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Aim: Due to the environmental usage, these substances can be applied to the placental blood industry due to the shelves and the deteriorated membrane transportation. It is intended that their environmental effects can be influenced by these transport proteins. Materials and Methods: Within the scope of the study, in the placenta of the owner and endotheliochorial dog; Good by analysis of 28 good (PCB, PBDE, PAH and Organic chlorinated pesticides); The expression profile of the placental whole genome was investigated by RNAseq, evaluated in silico (mole clamping) and in vitro (SLC and ABCB1 mRNA analysis in the placental cell line HTR8/SVneo treated with PCB 101, PCB118). Results: PCB101 826.4μg/kg in one of the 60 samples tested; In 23 samples, PCB118 was found to be between 0.14 and 41.9μg/kg. In 55 samples in the sequence analysis in bioinformatics, PCB was found in 742 genes between positive and negative (p

Objective: Due to widespread presence and exposure to environmental pollutants, structural and functional changes in membrane transporters could occur, leading to plasental transport of these compounds. In this study, the effects of PCBs on SLC abd ABCB1 membrane transport molecules were evaluated. Materials and Methods: Hemochorial structured human placenta and endotheliochorial structured dog placenta were analyzed for 28 pollutants (PCB, PBDE, PAH and Organochlorines) using GC-MS. The expression profile of the placental whole genome were investigated with RNAseq, and in silico (molecular chelation) and in vitro (SLC and ABCB1 mRNA expression in the placental cell line HTR8/SVneo treated with PCB 101, PCB118) were evaluated. Results: PCB101 826.4μg/kg in one sample out of 60 samples tested; In 23 samples, PCB118 was found to be between 0.14 and 41.9μg/kg. In the bioinformatics findings, there were differences in 742 genes between PCB positive and negative samples in 55 samples that were sequenced (p, Amaç: Çevresel kirletici maruziyetine bağlı olarak işlevselliği değişen ve bozulan membran transportları nedeniyle, bu maddeler plasental bariyeri geçerek plasental kan dolaşımına geçebilmektedir. Çalışmada, çevresel kirleticilerin bu transport proteinleriyle etkileşimlerinin moleküler boyutta incelenmesi amaçlanmaktadır. Gereç ve Yöntem: Araştırma kapsamında hemokoryal yapıya sahip insan ve endotelyokoryal yapıya sahip köpek plasentasında; 28 kirleticinin analizi GC-MS ile yapılmış (PCB, PBDE, PAH ve Organik klorlu pestisitler); RNAseq ile plasental tüm genom ifade profili araştırılmış, in siliko (moleküler kenetleme) ve in vitro (PCB 101, PCB118 uygulanan plasental hücre hattı HTR8/SVneo’da SLC ve ABCB1 mRNA ifadesi) değerlendirilmiştir. Bulgular: Test edilen 60 örnek içerisinde bir örnekte PCB101 826.4μg/kg; 23 örnekte ise PCB118 0.14 ile 41,9μg/kg arasında bulundu. Biyoinformatik bulgularda sekans analizi yapılan 55 numunede PCB pozitif ve negatif numuneler arasında 742 gende farklılık bulundu (p

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 Unido Fil: Tekin, Nilgun. Ankara Üniversitesi; Turquía Fil: Conget, Paulette. Universidad del Desarrollo; Chile Fil: 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; Argentina Fil: Timar, Botond. Semmelweis Egyetem; Hungría Fil: Gagyi, Eva. Semmelweis Egyetem; Hungría Fil: Basak, Ranjan. Tata Memorial Hospital; India Fil: Auewarakul, Chirayu. Mahidol University; Tailandia Fil: Sritana, Narongrit. Mahidol University; Tailandia Fil: Cerci, Juliano Julio. Department of Nuclear Medicine, Quanta Diagnóstico e Terapia; Brasil Fil: DImamay, Mark Pierre. St Luke's Medical Centre; Filipinas Fil: Gyorke, Tamas. Semmelweis University; Hungría Fil: Redondo, Francisca. Fundación Arturo López Pérez; Chile Fil: Nair, Reena. Tata Memorial Hospital; India Fil: Gorospe, Charity. St Luke's Medical Centre; Filipinas Fil: Paez, DIana. International Atomic Energy Agency; Austria Fil: Fanti, Stefano. Universidad de Bologna; Italia Fil: Ozdag, Hilal. Ankara Üniversitesi; Turquía Fil: Padua, Rose Ann. Université Paris Diderot - Paris 7; Francia Fil: Carr, Robert. Guy’s and St. Thomas’ Hospital; Reino Unido

Objectives: Our aim was to determine how well immunohistochemical analysis identified colon cancer patients with microsatellite instability in Turkish patients. Material and methods: Subjects were patients that underwent surgery for colorectal cancer in our institution between 2006 and 2011. Patients were grouped as: (1) suspected Lynch syndrome (n=14), (2) familial colorectal cancer (n=14), and (3) sporadic colorectal cancer groups (n=14). Mismatch repair proteins were analyzed by a four antibody-panel immunohistochemistry. Microsatellite instability analysis was conducted on DNA samples using MSI-PCR followed by fragment analysis. Results: The immunohistochemistry and PCR results had good concordance in 35/42 patients. Both microsatellite instability and at least one mismatch repair protein deficiency were detected in 11 patients, and both microsatellite stability and normal expression of mismatch repair proteins were detected in 24 patients. Test results were discordant in seven of the patients. Conclusion: As it is not feasible to perform expensive molecular tests in healthcare units in many developing countries, the four antibody-panel immunohistochemistry is a reliable and affordable method for screening for colorectal cancer, including Lynch syndrome and sporadic cases when suspected.

Background Genome-wide gene expression profiling analysis of FFPE tissue samples is indispensable for cancer research and provides the opportunity to evaluate links between molecular and clinical information, however, working with FFPE samples is challenging due to extensive cross-linking, fragmentation and limited quantities of nucleic acid. Thus, processing of FFPE tissue samples from RNA extraction to microarray analysis still needs optimization. Materials and methods In this study, a modified deparaffinization protocol was conducted prior to RNA isolation. Trizol, Qiagen RNeasy FFPE and Arcturus PicoPure RNA Isolation kits were used in parallel to compare their impact on RNA isolation. We also evaluated the effect of two different cRNA/cDNA preparation and labeling protocols with two different array platforms (Affymetrix Human Genome U133 Plus 2.0 and U133_X3P) on the percentage of present calls. Results Our optimization study shows that the Qiagen RNeasy FFPE kit with modified deparaffinization step gives better results (RNA quantity and quality) than the other two isolation kits. The Ribo-SPIA protocol gave a significantly higher percentage of present calls than the 3′ IVT cDNA amplification and labeling system. However, no significant differences were found between the two array platforms. Conclusion Our study paves the way for future high-throughput transcriptional analysis by optimizing FFPE tissue sample processing from RNA isolation to microarray analysis.

Background: Acute lymphoblastic leukemia (ALL) is a hematological malignancy characterized by the abnormal expansion of clonal lymphoblasts in the bone marrow (BM). The behavior of malignant lymphoblasts is not only dependent on their genomic abnormalities but also, on their complex and reciprocal relationships with their local niche. BM microenvironment is a dynamic network of growth factors, cytokines, and stromal cells, providing a permissive environment for leukemogenesis and progression. Despite some evidence about the implication of the bidirectional interaction between mesenchymal stromal cells (MSCs) and leukemic cell on growth and survival, it is still largely unknown. Although an increasing number of studies are reporting on the expression of specific genes in leukemic cells-interacting MSCs, gene expression profiling in cocultured MSCs (with respect to mono culture conditions) has not been done on a transcriptome-wide basis. Taking all this into consideration, we have established cocultures between BM-derived MSCs and the leukemic mononuclear cells and performed gene expression profile (GEP) studies on the MSC population to determine those deregulated genes due to the coculture condition with respect to MSCs in mono culture. Methods: Primary MSCs from BM samples of healthy donors (n=4) and pediatric pre-B ALL patients (n=4) were isolated and expanded and mononuclear cells were, also, isolated from patients peripheral blood. At passage 2, healthy/patient (h/p) MSCs were cocultured with the leukemic cells for 72 hours and subsequently subjected to GEP analyses. RNA isolated from h/pMSCs and biotinylated amplified RNA was synthesized. For the hybridization HG-U133 Plus, 2.0 GeneChip oligonucleotide arrays (Affymetrix) was used. Raw microarray data were processed into expression values through the Affy package in R. RMA (robust multi-array average) algorithm was used for preprocessing. The linear regression model package LIMMA (Linear Models for Microarray Data) was used to identify significant differential expression of genes (DEGs) compared to h/pMSCs after coculture with MSCs from the same origin in mono culture. Minimum 1.5 fold change and p-value < 0.001 were defined as the threshold. Functional enrichment, gene network and pathway analysis, were performed on selected sets of genes after differential expression analyses using two bioinformatics tools: DAVID Bioinformatics Resources 6.8 and WebGestalt 2019. Results: We identified 293 DEGs when analyzing pMSC samples vs. hMSC in coculture condition and 853 DEGs of pMSC vs. hMSC analyze in mono culture condition and only 15 DEGs common in both group. According to the result of functional enrichment analysis of pMSC vs. hMSC in coculture condition, 29 gene ontology (GO) term biological process including (top five) apoptotic process, axon guidance, regulation of JNK cascade, cell-cell adhesion and protein phosphorylation and 4 KEGG pathways of DEGs including axon guidance, FoxO signalling pathway, Wnt signalling pathway and signalling pathways regulating pluripotency of stem cells were determined. Comparing pMSC vs. hMSC in mono culture condition, 292 GO term biological process including extracellular matrix organization, skeletal system development, angiogenesis and signal transduction and 43 KEGG pathways of DEGs including pathways in cancer, TGFß signalling pathway, ECM-receptor interaction, p53 signalling pathway and PI3-Akt signalling pathway were determined.Five genes with upregulated expression after coculture (COL18A1, EFNA5, MAP3K8, CASP1, IGF1R) and after mono culture (MMP1, CXCL1, IL1B, PCDH10, CXCL6) were identified. Conclusions: Deregulated genes especially after coculture condition in axon guidance and ephrin receptor-mediated signalling pathway of which the importance is not yet understood in cancer microenvironment including EPHB1, ephrinA5, ephrinB3, p21 activated kinase 2 (PAK2), and ROBO3 showed highly differential expression pattern between pMSCs and hMSCs. This is the first report indicating the importance of axon guidance genes as a result of interaction between MSCs and leukemic cells. The elucidation of deregulated mechanisms and pathways provides new molecular insights to the contribution of these cells to ALL pathophysiology and understanding cross talk between these cells may lead to found new therapeutic targets. Disclosures No relevant conflicts of interest to declare.

BACKGROUND Therapy discontinuations and toxicities occur because of significant interindividual variations in 6-mercaptopurine (6-MP) and methotrexate (MTX) response during maintenance therapy of childhood acute lymphoblastic leukemia (ALL). 6-MP/MTX intolerance in some of the patients cannot be explained by thiopurine S-methyl transferase (TPMT) gene variants. In this study, we aimed to investigate candidate pharmacogenetic determinants of 6-MP and MTX intolerance in Turkish ALL children. METHODS In total, 48 children with ALL who had completed or were receiving maintenance therapy according to Children's Oncology Group (COG) protocols were enrolled. Fifteen single-nucleotide polymorphisms in 8 candidate genes that were related to drug toxicity or had a role in the 6-MP/MTX metabolism (TPMT, ITPA, MTHFR, IMPDH2, PACSIN2, SLCO1B1, ABCC4, and PYGL) were genotyped by competitive allele-specific PCR (KASP). Drug doses during maintenance therapy were modified according to the protocol. RESULTS The median drug dose intensity was 50% (28% to 92%) for 6-MP and 58% (27% to 99%) for MTX in the first year of maintenance therapy, which were lower than that scheduled in all patients. Among the analyzed polymorphisms, variant alleles in SLCO1B1 rs4149056 and rs11045879 were found to be associated with lower 6-MP/MTX tolerance. CONCLUSIONS SLCO1B1 rs4149056 and rs11045879 polymorphisms may be important genetic markers to individualize 6-MP/MTX doses.

Congenital plasminogen (Plg) deficiency leads to the development of ligneous membranes on mucosal surfaces. Here, we report our experience with local and intravenous fresh frozen plasma (FFP). We retrospectively reviewed medical files of 17 patients and their eight first-degree relatives. Conjunctivitis was the main complaint. Thirteen patients were treated both with intravenous and conjunctival FFP. Venous thrombosis did not develop in any. Genetic evaluation revealed heterogeneous mutations as well as polymorphisms. Diagnosis and treatment of Plg deficiency is challenging; topical and intravenous FFP may be an alternative treatment.

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; Turquía Fil: Omidvar, Nader. Cardiff University; Reino Unido Fil: Morris, Tim Peter. Clinical Trials Unit at University College. Medical Research Council; Reino Unido Fil: Conget, Paulette. Universidad del Desarrollo; Chile Fil: 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; Argentina Fil: Timar, Botond. Semmelweis University. Department of Pathology and Experimental Cancer Research; Hungría Fil: Gagyi, Eva. Semmelweis University. Department of Pathology and Experimental Cancer Research; Hungría Fil: Basak, Ranjan. Tata Memorial Hospital. Departments of Medical Oncology & Pathology; India Fil: Naik, Omkar. Tata Memorial Hospital. Departments of Medical Oncology & Pathology; India Fil: Auewarakul, Chirayu. Faculty of Medicine Sirira; Tailandia. Chulabhorn Cancer Centre; Tailandia Fil: Sritana, Narongrit. Faculty of Medicine Sirira; Tailandia. Chulabhorn Cancer Centre; Tailandia Fil: Levy, Debora. Chulabhorn Cancer Centre; Tailandia. Faculty of Medicine Sirira; Tailandia Fil: Cerci, Juliano Julio. Department of Nuclear Medicine. Quanta - Diagnóstico e Terapia; Brasil Fil: Bydlowski, Sergio Paulo. Universidade de Sao Paulo; Brasil Fil: Pereira, Juliana. Universidade de Sao Paulo; Brasil Fil: Dimamay, Mark Pierre. St. Lukes Medical. Research and Biotechnology Division; Filipinas Fil: Natividad, Filipinas. St. Lukes Medical. Research and Biotechnology Division; Filipinas Fil: Chung, June-Key. Seoul National University Hospital. Department of Nuclear Medicine; Corea del Sur Fil: Belder, Nevin. Ankara University. Biotechology Institute; Turquía Fil: Kuzu, Isinsu. Ankara University. Faculty of Medicina; Turquía Fil: Paez, Diana. International Atomic Energy Agency; Austria Fil: Dondi, Maurizio. International Atomic Energy Agency; Austria Fil: Carr, Robert. King’s College. Guy’s & St Thomas’ Hospital; Reino Unido Fil: Ozdag, Hilal. Ankara University. Faculty of Medicina; Turquía Fil: Padua, Rose Ann. Institut National de la Sante Et de la Recherche Médica; Francia. Université Paris-Diderot; Francia. Institut Universitaire d'Hématologie; Francia

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

The BRCA2 gene is mutated in familial breast and ovarian cancer, and its product is implicated in DNA repair and transcriptional regulation. Here we identify a protein, EMSY, which binds BRCA2 within a region (exon 3) deleted in cancer. EMSY is capable of silencing the activation potential of BRCA2 exon 3, associates with chromatin regulators HP1β and BS69, and localizes to sites of repair following DNA damage. EMSY maps to chromosome 11q13.5, a region known to be involved in breast and ovarian cancer. We show that the EMSY gene is amplified almost exclusively in sporadic breast cancer (13%) and higher-grade ovarian cancer (17%). In addition, EMSY amplification is associated with worse survival, particularly in node-negative breast cancer, suggesting that it may be of prognostic value. The remarkable clinical overlap between sporadic EMSY amplification and familial BRCA2 deletion implicates a BRCA2 pathway in sporadic breast and ovarian cancer.

The first observation of homozygote Hb Q-Iran (α1 75(EF4) Asp-His) is presented in this report. The clinical and hematological data of the index case, his father and mother showed that homozygous or heterozygous Hb Q-Iran has no clinical importance.Sivas kökenli anormal hemoglobini olan bir çocuğa moleküler analizle Homozigot Hb Q-Iran (α1 75(EF4) Asp-His tanısı konulmuştur.

Formalin-fixed paraffin-embedded (FFPE) tissue is a widely available clinical specimen for retrospective studies. The possibility of long-term clinical follow-up of FFPE samples makes them a valuable source to evaluate links between molecular and clinical information. Working with FFPE samples in the molecular research area, especially using high-throughput molecular techniques such as microarray gene expression profiling, has come into prominence. Because of the harmful effects of formalin fixation process such as degradation of nucleic acids, cross-linking with proteins, and chemical modifications on DNA and RNA, there are some limitations in gene expression profiling studies using FFPE samples. To date many studies have been conducted to evaluate gene expression profiling using microarrays (Thomas et al., Thomas et al. (2013) [1]; Scicchitano et al., Scicchitano et al. (2006) [2]; Frank et al., Frank et al. (2007) [3]; Fedorowicz et al., Fedorowicz et al. (2009) [4]). However, there is still no generally accepted, efficient and standardized procedure for microarray analysis of FFPE samples. This paper describes the microarray data presented in our recently accepted to be published article showing a standard protocol from deparaffinization of FFPE tissue sections and RNA extraction to microarray gene expression analysis. Here we represent our data in detail, deposited in the gene expression omnibus (GEO) database with the accession number GSE73883. Four combinations of two different cRNA/cDNA preparation and labeling protocols with two different array platforms (Affymetrix Human Genome U133 Plus 2.0 and U133_X3P) were evaluated to determine which combination gives the best percentage of present call. The study presents a dataset for comparative analysis which has a potential in terms of providing a robust protocol for gene expression profiling with FFPE tissue samples. Keywords: Microarray, Gene expression, FFPE, Optimization

The plasminogen (Plg) protein is the inactive proenzyme form of plasmin that dissolves fibrin thrombi by a process called fibrinolysis. It has been shown that homozygous or compound-heterozygous deficiency of this protein is a major cause of a rare inflammatory disease affecting mainly mucous membranes found in different body sites. In this study, five individual Turkish patients and nine Turkish families with type 1 Plg deficiency were investigated for PLG gene mutations. All of the coding regions of the PLG gene mutations were screened for mutations using denaturing high-pressure liquid chromatography (DHPLC). Samples showing a different DHPLC profile were subjected to DNA sequencing analysis. Here, we described five novel mutations namely, Cys49Ter, +1 IVS6 G>A, Gly218Val, Tyr283Cys, and Gly703Asp. Previously identified five nonsynonymous (Lys38Glu, Glu180Lys, Gly420Asp, Asp453Asn, Pro763Ser), five synonymous (330 C>T, 582 C>T, 771 T>C, 1083 A>G, 2286 T>G), and a 3' untranslated region (3' UTR) mutation (c.*45 A>G) were also reported in this present study. In this study, we have identified a total of eight mutations, five of which are novel. The mutations/polymorphisms identified in eight of the patients do not explain the disease phenotype. These cases probably carry other pathological mutations (homozygous or compound heterozygous) that cannot be detected by DHPLC. Copyright (C) 2016 Wolters Kluwer Health, Inc. All rights reserved.

Thalassemia is an inherited blood disorder which is divided into two groups: alpha and beta. HBA1 and HBA2 are the two genes associated with alpha thalassemia. The aim of this study is to investigate abnormal hemoglobin variants of alpha globin gene in healthy abnormal hemoglobin carrying individuals with intact beta globin gene. DNA was extracted from peripheral blood samples of seven healthy carrier individuals who have abnormal hemoglobin variants and 16 control individuals from Turkey. Complete coding and intronic sequences of HBA1 and HBA2 genes were amplified by polymerase chain reaction (PCR) and PCR products of HBA1 and HBA2 were sequenced. We were unable to find any base change in our carrier group in the HBA1 gene. We have observed an A/G polymorphism in the downstream untranslated region (+861 G>A) of the HBA2 gene. Our study showed that 14.29% (1/7 carriers) of the carrier group and 37.50% (6/16 controls) of the control group were heterozygous for the +861 G>A polymorphism. The distribution of allele frequencies and genotypes of HBA2 between carrier and control samples were analyzed and it is seen that the distribution of allele frequencies and that of genotypes were not statistically significant between carrier and control samples (P-value=0.4131, P-value=0.366, respectively). HBA2 +861 G>A nucleotide substitution is a neutral polymorphism previously reported in other populations. This is the first report in Turkish population.

Ataxia-telangiectasia (AT) is a complex disorder characterized by progressive neurodegeneration, immunodeficiency, hypersensitivity to DNA damaging agents and cancer predisposition. Clinical heterogeneity is observed even among the affected siblings with AT. Mutations of the ataxia-telangiectasia mutated (ATM) gene are responsible for AT. H2AX, an essential histone protein, is phosphorylated by ATM in response to double-strand breaks, and H2AX-deficient mice share some clinical and laboratory findings with AT. Therefore, we sought a possible modifier effect of H2AX gene on various clinical features in a group of patients with AT and healthy controls. We performed sequence analysis of H2AX gene in 81 patients with AT, and in 51 of them, we analysed methylation. We examined H2AX gene expression in 25 patients. We investigated 48 healthy individuals as a control group. We did not detect any mutation or sequence variation in the H2AX gene, or any altered methylation pattern in any of the patients. Although H2AX gene expression was markedly increased (2.5- to 11.8-fold) in five of 25 patients, and slightly increased (1.5- to 2.4-fold) in four patients, the correlations between H2AX gene expression and the evaluated clinical features of the patients were not significant. Other potential modifier genes that might be scrutinized in AT patients include p53, 53BP1 and TIP60, as well as the genes that effect mitochondrial function and the oxidative response.

YILMAZ, Engin/0000-0001-8873-7645; Akarsu, Nurten/0000-0001-5432-0032; Ozdag, Hilal/0000-0001-7940-2499; Liehr, Thomas/0000-0003-1672-3054; Alanay, Yasemin/0000-0003-0683-9731; von Eggeling, Ferdinand/0000-0002-8062-6999 WOS: 000278045300015 PubMed: 20451171 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. Scientific and Technological Research Council of Turkey (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [108S420]; European Research Area Network (E-RARE) [R07197KS] We are grateful to the families for their participation in the study. We thank Han Brunner for critical reading and comments, Ebru Oralli Bircan for illustrations, Hacettepe University Craniofacial Surgery Study Group members Yucel Erk, Emin Mavili, Aycan Kayikcioglu (Plastic and Reconstructive Surgery), Kemal Benli (Neurosurgery), Aysenur Cila (Radiology), Tulin Taner, and liken Kocadereli (Orthodonty) for evaluating the frontonasal malformation cases in the registry. This work was supported by the Scientific and Technological Research Council of Turkey (TUBITAK) (grant numbers 108S420 to N.A.A), and the overall consortium (CRANIRARE) was supported by the European Research Area Network (E-RARE) (project number R07197KS).

WOS: 000278045300016, PubMed: 20451170, More than 270 million people worldwide have hearing loss that affects normal communication. Although astonishing progress has been made in the identification of more than 50 genes for deafness during the past decade, the majority of deafness genes are yet to be identified. In this study, we mapped a previously unknown autosomal-recessive nonsyndromic sensorineural hearing loss locus (DENB91) to chromosome 6p25 in a consanguineous Turkish family. The degree of hearing loss was moderate to severe in affected individuals. We subsequently identified a nonsense mutation (p.E245X) in SERPINB6, which is located within the linkage interval for DENB91 and encodes for an intracellular protease inhibitor. The p.E245X mutation cosegregated in the family as a completely penetrant autosomal-recessive trait and was absent in 300 Turkish controls. The mRNA expression of SERPINB6 was reduced and production of protein was absent in the peripheral leukocytes of homozygotes, suggesting that the hearing loss is due to loss of function of SERPINB6. We also demonstrated that SERPINB6 was expressed primarily in the inner ear hair cells. We propose that SERPINB6 plays an important role in the inner ear in the protection against leakage of lysosomal content during stress and that loss of this protection results in cell death and sensorineural hearing loss., The Scientific AMP; Technological Research Council of Turkey [105S464, 108S045]; University of Miami; NIHUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [R01 DC006908]; National Natural Science Foundation of ChinaNational Natural Science Foundation of China [30728030]; Federick and Ines Yeatts [R01 DC005575]; Oticon Fonden, Denmark, We are thankful to all participating families. We thank Professor Phillip I. Bird from Monash University, Australia, for helpful suggestions and critical reading of the manuscript. This study was partially supported by The Scientific & Technological Research Council of Turkey Grants (105S464 and 108S045), funds from the University of Miami to M.T., NIH R01 DC006908 to Z.-Y.C., National Natural Science Foundation of China to Z.-Y.C. (30728030), the Federick and Ines Yeatts inner ear hair cell regeneration fellowship to M.H., R01 DC005575 to X.Z.L., and a grant from Oticon Fonden, Denmark, to M.B.P.

Rational drug discovery relies on pathognomonic molecular reporters of disease or biomarkers. Therefore biomarkers contain relational or contextual information about disease pathophysiology. Two broad pathways can be taken to identify biomarkers: a 'top-down', holistic approach that makes no assumptions about biomarker type, or the 'bottom-up' approach, which is hypothesis driven and relies on a priori information. Both approaches involve parallel or sequential methods that include genomic and proteomic profiling. Biomarker discovery and translational medicine owe much to isotopic techniques because these provide near-real-time information about disease status as diagnostics, in drug delivery and for monitoring treatment. Here, we provide an overview of recent developments and some insight into the future role of isotopes in biomarker discovery and disease therapy.

Using Affymetrix 10K arrays, we searched for regions of homozygosity in 51 Turkish families including at least three members with either congenital or prelingual autosomal recessive non-syndromic sensorineural hearing loss (ARNSSNHL), and identified four families whose deafness mapped to the DFNB6 locus on 3p21 containing the TMIE gene. Mutation analysis revealed the p.R84W mutation in all four families. Screening of this mutation in 254 families with ARNSSNHL, without GJB2 mutations, revealed four additional affected families. A novel mutation was found in a non-complementary marriage between a deaf couple who were homozygous for p.R84W and p.W57X, respectively with two affected children who were compound heterozygotes. Six of the TMIE families originated from southeastern Anatolia, making p.R84W a common cause of hearing loss in that region with a relative frequency of 10.3% (95% CI is 2.5-18.1%). The overall prevalence of the p.R84W mutation in ARNSSNHL in Turkey is 2.4% (95% CI is 0.7-4.0%). Genotyping of single-nucleotide polymorphisms flanking the TMIE gene revealed a conserved haplotype, suggesting a single origin for p.R84W from a common ancestor 1250 years ago (95% CI is 650-2500 years). We conclude that p.R84W could be a common mutation in other Middle Eastern populations and should be included in mutation screening offered to individuals with ARNSSNHL.

Genome wide homozygosity mapping using Affymetrix 10K arrays revealed the DFNB7/11 locus including the TMC1 gene in 5 of 35 Turkish families with autosomal recessive nonsyndromic severe to profound congenital or prelingual-onset sensorineural hearing loss (SNHL). Additional 51 families were later screened for co-segregation of the locus with the phenotype using microsatellite markers. GJB2 and mtDNA A1555G mutations were negative in probands from each family. Mutation analysis was performed in families showing co-segregation Of autosomal recessive SNHL with haplotypes at the DFNB7/11 locus. A total of six different mutations in seven families were identified, including novel missense alterations, p.G444R (c.1330G > A), p.R445C (c.1333C > T), and p.1677T (c.2030T > C), one novel splice site mutation IVS6+2 T > A (c.64+2T > A), and a novel large deletion ofapproximately 31 kb at the 3' region of the gene including exons 19-24, as well as a previously reported nonsense mutation, p.R34X (c.100C > T). All identified Mutations co-segregated with autosomal recessive SNHL in all families and were not found in Turkish hearing controls. These results expand the mutation spectrum of TMC1 with five novel mutations and provide data for the significant contribution of TMC1 mutations in hearing loss. (c) 2009 Elsevier Ireland Ltd. All rights reserved.

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.

Ağrı çeşitli etyolojik faktörlerin neden olduğu, yaşam kalitesinde ve işgücünde düşmeye yol açan bir halk sağlığı sorunudur. Tedavi amaçlı alınan ilaçlar her zaman istenilen sonucu verememekte, bu durum hastaların farklı yöntemler aramasına neden olmaktadır. Bu anlamda gelişmiş ülkelerde tek başına veya beraber kullanılan yöntemlerden biri de akupunkturdur. Çok çeşitli alanlarda tamamlayıcı tedavi olarak kullanılsa da; ağrı akupunktur tedavisinin en çok kullanıldığı endikasyonlardan biridir. Bu yazıda ağrı tedavisinde akupunktur kullanımı ile ilgili bazı bilimsel çalışmalar gözden geçirilmiştir., Pain is a public health problem caused by various etiological factors that leads to decrease in quality of life and labor. Medication can not always produce the desired result, so patients may search for different methods for threatment. In this sense, acupuncture is one the method that used alone or complementary treatment in developed countries. Also used as complementary treatment in various fields; pain is one of the most commonly used indications that the acupuncture treatment. In this article some scientific studies on the use of acupuncture in the treatment of pain have been reviewed.

C-type lectin domain family 12, member A (CLEC12A) is a C-type lectin-like pattern recognition receptor capable of recognizing monosodium urate crystals. Monosodium urate crystals, the causative agents of gout are also among the danger-associated molecular patterns reflecting cellular injury/cell death. In response to monosodium urate crystals, CLEC12A effectively inhibits granulocyte and monocyte/macrophage functions and hence acts as a negative regulator of inflammation. Behcet’s syndrome and gout are autoinflammatory disorders sharing certain pathological (neutrophilic inflammation), clinical (exaggerated response to monosodium urate crystals) and therapeutic (colchicine) features. We propose the hypothesis that decreased expression of CLEC12A is a common denominator in the hyperinflammatory responses observed in Behcet’s syndrome and gout. Major lines of evidence supporting this hypothesis are: (1) Downregulation/deficiency of CLEC12A is associated with hyperinflammatory responses. (2) CLEC12A polymorphisms with functional and clinical implications have been documented in other inflammatory diseases. (3) Colchicine, a fundamental therapeutic agent used both in Behcet’s syndrome and gout is shown to oppose the downregulation of CLEC12A. (4) Behcet’s syndrome and gout are characterized by a hyperinflammatory response to monosodium urate crystals and other than gout, Behcet’s syndrome is the only inflammatory condition exhibiting this exaggerated response. (5) Genomewide linkage and association studies of Behcet’s syndrome collectively point to 12p12–13, the chromosomal region harboring CLEC12A. (6) Patients with severe forms of Behcet’s syndrome underexpress CLEC12A with respect to patients with mild forms of the disease. If supported by well-designed, rigorous experiments, the forementioned hypothesis pertinent to CLEC12A will carry important implications for therapy, designing experimental models, and uncovering immunopathogenic mechanisms in Behcet’s syndrome and gout.

Sensitive and cost-effective detection of point mutations is important in genetics research. Denaturing high-performance liquid chromatography (DHPLC) is known to be one of the most sensitive techniques for point mutation detection. A more recent technique, high-resolution melting (HRM), is based on the melting behavior of PCR products. In this study, the efficiency and sensitivity of HRM and DHPLC for the detection of MEFV, F5, and F2 gene point mutations were evaluated. Materials and methods: We studied 15 patients with MEFV mutations (E148Q, M680I, M694V, or V726A), 7 patients with the F51691G>A mutation, and 12 patients with the F220210G>A mutation. All mutations were screened by HRM and DHPLC. Results: All mutations were successfully detected by HRM. However, only 4 (MEFV E148Q and M680I, F51691G>A, and F220210G>A) of 6 mutations were successfully detected with DHPLC. Conclusion: Our study showed that HRM is more sensitive than DHPLC for detection of the studied point mutations.

p300 and cyclic AMP response element-binding protein (CBP) are adenoviral E1A-binding proteins involved in multiple cellular processes, and function as transcriptional co-factors and histone acetyltransferases. Germline mutation of CBP results in Rubinstein-Taybi syndrome, which is characterized by an increased predisposition to childhood malignancies. Furthermore, somatic mutations of p300 and CBP occur in a number of malignancies. Chromosome translocations target CBP and, less commonly, p300 in acute myeloid leukemia and treatment-related hematological disorders. p300 mutations in solid tumors result in truncated p300 protein products or amino-acid substitutions in critical protein domains, and these are often associated with inactivation of the second allele. A mouse model confirms that p300 and CBP function as suppressors of hematological tumor formation. The involvement of these proteins in critical tumorigenic pathways (including TGF-beta, p53 and Rb) provides a mechanistic route as to how their inactivation could result in cancer.

Germ line BRCA1 and/or BRCA2 mutations were screened in 50 Turkish breast and/or ovarian cancer patients composed of hereditary, familial, early onset and male cancer groups. Genomic DNA samples were tested by heteroduplex analysis and DNA sequencing. Two truncating BRCA2 mutations, one novel (6880 insG) and one previously reported (3034 delAAAC), were found in two out of six (33%) hereditary breast and/or ovarian cancer patients. A novel truncating (1200 insA) and a missense (2080A!G) BRCA1 mutation was found in two of 27 (7%) individuals in the early onset group. A total of four (8%) disease-causing mutations in 50 breast cancer patients were identified in BRCA1 and BRCA2 genes. In addition, five BRCA1 sequence variants have been identified in 23 patients. These results indicate that BRCA1 and BRCA2 genes are involved in some, but not all, forms of hereditary predisposition to breast cancer in the Turkish population. # 2000 Published by Elsevier Science Ltd.

Mutation screening studies related with thrombosis revealed that prothrombin 20210A allele of the prothrombin gene leads to an increase in plasma prothrombin levels. The G20210A mutation screening has become a routine analysis in patients with thrombosis. For the detection of the mutation, several molecular techniques have been defined. Real-time polymerase chain reaction is an easy and feasible way to monitor this mutation according to the melting point analysis. Here we report a different pattern in the LightCycler melting point analysis of 2 patients with thrombosis. DNA sequencing of the prothrombin gene showed that these patients with an atypical melting point profile carry a 20209 C >T mutation along with a novel homozygous polymorphism at the 3' downstream region, +4 C >T.

A new deletion of the β-globin gene cluster was characterized in a Turkish family. A 6-year-old male and his father were heterozygotes for this deletion. They presented with mild hypochromic microcyti

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.

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. European Journal of Human Genetics (2011) 19, 915-920; doi:10.1038/ejhg.2011.51; published online 23 March 2011

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.

We identified nine individuals from three unrelated Turkish families with a unique autosomal recessive syndrome characterized by type I microtia, microdontia, and profound congenital deafness associated with a complete absence of inner ear structures (Michel aplasia). We later demonstrated three different homozygous mutations (p.S156P, p.R104X, and p.V206SfsX117) in the fibroblast growth factor 3 (FGF3) gene in affected members of these families, cosegregating with the autosomal recessive transmission as a completely penetrant phenotype. These findings demonstrate the involvement of FGF3 mutations in a human malformation syndrome for the first time and contribute to our understanding of the role this gene plays in embryonic development. Of particular interest is that the development of the inner ear is completely disturbed at a very early stage--or the otic vesicle is not induced at all--in all of the affected individuals who carried two mutant FGF3 alleles.

BackgroundPost-translational modification of histones resulting in chromatin remodelling plays a key role in the regulation of gene expression. Here we report characteristic patterns of expression of 12 members of 3 classes of chromatin modifier genes in 6 different cancer types: histone acetyltransferases (HATs)-EP300, CREBBP, andPCAF; histone deacetylases (HDACs)-HDAC1, HDAC2, HDAC4, HDAC5, HDAC7A, andSIRT1; and histone methyltransferases (HMTs)-SUV39H1andSUV39H2. Expression of each gene in 225 samples (135 primary tumours, 47 cancer cell lines, and 43 normal tissues) was analysedby QRT-PCR, normalized with 8 housekeeping genes, and given as a ratio by comparison with a universal reference RNA.ResultsThis involved a total of 13,000 PCR assays allowing for rigorous analysis by fitting a linear regression model to the data. Mutation analysis ofHDAC1, HDAC2, SUV39H1, andSUV39H2revealed only two out of 181 cancer samples (both cell lines) with significant coding-sequence alterations. Supervised analysis and Independent Component Analysis showed that expression of many of these genes was able to discriminate tumour samples from their normal counterparts. Clustering based on the normalized expression ratios of the 12 genes also showed that most samples were grouped according to tissue type. Using a linear discriminant classifier and internal cross-validation revealed that with as few as 5 of the 12 genes,SIRT1, CREBBP, HDAC7A, HDAC5andPCAF, most samples were correctly assigned.ConclusionThe expression patterns of HATs, HDACs, and HMTs suggest these genes are important in neoplastic transformation and have characteristic patterns of expression depending on tissue of origin, with implications for potential clinical application.

Amplification of 8p11–12 is a well-known alteration in human breast cancers but the driving oncogene has not been identified. We have developed a high-resolution comparative genomic hybridization array covering 8p11–12 and analysed 33 primary breast tumors, 20 primary ovarian tumors and 27 breast cancer cell lines. Expression analysis of the genes in the region was carried out by using real-time quantitative PCR and/or oligo-microarray profiling. In all, 24% (8/33) of the breast tumors, 5% (1/20) of the ovary tumors and 15% (4/27) of the cell lines showed 8p11–12 amplification. We identified a 1 Mb segment of common amplification that excludes previously proposed candidate genes. Some of the amplified genes did not show overexpression, whereas for others, overexpression was not specifically attributable to amplification. The genes FLJ14299, C8orf2, BRF2 and RAB11FIP, map within the 8p11–12 minimal amplicon, two have a putative function consistent with an oncogenic role, these four genes showed a strong correlation between amplification and overexpression and are therefore the best candidate driver oncogenes at 8p12.

Activation of the tumor suppressor p53 by DNA damage induces either cell cycle arrest or apoptosis, but what determines the choice between cytostasis and death is not clear. In this report, we show that the E1A-binding p300 nucleoprotein is a key determinant of p53-dependent cell fate in colorectal cancer cells: absence of p300 increases apoptosis in response to DNA damage. In addition, p300-deficient (p300 - ) cells fail to undergo G 1 /S arrest after UV irradiation. These abnormalities are associated with prolongation of p53 stability, reduced p53-acetylation, blunting of MDM2 activation, failure to transactivate p21, and a disproportionate increase in PUMA levels. When xenografted, p300 - cells are more sensitive to chemotherapy with doxorubicin. These results show that p300 is a key regulator of the p53 response and suggest that p300 inhibition could be used to modulate chemotherapy.

A large proportion of epithelial cancers show the chromosome-instability phenotype, in which they have many chromosome abnormalities. This is thought to be the result of mutations that disrupt chromosome maintenance, but the causative mutations are not known. We identified cell lines known to have mutations that might cause chromosome instability, and examined their karyotypes. Two cell lines, the breast cancer line HCC1937 and the pancreatic cancer line CAPAN-1, that have mutations respectively in BRCA1 and BRCA2, had very abnormal karyotypes, with many structural and numerical chromosome changes and substantial variation between metaphases. However, two colorectal cancer lines with mutations in BUB1, a spindle checkpoint protein involved in chromosome segregation, had rather simple near-tetraploid karyotypes, with minimal loss or gain of chromosomes other than the endoreduplication event, and minimal structural change. Apart from tetraploidy, these karyotypes were typical of colorectal lines considered to be chromosomally stable. Two lines derived from the same tumour, DLD-1 and HCT-15, with bi-allelic mutation of CHK2, had karyotypes that were typical of near-diploid colorectal lines considered chromosomally stable. The karyotypes observed supported the proposed role for BRCA1 and BRCA2 mutations in chromosomal instability, but showed that the tested mutations in BUB1 and CHK2 did not result in karyotypes that would have been predicted if they were sufficient for chromosomal instability.

In this study we screened the histone acetyltransferases CBP and PCAF for mutations in human epithelial cancer cell lines and primary tumours. We identified two CBP truncations (both in cell lines), seven PCAF missense variants and four CBP intronic microdeletions. These data suggest that neither gene is commonly inactivated in human epithelial cancers. British Journal of Cancer (2002) 87, 1162–1165. doi:10.1038/sj.bjc.6600554 www.bjcancer.com © 2002 Cancer Research UK