A pathogenic breakpoint at 566.8 kb from the 3′ end of the SATB2 leads to a 2q33.1 microdeletionlike phenotype

SATB2 is an AT-rich sequence-binding protein that binds to nuclear matrix attachment regions. It plays an important role in transcription regulation and chromatin loop remodelling. Deletions, chromosome translocations, as well as heterozygous nonsense mutations affecting this gene have been reported associated with overlapping conditions involving craniofacial anomalies such as the isolated cleft palate (OMIM 119540), 2q33.1 microdeletion syndrome (OMIN 612313) and Toriello–Carey syndrome (OMIM 217980). The aim of this study was the identification of the breakpoint sequences and candidate gene/s of a de novo t(1;2)(q14.1;q35) associated with severe mental retardation, behaviour disturbance, dysmorphic facies, dental anomalies, convergent strabismus and high palate but without clefting. The chromosome 2 breakpoint is localised at position 199,567,382 of the current human genome assembly (hg19), within IVS1 of the processed transcript AC019330.1. This breakpoint disrupts an evolutionarily conserved non-coding genomic element localised 566.8 kb from the 3′ end of the SATB2 gene. The chromosome 1 breakpoint is localised within IVS13 of the zyg-11 homolog A (Caenorhabditis elegans) ZYG11A gene,at position 53,355,744 (assembly hg19). Although the chromosome 1 breakpoint disrupts the ZYG11A, we consider that the SATB2 is the main candidate gene, which is substantiated by the overlap observed between the probands’ phenotype with the pathologies associated with this gene. The characterization of the translocation breakpoints allowed us to establish an accurate clinical diagnosis. As pathogenic mechanism, we propose the disruption of the genomic architecture of evolutionary conserved long-range regulatory elements leading to a socalled cis-ruption disorder. The elucidation of the pathogenic mechanism by which disruption of such an evolutionarily conserved sequence element leads to the aforementioned condition will allow us to consider new therapeutic strategies that may hinder progressive deterioration of the clinical condition in such “cis-ruption disorders”

Tricho-rhino-phalangeal syndrome type I as a “cis-ruption disorder” caused by a translocation

Tricho-rhino-phalangeal syndrome type I (TRPS I; OMIM 190350) and type II (OMIM 150230) are two forms of the rare autosomal-dominant TRP malformation syndrome localised in 8q23.3–24.1. TRPS I is generally caused by point mutations or deletions of the TRPS1 gene, whereas type II is characterised by the presence of multiple cartilage exostoses (EXT) and deletions comprising the TRPS1 and EXT1 genes. In the present study, we have mapped and sequenced the breakpoints of a balanced familial translocation [t(8;13)(q23.3;q21.32)] segregating with mild TRPS I and analysed the TRPS1 candidate gene. The proband, in addition to features compatible with TRPS I, also presented developmental delay and severe mental retardation. The pathogenic chromosome 8 breakpoint was localised within a transposon type I element at 116.768 Mb, 87 kb from the TRPS1 5′ end. The breakpoint on chromosome 13 was localised within a gene-poor region at 65.101 Mb, and the nearest gene, 1.5 Mb distal from the breakpoint, is protocadherin 9 (PCDH9). Analysis of the three affected relatives by the 33K tiling BAC array and of the proband by 2.7-M high-resolution oligonucleotide array painting did not reveal additional genomic variation. Furthermore, mutation screening of the TRPS1 also did not reveal any alteration. Finally, expression studies of TRPS1 performed from LCLs indicate that inter-individual variation is higher than the expected gene expression changes induced by the translocation. Although the reason underlying the severe mental retardation observed in the proband is unknown, the available data indicate that this is not associated with the translocation. As far as we know, this is the first reported case of position effect or “cis-ruption” causing TRPS I. Finally, further studies are necessary to unveil the molecular pathogenic mechanisms of this “cis-ruption disorder” triggered by chromosometranslocation

Rare diseases in Europe: the Portuguese framework

A EUCERD Joint Action (EJA) para as Doenças Raras (DR) integrou cinco domínios: planos nacionais e estratégias, nomenclatura internacional para DR, serviços sociais especializados, qualidade dos cuidados/centros de referência e integração de iniciativas em DR. O objetivo deste artigo é descrever o enquadramento português nas DR. Em novembro de 2014 foi realizado um workshop em Portugal com oito países participantes. Foi descrita a situação europeia para as DR e comparada com a realidade portuguesa. Estiveram presentes: autoridades europeias, parceiros da EJA, especialistas, investigadores, profissionais de saúde e associações de doentes. Realizou-se uma análise qualitativa dos conteúdos das apresentações, posteriormente atualizada através de análise documental. No domínio dos planos e estratégias foi aprovada a Estratégia Integrada para as Doenças Raras 2015-2020 que assenta numa cooperação interministerial, intersectorial e interinstitucional. Em relação à nomenclatura, foi discutida e proposta a utilização do Orphanumber. Foram descritas várias iniciativas no âmbito das DR e observados exemplos de boas práticas na área dos serviços socias especializados. Recentemente, Portugal reconheceu oficialmente vários Centros de Referência Nacionais, onde se incluem alguns para as DR. Em conclusão, Portugal tem vindo a desenvolver diversas atividades no domínio das DR sendo necessário continuar com a integração das mesmas.The EUCERD Joint Action (EJA) for Rare Diseases (RD) consists of five domains: national plans and strategies, international RD nomenclatures, specialized social services, quality of care/centres of expertise and integration of RD initiatives. This article intends to provide the Portuguese situation on RD. In November 2014, a workshop was held in Portugal and included participants from eight different countries. The European stateof- art in every domain was counterbalanced with the Portuguese reality. European authorities, EJA’s partners, experts, researchers, health care professionals and patients’ representatives were present. A qualitative data analysis of the presentations’ contents was performed and updated documental analysis. Concerning plans and strategies, a National Integrated Strategy 2015-2020, based on an inter-ministerial/sectoral/institutional cooperation, using medi cal, social, scientific and technological resources, for RD was approved. Regarding nomenclature, health professionals use different coding systems. A proposal for the ORPHA number system to be adopted in disease nomenclature was discussed. Among specialized social services, good practices examples were described and RD initiatives were observed. Finally, just recently, Portugal recognized officially national Reference Centres which include some for RD. In conclusion, regarding the different domains of RD, Portugal has been developing several activities and its integration needs to continue

Transcriptomics predicts compound synergy in drug and natural product treated glioblastoma cells.

Pathway analysis is an informative method for comparing and contrasting drug-induced gene expression in cellular systems. Here, we define the effects of the marine natural product fucoxanthin, separately and in combination with the prototypic phosphatidylinositol 3-kinase (PI3K) inhibitor LY-294002, on gene expression in a well-established human glioblastoma cell system, U87MG. Under conditions which inhibit cell proliferation, LY-294002 and fucoxanthin modulate many pathways in common, including the retinoblastoma, DNA damage, DNA replication and cell cycle pathways. In sharp contrast, we see profound differences in the expression of genes characteristic of pathways such as apoptosis and lipid metabolism, contributing to the development of a differentiated and distinctive drug-induced gene expression signature for each compound. Furthermore, in combination, fucoxanthin synergizes with LY-294002 in inhibiting the growth of U87MG cells, suggesting complementarity in their molecular modes of action and pointing to further treatment combinations. The synergy we observe between the dietary nutraceutical fucoxanthin and the synthetic chemical LY-294002 in producing growth arrest in glioblastoma, illustrates the potential of nutri-pharmaceutical combinations in targeting this challenging disease

Identifying disease-specific genes based on their topological significance in protein networks

BACKGROUND: The identification of key target nodes within complex molecular networks remains a common objective in scientific research. The results of pathway analyses are usually sets of fairly complex networks or functional processes that are deemed relevant to the condition represented by the molecular profile. To be useful in a research or clinical laboratory, the results need to be translated to the level of testable hypotheses about individual genes and proteins within the condition of interest. RESULTS: In this paper we describe novel computational methodology capable of predicting key regulatory genes and proteins in disease- and condition-specific biological networks. The algorithm builds shortest path network connecting condition-specific genes (e.g. differentially expressed genes) using global database of protein interactions from MetaCore. We evaluate the number of all paths traversing each node in the shortest path network in relation to the total number of paths going via the same node in the global network. Using these numbers and the relative size of the initial data set, we determine the statistical significance of the network connectivity provided through each node. We applied this method to gene expression data from psoriasis patients and identified many confirmed biological targets of psoriasis and suggested several new targets. Using predicted regulatory nodes we were able to reconstruct disease pathways that are in excellent agreement with the current knowledge on the pathogenesis of psoriasis. CONCLUSION: The systematic and automated approach described in this paper is readily applicable to uncovering high-quality therapeutic targets, and holds great promise for developing network-based combinational treatment strategies for a wide range of diseases

Complex X chromosome rearrangement associated with multiorgan autoimmunity

BACKGROUND: Turner syndrome, a congenital condition that affects 1/2,500 births, results from absence or structural alteration of the second sex chromosome. Turner syndrome is usually associated with short stature, gonadal dysgenesis and variable dysmorphic features. The classical 45,X karyotype accounts approximately for half of all patients, the remainder exhibit mosaicism or structural abnormalities of the X chromosome. However, complex intra-X chromosomal rearrangements involving more than three breakpoints are extremely rare. RESULTS: We present a unique case of a novel complex X chromosome rearrangement in a young female patient presenting successively a wide range of autoimmune diseases including insulin dependent diabetes mellitus, Hashimoto's thyroiditis, celiac disease, anaemia perniciosa, possible inner ear disease and severe hair loss. For the genetic evaluation, conventional cytogenetic analysis and FISH with different X specific probes were initially performed. The complexity of these results and the variety of autoimmune problems of the patient prompted us to identify the exact composition and breakpoints of the rearranged X as well as methylation status of the X chromosomes. The high resolution array-CGH (assembly GRCh37/hg19) detected single copy for the whole chromosome X short arm. Two different sized segments of Xq arm were present in three copies: one large size of 80,3 Mb from Xq11.1 to Xq27.3 region and another smaller (11,1 Mb) from Xq27.3 to Xq28 region. An 1,6 Mb Xq27.3 region of the long arm was present in two copies. Southern blot analysis identified a skewed X inactivation with approximately 70:30 % ratios of methylated/unmethylated fragments. The G-band and FISH patterns of the rearranged X suggested the aspect of a restructured i(Xq) chromosome which was shattered and fortuitously repaired. The X-STR genotype analysis of the family detected that the patient inherited intact maternal X chromosome and a rearranged paternal X chromosome. The multiple Xq breakages and fusions as well as inverted duplication would have been expected to cause a severe Turner phenotype. However, the patient lacks many of the classic somatic features of Turner syndrome, instead she presented multiorgan autoimmune diseases. CONCLUSIONS: The clinical data of the presented patient suggest that fragmentation of the i(Xq) chromosome elevates the risk of autoimmune diseases

Citogenética de Próxima Geração: Implementação e primeiros resultados em Portugal

Abstract publicado em: Nascer e Crescer. 2016 fev 26; Supl1:S29.Especial XLV conferências de genética Doutor Jacinto Magalhães. Disponível em: http://revistas.rcaap.pt/nascercrescer/article/view/10542/7563Introdução: As alterações cromossómicas estruturais provocam doenças de severidade variável que acarretam sofrimento individual e familiar signifi cativo. Para compreensão da sua etiologia e estabelecimento de um possível prognóstico, uma adequada correlação fenótipo-genótipo é fundamental. O presente estudo faz parte do projeto intitulado àCitogenética de Próxima Geração Irrompe nos Cuidados de Saúde e Contribui para Anotação do Genoma Humanoà, que visa a introdu- ção da sequenciação de próxima geração (NGS) na citogené- tica clínica, tirando partido dessa inovação única na deteção de variantes estruturais, com uma resolução de um nucleótido para a criação de uma citogenética de alto rendimento, catalisadora de notáveis avanços no diagnóstico clínico e resulta da colaboração entre seis Instituições nacionais e a Harvard Medical School. Estima-se que exista um número considerável de indivíduos portadores de diversas patologias, incluindo algumas de início tardio associadas a rearranjos genómicos por identifi car. Assim, é fundamental a identifi cação e a referência destes indivíduos com possíveis rearranjos cromossómicos associados a doenças.FCT HMSP-ICT/0016/2013info:eu-repo/semantics/publishedVersio