Estrategias estadístico-computacionales avanzadas para análisis de expresión de proteínas/genes en cáncer. Advanced statistical and computational strategies for protein/gene expression analysis in cancer.

El objetivo de este proyecto, enmarcado en el área de metodología de análisis en bioingeniería-biotecnología aplicadas al estudio del cancer, es el análisis y caracterización a través modelos estadísticos con efectos mixtos y técnicas de aprendizaje automático, de perfiles de expresión de proteínas y genes de las vías metabolicas asociadas a progresión tumoral. Dicho estudio se llevará a cabo mediante la utilización de tecnologías de alto rendimiento. Las mismas permiten evaluar miles de genes/proteínas en forma simultánea, generando así una gran cantidad de datos de expresión. Se hipotetiza que para un análisis e interpretación de la información subyacente, caracterizada por su abundancia y complejidad, podría realizarse mediante técnicas estadístico-computacionales eficientes en el contexto de modelos mixtos y técnias de aprendizaje automático. Para que el análisis sea efectivo es necesario contemplar los efectos ocasionados por los diferentes factores experimentales ajenos al fenómeno biológico bajo estudio. Estos efectos pueden enmascarar la información subycente y así perder informacion relavante en el contexto de progresión tumoral. La identificación de estos efectos permitirá obtener, eficientemente, los perfiles de expresión molecular que podrían permitir el desarrollo de métodos de diagnóstico basados en ellos. Con este trabajo se espera poner a disposición de investigadores de nuestro medio, herramientas y procedimientos de análisis que maximicen la eficiencia en el uso de los recursos asignados a la masiva captura de datos genómicos/proteómicos que permitan extraer información biológica relevante pertinente al análisis, clasificación o predicción de cáncer, el diseño de tratamientos y terapias específicos y el mejoramiento de los métodos de detección como así tambien aportar al entendimieto de la progresión tumoral mediante análisis computacional intensivo.

O polimorfismo VNTR no gene codificador do antagonista do receptor da interleucina-1 está associado com a doença arterial coronariana

FUNDAMENTO: A Doença Arterial Coronariana (DAC) é a aterosclerose das artérias coronárias que transportam o sangue para o coração. A aterosclerose é uma doença inflamatória. As variações gênicas das citocinas - como as associadas à família IL1 - fazem parte da patogênese da aterosclerose. OBJETIVO: O objetivo deste estudo foi determinar a relação entre os polimorfismos da família IL1 (VNTR do IL1RN, posições -511 e +3953 do IL1B) e a DAC na população turca. MÉTODOS: Um total de 427 indivíduos foram submetidos à angiografia coronariana e em seguida divididos da seguinte forma: 170 no grupo controle e 257 no grupo de pacientes com DAC. Os sujeitos com DAC foram divididos em dois subgrupos: 91 no grupo de Doença Coronariana em um único vaso (Single Vessel Disease - SVD) e 166 no grupo Doença Coronariana em múltiplos vasos (Multiple Vessel Disease - MVD). Os genótipos de IL1RN e IL1B (-511, +3953) foram determinados por reação em cadeia da polimerase (RCP), seguida de análise da digestão por enzima de restrição. RESULTADOS: Não foram observadas diferenças significantes nas distribuições de genótipos de IL1RN e IL1B (-511 e +3953) entre os sujeitos com DAC e os controles, ou entre sujeitos com MVD e controles. No entanto, observou-se uma relação significante no genótipo IL1RN 2/2 entre sujeitos portadores de SVD e controles (P= 0,016, x2: 10,289, OR: 2,94IC 95% 1,183 - 7,229). Tampouco foi observada diferença estatisticamente significante nas freqüências dos alelos de IL1RN e IL1B (-511 e +3953) entre os sujeitos com DAC e controles, os sujeitos com MVD e controles, ou ainda os sujeitos SVD e controles. CONCLUSÃO: Não foi observada nenhuma relação na freqüência alélica e nem na distribuição genotípica dos polimorfismos de IL1RN e IL1B entre sujeitos com DAC e grupos controle. No entanto, o genótipo IL1RN 2/2 pode representar um fator de risco para sujeitos com SVD na população turca.

Polimorfismo K121Q do gene ENPP1 e cardiopatia isquêmica em pacientes com diabete melito

FUNDAMENTO: O gene ecto-nucleotídeo pirofosfatase/fosfodiesterase 1 (ENPP1) é um gene candidato à resistência insulínica. A resistência à insulina é um componente importante da síndrome metabólica e tem sido implicada no desenvolvimento de doença cardíaca isquêmica (DCI). OBJETIVO: Avaliar a associação entre o polimorfismo K121Q do gene ENPP1 e a presença da DCI em pacientes caucasianos com diabete melito (DM) tipo 2. MÉTODOS: Estudo transversal foi realizado em pacientes com DM tipo 2 (n=573; 50,6% homens; idade 59,5±10,4 anos). DCI foi definida pela presença de angina ou infarto agudo do miocárdio pelo questionário cardiovascular da Organização Mundial da Saúde e/ou alterações compatíveis no ECG (código Minnesota) ou cintilografia miocárdica. O polimorfismo K121Q foi genotipado através da técnica de PCR e digestão enzimática. RESULTADOS: DCI esteve presente em 209 (36,5%) pacientes. A frequência dos genótipos KK, KQ e QQ entre os pacientes com DCI foi 60,8%, 34,4% e 4,8%, semelhante à distribuição dos genótipos entre os pacientes sem DCI (64,0%, 32,7% e 3,3%, P = 0,574). Não se observou diferença nas características clínicas ou laboratoriais entre os três genótipos, nem em relação à presença de síndrome metabólica. CONCLUSÃO: Nenhuma associação foi encontrada entre o polimorfismo K121A do gene ENPP1 e a presença de DCI ou características fenotípicas de resistência insulínica.

Efeitos da atorvastatina e do polimorfismo T-786C do gene eNOS sobre parâmetros do metabolismo lipídico plasmático

FUNDAMENTO: A atividade do óxido nítrico sintase endotelial (eNOS) pode ser modulada pelo colesterol da lipoproteína de alta densidade (HDL-C), estatinas ou polimorfismos, como o T-786C de eNOS. OBJETIVO: Este estudo teve como objetivo avaliar se o polimorfismo T-786C está associado a alterações nos efeitos da atorvastatina no perfil lipídico, nas concentrações de metabólitos de óxido nítrico (NO) e da proteína C reativa de alta sensibilidade (PCR-as). MÉTODOS: Trinta voluntários do sexo masculino, assintomáticos, com idade entre 18-56 anos foram genotipados e classificados de acordo com a ausência (TT, n = 15) ou presença (CC, n = 15) do polimorfismo. Eles foram selecionados aleatoriamente para a utilização de placebo e atorvastatina (10 mg/dia por 14 dias). Após cada tratamento foram medidos lípides, lipoproteínas, frações HDL2 e HDL3, atividade da proteína de transferência de colesteril éster (CETP), metabólitos de NO e PCR-as. RESULTADOS: As comparações entre genótipos após a administração de placebo mostraram aumento da atividade da CETP polimorfismo-dependente (TT, 12 ± 7; CC, 22 ± 12, p < 0,05). As análises da interação entre os tratamentos indicaram que a atorvastatina tem efeito sobre colesterol, LDL, nitrito e razões lípides/proteínas (HDL2 e HDL3) (p < 0,001) em ambos os genótipos. É interessante notar as interações genótipo/droga sobre a CETP (p < 0,07) e a lipoproteína (a) [Lp(a)] (p < 0,056), levando a uma diminuição limítrofe da CETP, embora sem afetar a Lp(a). A PRC-as não mostrou alterações. CONCLUSÃO: Os resultados sugerem que o tratamento com estatinas pode ser relevante para a prevenção primária da aterosclerose em pacientes com o polimorfismo T-786C do eNOS, considerando os efeitos no metabolismo lipídico.

O polimorfismo do gene AKL7 está associado ao risco de síndrome metabólica e à remodelação cardiovascular

FUNDAMENTO: Quinase Tipo Receptor de Ativina 7 (ALK7) é um tipo de receptor I para a superfamília TGF-β e recentemente apresentou ter uma função importante na manutenção de homeostase metabólica. OBJETIVO: Investigar a associação do polimorfismo do gene ALK7 à síndrome metabólica (SMet) e remodelação cardiovascular em pacientes com SMet. MÉTODOS: O polimorfismo de nucleotídeo único rs13010956 no gene ALK7 foi genotipado em 351 indivíduos chineses submetidos à ultrassonografia cardíaca e das carótidas. As associações do polimorfismo do gene ALK7 ao fenótipo e aos parâmetros da síndrome metabólica e características ultrassônicas cardiovasculares foram analisadas. RESULTADOS: O polimorfismo de rs13010956 no gene ALK7 foi considerado significativamente relacionado ao fenótipo de SMet em mulheres (p < 0,05) e significativamente associado à pressão sanguínea em populações totais (p < 0,05) e femininas (p < 0,01). Outras análises revelaram que rs13010956 estava associado à média da espessura íntima-média de artérias carótidas em mulheres (p < 0,05). Após o controle do índice de massa corporal, pressão arterial, glicemia em jejum e triglicérides, o rs13010956 também foi considerado significativamente associado ao índice de massa do ventrículo esquerdo em populações totais (p < 0,05) e femininas (p < 0,05). CONCLUSÃO: Nossos achados sugeriram que o polimorfismo de rs13010956 do gene ALK7 estava significativamente vinculado ao risco de SMet em mulheres e pode estar envolvido na remodelação cardiovascular em pacientes com SMet.

Analyse der Informationsverarbeitung in CHL1-defizienten Mäusen mittels metabolischer Markierung, Expressionsstudien der Immediate-Early-Gene c-fos und arg3.1/arc sowie verhaltensbiologischer Tests

Close homolog of L1, neural cell recognition molecules, c-fos, arg3.1, arc, immediat early genes, novelty, information processing, behavioral tests

Effects of neural nitric oxide synthase gene inactivation on the neurodocrine stress response in mice

Neural nitric oxide synthase, neuroendocrine stress response, forced swimming, nNOS KO mice, hypothalamus, adrenal gland

APOE and LDLR Gene Polymorphisms and Dyslipidemia Tracking. Rio de Janeiro Study

Background:Studies show an association between changes in apolipoprotein E (ApoE) and LDLR receptor with the occurrence of dyslipidemia.Objectives:To investigate the association between polymorphisms of the APOE (ε2, ε3, ε4) and LDLR (A370T) genes with the persistence of abnormal serum lipid levels in young individuals followed up for 17 years in the Rio de Janeiro Study.Methods:The study included 56 individuals (35 males) who underwent three assessments at different ages: A1 (mean age 13.30 ± 1.53 years), A2 (22.09 ± 1.91 years) and A3 (31.23 ± 1.99 years). Clinical evaluation with measurement of blood pressure (BP) and body mass index (BMI) was conducted at all three assessments. Measurement of waist circumference (WC) and serum lipids, and analysis of genetic polymorphisms by PCR-RFLP were performed at A2 and A3. Based on dyslipidemia tracking, three groups were established: 0 (no abnormal lipid value at A2 and A3), 1 (up to one abnormal lipid value at A2 or A3) and 2 (one or more abnormal lipid values at A2 and A3).Results:Compared with groups 0 and 1, group 2 presented higher mean values of BP, BMI, WC, LDL-c and TG (p < 0.01) and lower mean values of HDL-c (p = 0.001). Across the assessments, all individuals with APOE genotypes ε2/ε4 and ε4/ε4 maintained at least one abnormal lipid variable, whereas those with genotype ε2/ε3 did not show abnormal values (χ2 = 16.848, p = 0.032). For the LDLR genotypes, there was no significant difference among the groups.Conclusions:APOE gene polymorphisms were associated with dyslipidemia in young individuals followed up longitudinally from childhood.

A ação dos gens gametofíticos com referência especial ao milho

1) The first part deals with the different processes which may complicate Mendelian segregation and which may be classified into three groups, according to BRIEGER (1937b) : a) Instability of genes, b) Abnormal segregation due to distur- bances during the meiotic divisions, c) obscured segregation, after a perfectly normal meiosis, caused by elimination or during the gonophase (gametophyte in higher plants), or during zygophase (sporophyte). Without entering into detail, it is emphasized that all the above mentioned complications in the segregation of some genes may be caused by the action of other genes. Thus in maize, the instability of the Al factor is observed only when the gene dt is presente in the homozygous conditions (RHOADES 1938). In another case, still under observation in Piracicaba, an instability is observed in Mirabilis with regard to two pairs of alleles both controlling flower color. Several cases are known, especially in corn, where recessive genes, when homozigous, affect the course of meiosis, causing asynapsis (asyndesis) (BEADLE AND MC CLINTOCK 1928, BEADLE 1930), sticky chromosomes (BEADLE 1932), supermunmerary divisions (BEADLE 1931). The most extreme case of an obscured segregatiou is represented by the action of the S factors in self stetrile plants. An additional proof of EAST AND MANGELSDORF (1925) genetic formula of self sterility has been contributed by the studies on Jinked factors in Nicotina (BRIEGER AND MANGELSDORF (1926) and Antirrhinum (BRIEGER 1930, 1935), In cases of a incomplete competition and selection between pollen tubes, studies of linked indicator-genes are indispensable in the genetic analysis, since it is impossible to analyse the factors for gametophyte competition by direct aproach. 2) The flower structure of corn is explained, and stated that the particularites of floral biology make maize an excellent object for the study of gametophyte factors. Since only one pollen tube per ovule may accomplish fertilization, the competition is always extremely strong, as compared with other species possessing multi-ovulate ovaries. The lenght of the silk permitts the study of pollen tube competitions over a varying distance. Finally the genetic analysis of grains characters (endosperm and aleoron) simpliflen the experimental work considerably, by allowing the accumulation of large numbers for statistical treatment. 3) The four methods for analyzing the naturing of pollen tube competition are discussed, following BRIEGER (1930). Of these the first three are: a) polinization with a small number of pollen grains, b) polinization at different times and c) cut- ting the style after the faster tubes have passe dand before the slower tubes have reached the point where the stigma will be cut. d) The fourth method, alteration of the distatice over which competition takes place, has been applied largely in corn. The basic conceptions underlying this process, are illustrated in Fig. 3. While BRINK (1925) and MANGELSDORF (1929) applied pollen at different levels on the silks, the remaining authors (JONES, 1922, MANGELSDORF 1929, BRIEGER, at al. 1938) have used a different process. The pollen was applied as usual, after removing the main part of the silks, but the ears were divided transversally into halves or quarters before counting. The experiments showed generally an increase in the intensity of competition when there was increase of the distance over which they had to travel. Only MANGELSDORF found an interesting exception. When the distance became extreme, the initially slower tubes seemed to become finally the faster ones. 4) Methods of genetic and statistical analysis are discussed, following chiefly BRIEGER (1937a and 1937b). A formula is given to determine the intensity of ellimination in three point experiments. 5) The few facts are cited which give some indication about the physiological mechanism of gametophyte competition. They are four in number a) the growth rate depends-only on the action of gametophyte factors; b) there is an interaction between the conductive tissue of the stigma or style and the pollen tubes, mainly in self-sterile plants; c) after self-pollination necrosis starts in the tissue of the stigma, in some orchids after F. MÜLLER (1867); d) in pollon mixtures there is an inhibitory interaction between two types of pollen and the female tissue; Gossypium according to BALLS (1911), KEARNEY 1923, 1928, KEARNEY AND HARRISON (1924). A more complete discussion is found in BRIEGER 1930). 6) A list of the gametophyte factors so far localized in corn is given. CHROMOSOME IV Ga 1 : MANGELSDORF AND JONES (1925), EMERSON 1934). Ga 4 : BRIEGER (1945b). Sp 1 : MANGELSDORF (1931), SINGLETON AND MANGELSDORF (1940), BRIEGER (1945a). CHROMOSOME V Ga 2 : BRIEGER (1937a). CHROMOSOME VI BRIEGER, TIDBURY AND TSENG (1938) found indications of a gametophyte factor altering the segregation of yellow endosperm y1. CHROMOSOME IX Ga 3 : BRIEGER, TIDBURY AND TSENG (1938). While the competition in these six cases is essentially determined by one pair of factors, the degree of elimination may be variable, as shown for Ga2 (BRIEGER, 1937), for Ga4 (BRIEGER 1945a) and for Spl (SINGLETON AND MANGELSDORF 1940, BRIEGER 1945b). The action of a gametophyte factor altering the segregation of waxy (perhaps Ga3) is increased by the presence of the sul factor which thus acts as a modifier (BRINCK AND BURNHAM 1927). A polyfactorial case of gametophyte competition has been found by JONES (1922) and analysed by DEMEREC (1929) in rice pop corn which rejects the pollen tubes of other types of corn. Preference for selfing or for brothers-sister mating and partial elimination of other pollen tubes has been described by BRIEGER (1936). 7) HARLAND'S (1943) very ingenious idea is discussed to use pollen tube factors in applied genetics in order to build up an obstacle to natural crossing as a consequence of the rapid pollen tube growth after selfing. Unfortunately, HARLAND could not obtain the experimental proof of the praticability of his idea, during his experiments on selection for minor modifiers for pollen tube grouth in cotton. In maize it should be possible to employ gametophyte factors to build up lines with preference for crossing, though the method should hardly be of any practical advantage.

mRNA metabolism: nonsense mediated mRNA decay as a tool for gene therapy and the role of human DIS3L2 in transcript degradation

Tese de mestrado em Biologia Humana e Ambiente, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2015

Changes in reproductive roles are associated with changes in gene expression in fire ant queens.

Abstract In species with social hierarchies, the death of dominant individuals typically upheaves the social hierarchy and provides an opportunity for subordinate individuals to become reproductives. Such a phenomenon occurs in the monogyne form of the fire ant, Solenopsis invicta, where colonies typically contain a single wingless reproductive queen, thousands of workers and hundreds of winged nonreproductive virgin queens. Upon the death of the mother queen, many virgin queens shed their wings and initiate reproductive development instead of departing on a mating flight. Workers progressively execute almost all of them over the following weeks. To identify the molecular changes that occur in virgin queens as they perceive the loss of their mother queen and begin to compete for reproductive dominance, we collected virgin queens before the loss of their mother queen, 6 h after orphaning and 24 h after orphaning. Their RNA was extracted and hybridized against microarrays to examine the expression levels of approximately 10 000 genes. We identified 297 genes that were consistently differentially expressed after orphaning. These include genes that are putatively involved in the signalling and onset of reproductive development, as well as genes underlying major physiological changes in the young queens.

IFN stimulated gene expression in the liver is a better predictor of treatment response in chronic hepatitis c than the IL28b (IFN lambda 3) genotype

Background: Therapy of chronic hepatitis C (CHC) with pegIFNa/ribavirin achieves sustained virologic response (SVR) in ~55%. Pre-activation of the endogenous interferon system in the liver is associated non-response (NR). Recently, genome-wide association studies described associations of allelic variants near the IL28B (IFNλ3) gene with treatment response and with spontaneous clearance of the virus. We investigated if the IL28B genotype determines the constitutive expression of IFN stimulated genes (ISGs) in the liver of patients with CHC. Methods: We genotyped 93 patients with CHC for 3 IL28B single nucleotide polymorphisms (SNPs, rs12979860, rs8099917, rs12980275), extracted RNA from their liver biopsies and quantified the expression of IL28B and of 8 previously identified classifier genes which discriminate between SVR and NR (IFI44L, RSAD2, ISG15, IFI22, LAMP3, OAS3, LGALS3BP and HTATIP2). Decision tree ensembles in the form of a random forest classifier were used to calculate the relative predictive power of these different variables in a multivariate analysis. Results: The minor IL28B allele (bad risk for treatment response) was significantly associated with increased expression of ISGs, and, unexpectedly, with decreased expression of IL28B. Stratification of the patients into SVR and NR revealed that ISG expression was conditionally independent from the IL28B genotype, i.e. there was an increased expression of ISGs in NR compared to SVR irrespective of the IL28B genotype. The random forest feature score (RFFS) identified IFI27 (RFFS = 2.93), RSAD2 (1.88) and HTATIP2 (1.50) expression and the HCV genotype (1.62) as the strongest predictors of treatment response. ROC curves of the IL28B SNPs showed an AUC of 0.66 with an error rate (ERR) of 0.38. A classifier with the 3 best classifying genes showed an excellent test performance with an AUC of 0.94 and ERR of 0.15. The addition of IL28B genotype information did not improve the predictive power of the 3-gene classifier. Conclusions: IL28B genotype and hepatic ISG expression are conditionally independent predictors of treatment response in CHC. There is no direct link between altered IFNλ3 expression and pre-activation of the endogenous system in the liver. Hepatic ISG expression is by far the better predictor for treatment response than IL28B genotype.

Flippase (FLP) recombinase-mediated marker recycling in the dermatophyte Arthroderma vanbreuseghemii.

Biological processes can be elucidated by investigating complex networks of relevant factors and genes. However, this is not possible in species for which dominant selectable markers for genetic studies are unavailable. To overcome the limitation in selectable markers for the dermatophyte Arthroderma vanbreuseghemii (anamorph: Trichophyton mentagrophytes), we adapted the flippase (FLP) recombinase-recombination target (FRT) site-specific recombination system from the yeast Saccharomyces cerevisiae as a selectable marker recycling system for this fungus. Taking into account practical applicability, we designed FLP/FRT modules carrying two FRT sequences as well as the flp gene adapted to the pathogenic yeast Candida albicans (caflp) or a synthetic codon-optimized flp (avflp) gene with neomycin resistance (nptII) cassette for one-step marker excision. Both flp genes were under control of the Trichophyton rubrum copper-repressible promoter (PCTR4). Molecular analyses of resultant transformants showed that only the avflp-harbouring module was functional in A. vanbreuseghemii. Applying this system, we successfully produced the Ku80 recessive mutant strain devoid of any selectable markers. This strain was subsequently used as the recipient for sequential multiple disruptions of secreted metalloprotease (fungalysin) (MEP) or serine protease (SUB) genes, producing mutant strains with double MEP or triple SUB gene deletions. These results confirmed the feasibility of this system for broad-scale genetic manipulation of dermatophytes, advancing our understanding of functions and networks of individual genes in these fungi.

Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.

Metabolic traits are molecular phenotypes that can drive clinical phenotypes and may predict disease progression. Here, we report results from a metabolome- and genome-wide association study on (1)H-NMR urine metabolic profiles. The study was conducted within an untargeted approach, employing a novel method for compound identification. From our discovery cohort of 835 Caucasian individuals who participated in the CoLaus study, we identified 139 suggestively significant (P<5×10(-8)) and independent associations between single nucleotide polymorphisms (SNP) and metabolome features. Fifty-six of these associations replicated in the TasteSensomics cohort, comprising 601 individuals from São Paulo of vastly diverse ethnic background. They correspond to eleven gene-metabolite associations, six of which had been previously identified in the urine metabolome and three in the serum metabolome. Our key novel findings are the associations of two SNPs with NMR spectral signatures pointing to fucose (rs492602, P = 6.9×10(-44)) and lysine (rs8101881, P = 1.2×10(-33)), respectively. Fine-mapping of the first locus pinpointed the FUT2 gene, which encodes a fucosyltransferase enzyme and has previously been associated with Crohn's disease. This implicates fucose as a potential prognostic disease marker, for which there is already published evidence from a mouse model. The second SNP lies within the SLC7A9 gene, rare mutations of which have been linked to severe kidney damage. The replication of previous associations and our new discoveries demonstrate the potential of untargeted metabolomics GWAS to robustly identify molecular disease markers.