Investigation on the relationship between violent death, cocaine abuse and single nucleotide polymorphisms / Estudo da relação entre morte violenta, uso de cocaína e polimorfismos de nucleotídeo único

Violence is a dreadful phenomenon spread throughout the world, resulting in unfortunate events that can ultimately cause death. It is known that some countries play a much worrying role in this scenario than others. Brazil is one of them. The present study has focused on identifying the use of cocaine within 105 postmortem cases arriving at the Institute of Legal Medicine of São Paulo (IML-SP) through analytic toxicological methods and latter applying genetic testing to see whether the presence of certain single nucleotide polymorphisms (SNPs) is more predominant within users rather than non-users, which would help to better understand one's susceptibility to abuse the drug. Both blood and hair samples have been analysed through ultra-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) in order to distinguish between recent or chronic cocaine use among violent individuals whose violence has ultimately leaded to their death. Two dilute-and-shoot methods have been validated and used for this purpose, and the final residue was analysed through the UPLC-ESIMS/ MS system. From the 105 postmortem cases, a rather high proportion of cocaine and its metabolites was found. A chronic use of the drug was denoted in 53% of the cases, which were positive for cocaine and benzoylecgonine, followed by 43% for norcocaine, 40% for cocaethylene and 13% for anhydroecgonine methyl ester, in hair. As for blood, reflecting the use of cocaine prior to death, 51% of the cases have shown to be positive for benzoylecgonine, followed by 41% for cocaine, 23% for cocaethylene and 20% for norcocaine. These findings suggest a probable association between the use of the drug and risky/violent behaviours. Genetic wise, a significant difference has been observed for SNP rs4263329 from the BCHE gene in its dominant model, with higher frequencies of the genotypes A/G and G/G seen in cocaine users rather than non-users (OR=8.91; 95%CI=1.58-50.21; ρ=0.01). Likewise, also SNP rs6280 from the DRD3> gene presented a significant association in both its additive and dominant model, suggesting that the C allele may be playing a role in cocaine use as both genotypes T/C and C/C were significantly more frequent in users than non-users. This association was not lost when adjusted for covariants using logistic regression (OR=4.96; 95%CI=1.07; ρ=0.04). Finally, a statistically significant association (ρ = 0.003) was also encountered among individuals with both A/G and G/G genotypes within SNP rs4263329 and the use of cocaine HCl (f(A/G+G/G)=44.7%) versus crack-cocaine (f(A/G+G/G)=7.7%) and nonusers (f(A/G+G/G)=16.2%). In conclusion, this study has found significant associations within two SNPs related to cocaine use, however, due to several inherent limitations, these must be confirmed by further studies with a higher number of subjects and within a more controlled setting. Definite assumptions may not be made at this point and future researches are to be conducted

A violência é um fenômeno aterrador espalhado por todo o mundo, resultando em eventos que podem, em última instância, causar a morte. Sabe-se que, em alguns países esse cenário é mais preocupante que em outros. O Brasil é um deles. O presente estudo teve como objetivo identificar o uso de cocaína em 105 casos postmortem provenientes do Instituto de Medicina Legal de São Paulo (IML-SP) por meio de métodos toxicológicos analíticos e posterior aplicação de testes genéticos para verificar se a presença de determinados polimorfismos de nucleotídeo único (SNPs) é mais predominante dentro dos usuários do que dos não usuários, o que explicaria uma possível suscetibilidade de um indivíduo ao abuso da droga. Amostras de sangue e cabelo foram analisadas através de cromatografia líquida de ultra-eficiência acoplada a espectrometria de massas e ionização por electrospray (UPLC-ESI-MS/MS) para distinguir entre uso recente ou crônico de cocaína entre indivíduos violentos cuja violência levou à sua morte. Para tal, dois métodos de extração baseados na técnica de "dilute-and-shoot" foram validados e utilizados para esse fim, e o resíduo final foi analisado através de um sistema UPLC-ESI-MS/MS. Dos 105 casos postmortem, foi encontrada uma proporção significativa de cocaína e seus produtos de biotransformação. O uso crônico da droga foi denotado em 53% dos casos, sendo estes positivos para cocaína e benzoilecgonina, seguidos de 43% para norcocaína, 40% para cocaetileno e 13% para anidroecgonina metil éster, no cabelo. Quanto ao sangue, refletindo o uso de cocaína antes da morte, 51% dos casos mostraram-se positivos para benzoilecgonina, seguido de 41% para cocaína, 23% para cocaetileno e 20% para norcocaína. Esses dados corroboram a hipótese provável da relação entre o uso da droga e comportamentos de risco/violentos. Quanto à genética, uma diferença significativa foi observada para o SNP rs4263329 do gene BCHE em seu modelo dominante, com maiores frequências dos genótipos A/G e G/G vistos em usuários de cocaína ao contrário de não usuários (OR=8,91; 95%IC=1,58-50,21; ρ=0,01). Da mesma forma, também o SNP rs6280 do gene DRD3 apresentou uma associação significativa tanto no seu modelo aditivo quanto dominante, sugerindo que o alelo C pode estar desempenhando um papel no uso de cocaína, pois ambos os genótipos T/C e C/C foram significativamente mais frequentes nos usuários do que não usuários. Essa associação não foi perdida quando ajustada para co-variáveis usando regressão logística (OR=4,96; 95%IC=1,07; ρ=0,04). Finalmente, uma associação estatisticamente significativa (ρ=0,003) também foi encontrada entre indivíduos com ambos os genótipos A/G e G/G dentro do SNP rs4263329 e o uso de cocaína HCl (f(A/G + G/G)=44,7%) versus crack (f(A/G + G/G)=7,7%) e não usuários (f(A/G + G/G)=16,2%). Em conclusão, este estudo encontrou associações significativas em dois SNPs relacionados ao uso de cocaína, no entanto, devido a várias limitações inerentes, estas devem ser confirmadas por mais estudos com um maior número de indivíduos e dentro de um cenário mais controlado. Hipóteses definitivas não poderão ser feitas neste momento e futuras pesquisas devem ser conduzidas

Cross-platform comparison of microarray-based multiple-class prediction.

High-throughput microarray technology has been widely applied in biological and medical decision-making research during the past decade. However, the diversity of platforms has made it a challenge to re-use and/or integrate datasets generated in different experiments or labs for constructing array-based diagnostic models. Using large toxicogenomics datasets generated using both Affymetrix and Agilent microarray platforms, we carried out a benchmark evaluation of cross-platform consistency in multiple-class prediction using three widely-used machine learning algorithms. After an initial assessment of model performance on different platforms, we evaluated whether predictive signature features selected in one platform could be directly used to train a model in the other platform and whether predictive models trained using data from one platform could predict datasets profiled using the other platform with comparable performance. Our results established that it is possible to successfully apply multiple-class prediction models across different commercial microarray platforms, offering a number of important benefits such as accelerating the possible translation of biomarkers identified with microarrays to clinically-validated assays. However, this investigation focuses on a technical platform comparison and is actually only the beginning of exploring cross-platform consistency. Further studies are needed to confirm the feasibility of microarray-based cross-platform prediction, especially using independent datasets.

A molecular bar-coded DNA repair resource for pooled toxicogenomic screens.

DNA damage from exogenous and endogenous sources can promote mutations and cell death. Fortunately, cells contain DNA repair and damage signaling pathways to reduce the mutagenic and cytotoxic effects of DNA damage. The identification of specific DNA repair proteins and the coordination of DNA repair pathways after damage has been a central theme to the field of genetic toxicology and we have developed a tool for use in this area. We have produced 99 molecular bar-coded Escherichia coli gene-deletion mutants specific to DNA repair and damage signaling pathways, and each bar-coded mutant can be tracked in pooled format using bar-code specific microarrays. Our design adapted bar-codes developed for the Saccharomyces cerevisiae gene-deletion project, which allowed us to utilize an available microarray product for pooled gene-exposure studies. Microarray-based screens were used for en masse identification of individual mutants sensitive to methyl methanesulfonate (MMS). As expected, gene-deletion mutants specific to direct, base excision, and recombinational DNA repair pathways were identified as MMS-sensitive in our pooled assay, thus validating our resource. We have demonstrated that molecular bar-codes designed for S. cerevisiae are transferable to E. coli, and that they can be used with pre-existing microarrays to perform competitive growth experiments. Further, when comparing microarray to traditional plate-based screens both overlapping and distinct results were obtained, which is a novel technical finding, with discrepancies between the two approaches explained by differences in output measurements (DNA content versus cell mass). The microarray-based classification of Deltatag and DeltadinG cells as depleted after MMS exposure, contrary to plate-based methods, led to the discovery that Deltatag and DeltadinG cells show a filamentation phenotype after MMS exposure, thus accounting for the discrepancy. A novel biological finding is the observation that while DeltadinG cells filament in response to MMS they exhibit wild-type sulA expression after exposure. This decoupling of filamentation from SulA levels suggests that DinG is associated with the SulA-independent filamentation pathway.

Application of visualization tools to the analysis of histopathological data enhances biological insight and interpretation.

Gene expression profiling, metabolomic screens, and other high-dimensional methods have become an integral part of many biological investigations. To facilitate interpretation of these data, it is important to have detailed phenotypic data--including histopathology--to which these data can be associated, or anchored. However, as the amount of phenotypic data increases, associations within and across these data can be difficult to visualize and interpret. We have developed an approach for categorizing and clustering biologically related histopathological diagnoses to facilitate their visualization, thereby increasing the possibility of identifying associations and facilitating the comparison with other data streams. In this study, we utilize histopathological data generated as part of a standardized toxicogenomics compendium study to generate composite histopathological scores and to develop visualizations that facilitate biological insight. The validity of this approach is illustrated by the identification of transcripts that correlate with the pathology diagnoses that comprise the categories of "response to hepatocellular injury" and "repair." This approach is broadly applicable to studies in which histopathology is used to phenotypically anchor other data, and results in visualizations that facilitate biological interpretation and the identification of associations and relationships within the data.