Using genomics for drug discovery in medulloblastoma

Tese de doutoramento, Medicina (Neurocirurgia), Universidade de Lisboa, Faculdade de Medicina, 2014

Harmonization guidelines for HLA-peptide multimer assays derived from results of a large scale international proficiency panel of the Cancer Vaccine Consortium.

PURPOSE: The Cancer Vaccine Consortium of the Cancer Research Institute (CVC-CRI) conducted a multicenter HLA-peptide multimer proficiency panel (MPP) with a group of 27 laboratories to assess the performance of the assay. EXPERIMENTAL DESIGN: Participants used commercially available HLA-peptide multimers and a well characterized common source of peripheral blood mononuclear cells (PBMC). The frequency of CD8+ T cells specific for two HLA-A2-restricted model antigens was measured by flow cytometry. The panel design allowed for participants to use their preferred staining reagents and locally established protocols for both cell labeling, data acquisition and analysis. RESULTS: We observed significant differences in both the performance characteristics of the assay and the reported frequencies of specific T cells across laboratories. These results emphasize the need to identify the critical variables important for the observed variability to allow for harmonization of the technique across institutions. CONCLUSIONS: Three key recommendations emerged that would likely reduce assay variability and thus move toward harmonizing of this assay. (1) Use of more than two colors for the staining (2) collect at least 100,000 CD8 T cells, and (3) use of a background control sample to appropriately set the analytical gates. We also provide more insight into the limitations of the assay and identified additional protocol steps that potentially impact the quality of data generated and therefore should serve as primary targets for systematic analysis in future panels. Finally, we propose initial guidelines for harmonizing assay performance which include the introduction of standard operating protocols to allow for adequate training of technical staff and auditing of test analysis procedures.

The relationship between subjective experiences during first use of tobacco and cannabis and the effect of the substance experienced first.

INTRODUCTION: We examined the positive and negative subjective feelings associated with initial tobacco and cannabis use as well as the role of these experiences in regular use. Additionally, we investigated the effect of the first substance experienced on initial subjective experiences and later regular use. METHODS: Baseline data from a representative sample of young Swiss men were obtained from an ongoing Cohort Study on Substance Use Risk Factors, which includes 2,321 lifetime tobacco and cannabis users. We assessed the age of first tobacco and cannabis use along with the subjective experiences associated with initial use. Additionally, subjective experiences related to regular use of both substances were analyzed. RESULTS: The initial subjective experiences were divided into positive and negative for each substance, and we found that the feelings associated with first use of tobacco and cannabis were similar. Moreover, the participants who used cannabis before tobacco reported fewer negative experiences associated with first tobacco use, whereas the participants who initially used tobacco reported more negative experiences related to first cannabis use. Also, we identified that regular use was encouraged by positive experiences and that negative experiences were more adverse for regular use of cannabis compared with tobacco. CONCLUSIONS: Taken together, these results indicate that similar subjective experiences were associated with the first use of tobacco and cannabis. Also, the use of cannabis before tobacco, which occurred in only a minority of users, had the potential to enhance the effects of initial tobacco use.

Profiles of drug users in Switzerland and effects of early-onset intensive use of alcohol, tobacco and cannabis on other illicit drug use.

QUESTIONS UNDER STUDY / PRINCIPLES: The main aim of this study was to investigate profiles of drug users, with a particular focus on illicit drugs other than cannabis, and to explore the effect of early-onset intensive use (drunkenness, daily smoking, high on cannabis) on profiles of illicit drug use. METHODS: Baseline data from a representative sample of 5,831 young Swiss men in the ongoing Cohort Study on Substance Use Risk Factors were used. Substance use (alcohol, tobacco, cannabis and 15 types of other illicit drug) and age of onset of intensive use were assessed. The Item Response Theory (IRT) and prevalence rates at different ages of onset were used to reveal different profiles of illicit drug use. RESULTS: In addition to cannabis, there were two profiles of other illicit drug use: (a) "softer" drug users (uppers, hallucinogens and inhaled drugs), among which ecstasy had the highest discriminatory potential (IRT slope = 4.68, standard error (SE) = 0.48; p <0.001); and (b) "harder" drug users (heroin, ketamine, gamma-hydroxybutyrate/gamma-hydroxylactone, research chemicals, crystal meth and spice), among which ketamine had the highest discriminatory potential (slope = 4.05; SE = 0.63; p <0.001). Onset of intensive use at the age of 12 years or younger also discriminated between these two profiles. CONCLUSION: Both the IRT model and the effect of onset of intensive use enabled two groups of illicit drugs to be identified. In particular, very early onset (at 12 years or younger) intensive use of any substance was a marker for later use of the second group of drugs.

E-Cigarettes: A Review of New Trends in Cannabis Use.

The emergence of electronic cigarettes (e-cigs) has given cannabis smokers a new method of inhaling cannabinoids. E-cigs differ from traditional marijuana cigarettes in several respects. First, it is assumed that vaporizing cannabinoids at lower temperatures is safer because it produces smaller amounts of toxic substances than the hot combustion of a marijuana cigarette. Recreational cannabis users can discretely "vape" deodorized cannabis extracts with minimal annoyance to the people around them and less chance of detection. There are nevertheless several drawbacks worth mentioning: although manufacturing commercial (or homemade) cannabinoid-enriched electronic liquids (e-liquids) requires lengthy, complex processing, some are readily on the Internet despite their lack of quality control, expiry date, and conditions of preservation and, above all, any toxicological and clinical assessment. Besides these safety problems, the regulatory situation surrounding e-liquids is often unclear. More simply ground cannabis flowering heads or concentrated, oily THC extracts (such as butane honey oil or BHO) can be vaped in specially designed, pen-sized marijuana vaporizers. Analysis of a commercial e-liquid rich in cannabidiol showed that it contained a smaller dose of active ingredient than advertised; testing our laboratory-made, purified BHO, however, confirmed that it could be vaped in an e-cig to deliver a psychoactive dose of THC. The health consequences specific to vaping these cannabis preparations remain largely unknown and speculative due to the absence of comprehensive, robust scientific studies. The most significant health concerns involve the vaping of cannabinoids by children and teenagers. E-cigs could provide an alternative gateway to cannabis use for young people. Furthermore, vaping cannabinoids could lead to environmental and passive contamination.

Changes in cannabis and tobacco use trajectories from age 17 to age 23

Much like the first volume published in 2011, the second volume of this anthology series gathers a selection of analyses which are empirically based on the data of the Swiss panel study TREE (Transitions from Education to Employment). The contributions of this volume carry on the investigation of the critical transitions during youth and young adulthood, drawing on sociological, economic, psychological and pedagogical research questions and thus highlighting the analytic and pluri-disciplinary research potential of the TREE data. One of the topical foci is the long-term influence of social origin on education and labour market pathways, particularly with regard to access to higher education.

L’évaluation du risque comme facteur influençant les opinions et comportements en lien avec le tabac et le cannabis

S’inscrivant dans le cadre d’une étude pancanadienne portant sur la normalisation du cannabis et la stigmatisation du tabac, le principal objectif de cette recherche était de comprendre quelle place occupe l’évaluation des risques dans la compréhension des perceptions et comportements liés aux deux substances. Pour ce faire, à partir d’un devis mixte – quantitatif et qualitatif, nous avons 1) décrit les perceptions et opinions des participants quant à leur propre consommation de cannabis et/ou de tabac et quant à la consommation que font les gens en général des mêmes substances. Nous avons aussi 2) décrit comment les participants évaluent les risques liés à chacune des substances. Enfin, sachant que la perception du risque est intimement liée au comportement d’un individu, nous avons cherché 3) à préciser comment l’évaluation du risque agit sur les comportements et les opinions des quelques 50 participants, hommes et femmes âgés entre 20 et 49 ans, bien intégrés socialement, envers le tabac et le cannabis. Il s’avère que les fumeurs de cannabis, qui ont insisté sur la distinction à faire entre la manière dont ils font usage de la substance et une consommation abusive, valorisait le contrôle que leur permettait, selon eux, la consommation de cannabis. La consommation de cigarettes, quant à elle, était perçue négativement pour des raisons opposées puisque de l’avis des participants à l’étude, elle engendrerait chez le fumeur une incapacité à se maîtriser et un besoin compulsif de fumer. Dans cette optique, les risques liés au cannabis étaient perçus, par la plupart, comme étant contrôlables, à l’exception du jugement d’autrui qui demeurerait incertain et sur lequel il serait impossible d’avoir du contrôle. La réaction de certaines personnes de leur entourage étant ou bien imprévisible ou négative, c’est ce qui les amènerait à fumer principalement en privé. Le contrôle social formel aurait finalement peu d’influence étant donné le fort sentiment qu’ont les répondants qu’il ne s’appliquera tout simplement pas à eux.

Le rôle modérateur de la pratique d’un sport organisé dans la relation entre les amis déviants et l’intoxication à l’alcool et la consommation de cannabis à l’adolescence

La consommation de substances psychoactives débute généralement à l’adolescence. Cette pratique, bien qu’illégale, est répandue à cet âge. Toutefois, elle peut avoir de graves répercussions sur le développement de l’individu. Il est important de mieux connaître les facteurs pouvant influencer sa fréquence d’utilisation afin d’en diminuer les risques. Ce mémoire vise à examiner le rôle des amis déviants et de la pratique d’un sport organisé dans le développement de l’intoxication à l’alcool et la consommation de cannabis à l’adolescence. Plus précisément, l’étude vise à déterminer si la pratique d’un sport organisé a des effets modérateurs sur la relation entre les amis déviants et l’intoxication à l’alcool et la consommation de cannabis. Les analyses ont été réalisées séparément pour l’alcool et le cannabis. L’échantillon utilisé provient de l’étude longitudinale de la Stratégie d’Intervention Agir Autrement et comprend 4219 adolescents. Des régressions probit ont été effectuées. Tel qu’attendu, les résultats montrent que la fréquentation d’amis déviants est associée au risque d’intoxication à l’alcool et de consommation de cannabis. De plus, les résultats ont démontré le rôle modérateur protecteur de la pratique d’un sport organisé pour l’alcool. Un jeune qui a des amis déviants et qui participe à un sport organisé consommerait généralement moins d’alcool qu’un jeune qui a des amis déviants et qui ne participe pas une activité sportive organisée. Les implications de ces résultats pour la recherche sont discutées.

Consommation de cannabis et symptômes dépressifs à l'adolescence : le rôle modérateur de la qualité de la relation parent-adolescent

La dépression est une psychopathologie répandue qui débute fréquemment au cours de l’adolescence. Maintes répercussions tant personnelles qu’économiques et sociales ont été associées à ce trouble. Plusieurs facteurs, dont la consommation de cannabis, ont été identifiés comme étant susceptibles d’influencer l’apparition et le développement de symptômes dépressifs. Il existe toutefois une absence de consensus par rapport au lien entre la consommation de cannabis et les symptômes dépressifs à l’adolescence, qui pourrait notamment résulter de différences méthodologiques telles que le contrôle de tierces variables. Parmi ces variables, la relation parent-adolescent pourrait modérer la relation entre la consommation de cannabis et les symptômes dépressifs. Ce mémoire vise d’une part à vérifier la relation entre la consommation de cannabis et la manifestation de symptômes dépressifs à l’adolescence et, d’autre part, le rôle modérateur de la relation parent-adolescent sur ce lien. L’échantillon compte 1 740 adolescents québécois suivis longitudinalement du secondaire II au secondaire IV. Des analyses de régression multiple hiérarchique ont été effectuées afin de tester les hypothèses à l’étude. Les résultats démontrent une faible relation positive entre la consommation de cannabis en secondaire II et les symptômes dépressifs évalués deux ans plus tard. Par ailleurs, une seule dimension de la relation parent-adolescent, soit le faible soutien parental, a été identifiée comme ayant un pouvoir prédictif sur les symptômes dépressifs. Cet effet d’interaction explique néanmoins une variance insuffisante pour être significatif d’un point de vue clinique. Les implications de ces résultats pour la recherche sont discutées.

The dynamics of local hiv-1 epidemics: the colombian and belgian cohorts

We aimed to characterize the HIV-1 epidemic of the Belgian and Colombian cohorts using an integrated approach that includes socio-demographic information, clinical data, and viral sequences, analyzed with statistical and phylogenetic approaches.

Models, mathematics and meaning in interdisciplinary research

Interdisciplinary research presents particular challenges for unambiguous communication. Frequently, the meanings of words differ markedly between disciplines, leading to apparent consensus masking fundamental misunderstandings. Researchers can agree on the need for models, but conceive of models fundamentally differently. While mathematics is frequently seen as an elitist language reinforcing disciplinary distinctions, both mathematics and modelling can also offer scope to bridge disciplinary epistemological divisions and create common ground on which very different disciplines can meet. This paper reflects on the role and scope for mathematics and modelling to present a common epistemological space in interdisciplinary research spanning the social, natural and engineering sciences.

The challenges for molecular nutrition research 1: linking genotype to healthy nutrition

Nutrition science finds itself at a major crossroad. On the one hand we can continue the current path, which has resulted in some substantial advances, but also many conflicting messages which impair the trust of the general population, especially those who are motivated to improve their health through diet. The other road is uncharted and is being built over the many exciting new developments in life sciences. This new era of nutrition recognizes the complex relation between the health of the individual, its genome, and the life-long dietary exposure, and has lead to the realisation that nutrition is essentially a gene - environment interaction science. This review on the relation between genotype, diet and health is the first of a series dealing with the major challenges in molecular nutrition, analyzing the foundations of nutrition research. With the unravelling of the human genome and the linking of its variability to a multitude of phenotypes from " healthy'' to an enormously complex range of predispositions, the dietary modulation of these propensities has become an area of active research. Classical genetic approaches applied so far in medical genetics have steered away from incorporating dietary effects in their models and paradoxically, most genetic studies analyzing diet-associated phenotypes and diseases simply ignore diet. Yet, a modest but increasing number of studies are accounting for diet as a modulator of genetic associations. These range from observational cohorts to intervention studies with prospectively selected genotypes. New statistical and bioinformatics approaches are becoming available to aid in design and evaluation of these studies. This review discusses the various approaches used and provides concrete recommendations for future research.

Cannabis sativa and the endogenous cannabinoid system: therapeutic potential for appetite regulation

The herb Cannabis sativa (C. sativa) has been used in China and on the Indian subcontinent for thousands of years as a medicine. However, since it was brought to the UK and then the rest of the western world in the late 19th century, its use has been a source of controversy. Indeed, its psychotropic side effects are well reported but only relatively recently has scientific endeavour begun to find valuable uses for either the whole plant or its individual components. Here, we discuss evidence describing the endocannabinoid system, its endogenous and exogenous ligands and their varied effects on feeding cycles and meal patterns. Furthermore we also critically consider the mounting evidence which suggests non‐tetrahydrocannabinol phytocannabinoids play a vital role in C. sativa‐induced feeding pattern changes. Indeed, given the wide range of phytocannabinoids present in C. sativa and their equally wide range of intra‐, inter‐ and extra‐cellular mechanisms of action, we demonstrate that non‐Δ9tetrahydrocannabinol phytocannabinoids retain an important and, as yet, untapped clinical potential.