Integrated methodologies to study human transcriptional regulation from functional genomics data

Abstract : The human body is composed of a huge number of cells acting together in a concerted manner. The current understanding is that proteins perform most of the necessary activities in keeping a cell alive. The DNA, on the other hand, stores the information on how to produce the different proteins in the genome. Regulating gene transcription is the first important step that can thus affect the life of a cell, modify its functions and its responses to the environment. Regulation is a complex operation that involves specialized proteins, the transcription factors. Transcription factors (TFs) can bind to DNA and activate the processes leading to the expression of genes into new proteins. Errors in this process may lead to diseases. In particular, some transcription factors have been associated with a lethal pathological state, commonly known as cancer, associated with uncontrolled cellular proliferation, invasiveness of healthy tissues and abnormal responses to stimuli. Understanding cancer-related regulatory programs is a difficult task, often involving several TFs interacting together and influencing each other's activity. This Thesis presents new computational methodologies to study gene regulation. In addition we present applications of our methods to the understanding of cancer-related regulatory programs. The understanding of transcriptional regulation is a major challenge. We address this difficult question combining computational approaches with large collections of heterogeneous experimental data. In detail, we design signal processing tools to recover transcription factors binding sites on the DNA from genome-wide surveys like chromatin immunoprecipitation assays on tiling arrays (ChIP-chip). We then use the localization about the binding of TFs to explain expression levels of regulated genes. In this way we identify a regulatory synergy between two TFs, the oncogene C-MYC and SP1. C-MYC and SP1 bind preferentially at promoters and when SP1 binds next to C-NIYC on the DNA, the nearby gene is strongly expressed. The association between the two TFs at promoters is reflected by the binding sites conservation across mammals, by the permissive underlying chromatin states 'it represents an important control mechanism involved in cellular proliferation, thereby involved in cancer. Secondly, we identify the characteristics of TF estrogen receptor alpha (hERa) target genes and we study the influence of hERa in regulating transcription. hERa, upon hormone estrogen signaling, binds to DNA to regulate transcription of its targets in concert with its co-factors. To overcome the scarce experimental data about the binding sites of other TFs that may interact with hERa, we conduct in silico analysis of the sequences underlying the ChIP sites using the collection of position weight matrices (PWMs) of hERa partners, TFs FOXA1 and SP1. We combine ChIP-chip and ChIP-paired-end-diTags (ChIP-pet) data about hERa binding on DNA with the sequence information to explain gene expression levels in a large collection of cancer tissue samples and also on studies about the response of cells to estrogen. We confirm that hERa binding sites are distributed anywhere on the genome. However, we distinguish between binding sites near promoters and binding sites along the transcripts. The first group shows weak binding of hERa and high occurrence of SP1 motifs, in particular near estrogen responsive genes. The second group shows strong binding of hERa and significant correlation between the number of binding sites along a gene and the strength of gene induction in presence of estrogen. Some binding sites of the second group also show presence of FOXA1, but the role of this TF still needs to be investigated. Different mechanisms have been proposed to explain hERa-mediated induction of gene expression. Our work supports the model of hERa activating gene expression from distal binding sites by interacting with promoter bound TFs, like SP1. hERa has been associated with survival rates of breast cancer patients, though explanatory models are still incomplete: this result is important to better understand how hERa can control gene expression. Thirdly, we address the difficult question of regulatory network inference. We tackle this problem analyzing time-series of biological measurements such as quantification of mRNA levels or protein concentrations. Our approach uses the well-established penalized linear regression models where we impose sparseness on the connectivity of the regulatory network. We extend this method enforcing the coherence of the regulatory dependencies: a TF must coherently behave as an activator, or a repressor on all its targets. This requirement is implemented as constraints on the signs of the regressed coefficients in the penalized linear regression model. Our approach is better at reconstructing meaningful biological networks than previous methods based on penalized regression. The method is tested on the DREAM2 challenge of reconstructing a five-genes/TFs regulatory network obtaining the best performance in the "undirected signed excitatory" category. Thus, these bioinformatics methods, which are reliable, interpretable and fast enough to cover large biological dataset, have enabled us to better understand gene regulation in humans.

Shared decision making development in Switzerland: room for improvement!

In Switzerland there is a strong movement at a national policy level towards strengthening patient rights and patient involvement in health care decisions. Yet, there is no national programme promoting shared decision making. First decision support tools (prenatal diagnosis and screening) for the counselling process have been developed and implemented. Although Swiss doctors acknowledge that shared decision making is important, hierarchical structures and asymmetric physician-patient relationships are still prevailing. The last years have seen some promising activities regarding the training of medical students and the development of patient support programmes. Swiss direct democracy and the habit of consensual decision making and citizen involvement in general may provide a fertile ground for SDM development in the primary care setting.

Integrated Ladinian bio-chronostratigraphy and geochrononology of Monte San Giorgio (Southern Alps, Switzerland)

New biostratigraphic data significantly improve the age assignment of the Ladinian succession of Monte San Giorgio (UNESCO World Heritage List site, Southern Alps, Switzerland), whose world-famous fossil marine vertebrate faunas are now dated to the substage and zone levels. High-resolution single-zircon U-Pb dating was performed using ID-TIMS and chemical abrasion (CA) pre-treatment technique on volcanic ash layers intercalated in the biostratigraphically-defined intervals of the Meride Limestone. It yielded ages of 241.07 +/- 0.13 Ma (Cava superiore beds, P. gredleri Zone), 240.63 +/- 0.13 Ma (Cassina beds, P gredleri/P. archelaus transition Zone) and 239.51 +/- 0.15 Ma (Lower Kalkschieferzone, P. archelaus Zone). Our results suggest that the time interval including the vertebrate-bearing Middle Triassic section spans around 4 Myr and is thus significantly shorter than so far assumed. The San Giorgio Dolomite and the Meride Limestone correlate with intervals of the Buchenstein Formation and the Wengen Formation in the reference section at Bagolino, where the Global boundary Stratotype Section and Point (GSSP) for the base of the Ladinian was defined. The new radio-isotopic ages of the Meride Limestone are up to 2 Myr older than those published for the biostratigraphically-equivalent intervals at Bagolino but they are consistent with the recent re-dating of the underlying Besano Formation, also performed using the CA technique. Average sedimentation rates at Monte San Giorgio are by more than an order of magnitude higher compared to those assumed for the Buchenstein Formation, which formed under sediment-starved pelagic conditions, and reflect prevailing high subsidence and high carbonate mud supply from the adjoining Salvatore/Esino platforms. Finally, the high-resolution U-Pb ages allow a correlation of the vertebrate faunas of the Cava superiore/Cava inferiore beds with the marine vertebrate record of the Prosanto Formation (Upper Austroalpine), so far precluded by the poor biostratigraphic control of the latter.

The InterActive Choice Aid: A new approach to supporting online consumer decision making

Interactive Choice Aid (ICA) is a decision aid, introduced in this paper, that systematically assists consumers with online purchase decisions. ICA integrates aspects from prescriptive decision theory, insights from descriptive decision research, and practical considerations; thereby combining pre-existing best practices with novel features. Instead of imposing an objectively ideal but unnatural decision procedure on the user, ICA assists the natural process of human decision-making by providing explicit support for the execution of the user's decision strategies. The application contains an innovative feature for in-depth comparisons of alternatives through which users' importance ratings are elicited interactively and in a playful way. The usability and general acceptance of the choice aid was studied; results show that ICA is a promising contribution and provides insights that may further improve its usability.

Toxic substances in blood: an analysis of current recommendations under a Bayesian (decision) approach

This article extends existing discussion in literature on probabilistic inference and decision making with respect to continuous hypotheses that are prevalent in forensic toxicology. As a main aim, this research investigates the properties of a widely followed approach for quantifying the level of toxic substances in blood samples, and to compare this procedure with a Bayesian probabilistic approach. As an example, attention is confined to the presence of toxic substances, such as THC, in blood from car drivers. In this context, the interpretation of results from laboratory analyses needs to take into account legal requirements for establishing the 'presence' of target substances in blood. In a first part, the performance of the proposed Bayesian model for the estimation of an unknown parameter (here, the amount of a toxic substance) is illustrated and compared with the currently used method. The model is then used in a second part to approach-in a rational way-the decision component of the problem, that is judicial questions of the kind 'Is the quantity of THC measured in the blood over the legal threshold of 1.5 μg/l?'. This is pointed out through a practical example.

Altered decision-making in multiple sclerosis: a sign of impaired emotional reactivity?

We assessed decision-making capacity and emotional reactivity in 20 patients with multiple sclerosis (MS) and in 16 healthy subjects using the Gambling Task (GT), a model of real-life decision making, and the skin conductance response (SCR). Demographic, neurological, affective, and cognitive parameters were analyzed in MS patients for their effect on decision-making performance. MS patients persisted longer (slope, -3.6%) than the comparison group (slope, -6.4%) in making disadvantageous choices as the GT progressed (p < 0.001), suggesting significant slower learning in MS. Patients with higher Expanded Disability Status Scale scores (EDSS >2.0) showed a different pattern of impairment in the learning process compared with patients with lower functional impairment (EDSS </=2.0). This slower learning was associated with impaired emotional reactivity (anticipatory SCR 3.9 vs 6.1 microSiemens [microS] for patients vs the comparison group, p < 0.0001; post-choice SCR 3.9 vs 6.2 microS, p < 0.0001), but not with executive dysfunction. Impaired emotional dimensions of behavior (assessed using the Dysexecutive Questionnaire, p < 0.002) also correlated with slower learning. Given the considerable consequences that impaired decision making can have on daily life, we suggest that this factor may contribute to handicap and altered quality of life secondary to MS and is dependent on emotional experience. Ann Neurol 2004.

An integrated encyclopedia of DNA elements in the human genome.

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

Constraining ACT-R models of decision strategies: An experimental paradigm

It has been repeatedly debated which strategies people rely on in inference. These debates have been difficult to resolve, partially because hypotheses about the decision processes assumed by these strategies have typically been formulated qualitatively, making it hard to test precise quantitative predictions about response times and other behavioral data. One way to increase the precision of strategies is to implement them in cognitive architectures such as ACT-R. Often, however, a given strategy can be implemented in several ways, with each implementation yielding different behavioral predictions. We present and report a study with an experimental paradigm that can help to identify the correct implementations of classic compensatory and non-compensatory strategies such as the take-the-best and tallying heuristics, and the weighted-linear model.

Enseignement de la médecine de famille: nouvelles évolutions à Lausanne [Teaching family medicine in Lausanne].

The Faculty of Biology and Medicine of Lausanne has integrated education of family medicine all along its new undergraduate medical curriculum. The Institute of general medicine is in charge to implement those offers among which two are presented hereafter. In the new module "Generalism" several courses cover the specificities of the discipline as for example medical decision in the practice. A mandatory one-month internship in the medical practice offers an experiential immersion into family medicine for all students. In a meeting at the end of their internship, students discuss in group with their peers their individual experiences and are asked to identify, based on their personal experience, the general concepts of the specialty of family medicine and general practice.

The 2005 Pakistan earthquake revisited: Methods for integrated landslide assessment

Five years after the 2005 Pakistan earthquake that triggered multiple mass movements, landslides continue to pose a threat to the population of Azad Kashmir, especially during heavy monsoon rains. The thousands of landslides that were triggered by the 7.6 magnitude earthquake in 2005 were not just due to a natural phenomenon but largely induced by human activities, namely, road building, grazing, and deforestation. The damage caused by the landslides in the study area (381 km2) is estimated at 3.6 times the annual public works budget of Azad Kashmir for 2005 of US$ 1 million. In addition to human suffering, this cost constitutes a significant economic setback to the region that could have been reduced through improved land use and risk management. This article describes interdisciplinary research conducted 18 months after the earthquake to provide a more systemic approach to understanding risks posed by landslides, including the physical, environmental, and human contexts. The goal of this research is twofold: to present empirical data on the social, geological, and environmental contexts in which widespread landslides occurred following the 2005 earthquake; and, second, to describe straightforward methods that can be used for integrated landslide risk assessments in data-poor environments. The article analyzes limitations of the methodologies and challenges for conducting interdisciplinary research that integrates both social and physical data. This research concludes that reducing landslide risk is ultimately a management issue, based in land use decisions and governance.