Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets.

Anti-cancer therapies often exhibit only short-term effects. Tumors typically develop drug resistance causing relapses that might be tackled with drug combinations. Identification of the right combination is challenging and would benefit from high-content, high-throughput combinatorial screens directly on patient biopsies. However, such screens require a large amount of material, normally not available from patients. To address these challenges, we present a scalable microfluidic workflow, called Combi-Seq, to screen hundreds of drug combinations in picoliter-size droplets using transcriptome changes as a readout for drug effects. We devise a deterministic combinatorial DNA barcoding approach to encode treatment conditions, enabling the gene expression-based readout of drug effects in a highly multiplexed fashion. We apply Combi-Seq to screen the effect of 420 drug combinations on the transcriptome of K562 cells using only ~250 single cell droplets per condition, to successfully predict synergistic and antagonistic drug pairs, as well as their pathway activities.

Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy.

Tissue development and disease progression are multi-stage processes controlled by an evolving set of key regulatory factors, and identifying these factors necessitates a dynamic analysis spanning relevant time scales. Current omics approaches depend on incomplete biological databases to identify critical cellular processes. Herein, we present TRACER (TRanscriptional Activity CEll aRrays), which was employed to quantify the dynamic activity of numerous transcription factor (TFs) simultaneously in 3D and networks for TRACER (NTRACER), a computational algorithm that allows for cellular rewiring to establish dynamic regulatory networks based on activity of TF reporter constructs. We identified major hubs at various stages of culture associated with normal and abnormal tissue growth (i.e., ELK-1 and E2F1, respectively) and the mechanism of action for a targeted therapeutic, lapatinib, through GATA-1, which were confirmed in human ErbB2 positive breast cancer patients and human ErbB2 positive breast cancer cell lines that were either sensitive or resistant to lapatinib.

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.

Systems biology has to increasingly cope with large- and multi-scale biological systems. Many successful in silico representations and simulations of various cellular modules proved mathematical modelling to be an important tool in gaining a solid understanding of biological phenomena. However, models spanning different functional layers (e.g. metabolism, signalling and gene regulation) are still scarce. Consequently, model integration methods capable of fusing different types of biological networks and various model formalisms become a key methodology to increase the scope of cellular processes covered by mathematical models. Here we propose a new integration approach to couple logical models of signalling or/and gene-regulatory networks with kinetic models of metabolic processes. The procedure ends up with an integrated dynamic model of both layers relying on differential equations. The feasibility of the approach is shown in an illustrative case study integrating a kinetic model of central metabolic pathways in hepatocytes with a Boolean logical network depicting the hormonally induced signal transduction and gene regulation events involved. In silico simulations demonstrate the integrated model to qualitatively describe the physiological switch-like behaviour of hepatocytes in response to nutritionally regulated changes in extracellular glucagon and insulin levels. A simulated failure mode scenario addressing insulin resistance furthermore illustrates the pharmacological potential of a model covering interactions between signalling, gene regulation and metabolism.

Estudio epidemiológico del suicidio en el partido judicial de Priego de Córdoba durante el periodo desde el año 1960 al 1990 / Epidemiological study of suicide in the Priego de Córdoba

La conducta suicida es un verdadero problema de salud pública del que nos viene advirtiendo la Organización Mundial de la Salud (OMS) desde hace años. Este trabajo es un estudio epidemiológico retrospectivo de la mortalidad por suicidio en la serie histórica desde el año 1960 al 1990 en el partido judicial de Priego de Córdoba, una demarcación territorial situada entre Córdoba y Granada. El número de suicidios en dichas localidades triplica la media nacional durante este periodo, correspondiendo la modalidad mayoritariamente a la ahorcadura, que casi duplica las cifras a nivel nacional. De las variables estudiadas, las que resultan con significación estadística son: sexo (más frecuente en hombres), edad (más frecuente entre los 50 y los 59 años), estación del año (más frecuente en primavera y verano) y distribución horaria (más frecuente entre las 8 y las 16 horas) (AU)

Suicide behaviour is a real publichealth problem, as the World Health Organization (WHO) has been warning since some years. Our work is an epidemiological study of mortality due to suicide in a historical series of cases between 1960 to 1990. Suicide cases were extracted from data in regional archives and from autopsy reports in the Priego de Córdoba court registry office, located among the territories of Córdoba and Granada. The number of suicides in this area triples the average of suicides in Spain during this period. The most common method used was hanging, doubling the average of this category in Spain. Our results with statistical significance were: Suicide occurred more frequently in males, and in the 50-59 year old population. With relation to temporal distribution, suicides were more frequent in spring and summer, as well as more frequent between 8:00 and 16:00 hours (AU)

Multistability of signal transduction motifs.

Protein domains are the basic units of signalling processes. The mechanisms they are involved in usually follow recurring patterns, such as phosphorylation/dephosphorylation cycles. A set of common motifs was defined and their dynamic models were analysed with respect to number and stability of steady states. In a first step, Feinberg's chemical reaction network theory was used to determine whether a motif can show multistationarity or not. The analysis revealed that, apart from double-step activation motifs including a distributive mechanism, only those motifs involving an autocatalytic reaction can show multistationarity. To further characterise these motifs, a large number of randomly chosen parameter sets leading to bistability was generated, followed by a bifurcation analysis of each parameter set and a statistical evaluation of the results. The statistical results can be used to explore robustness against noise, pointing to the observation that multistationarity at the single-motif level may not be a robust property; the range of protein concentrations compatible with multistationarity is fairly narrow. Furthermore, experimental evidence suggests that protein concentrations vary substantially between cells. Considering a motif designed to be a bistable switch, this implies that fluctuation of protein concentrations between cells would prevent a significant proportion of motifs from acting as a switch. The authors consider this to be a first step towards a catalogue of fully characterised signalling modules.

Systems biology--an engineering perspective.

The interdisciplinary field of systems biology has evolved rapidly over the last years. Different disciplines have aided the development of both its experimental and theoretical branches. One field, which has played a significant role is engineering science and, in particular chemical engineering. Here, we review and illustrate some of these contributions, ranging from modeling approaches to model analysis with a special focus on technique which have not yet been substantially exploited but can be potentially useful in the analysis of biochemical systems.

Using chemical reaction network theory to discard a kinetic mechanism hypothesis.

Feinberg's chemical reaction network theory (CRNT) connects the structure of a biochemical reaction network to qualitative properties of the corresponding system of ordinary differential equations. No information about parameter values is needed. As such, it seems to be well suited for application in systems biology, where parameter uncertainty is predominant. However, its application in this area is rare. To demonstrate the potential benefits from its application, different reaction networks representing a single layer of the well-studied mitogen-activated protein kinase (MAPK) cascade are analysed. Recent results from Markevich et al. (2004) show that, unexpectedly, multilayered protein kinase cascades can exhibit multistationarity, even on a single cascade level. Using CRNT, we show that their assumption of a distributive mechanism for double phosphorylation and dephosphorylation is crucial for multistationarity on the single cascade level.

Reduction of mathematical models of signal transduction networks: simulation-based approach applied to EGF receptor signalling.

Biological systems and, in particular, cellular signal transduction pathways are characterised by their high complexity. Mathematical models describing these processes might be of great help to gain qualitative and, most importantly, quantitative knowledge about such complex systems. However, a detailed mathematical description of these systems leads to nearly unmanageably large models, especially when combining models of different signalling pathways to study cross-talk phenomena. Therefore, simplification of models becomes very important. Different methods are available for model reduction of biological models. Importantly, most of the common model reduction methods cannot be applied to cellular signal transduction pathways. Using as an example the epidermal growth factor (EGF) signalling pathway, we discuss how quantitative methods like system analysis and simulation studies can help to suitably reduce models and additionally give new insights into the signal transmission and processing of the cell.

Abordaje multidisciplinar en el maltrato a la mujer / Multidisciplinary approach in the battered women

Este trabajo propone una serie de actuaciones que deben realizar los distintos profesionales que intervenienen en los casos de agresión a la mujer: Médicos de Atención Primaria, Médicos Forenses, Miembros de las Fuerzas y Cuerpos de Seguridad del Estado, jueces, Fiscales, Abogados, Psicólogos, Trabajadores Sociales, ...El objetivo es conseguir entre todos disminuir la incidencia del llamado Síndrome de la Mujer Maltratada, algo que, por su extraordinaria frecuencia, constituye, según la propia Organización Mundial de la Salud, "un problema de salud internacional" (AU)