Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms

The development of computational approaches in systems biology has reached a state of maturity that allows their transition to systems medicine. Despite this progress, intuitive visualisation and context-dependent knowledge representation still present a major bottleneck. In this paper, we describe the Disease Maps Project, an effort towards a community-driven computationally readable comprehensive representation of disease mechanisms. We outline the key principles and the framework required for the success of this initiative, including use of best practices, standards and protocols. We apply a modular approach to ensure efficient sharing and reuse of resources for projects dedicated to specific diseases. Community-wide use of disease maps will accelerate the conduct of biomedical research and lead to new disease ontologies defined from mechanism-based disease endotypes rather than phenotypes.

Cylindrospermopsis raciborskii exudate-Cu complexes: impact on copper dynamics and bioavailability in an aquatic food chain

INTRODUCTION

The increasing contamination of aquatic environments motivates studies on the interactions among natural dissolved organic matter, metals, and the biota. This investigation focused on the organic exudates of the toxic cyanobacteria Cylindrospermopsis raciborskii as a Cu carrier through a three-level aquatic trophic chain (bacteria, protozoa, and copepod).

DISCUSSION

The effects of bacteria activity and growth on the metal-organic complexes were evaluated through changes in free Cu(2+) ions, total dissolved, and total particulate Cu. To be sure that the added copper would be complexed to the exudates, its complexing properties were previously determined. The cyanobacteria exudate-Cu complexes were furnished to bacteria that were further used as a food source to the protozoan Paramercium caudatum. This was then furnished as food to the copepod Mesocyclops sp. The results showed that, in general, the cyanobacterial exudates decreased Cu bioavailability and toxicity to the first trophic level (bacteria), but because the heterotrophic bacteria accumulated Cu, they were responsible for the transference for the otherwise low availability metal form. Both the bacteria and protozoan organisms accumulated Cu, but no metal accumulation was detected in the copepods.

Natural DOM affects copper speciation and bioavailability to bacteria and ciliate

This study aimed to investigate the influence of natural dissolved organic materials (DOM) on copper speciation (total dissolved, particulate, and free Cu2+ ions) and bioavailability during a two-level experimental microbial food chain. Bacteria were used as the first trophic level, and Paramecium caudatum (protozoan) as the second. The organisms were obtained from a freshwater reservoir and kept under controlled laboratory conditions. Three experimental treatments were performed: exposure of the organisms to copper in the absence of DOM, exposure to DOM in the absence of copper, and exposure to both copper and DOM. Freshwater medium containing natural DOM and copper at a total dissolved concentration of 1.8 x 10(-6) mol L(-1) was furnished to bacteria, which was further used as food to the protozoan. The results showed that after bacterial growth, DOM concentration decreased as quantified by total organic carbon determinations. At the same time, free Cu2+ ions concentration increased in the medium. A lower copper concentration was detected in both microorganisms in the presence of DOM. We conclude that natural DOM reduced copper accumulation in the organisms on the first and second trophic levels, thus reducing the entrance of copper into the aquatic microbial food chain.

The effects of Anabaena spiroides exopolysaccharides on copper accumulation in an aquatic food chain

The influence of Anabaena spiroides exopolysaccharides (EPS) on copper speciation (total dissolved, particulate and free Cu(2+) ions) and bioavailability in aquatic organisms was investigated. Bacteria were used as the first trophic level, Paramecium caudatum (protozoan) as the second and the copepod cyclopoid Metacyclops mendocinus as the third level. The organisms were obtained from a freshwater reservoir and held under continuous laboratory controlled conditions. Freshwater media containing EPS excreted by A. spiroides (10mgL(-1)) and copper (1.0x10(-6)molL(-1)) were used for bacteria growth. Contamined bacteria were used as food source to protozoan, which was further furnished to copepods. The results showed a reduction of EPS concentration during bacteria growth and also a smaller copper accumulation by microorganisms in the presence of EPS. We concluded that A. spiroides exopolysaccharides have reduced copper entrance into the experimental aquatic microbial food chain.

Constitutive and specific activation of STAT3 by BCR-ABL in embryonic stem cells

BCR-ABL oncogene, the molecular hallmark of chronic myelogenous leukemia (CML) arises in a primitive hematopoietic stem cell with both differentiation and self-renewal ability. To study the phenotypic effects of BCR-ABL in a clonal in vitro self-renewal and differentiation model, we have introduced BCR-ABL in the ES cell line CCE. The major effect of BCR-ABL expression was the persistence of primitive morphology of ES cells despite LIF deprivation, correlated with a constitutive activation of STAT3, the major self-renewal factor of ES cells, but no evidence of activation of STAT5. The enforced expression of BCR-ABL in an ES cell line, engineered to express a tetracycline-inducible dominant-negative form of a STAT3, triggered ES cell differentiation with an increased generation of hematopoietic cells expressing erythroid and megakaryocytic phenotypes. RT-PCR analysis for Oct4, Brachyury and beta-globin expression confirmed a delay of differentiation in BCR-ABL expressing clones, which could be entirely reversed upon activation of the dominant-negative form of STAT3. To study the possible relevance of STAT3 activation by BCR-ABL in human CML, Western blot analyses performed on the CD34+ cells, purified from CML patients at different stages of their disease, also demonstrated increased levels of STAT3 proteins phosphorylated both on tyrosine and serine residues. These results represent to our knowledge the first functional link between BCR-ABL oncogene and a self-renewal in the context of ES cells through constitutive activation of STAT3. Thus, the BCR-ABL embryonic stem cell model that we developed as well as the results obtained in human CML samples suggests a role for STAT3 in the pathogenesis of human CML.

Expression of CD41 on hematopoietic progenitors derived from embryonic hematopoietic cells

In this study, we have characterized the early steps of hematopoiesis during embryonic stem cell differentiation. The immunophenotype of hematopoietic progenitor cells derived from murine embryonic stem cells was determined using a panel of monoclonal antibodies specific for hematopoietic differentiation antigens. Surprisingly, the CD41 antigen (αIIb integrin, platelet GPIIb), essentially considered to be restricted to megakaryocytes, was found on a large proportion of cells within embryoid bodies although very few megakaryocytes were detected. In clonogenic assays, more than 80% of all progenitors (megakaryocytic, granulo-macrophagic, erythroid and pluripotent) derived from embryoid bodies expressed the CD41 antigen. CD41 was the most reliable marker of early steps of hematopoiesis. However, CD41 remained a differentiation marker because some CD41– cells from embryoid bodies converted to CD41+ hematopoietic progenitors, whereas the inverse switch was not observed. Immunoprecipitation and western blot analysis confirmed that CD41 was present in cells from embryoid bodies associated with CD61 (β3 integrin, platelet GPIIIa) in a complex. Analysis of CD41 expression during ontogeny revealed that most yolk sac and aorta-gonad-mesonephros hematopoietic progenitor cells were also CD41+, whereas only a minority of bone marrow and fetal liver hematopoietic progenitors expressed this antigen. Differences in CD34 expression were also observed: hematopoietic progenitor cells from embryoid bodies, yolk sac and aorta-gonad-mesonephros displayed variable levels of CD34, whereas more than 90% of fetal liver and bone marrow progenitor cells were CD34+.

Thus, these results demonstrate that expression of CD41 is associated with early stages of hematopoiesis and is highly regulated during hematopoietic development. Further studies concerning the adhesive properties of hematopoietic cells are required to assess the biological significance of these developmental changes.

Embryonic stem cell differentiation to hematopoietic cells: A model to study the function of various regions of the intracytoplasmic domain of cytokine receptors in vitro

To examine whether the in vitro model of embryonic stem (ES) cell hematopoietic differentiation is suitable to study the function of intracytoplasmic regions of cytokine receptors, we used the thrombopoietin receptor Mpl as a typical cytokine receptor.ES cells deficient in c-mpl (mpl(-/)-) were transfected with genes encoding the full-length or two mutated forms of the intracytoplasmic domain of Mpl using the pEF-BOS expression vector. The mutated forms lack box1 or box2.pEF-BOS was able to maintain protein production during ES cell differentiation. Reintroduction of full-length-c-mpl into mpl(-/)- ES cells restored the response of megakaryocyte progenitors to a truncated form of human Mpl-ligand conjugated to polyethylene glycol (PEG-rhuMGDF) and the formation of platelets, for which mpl(-/)- ES cells are defective. In addition, enforced expression of Mpl resulted in the development of all myeloid progenitors and mature cells in the presence of PEG-rhuMGDF. Blast colony-forming cells, the in vitro equivalent of the hemangioblast, also generated blast cell colonies with a hematopoietic potential equivalent to that of the wild type in the presence of PEG-rhuMGDF, although its growth is normally dependent on vascular endothelial cell growth factor (VEGF). Thus, Mpl acts as a substitute for other cytokine receptors and for a tyrosine kinase receptor, Flk-1, indicating that Mpl has no instructive role in hematopoietic cell commitment and differentiation. The Mpl mutant forms lacking box1 or box2 prevented response of ES cell-derived blast colony-forming cells or progenitors to PEG-rhuMGDF. Therefore, these two regions, essential for signaling by cytokine receptors, are required for the responses of ES cell-derived hematopoietic cells to PEG-rhuMGDF.These results show that the in vitro hematopoietic differentiation of ES cells is suitable for studying the role of various intracytoplasmic regions of cytokine receptors.

Regulation of Id gene expression during embryonic stem cell-derived hematopoietic differentiation

To elucidate the role of helix-loop-helix (HLH) Id proteins in hematopoietic differentiation, we used a model of embryonic stem (ES) cell differentiation in vitro which gives access not only to hematopoietic myeloid progenitor cells but also to the more primitive blast colony-forming cell (BL-CFC), the in vitro equivalent of the hemangioblast that gives rise to blast cell colonies in the presence of VEGF. We first demonstrated that ES cell-derived blast cell colonies could be used as a model to study hematopoietic differentiation and maturation. We next established the expression profile of Id genes in this model. Transcripts of the four Id genes were present in ES cells. Id1, Id3 and Id4 gene expression was down-regulated during the development of blast cell colonies while that of Id2 was maintained. Thus, Id1, Id3, and Id4 proteins are candidates for being negative regulators of hematopoiesis in the model of hematopoietic ES cell differentiation in vitro.