Predictive integration of gene functional similarity and co-expression defines treatment response of endothelial progenitor cells

<p>Abstract</p> <p>Background</p> <p>Endothelial progenitor cells (EPCs) have been implicated in different processes crucial to vasculature repair, which may offer the basis for new therapeutic strategies in cardiovascular disease. Despite advances facilitated by functional genomics, there is a lack of systems-level understanding of treatment response mechanisms of EPCs. In this research we aimed to characterize the EPCs response to adenosine (Ado), a cardioprotective factor, based on the systems-level integration of gene expression data and prior functional knowledge. Specifically, we set out to identify novel biosignatures of Ado-treatment response in EPCs.</p> <p>Results</p> <p>The predictive integration of gene expression data and standardized functional similarity information enabled us to identify new treatment response biosignatures. Gene expression data originated from Ado-treated and -untreated EPCs samples, and functional similarity was estimated with Gene Ontology (GO)-based similarity information. These information sources enabled us to implement and evaluate an integrated prediction approach based on the concept of <it>k</it>-nearest neighbours learning (<it>k</it>NN). The method can be executed by expert- and data-driven input queries to guide the search for biologically meaningful biosignatures. The resulting <it>integrated kNN </it>system identified new candidate EPC biosignatures that can offer high classification performance (areas under the operating characteristic curve > 0.8). We also showed that the proposed models can outperform those discovered by standard gene expression analysis. Furthermore, we report an initial independent <it>in vitro </it>experimental follow-up, which provides additional evidence of the potential validity of the top biosignature.</p> <p>Conclusion</p> <p>Response to Ado treatment in EPCs can be accurately characterized with a new method based on the combination of gene co-expression data and GO-based similarity information. It also exploits the incorporation of human expert-driven queries as a strategy to guide the automated search for candidate biosignatures. The proposed biosignature improves the systems-level characterization of EPCs. The new integrative predictive modeling approach can also be applied to other phenotype characterization or biomarker discovery problems.</p

Therapeutic metabolic inhibition: hydrogen sulfide significantly mitigates skeletal muscle ischemia reperfusion injury in vitro and in vivo

BACKGROUND:: Recent evidence suggests that hydrogen sulfide is capable of mitigating the degree of cellular damage associated with ischemia-reperfusion injury. The purpose of this study was to determine whether it is protective in skeletal muscle. METHODS:: This study used both in vitro (cultured myotubes subjected to sequential anoxia and normoxia) and in vivo (mouse hind-limb ischemia followed by reperfusion) models in which hydrogen sulfide (0 to 1000 μM) was delivered before the onset of oxygen deficiency. Injury score and apoptotic index were determined by analysis of specimens stained with hematoxylin and eosin and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling, respectively. RESULTS:: In vitro, hydrogen sulfide reduced the apoptotic index by as much as 99 percent (p = 0.001), with optimal protection conferred by raising intravascular hydrogen sulfide to 10 μM. In vivo, 10 μM hydrogen sulfide delivered before 3 hours of hind-limb ischemia followed by 3 hours of reperfusion resulted in protection against ischemia-reperfusion injury-induced cellular changes, as evidenced by significant decreases in injury score and apoptotic index (by as much as 91 percent; p = 0.001). These findings were consistent at 4 weeks after injury and reperfusion. CONCLUSION:: These findings confirm that the preischemic delivery of hydrogen sulfide limits ischemia-reperfusion injury-induced cellular damage in myotubes and skeletal muscle and suggests that, when given in the appropriate dose, this molecule may have significant therapeutic applications in multiple clinical scenario

Pulmonary oedema fluid induces non-α-ENaC-dependent Na+ transport and fluid absorption in the distal lung

To determine if pulmonary oedema fluid (EF) alters ion and fluid transport of distal lung epithelium (DLE), EF was collected from rats in acute heart failure. EF, but not plasma, increased amiloride-insensitive short circuit current (Isc) and Na+–K+ ATPase protein content and pump activity of DLE grown in primary culture. Inhibitors of Cl− transport or cGMP-gated cation channels had a significant (P < 0.05), but limited ability to block the increased Isc. EF increased amiloride-insensitive, but not amiloride-sensitive, DLE apical membrane Na+ conductance. The level of mRNA encoding epithelial sodium channel (ENaC) subunits was unchanged (α, β), or decreased (γ, P < 0.05) in EF-exposed DLE. EF also induced an amiloride-insensitive increase in the potential difference across murine tracheal cysts. Distal lung explants from late gestation wild-type and α-ENaC-deficient fetal mice, which normally expand due to liquid secretion, decreased in size due to liquid absorption when exposed to EF. Trypsin digestion or heat treatment of EF abrogated the ability of EF to increase amiloride-insensitive Isc in DLE and liquid absorption by distal lung explants. Thus proteins or protein-dependent factors within cardiogenic EF induce an α-ENaC-independent and amiloride-insensitive apical membrane Na+ conductance and liquid absorption in the distal lung

Isolation and characterization of mouse bone marrow-derived Lin-/VEGF-R2 + progenitor cells

Circulating endothelial progenitor cells (EPCs) in the peripheral blood (PB) have physiological roles in the maintenance of the existing vascular beds and rescue of vascular injury. In this study, we have evaluated the properties of Lin-/VEGF-R2+ progenitor cells isolated from the mouse bone marrow (BM) and further studied their distribution and integration in an animal model of laser-induced retinal vascular injury. Lin-/VEGF-R2+ cells were enriched from C57BL/6 mice BM using magnetic cell sorting with hematopoietic lineage (Lin) depletion followed by VEGF-R2 positive selection. Lin-/VEGF-R2+ BM cells were characterized using flow cytometry and immunocytochemistry and further tested for colony formation during culture and tube formation on Matrigel®. Lin-/VEGF-R2+ BM cells possessed typical EPC properties such as forming cobble-stone shaped colonies after 3 to 4 weeks of culture, CD34+ expression, take up of Dil-acLDL and binding to Ulex europaeus agglutinin. However, they did not form tube-like structures on Matrigel®. The progenitor cells retained their phenotype over extended period of culture. After intravitreal transplantation in eyes subjected to the laser-induced retinal vascular injury, some Lin-/VEGF-R2+ cells were able to integrate into the damaged retinal vasculature but the level of cell integration seemed less efficient when compared with previous reports in which EPCs from the human PB were employed. Our results indicate that Lin-/VEGF-R2+ cells isolated from the mouse BM share some similarities to EPCs from the human PB but most of them are at a very early stage of maturation and remain quiescent during culture and after intravitreal transplantation