Dynamic interaction networks in a hierarchically organized tissue

We have integrated gene expression profiling with database and literature mining, mechanistic modeling, and cell culture experiments to identify intercellular and intracellular networks regulating blood stem cell self-renewal.Blood stem cell fate in vitro is regulated non-autonomously by a coupled positive–negative intercellular feedback circuit, composed of megakaryocyte-derived stimulatory growth factors (VEGF, PDGF, EGF, and serotonin) versus monocyte-derived inhibitory factors (CCL3, CCL4, CXCL10, TGFB2, and TNFSF9).The antagonistic signals converge in a core intracellular network focused around PI3K, Raf, PLC, and Akt.Model simulations enable functional classification of the novel endogenous ligands and signaling molecules

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

The Systematic Production of Cells for Cell Therapies

Stem cells have emerged as the starting material of choice for bioprocesses to produce cells and tissues to treat degenerative, genetic, and immunological disease. Translating the biological properties and potential of stem cells into therapies will require overcoming significant cell-manufacturing and regulatory challenges. Bioprocess engineering fundamentals, including bioreactor design and process control, need to be combined with cellular systems biology principles to guide the development of next-generation technologies capable of producing cell-based products in a safe, robust, and cost-effective manner. The step-wise implementation of these bioengineering strategies will enhance cell therapy product quality and safety, expediting clinical development

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks

Background: Understanding the information-processing capabilities of signal transduction networks, how those networks are disrupted in disease, and rationally designing therapies to manipulate diseased states require systematic and accurate reconstruction of network topology. Data on networks central to human physiology, such as the inflammatory signalling networks analyzed here, are found in a multiplicity of on-line resources of pathway and interactome databases (Cancer CellMap, GeneGo, KEGG, NCI-Pathway Interactome Database (NCI-PID), PANTHER, Reactome, I2D, and STRING). We sought to determine whether these databases contain overlapping information and whether they can be used to construct high reliability prior knowledge networks for subsequent modeling of experimental data. Results: We have assembled an ensemble network from multiple on-line sources representing a significant portion of all machine-readable and reconcilable human knowledge on proteins and protein interactions involved in inflammation. This ensemble network has many features expected of complex signalling networks assembled from high-throughput data: a power law distribution of both node degree and edge annotations, and topological features of a &#8220;bow tie&#8221; architecture in which diverse pathways converge on a highly conserved set of enzymatic cascades focused around PI3K/AKT, MAPK/ERK, JAK/STAT, NF&#954;B, and apoptotic signaling. Individual pathways exhibit &#8220;fuzzy&#8221; modularity that is statistically significant but still involving a majority of &#8220;cross-talk&#8221; interactions. However, we find that the most widely used pathway databases are highly inconsistent with respect to the actual constituents and interactions in this network. Using a set of growth factor signalling networks as examples (epidermal growth factor, transforming growth factor-beta, tumor necrosis factor, and wingless), we find a multiplicity of network topologies in which receptors couple to downstream components through myriad alternate paths. Many of these paths are inconsistent with well-established mechanistic features of signalling networks, such as a requirement for a transmembrane receptor in sensing extracellular ligands. Conclusions: Wide inconsistencies among interaction databases, pathway annotations, and the numbers and identities of nodes associated with a given pathway pose a major challenge for deriving causal and mechanistic insight from network graphs. We speculate that these inconsistencies are at least partially attributable to cell, and context-specificity of cellular signal transduction, which is largely unaccounted for in available databases, but the absence of standardized vocabularies is an additional confounding factor. As a result of discrepant annotations, it is very difficult to identify biologically meaningful pathways from interactome networks a priori. However, by incorporating prior knowledge, it is possible to successively build out network complexity with high confidence from a simple linear signal transduction scaffold. Such reduced complexity networks appear suitable for use in mechanistic models while being richer and better justified than the simple linear pathways usually depicted in diagrams of signal transduction.National Institutes of Health (U.S.) (NIH grant U54-HG006097)Boehringer Ingelheim Pharmaceutical

HER2+ Cancer Cell Dependence on PI3K <i>vs</i>. MAPK Signaling Axes Is Determined by Expression of EGFR, ERBB3 and CDKN1B

<div><p>Understanding the molecular pathways by which oncogenes drive cancerous cell growth, and how dependence on such pathways varies between tumors could be highly valuable for the design of anti-cancer treatment strategies. In this work we study how dependence upon the canonical PI3K and MAPK cascades varies across HER2+ cancers, and define biomarkers predictive of pathway dependencies. A panel of 18 HER2+ (<i>ERBB2</i>-amplified) cell lines representing a variety of indications was used to characterize the functional and molecular diversity within this oncogene-defined cancer. PI3K and MAPK-pathway dependencies were quantified by measuring <i>in vitro</i> cell growth responses to combinations of AKT (MK2206) and MEK (GSK1120212; trametinib) inhibitors, in the presence and absence of the ERBB3 ligand heregulin (NRG1). A combination of three protein measurements comprising the receptors EGFR, ERBB3 (HER3), and the cyclin-dependent kinase inhibitor p27 (CDKN1B) was found to accurately predict dependence on PI3K/AKT vs. MAPK/ERK signaling axes. Notably, this multivariate classifier outperformed the more intuitive and clinically employed metrics, such as expression of phospho-AKT and phospho-ERK, and PI3K pathway mutations (<i>PIK3CA</i>, <i>PTEN</i>, and <i>PIK3R1</i>). In both cell lines and primary patient samples, we observed consistent expression patterns of these biomarkers varies by cancer indication, such that ERBB3 and CDKN1B expression are relatively high in breast tumors while EGFR expression is relatively high in other indications. The predictability of the three protein biomarkers for differentiating PI3K/AKT vs. MAPK dependence in HER2+ cancers was confirmed using external datasets (Project Achilles and GDSC), again out-performing clinically used genetic markers. Measurement of this minimal set of three protein biomarkers could thus inform treatment, and predict mechanisms of drug resistance in HER2+ cancers. More generally, our results show a single oncogenic transformation can have differing effects on cell signaling and growth, contingent upon the molecular and cellular context.</p></div

Canonical PI3K/AKT and MAPK/ERK signaling nodes and their statistical association with biomarker-defined cell line subsets represented in Project Achilles.

<p>Canonical PI3K/AKT and MAPK/ERK signaling nodes and their statistical association with biomarker-defined cell line subsets represented in Project Achilles.</p