Integrating biological knowledge into variable selection : an empirical Bayes approach with an application in cancer biology

Background: An important question in the analysis of biochemical data is that of identifying subsets of molecular variables that may jointly influence a biological response. Statistical variable selection methods have been widely used for this purpose. In many settings, it may be important to incorporate ancillary biological information concerning the variables of interest. Pathway and network maps are one example of a source of such information. However, although ancillary information is increasingly available, it is not always clear how it should be used nor how it should be weighted in relation to primary data. Results: We put forward an approach in which biological knowledge is incorporated using informative prior distributions over variable subsets, with prior information selected and weighted in an automated, objective manner using an empirical Bayes formulation. We employ continuous, linear models with interaction terms and exploit biochemically-motivated sparsity constraints to permit exact inference. We show an example of priors for pathway- and network-based information and illustrate our proposed method on both synthetic response data and by an application to cancer drug response data. Comparisons are also made to alternative Bayesian and frequentist penalised-likelihood methods for incorporating network-based information. Conclusions: The empirical Bayes method proposed here can aid prior elicitation for Bayesian variable selection studies and help to guard against mis-specification of priors. Empirical Bayes, together with the proposed pathway-based priors, results in an approach with a competitive variable selection performance. In addition, the overall procedure is fast, deterministic, and has very few user-set parameters, yet is capable of capturing interplay between molecular players. The approach presented is general and readily applicable in any setting with multiple sources of biological prior knowledge

Vav3-induced cytoskeletal dynamics contribute to heterotypic properties of endothelial barriers

© 2018 Hilfenhaus et al.Through multiple cell–cell and cell–matrix interactions, epithelial and endothelial sheets form tight barriers. Modulators of the cytoskeleton contribute to barrier stability and act as rheostats of vascular permeability. In this study, we sought to identify cytoskeletal regulators that underlie barrier diversity across vessels. To achieve this, we correlated functional and structural barrier features to gene expression of endothelial cells (ECs) derived from different vascular beds. Within a subset of identified candidates, we found that the guanosine nucleotide exchange factor Vav3 was exclusively expressed by microvascular ECs and was closely associated with a high-resistance barrier phenotype. Ectopic expression of Vav3 in large artery and brain ECs significantly enhanced barrier resistance and cortical rearrangement of the actin cytoskeleton. Mechanistically, we found that the barrier effect of Vav3 is dependent on its Dbl homology domain and downstream activation of Rap1. Importantly, inactivation of Vav3 in vivo resulted in increased vascular leakage, highlighting its function as a key regulator of barrier stability.Deutsche Forschungsgemeinschaft (STE 2045/1-1) Fundación Ramón Areces (NO AWARD) Ministerio de Economía y Competitividad (NO AWARD) National Institutes of Health (P40OD018537) Worldwide Cancer Research (13-0170

Vav3-induced cytoskeletal dynamics contribute to heterotypic properties of endothelial barriers

[EN]Through multiple cell-cell and cell-matrix interactions, epithelial and endothelial sheets form tight barriers. Modulators of the cytoskeleton contribute to barrier stability and act as rheostats of vascular permeability. In this study, we sought to identify cytoskeletal regulators that underlie barrier diversity across vessels. To achieve this, we correlated functional and structural barrier features to gene expression of endothelial cells (ECs) derived from different vascular beds. Within a subset of identified candidates, we found that the guanosine nucleotide exchange factor Vav3 was exclusively expressed by microvascular ECs and was closely associated with a high-resistance barrier phenotype. Ectopic expression of Vav3 in large artery and brain ECs significantly enhanced barrier resistance and cortical rearrangement of the actin cytoskeleton. Mechanistically, we found that the barrier effect of Vav3 is dependent on its Dbl homology domain and downstream activation of Rap1. Importantly, inactivation of Vav3 in vivo resulted in increased vascular leakage, highlighting its function as a key regulator of barrier stability. © 2018 Hilfenhaus et al

Integrated analysis of breast cancer cell lines reveals unique signaling pathways

Mapping of sub-networks in the EGFR-MAPK pathway in different breast cancer cell lines reveals that PAK1 may be a marker for sensitivity to MEK inhibitors

A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047

<p>Abstract</p> <p>Background</p> <p>Polyamines regulate important cellular functions and polyamine dysregulation frequently occurs in cancer. The objective of this study was to use a systems approach to study the relative effects of PG-11047, a polyamine analogue, across breast cancer cells derived from different patients and to identify genetic markers associated with differential cytotoxicity.</p> <p>Methods</p> <p>A panel of 48 breast cell lines that mirror many transcriptional and genomic features present in primary human breast tumours were used to study the antiproliferative activity of PG-11047. Sensitive cell lines were further examined for cell cycle distribution and apoptotic response. Cell line responses, quantified by the GI₅₀(dose required for 50% relative growth inhibition) were correlated with the omic profiles of the cell lines to identify markers that predict response and cellular functions associated with drug sensitivity.</p> <p>Results</p> <p>The concentrations of PG-11047 needed to inhibit growth of members of the panel of breast cell lines varied over a wide range, with basal-like cell lines being inhibited at lower concentrations than the luminal cell lines. Sensitive cell lines showed a significant decrease in S phase fraction at doses that produced little apoptosis. Correlation of the GI₅₀values with the omic profiles of the cell lines identified genomic, transcriptional and proteomic variables associated with response.</p> <p>Conclusions</p> <p>A 13-gene transcriptional marker set was developed as a predictor of response to PG-11047 that warrants clinical evaluation. Analyses of the pathways, networks and genes associated with response to PG-11047 suggest that response may be influenced by interferon signalling and differential inhibition of aspects of motility and epithelial to mesenchymal transition.</p> <p>See the related commentary by Benes and Settleman: <url>http://www.biomedcentral.com/1741-7015/7/78</url></p

Endothelial Mutagenesis Uncovers Key Regulatory Pathways that Maintain Vascular Homeostasis

The purpose of the vascular system is to distribute oxygen rich blood to all organs and extremities, to mediate the transport of nutrients and waste, and to deliver immune cells to sites of infection. It is comprised of the heart and a complex, hierarchically branched network of blood vessels through which the blood is pumped. The principal cell type of the blood vessel is the endothelial cell (EC). They are a subclass of epithelial cells that line the blood vessels and like ceramic tiles, provide a flat-slippery surface for the blood to flow past. Healthy blood circulation is critical for organs to be well oxygenated with the transport of red blood cell and free of infection through the delivery of white blood cells. Under normal physiological conditions, adult EC are quiescent and do not proliferate. However, in pathological conditions like wound healing and cancer, secreted growth factors and inflammatory cytokines induce endothelial cells to turn on an angiogenesis program. On the other hand, transformed ECs can be the primary cell type of pathology. One such endothelial cell pathology is vascular anomalies (VAs). The emergence of these lesions requires endothelial cells to accumulate mutations causing them to form malformed vessels or solid tumors. It has been predicted that half of the mutations underlying vascular malformations are unknown, especially those that are non-hereditary and triggered by sporadic, somatic mutations. What is known has been determined through genetic linkage analysis of familial forms of the disease. Here we present the novel results of an in vivo forward genetic screen in murine endothelial cells that modeled vascular anomalies. The majority of the approximately 100 disrupted genes identified have not been previously associated with vascular anomalies. Furthermore, we validated a tumor suppressor (Fndc3b) and an oncogene (Pdgfrb) and demonstrated their causation in endothelial dysfunction. The major significant finding of this study is that endothelial cell homeostasis is heavily governed by regulation of the actin cytoskeleton, cytokine and growth factor signaling, and Hippo signaling pathways. Also a result of the screen was the revelation that a pathological relationship exists between hemogenic endothelial cells and leukemia. Using the same forward genetic approach in a mouse model, we were able to induced mutagenesis at E9.5 in endothelial cells one day before they turned on their hemogenic program at E10.5. Not only were hematopoietic malignancies generated (both myeloid and lymphoid), but novel mutations associated with these cancers were identified. Here we also present data demonstrating the novel role of Pi4ka (identified in association with myeloid leukemia) in hematopoiesis. Together this work takes a look at the critical role of endothelial cells from three different perspectives (tumor angiogenesis, vascular anomalies, and hemogenic endothelial contribution to leukemia), highlighting their importance in physiology and pathology

Endothelial Mutagenesis Uncovers Key Regulatory Pathways that Maintain Vascular Homeostasis

The purpose of the vascular system is to distribute oxygen rich blood to all organs and extremities, to mediate the transport of nutrients and waste, and to deliver immune cells to sites of infection. It is comprised of the heart and a complex, hierarchically branched network of blood vessels through which the blood is pumped. The principal cell type of the blood vessel is the endothelial cell (EC). They are a subclass of epithelial cells that line the blood vessels and like ceramic tiles, provide a flat-slippery surface for the blood to flow past. Healthy blood circulation is critical for organs to be well oxygenated with the transport of red blood cell and free of infection through the delivery of white blood cells. Under normal physiological conditions, adult EC are quiescent and do not proliferate. However, in pathological conditions like wound healing and cancer, secreted growth factors and inflammatory cytokines induce endothelial cells to turn on an angiogenesis program. On the other hand, transformed ECs can be the primary cell type of pathology. One such endothelial cell pathology is vascular anomalies (VAs). The emergence of these lesions requires endothelial cells to accumulate mutations causing them to form malformed vessels or solid tumors. It has been predicted that half of the mutations underlying vascular malformations are unknown, especially those that are non-hereditary and triggered by sporadic, somatic mutations. What is known has been determined through genetic linkage analysis of familial forms of the disease. Here we present the novel results of an in vivo forward genetic screen in murine endothelial cells that modeled vascular anomalies. The majority of the approximately 100 disrupted genes identified have not been previously associated with vascular anomalies. Furthermore, we validated a tumor suppressor (Fndc3b) and an oncogene (Pdgfrb) and demonstrated their causation in endothelial dysfunction. The major significant finding of this study is that endothelial cell homeostasis is heavily governed by regulation of the actin cytoskeleton, cytokine and growth factor signaling, and Hippo signaling pathways. Also a result of the screen was the revelation that a pathological relationship exists between hemogenic endothelial cells and leukemia. Using the same forward genetic approach in a mouse model, we were able to induced mutagenesis at E9.5 in endothelial cells one day before they turned on their hemogenic program at E10.5. Not only were hematopoietic malignancies generated (both myeloid and lymphoid), but novel mutations associated with these cancers were identified. Here we also present data demonstrating the novel role of Pi4ka (identified in association with myeloid leukemia) in hematopoiesis. Together this work takes a look at the critical role of endothelial cells from three different perspectives (tumor angiogenesis, vascular anomalies, and hemogenic endothelial contribution to leukemia), highlighting their importance in physiology and pathology

Canonical and noncanonical vascular endothelial growth factor pathways: new developments in biology and signal transduction.

The past 5 years have witnessed a significant expansion in our understanding of vascular endothelial growth factor (VEGF) signaling. In particular, the process of canonical activation of VEGF receptor tyrosine kinases by homodimeric VEGF molecules has now been broadened by the realization that heterodimeric ligands and receptors are also active participants in the signaling process. Although heterodimer receptors were described 2 decades ago, their impact, along with the effect of additional cell surface partners and novel autocrine VEGF signaling pathways, are only now starting to be clarified. Furthermore, ligand-independent signaling (noncanonical) has been identified through galectin and gremlin binding and upon rise of intracellular levels of reactive oxygen species. Activation of the VEGF receptors in the absence of ligand holds immediate implications for therapeutic approaches that exclusively target VEGF. The present review provides a concise summary of the recent developments in both canonical and noncanonical VEGF signaling and places these findings in perspective to their potential clinical and biological ramifications