Using MIMs in coordination with gene expression datasets to unravel cell regulatory networks This project is based on the premise that genes that are co-regulated in a variety of cell types are likely to be functionally related. We developed that concept utilizing (1) expression data for the approximately 16,000 genes in the NCI-60 panel of human tumor cell lines;(2) data mining software, developed in our Laboratory (particularly CellMiner) for efficient access to that data;(3) NCI-60 gene expression clusters related to function categories derived by a novel procedure developed by Zeeberg et al (manuscript in preparation);(4) PathVisio-MIM diagram production software (see below);and (5) free access to the relevant scientific literature via PubMed. Utilizing those facilities, we investigated control networks involved in cell migration/invasion, functions specific to melanomas, and molecular interactions specific to cells having epithelial character, as follows. Molecular interaction network model of cell migration/invasion processes Using a set of genes derived by a new clustering procedure designed by Zeeberg et al. (manuscript in preparation) that links expression in the NCI-60 panel of human tumor cells with functions assigned by the Gene Ontology (GO) database, we assembled available information about the molecular interactions of a set of 70 expression-correlated genes. We found that about 70% of those genes could be depicted in 3 overlapping molecular interaction maps (MIMs) related to cell migration: (1) interactions with extracellular matrix;(2) interactions with the actin cytoskeleton;(3) interactions implicating proteoglycans in the extracellular matrix. Melanoma-specific Gene Expression Patterns in the NCI-60 Human Tumor Cell Lines. This project aims to elucidate the regulatory mechanisms specific to melanomas by characterizing distinct gene expression patterns and molecular interaction networks. That increased level of detail may provide new definitions of distinct melanoma subtypes that could improve the design and selection of targeted therapies.
We aim to organize what is known about the molecular interactions involved in functions specific to melanoma cells and their cell type of origin, the melanocyte or a precursor thereof. It has been pointed out that melanocytes provide an excellent system for studying complex regulatory networks (Schepsky et al., 2006). Melanomas and melanocytes specifically express the pathways for melanin biosynthesis and melanosome production. Studies of gene actions involved specifically in these processes therefore spotlight the mechanisms involved in those cell types and sharply focuses investigations of a particular set of interrelated molecular control systems. Epithelial gene expression signatures from the NCI-60 human tumor cell lines. In a new approach to the characterization of cells having epithelial character, we focused on the expression of genes for the proteins involved in tight-junctions, structures that are required to maintain polarity of epithelial cells. We found that gene expression of tight-junction proteins in the NCI-60 cell lines is consistent with and more specific than previous epithelial cell characterizations based on expression ratios of E-cadherin and vimentin. Enhancing the utility of our Molecular Interaction Map (MIM) notation In order to make the MIM notation readily accessible to the scientific community and make it easier to learn, as well as to provide tools for developers of MIM applications, we have developed the following software: PathVisio-MIM PathVisio is a tool for creating and editing pathway diagrams (www.pathvisio.org). We developed and published a plug-in to PathVisio for creating and editing MIMs: Luna, A., Sunshine, M.L., van Iersel, M.P., Aladjem, M.I., and Kohn, K.W. (2011). PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). Bioinformatics 27, 2165-2166. We now use PathVisio-MIM to create all of our MIM diagrams and find it much easier and faster than the graphics programs we previously used. It greatly facilitates editing or modifying the diagrams, particularly when sections of a diagram have to be moved to provide space for additions. It will make it much easier for new MIM users, because the proper MIM graphics elements are at hand and identified either in pull-down menus or as icons. Also of help for both new and proficient users will be the coordinated use of the Validator plugin described below. Tools for MIM developers In order to provide tools for MIM software development based on our MIM notation rules (Kohn et al., Mol. Biol. Cell 17: 1-13, 2006), we published the following Research Article: Luna, A., Karac, E.I., Sunshine, M., Chang, L., Nussinov, R., Aladjem, M.I., and Kohn, K.W. (2011). A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. BMC Bioinformatics 12:167. This publication makes available a Java-based application programming interface (API) that can be used by developers to help incorporate support for our new MIMML format. In addition, we have created and included validation software for MIMML datasets that allows MIM users to know if their diagrams conform to syntactic rules outlined by the new MIM specification. We provided documentation and examples for the use of the MIM API and for the validation of the MIMML, as well as a set of MIM diagram examples. PathVisio Validator We collaborated with developers of PathVisio and SBGN (Systems Biology Graphics Notation) to develop a validation framework in PathVisio that can be used with rule sets for MIM or other diagram notations, and we have submitted the following Systems Biology note: Kumar Chandan, Martijn P. van Iersel, Mirit I. Aladjem, Kurt W. Kohn and Augustin Luna (2011). PathVisio Validator: A Rule-based Validation Plugin for Pathway Graphical Notations in PathVisio. The Validator will help users check whether their diagrams conform to a standard rule set, such as for MIM, so as to make the diagrams unambiguous and coded in a manner suitable for exchange with other users. That will be important also for development of automation. The Validator plugin is free and open source. It works with versions of PathVisio 2.0.11 and later on Windows, Mac OS X, and Linux. The plugin along with instructions, example rulesets, and Java source code can be downloaded at http://pathvisio.org/wiki/PathwayValidatorHelp. Functions of MdmX in Fine-Tuning the Response of p53 to DNA Damage Based on a molecular interaction map (MIM) of the p53-Mdm2-MdmX control network, we simulated simplified models and surveyed parameter space to disclose regions where oscillatory behavior did or did not occur: Kim S, Aladjem MI, McFadden GB, Kohn KW. Predicted functions of MdmX in fine-tuning the response of p53 to DNA damage. PLoS Comput Biol. 6(2):e1000665, 2010. A major finding was that MdmX can dampen the p53 oscillations that occur after DNA damage. That action may prevent high transient p53 activity at could lead to unnecessary cell death. MdmX thus may protect against p53 excess. We are currently testing this novel hypothesis in cell culture. We have engineered the needed cell lines and have preliminary data supporting our hypothesis.
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