Olga V Saik1,2, Vadim V Nimaev3,4, Dilovarkhuja B Usmonov4,5, Pavel S Demenkov6,4, Timofey V Ivanisenko6,4, Inna N Lavrik6,7, Vladimir A Ivanisenko6,4. 1. Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. saik@bionet.nsc.ru. 2. Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090, Russia. saik@bionet.nsc.ru. 3. Laboratory of Surgical Lymphology and Lymphodetoxication, Research Institute of Clinical and Experimental Lymрhology - Branch of the Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, st. Timakova 2, Novosibirsk, 630117, Russia. 4. Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090, Russia. 5. Department of Neurosurgery, Ya. L. Tsivyan Novosibirsk Research Institute of Traumatology and Orthopedics, Ministry of Health of the Russian Federation, st. Frunze 17, Novosibirsk, 630091, Russia. 6. Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. 7. Translational Inflammation Research, Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, Medical Faculty, Pfalzer Platz 28, 39106, Magdeburg, Germany.
Abstract
BACKGROUND: Currently, more than 150 million people worldwide suffer from lymphedema. It is a chronic progressive disease characterized by high-protein edema of various parts of the body due to defects in lymphatic drainage. Molecular-genetic mechanisms of the disease are still poorly understood. Beginning of a clinical manifestation of primary lymphedema in middle age and the development of secondary lymphedema after treatment of breast cancer can be genetically determined. Disruption of endothelial cell apoptosis can be considered as one of the factors contributing to the development of lymphedema. However, a study of the relationship between genes associated with lymphedema and genes involved in endothelial apoptosis, in the associative gene network was not previously conducted. METHODS: In the current work, we used well-known methods (ToppGene and Endeavour), as well as methods previously developed by us, to prioritize genes involved in endothelial apoptosis and to find potential participants of molecular-genetic mechanisms of lymphedema among them. Original methods of prioritization took into account the overrepresented Gene Ontology biological processes, the centrality of vertices in the associative gene network, describing the interactions of endothelial apoptosis genes with genes associated with lymphedema, and the association of the analyzed genes with diseases that are comorbid to lymphedema. RESULTS: An assessment of the quality of prioritization was performed using criteria, which involved an analysis of the enrichment of the top-most priority genes by genes, which are known to have simultaneous interactions with lymphedema and endothelial cell apoptosis, as well as by genes differentially expressed in murine model of lymphedema. In particular, among genes involved in endothelial apoptosis, KDR, TNF, TEK, BMPR2, SERPINE1, IL10, CD40LG, CCL2, FASLG and ABL1 had the highest priority. The identified priority genes can be considered as candidates for genotyping in the studies involving the search for associations with lymphedema. CONCLUSIONS: Analysis of interactions of these genes in the associative gene network of lymphedema can improve understanding of mechanisms of interaction between endothelial apoptosis and lymphangiogenesis, and shed light on the role of disturbance of these processes in the development of edema, chronic inflammation and connective tissue transformation during the progression of the disease.
BACKGROUND: Currently, more than 150 million people worldwide suffer from lymphedema. It is a chronic progressive disease characterized by high-protein edema of various parts of the body due to defects in lymphatic drainage. Molecular-genetic mechanisms of the disease are still poorly understood. Beginning of a clinical manifestation of primary lymphedema in middle age and the development of secondary lymphedema after treatment of breast cancer can be genetically determined. Disruption of endothelial cell apoptosis can be considered as one of the factors contributing to the development of lymphedema. However, a study of the relationship between genes associated with lymphedema and genes involved in endothelial apoptosis, in the associative gene network was not previously conducted. METHODS: In the current work, we used well-known methods (ToppGene and Endeavour), as well as methods previously developed by us, to prioritize genes involved in endothelial apoptosis and to find potential participants of molecular-genetic mechanisms of lymphedema among them. Original methods of prioritization took into account the overrepresented Gene Ontology biological processes, the centrality of vertices in the associative gene network, describing the interactions of endothelial apoptosis genes with genes associated with lymphedema, and the association of the analyzed genes with diseases that are comorbid to lymphedema. RESULTS: An assessment of the quality of prioritization was performed using criteria, which involved an analysis of the enrichment of the top-most priority genes by genes, which are known to have simultaneous interactions with lymphedema and endothelial cell apoptosis, as well as by genes differentially expressed in murine model of lymphedema. In particular, among genes involved in endothelial apoptosis, KDR, TNF, TEK, BMPR2, SERPINE1, IL10, CD40LG, CCL2, FASLG and ABL1 had the highest priority. The identified priority genes can be considered as candidates for genotyping in the studies involving the search for associations with lymphedema. CONCLUSIONS: Analysis of interactions of these genes in the associative gene network of lymphedema can improve understanding of mechanisms of interaction between endothelial apoptosis and lymphangiogenesis, and shed light on the role of disturbance of these processes in the development of edema, chronic inflammation and connective tissue transformation during the progression of the disease.
Authors: M G Achen; S Roufail; T Domagala; B Catimel; E C Nice; D M Geleick; R Murphy; A M Scott; C Caesar; T Makinen; K Alitalo; S A Stacker Journal: Eur J Biochem Date: 2000-05
Authors: Vladimir A Ivanisenko; Olga V Saik; Nikita V Ivanisenko; Evgeny S Tiys; Timofey V Ivanisenko; Pavel S Demenkov; Nikolay A Kolchanov Journal: BMC Syst Biol Date: 2015-04-15
Authors: Germaine D Agollah; Manuel L Gonzalez-Garay; John C Rasmussen; I-Chih Tan; Melissa B Aldrich; Chinmay Darne; Caroline E Fife; Renie Guilliod; Erik A Maus; Philip D King; Eva M Sevick-Muraca Journal: PLoS One Date: 2014-11-10 Impact factor: 3.240