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Volume 2012 (2012), Article ID 820254, 12 pages
Putative Multifunctional Signature of Lung Metastases in Dedifferentiated Chondrosarcoma
1Cancer Biology and Epigenomics Program, Children’s Memorial Research Center, and Department of Pediatrics, Northwestern University Feinberg School of Medicine, 2430 N. Halstead Street, Chicago, IL 60614, USA
2GeneGo, Inc., 500 Renaissance Drive, No. 106, St. Joseph, MI 49085, USA
3Department of Pathology and Laboratory Medicine, Children’s Memorial Hospital 2300 Children’s Plaza, Chicago, IL 60614, USA
4Center for Bioinformatics and Computation Biology, University of Iowa, 5316 Seamans Center, Iowa City, IA 52242, USA
5Department of Orthopaedics and Rehabilitation, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
6Vavilov Institute for General Genetics, Russian Academy of Sciences, 3 Gubkina Street, Moscow 117093, Russia
7Department of Urology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
8Department of Hematology/Oncology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
9Department of Surgical Pathology, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
10Lung Cancer and Thoracic Oncology Program, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
11Department of Pediatrics, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
Received 12 May 2011; Revised 21 October 2011; Accepted 3 November 2011
Academic Editor: Alessandro Gronchi
Copyright © 2012 Sergey Malchenko et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Supplemental Table 1: The differential expression of a subset of genes in the “biased multifunctional signature” was validated by quantitative real-time PCR. The Pfaffl method was used to calculate the relative gene expression levels.
Supplemental Table 2: Datasets for the functional analysis: Up or Down-regulated genes in all the Met.- cell lines, Multi-functional genes “commonly” expressed in the metastases and in the virtual non-metastatic tumor, Metastasis associated literature (GeneGo), “Multi-functional” grid (GeneGo).
Supplemental Table 3: Distribution of the SAGE tags cluster sizes that were significantly differentially expressed relative to those SAGE tags that did not exhibit differential expression in the metastases.
Supplemental Table 4: A. Pair-wise comparisons between the genes expressed in Met. 1 (4,205 genes) and those expressed in each of the other metastases, i.e. Met. 2–5. B. Similar pair-wise comparisons were performed between the subset of 105 “metastasis-associated” genes identified in Met. 1 and those expressed in each of the other metastases. C. Similar pair-wise comparisons were performed between the subset of 52 “Multi-functional” genes identified in Met. 1 and those expressed in each of the other metastases.
Supplemental Table 5: A. Expression of chondrocyte markers and markers of conventional chondrosarcoma in the metastases and the virtual non-metastatic tumor. B. Genes with altered expression in the dedifferentiated chondrosarcoma metastases, which also differentially expressed during chondrogenic differentiation of MSC. C. Evaluation of tumor cell invasion of the metastatic and non-metastatic cell lines.
Supplemental Figure 1: The network built for the “biased” multi-functional signature using shortest path (SP) algorithm. SP algorithm allows incorporation of certain nodes from the MetaCore database, which are not in the input list of 15 genes, in such a way that all the 15 input genes are connected by the smallest possible number of direct interactions. Red solid circle indicates expression of the gene in the metastases. Blue square indicates consistently down-regulated gene in the metastases, relative to the virtual NM-cell line.