Comment[ArrayExpressAccession] E-GEOD-45832 MAGE-TAB Version 1.1 Public Release Date 2013-08-07 Investigation Title KB001-Gene expression profiling of histiocytic sarcomas in a canine model: the predisposed Flatcoated retriever dog Comment[Submitted Name] KB001-Gene expression profiling of histiocytic sarcomas in a canine model: the predisposed Flatcoated retriever dog Experiment Description Background: The determination of altered expression of genes in specific tumor types and their effect upon cellular processes may create insight in tumorigenesis and help to design better treatments. The Flatcoated retriever is a dog breed with an exceptionally high incidence of histiocytic sarcomas. The breed develops two distinct entities of histiocytic neoplasia, a soft tissue form and a visceral form. Gene expression studies of these tumors has value for comparable human diseases such as histiocytic/dendritic cell sarcoma for which knowledge is difficult to accrue due to their rare occurrence. In addition, such studies may help in the search for genetic aberrations underlying the genetic predisposition in this dog breed. Methods: Microarray analysis and pathway analyses were performed on fresh-frozen tissues obtained from Flatcoated retrievers with localized, soft tissue histiocytic sarcomas (STHS) and disseminated, visceral histiocytic sarcomas (VHS) and on normal canine spleens from various breeds. Expression differences of nine genes were validated with quantitative real-time PCR (qPCR) analyses. Results: QPCR analyses identified the significantly altered expression of nine genes; PPBP, SpiC, VCAM1, ENPEP, ITGAD (down-regulated), and GTSF1, Col3a1, CD90 and LUM (up-regulated) in the comparison of both the soft tissue and the visceral form with healthy spleen. DAVID pathway analyses revealed 24 pathways that were significantly involved in the development of HS in general, most of which were involved in the DNA repair and replication process. Conclusions: This study identified altered expression of nine genes not yet implicated in histiocytic sarcoma manifestations in the dog nor in comparable human histiocytic/dendritic sarcomas. Extraploration of this downside effect of canine inbreeding strategies for the study of similar sarcomas in humans might also lead to the identification of genes related to these rare malignancies in the human. Microarray expression dataset including STHS: Soft Tissue (localized) Histiocytic Sarcoma; VHS: Visceral (disseminated)Histiocytic Sarcoma; together with normal spleen (NS) samples. Comparisons were analysed in dyeswap on a 2-color platform against a common reference sample, consisting of a multitude of canine organs, including liver, spleen, kidney, lung, hart, intestine and bone. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Groot Koerkamp M. Boerkamp van der Kooij van Steenbeek van Wolferen Koerkamp van Leenen Grinwis Penning Wiemer Rutteman Person First Name Marian Kim Marieke Frank Monique Marian Dik Guy Louis Erik Gerard Person Mid Initials G E G C C A R Person Email M.J.A.GrootKoerkamp@umcutrecht.nl Person Affiliation UMC Utrecht, Netherlands Person Phone 31887568984 Person Address Molecular Cancer Research, UMC Utrecht, Netherlands, Universiteitsweg 100, Utrecht, Utrecht, Netherlands Person Roles submitter Protocol Name P-GSE45832-1 P-GSE45832-2 P-GSE45832-4 P-GSE45832-5 P-GSE45832-3 P-GSE45832-6 Protocol Description Features were extracted using Imagene software from Biodiscovery. Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009 ID_REF = VALUE = normalized log2 ratio (Cy5/Cy3) Signal Norm_Cy5 = Signal Norm_Cy3 = Features were extracted using Imagene software from Biodiscovery. Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009 ID_REF = VALUE = normalized log2 ratio (test/reference) Signal Norm_Cy5 = Signal Norm_Cy3 = INV_VALUE = normalized log2 ratio (Cy5/Cy3) robot amplification and labeling v1.0 Tecan HS4800 hybridization RNA isolation using Trizol v1.0 (tissue sections) scanning of slides using Agilent G256BA Protocol Type normalization data transformation protocol normalization data transformation protocol labelling protocol hybridization protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name SAMPLE TYPE ID ORGANISM PART Experimental Factor Type sample type ID organism part Comment[SecondaryAccession] GSE45832 Comment[GEOReleaseDate] 2013-08-07 Comment[ArrayExpressSubmissionDate] 2013-04-05 Comment[GEOLastUpdateDate] 2013-08-08 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-45832.sdrf.txt