Expression profiling in canine osteosarcoma: identification of biomarkers and pathways associated with outcome

Abstract

BackgroundOsteosarcoma (OSA) spontaneously arises in the appendicular skeleton of large breed dogs and shares many physiological and molecular biological characteristics with human OSA. The standard treatment for OSA in both species is amputation or limb-sparing surgery, followed by chemotherapy. Unfortunately, OSA is an aggressive cancer with a high metastatic rate. Characterization of OSA with regard to its metastatic potential and chemotherapeutic resistance will improve both prognostic capabilities and treatment modalities.MethodsWe analyzed archived primary OSA tissue from dogs treated with limb amputation followed by doxorubicin or platinum-based drug chemotherapy. Samples were selected from two groups: dogs with disease free intervals (DFI) of less than 100 days (n = 8) and greater than 300 days (n = 7). Gene expression was assessed with Affymetrix Canine 2.0 microarrays and analyzed with a two-tailed t-test. A subset of genes was confirmed using qRT-PCR and used in classification analysis to predict prognosis. Systems-based gene ontology analysis was conducted on genes selected using a standard J5 metric. The genes identified using this approach were converted to their human homologues and assigned to functional pathways using the GeneGo MetaCore platform.ResultsPotential biomarkers were identified using gene expression microarray analysis and 11 differentially expressed (p < 0.05) genes were validated with qRT-PCR (n = 10/group). Statistical classification models using the qRT-PCR profiles predicted patient outcomes with 100% accuracy in the training set and up to 90% accuracy upon stratified cross validation. Pathway analysis revealed alterations in pathways associated with oxidative phosphorylation, hedgehog and parathyroid hormone signaling, cAMP/Protein Kinase A (PKA) signaling, immune responses, cytoskeletal remodeling and focal adhesion.ConclusionsThis profiling study has identified potential new biomarkers to predict patient outcome in OSA and new pathways that may be targeted for therapeutic intervention.

SATB2 enhances migration and invasion in osteosarcoma by regulating genes involved in cytoskeletal organization

“…Moreover, our finding is also in agreement with previous gene expression profiling studies using both in vitro and in vivo models that identified both cytoskeletonremodeling and focal adhesion as metastatic pathways in OS. [32][33][34][35] Consistent with our pathway analyses, OS cells with SATB2 knockdown were characterized by morphological differences in the actin cytoskeleton. Sh-SATB2 cells were more elongated with increased stress fiber formation.…”

Expression of three topologically distinct membrane proteins elicits unique stress response pathways in the yeastSaccharomyces cerevisiae

“…Efficiency analysis identified the J5 test (123) as the most internally consistent test (compared to fold-change, the D1 test, the t-test, and random feature selection) after z-transform for the first two comparisons and after mean normalization for the third comparison. The J5 test is especially useful for datasets with a small number of replicates and may reduce the number of false positives generated through other analytical methods (19,123), and this test has previously been used to analyze microarray data from diverse sources (18,25,42,106,118,128,131,144). Missing values were imputed using k-nearest neighbors.…”

Application of post-genomic techniques in dog cancer research

“…A number of 51 transcripts were found to be differentially expressed and hierarchical clustering, validated by reverse transcriptase polymerase chain reaction (RT-PCR) analysis, revealed that four genes, namely ANKRRD17, MGST1, MRPS31, and NCOR1, were overexpressed in the short survival group. Expression profiling following the same technique identified both biomarkers and pathways associated with the clinical outcome 102 in dogs that View Article Online responded poorly to chemotherapy and dogs that responded well, as defined by the disease-free intervals (o100 days and 4300 days). Differentially expressed genes related to the hedgehog signalling pathway, such as HHIP, were found to be upregulated in the poor responder cohort.…”