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Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression.

Paoloni M, Davis S, Lana S, Withrow S, Sangiorgi L, Picci P, Hewitt S, Triche T, Meltzer P, Khanna C - BMC Genomics (2009)

Bottom Line: Expression of these genes in an independent population of pediatric osteosarcoma patients was associated with poor outcome (p = 0.020 and p = 0.026, respectively).Validation of IL-8 and SLC1A3 protein expression in pediatric osteosarcoma tissues further supported the potential value of these novel targets.Ongoing evaluation will validate the biological significance of these targets and their associated pathways.

View Article: PubMed Central - HTML - PubMed

Affiliation: Comparative Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. paolonim@mail.nih.gov

ABSTRACT

Background: Pulmonary metastasis continues to be the most common cause of death in osteosarcoma. Indeed, the 5-year survival for newly diagnosed osteosarcoma patients has not significantly changed in over 20 years. Further understanding of the mechanisms of metastasis and resistance for this aggressive pediatric cancer is necessary. Pet dogs naturally develop osteosarcoma providing a novel opportunity to model metastasis development and progression. Given the accelerated biology of canine osteosarcoma, we hypothesized that a direct comparison of canine and pediatric osteosarcoma expression profiles may help identify novel metastasis-associated tumor targets that have been missed through the study of the human cancer alone.

Results: Using parallel oligonucleotide array platforms, shared orthologues between species were identified and normalized. The osteosarcoma expression signatures could not distinguish the canine and human diseases by hierarchical clustering. Cross-species target mining identified two genes, interleukin-8 (IL-8) and solute carrier family 1 (glial high affinity glutamate transporter), member 3 (SLC1A3), which were uniformly expressed in dog but not in all pediatric osteosarcoma patient samples. Expression of these genes in an independent population of pediatric osteosarcoma patients was associated with poor outcome (p = 0.020 and p = 0.026, respectively). Validation of IL-8 and SLC1A3 protein expression in pediatric osteosarcoma tissues further supported the potential value of these novel targets. Ongoing evaluation will validate the biological significance of these targets and their associated pathways.

Conclusions: Collectively, these data support the strong similarities between human and canine osteosarcoma and underline the opportunities provided by a comparative oncology approach as a means to improve our understanding of cancer biology and therapies.

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Algorithm depicting the selection process for dog specific osteosarcoma genes using a fold-expression methodology. In order to define a list of dog specific osteosarcoma genes that are variably expressed in human osteosarcoma, probe sets with matching gene names or symbols across both species were evaluated (14,391 probe sets). An initial list of dog osteosarcoma defining genes was generated by identifying those probe sets with the highest fold expression differentials between the canine tumors and their normal tissues and present expression in the human tumors and their normal tissues (dog: > 8-fold up-regulation in tumors versus normal; human: <2-fold upregulation in tumors versus normal). This yielded 27 probe sets, representing 15 unique genes. Those genes that also had representative probe sets upregulated in both dog and man (> 8 fold expression) were then excluded, leaving 10 genes. This was further filtered by retaining only those genes with consistent expression across all their Affymetrix probe sets; using these stringent criteria 4 dog-like specific osteosarcoma genes were defined.
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Figure 3: Algorithm depicting the selection process for dog specific osteosarcoma genes using a fold-expression methodology. In order to define a list of dog specific osteosarcoma genes that are variably expressed in human osteosarcoma, probe sets with matching gene names or symbols across both species were evaluated (14,391 probe sets). An initial list of dog osteosarcoma defining genes was generated by identifying those probe sets with the highest fold expression differentials between the canine tumors and their normal tissues and present expression in the human tumors and their normal tissues (dog: > 8-fold up-regulation in tumors versus normal; human: <2-fold upregulation in tumors versus normal). This yielded 27 probe sets, representing 15 unique genes. Those genes that also had representative probe sets upregulated in both dog and man (> 8 fold expression) were then excluded, leaving 10 genes. This was further filtered by retaining only those genes with consistent expression across all their Affymetrix probe sets; using these stringent criteria 4 dog-like specific osteosarcoma genes were defined.

Mentions: The compelling likeness between canine and human osteosarcoma expression profiles prompted us to ask if new insights could be gleaned using our cross-species approach that would be overlooked if only the human data set was examined. Based on the fact that canine osteosarcoma may be associated with a more aggressive clinical course than human osteosarcoma, we hypothesized that genes that were more "dog-like" but nonetheless expressed in human osteosarcoma, would be more likely to be linked to metastatic progression or poorest clinical outcome in human patients. Using a fold expression approach we identified 74 genes with greater expression in the dog vs. human. From this list 15 strongly "dog-like" osteosarcoma defining genes (Table 2) were highly linked to dog osteosarcoma (highest fold expression difference between canine tumors and canine normal tissues; > 8-fold expression in tumors versus dog normals) but were nonetheless expressed in human osteosarcoma (expressed in human tumors compared to human normal tissues; <2-fold expression in tumors vs. normal) (Figure 3). Next, expression consistency in all Affymetrix probe sets, defined as concordant direction of differential expression for all probesets associated with a given gene, yielded four "dog-like" genes of interest: IL-8, SLC1A3, TFPI2, (tissue factor pathway inhibitor 2), and RBP4 (retinol binding protein 4, plasma). Each of these "dog-like" genes were examined in a distinct population of 34 human osteosarcoma patient samples (see Additional File 1, Table S1) that had previously undergone gene expression analysis and were linked to clinical outcome. The median survival time for this population of human patients was 10.3 years (see Additional File 1, Table S1)). High expression of two of the four "dog-like" genes (IL-8 and SLC1A3) linked to poor outcome in human osteosarcoma using Kaplan Meier analysis (IL-8, p = 0.0201; SLC1A3, p = 0.0264, Figure 4). This finding of two potentially informative genes is noteworthy since the survival signature generated via Cox Regression of the entire dataset suggested it was unlikely that individual genes would be predictive of clinical outcome (data not shown). Fisher exact analysis supported the strength of the association between these "dog-like" genes and survival when compared to 24 previously identified cancer candidate genes (p-value = 0.0189) where no association with survival was found. After multiple test corrections, using random permutation testing, increased IL-8 expression was continuously linked with poor survival (p = 0.02). (Figure 4).


Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression.

Paoloni M, Davis S, Lana S, Withrow S, Sangiorgi L, Picci P, Hewitt S, Triche T, Meltzer P, Khanna C - BMC Genomics (2009)

Algorithm depicting the selection process for dog specific osteosarcoma genes using a fold-expression methodology. In order to define a list of dog specific osteosarcoma genes that are variably expressed in human osteosarcoma, probe sets with matching gene names or symbols across both species were evaluated (14,391 probe sets). An initial list of dog osteosarcoma defining genes was generated by identifying those probe sets with the highest fold expression differentials between the canine tumors and their normal tissues and present expression in the human tumors and their normal tissues (dog: > 8-fold up-regulation in tumors versus normal; human: <2-fold upregulation in tumors versus normal). This yielded 27 probe sets, representing 15 unique genes. Those genes that also had representative probe sets upregulated in both dog and man (> 8 fold expression) were then excluded, leaving 10 genes. This was further filtered by retaining only those genes with consistent expression across all their Affymetrix probe sets; using these stringent criteria 4 dog-like specific osteosarcoma genes were defined.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2803201&req=5

Figure 3: Algorithm depicting the selection process for dog specific osteosarcoma genes using a fold-expression methodology. In order to define a list of dog specific osteosarcoma genes that are variably expressed in human osteosarcoma, probe sets with matching gene names or symbols across both species were evaluated (14,391 probe sets). An initial list of dog osteosarcoma defining genes was generated by identifying those probe sets with the highest fold expression differentials between the canine tumors and their normal tissues and present expression in the human tumors and their normal tissues (dog: > 8-fold up-regulation in tumors versus normal; human: <2-fold upregulation in tumors versus normal). This yielded 27 probe sets, representing 15 unique genes. Those genes that also had representative probe sets upregulated in both dog and man (> 8 fold expression) were then excluded, leaving 10 genes. This was further filtered by retaining only those genes with consistent expression across all their Affymetrix probe sets; using these stringent criteria 4 dog-like specific osteosarcoma genes were defined.
Mentions: The compelling likeness between canine and human osteosarcoma expression profiles prompted us to ask if new insights could be gleaned using our cross-species approach that would be overlooked if only the human data set was examined. Based on the fact that canine osteosarcoma may be associated with a more aggressive clinical course than human osteosarcoma, we hypothesized that genes that were more "dog-like" but nonetheless expressed in human osteosarcoma, would be more likely to be linked to metastatic progression or poorest clinical outcome in human patients. Using a fold expression approach we identified 74 genes with greater expression in the dog vs. human. From this list 15 strongly "dog-like" osteosarcoma defining genes (Table 2) were highly linked to dog osteosarcoma (highest fold expression difference between canine tumors and canine normal tissues; > 8-fold expression in tumors versus dog normals) but were nonetheless expressed in human osteosarcoma (expressed in human tumors compared to human normal tissues; <2-fold expression in tumors vs. normal) (Figure 3). Next, expression consistency in all Affymetrix probe sets, defined as concordant direction of differential expression for all probesets associated with a given gene, yielded four "dog-like" genes of interest: IL-8, SLC1A3, TFPI2, (tissue factor pathway inhibitor 2), and RBP4 (retinol binding protein 4, plasma). Each of these "dog-like" genes were examined in a distinct population of 34 human osteosarcoma patient samples (see Additional File 1, Table S1) that had previously undergone gene expression analysis and were linked to clinical outcome. The median survival time for this population of human patients was 10.3 years (see Additional File 1, Table S1)). High expression of two of the four "dog-like" genes (IL-8 and SLC1A3) linked to poor outcome in human osteosarcoma using Kaplan Meier analysis (IL-8, p = 0.0201; SLC1A3, p = 0.0264, Figure 4). This finding of two potentially informative genes is noteworthy since the survival signature generated via Cox Regression of the entire dataset suggested it was unlikely that individual genes would be predictive of clinical outcome (data not shown). Fisher exact analysis supported the strength of the association between these "dog-like" genes and survival when compared to 24 previously identified cancer candidate genes (p-value = 0.0189) where no association with survival was found. After multiple test corrections, using random permutation testing, increased IL-8 expression was continuously linked with poor survival (p = 0.02). (Figure 4).

Bottom Line: Expression of these genes in an independent population of pediatric osteosarcoma patients was associated with poor outcome (p = 0.020 and p = 0.026, respectively).Validation of IL-8 and SLC1A3 protein expression in pediatric osteosarcoma tissues further supported the potential value of these novel targets.Ongoing evaluation will validate the biological significance of these targets and their associated pathways.

View Article: PubMed Central - HTML - PubMed

Affiliation: Comparative Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. paolonim@mail.nih.gov

ABSTRACT

Background: Pulmonary metastasis continues to be the most common cause of death in osteosarcoma. Indeed, the 5-year survival for newly diagnosed osteosarcoma patients has not significantly changed in over 20 years. Further understanding of the mechanisms of metastasis and resistance for this aggressive pediatric cancer is necessary. Pet dogs naturally develop osteosarcoma providing a novel opportunity to model metastasis development and progression. Given the accelerated biology of canine osteosarcoma, we hypothesized that a direct comparison of canine and pediatric osteosarcoma expression profiles may help identify novel metastasis-associated tumor targets that have been missed through the study of the human cancer alone.

Results: Using parallel oligonucleotide array platforms, shared orthologues between species were identified and normalized. The osteosarcoma expression signatures could not distinguish the canine and human diseases by hierarchical clustering. Cross-species target mining identified two genes, interleukin-8 (IL-8) and solute carrier family 1 (glial high affinity glutamate transporter), member 3 (SLC1A3), which were uniformly expressed in dog but not in all pediatric osteosarcoma patient samples. Expression of these genes in an independent population of pediatric osteosarcoma patients was associated with poor outcome (p = 0.020 and p = 0.026, respectively). Validation of IL-8 and SLC1A3 protein expression in pediatric osteosarcoma tissues further supported the potential value of these novel targets. Ongoing evaluation will validate the biological significance of these targets and their associated pathways.

Conclusions: Collectively, these data support the strong similarities between human and canine osteosarcoma and underline the opportunities provided by a comparative oncology approach as a means to improve our understanding of cancer biology and therapies.

Show MeSH
Related in: MedlinePlus