Limits...
The stromal genome heterogeneity between breast and prostate tumors revealed by a comparative transcriptomic analysis.

He K, Lv W, Zheng D, Cheng F, Zhou T, Ye S, Ban Q, Ying Q, Huang B, Chen L, Wu G, Liu D - Oncotarget (2015)

Bottom Line: As a result, 8 up-regulated pathways and 73 down-regulated pathways were identified in the breast tumor stroma, while 32 up-regulated pathways and 18 down-regulated pathways were identified in the prostate tumor stroma.Several essential tumors stromal marker genes were also significantly identified.For example, CDH3 was significantly up-regulated in the stromals of both breast and prostate tumors, however EGFR was only significantly down-regulated in the stromal of breast tumor.

View Article: PubMed Central - PubMed

Affiliation: Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei City, Anhui, China.

ABSTRACT
Stromal microenvironment increases tumor cell survival, proliferation and migration, and promotes angiogenesis. In order to provide comprehensive information on the stromal heterogeneity of diverse tumors, here we employed the microarray datasets of human invasive breast and prostate cancer-associated stromals and applied Gene Set Enrichment Analysis (GSEA) to compare the gene expression profiles between them. As a result, 8 up-regulated pathways and 73 down-regulated pathways were identified in the breast tumor stroma, while 32 up-regulated pathways and 18 down-regulated pathways were identified in the prostate tumor stroma. Only 9 pathways such as tryptophan metabolism were commonly up or down regulated, but most of them (including ABC transporters) were specific for these two tumors. Several essential tumors stromal marker genes were also significantly identified. For example, CDH3 was significantly up-regulated in the stromals of both breast and prostate tumors, however EGFR was only significantly down-regulated in the stromal of breast tumor. Our study would be helpful for future therapeutic and predictive applications in breast and prostate cancers.

No MeSH data available.


Related in: MedlinePlus

Comparison of stromal related genes between DEGA and GSEA results for breast tumor and prostate tumor(A) Venn diagram showing the overlapping significantly identified genes by the comparison of stromal related genes between DEGA and GSEA results for breast cancer. By comparison, there were 84 common genes between DEGA and GSEA results for breast tumor stromal. The significance of overlapping was p=2.95E-11. (B) Comparison of stromal related genes between DEGA and GSEA results for prostate cancer. Venn diagram showing the overlapping significantly identified genes by the comparison of stromal related genes between DEGA and GSEA results for prostate cancer. For prostate tumor, the common genes number was 17 with the overlapping significance of p=4.65E-02.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4496176&req=5

Figure 1: Comparison of stromal related genes between DEGA and GSEA results for breast tumor and prostate tumor(A) Venn diagram showing the overlapping significantly identified genes by the comparison of stromal related genes between DEGA and GSEA results for breast cancer. By comparison, there were 84 common genes between DEGA and GSEA results for breast tumor stromal. The significance of overlapping was p=2.95E-11. (B) Comparison of stromal related genes between DEGA and GSEA results for prostate cancer. Venn diagram showing the overlapping significantly identified genes by the comparison of stromal related genes between DEGA and GSEA results for prostate cancer. For prostate tumor, the common genes number was 17 with the overlapping significance of p=4.65E-02.

Mentions: According to the approach of differentially expressed gene analysis (DEGA) studied by Planche et al., 643 and 319 differentially expressed genes between tumor and normal stroma were identified for breast cancer and prostate cancer, respectively (shown in Supplementary File 1) [24]. The DEGA approach was based on a paired analysis of differential expression using the package of limma with the cutoff of false positive rate (FDR) as 0.01. Here, we used standardized microarray preprocessing and GSEA with comprehensive expression profiles in order to find greater data convergence and provide a systematic insight into the associated pathways in both human breast and prostate tumor stromals. In our study, 8 up-regulated and 73 down-regulated pathways were significantly identified in breast tumor stromal, while 32 up-regulated and 18 down-regulated pathways were significantly identified in prostate tumor stromal based on the approach of GSEA. Totally, 3337 and 2145 genes were dysregulated in breast and prostate tumor stromal, respectively (shown in Supplementary File 2). By comparison, there were 84 common genes between DEGA and GSEA results for breast tumor stromal. The significance of overlapping was p=2.95E-11 (Figure 1A). For prostate tumor, the common genes number was 17 with the overlapping significance of p=4.65E-02 (Figure 1B). It indicated that our GSEA results would be not only consistent with the previous DEGA results but also more comprehensive. In addition, 360 and 342 dysregulated transcription factors (TFs) were further identified in breast tumor and prostate tumor stromal, respectively (shown in Supplementary File 3).


The stromal genome heterogeneity between breast and prostate tumors revealed by a comparative transcriptomic analysis.

He K, Lv W, Zheng D, Cheng F, Zhou T, Ye S, Ban Q, Ying Q, Huang B, Chen L, Wu G, Liu D - Oncotarget (2015)

Comparison of stromal related genes between DEGA and GSEA results for breast tumor and prostate tumor(A) Venn diagram showing the overlapping significantly identified genes by the comparison of stromal related genes between DEGA and GSEA results for breast cancer. By comparison, there were 84 common genes between DEGA and GSEA results for breast tumor stromal. The significance of overlapping was p=2.95E-11. (B) Comparison of stromal related genes between DEGA and GSEA results for prostate cancer. Venn diagram showing the overlapping significantly identified genes by the comparison of stromal related genes between DEGA and GSEA results for prostate cancer. For prostate tumor, the common genes number was 17 with the overlapping significance of p=4.65E-02.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4496176&req=5

Figure 1: Comparison of stromal related genes between DEGA and GSEA results for breast tumor and prostate tumor(A) Venn diagram showing the overlapping significantly identified genes by the comparison of stromal related genes between DEGA and GSEA results for breast cancer. By comparison, there were 84 common genes between DEGA and GSEA results for breast tumor stromal. The significance of overlapping was p=2.95E-11. (B) Comparison of stromal related genes between DEGA and GSEA results for prostate cancer. Venn diagram showing the overlapping significantly identified genes by the comparison of stromal related genes between DEGA and GSEA results for prostate cancer. For prostate tumor, the common genes number was 17 with the overlapping significance of p=4.65E-02.
Mentions: According to the approach of differentially expressed gene analysis (DEGA) studied by Planche et al., 643 and 319 differentially expressed genes between tumor and normal stroma were identified for breast cancer and prostate cancer, respectively (shown in Supplementary File 1) [24]. The DEGA approach was based on a paired analysis of differential expression using the package of limma with the cutoff of false positive rate (FDR) as 0.01. Here, we used standardized microarray preprocessing and GSEA with comprehensive expression profiles in order to find greater data convergence and provide a systematic insight into the associated pathways in both human breast and prostate tumor stromals. In our study, 8 up-regulated and 73 down-regulated pathways were significantly identified in breast tumor stromal, while 32 up-regulated and 18 down-regulated pathways were significantly identified in prostate tumor stromal based on the approach of GSEA. Totally, 3337 and 2145 genes were dysregulated in breast and prostate tumor stromal, respectively (shown in Supplementary File 2). By comparison, there were 84 common genes between DEGA and GSEA results for breast tumor stromal. The significance of overlapping was p=2.95E-11 (Figure 1A). For prostate tumor, the common genes number was 17 with the overlapping significance of p=4.65E-02 (Figure 1B). It indicated that our GSEA results would be not only consistent with the previous DEGA results but also more comprehensive. In addition, 360 and 342 dysregulated transcription factors (TFs) were further identified in breast tumor and prostate tumor stromal, respectively (shown in Supplementary File 3).

Bottom Line: As a result, 8 up-regulated pathways and 73 down-regulated pathways were identified in the breast tumor stroma, while 32 up-regulated pathways and 18 down-regulated pathways were identified in the prostate tumor stroma.Several essential tumors stromal marker genes were also significantly identified.For example, CDH3 was significantly up-regulated in the stromals of both breast and prostate tumors, however EGFR was only significantly down-regulated in the stromal of breast tumor.

View Article: PubMed Central - PubMed

Affiliation: Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei City, Anhui, China.

ABSTRACT
Stromal microenvironment increases tumor cell survival, proliferation and migration, and promotes angiogenesis. In order to provide comprehensive information on the stromal heterogeneity of diverse tumors, here we employed the microarray datasets of human invasive breast and prostate cancer-associated stromals and applied Gene Set Enrichment Analysis (GSEA) to compare the gene expression profiles between them. As a result, 8 up-regulated pathways and 73 down-regulated pathways were identified in the breast tumor stroma, while 32 up-regulated pathways and 18 down-regulated pathways were identified in the prostate tumor stroma. Only 9 pathways such as tryptophan metabolism were commonly up or down regulated, but most of them (including ABC transporters) were specific for these two tumors. Several essential tumors stromal marker genes were also significantly identified. For example, CDH3 was significantly up-regulated in the stromals of both breast and prostate tumors, however EGFR was only significantly down-regulated in the stromal of breast tumor. Our study would be helpful for future therapeutic and predictive applications in breast and prostate cancers.

No MeSH data available.


Related in: MedlinePlus