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SYK allelic loss and the role of Syk-regulated genes in breast cancer survival.

Blancato J, Graves A, Rashidi B, Moroni M, Tchobe L, Ozdemirli M, Kallakury B, Makambi KH, Marian C, Mueller SC - PLoS ONE (2014)

Bottom Line: In cases without immune cell infiltration, loss of SYK copy number was associated with a significant reduction of SYK mRNA.We found that overall survival was significantly reduced in IDC and Luminal A+B cases where copy number and mutations of these 55 genes were affected (Kaplan-Meier, Logrank test p-value 0.007141 and Logrank test p-value 0.001198, respectively).We conclude that reduction in Syk expression and contributions of genomic instability to copy number and mutations in the 55 Syk interacting genes significantly contribute to poorer overall patient survival.

View Article: PubMed Central - PubMed

Affiliation: Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D. C., United States of America.

ABSTRACT
Heterozygotic loss of SYK, a non-receptor tyrosine kinase, gives rise to mouse mammary tumor formation where Syk protein levels are reduced by about half; loss of SYK mRNA is correlated with invasive cell behavior in in vitro models; and SYK loss has been correlated with distant metastases in patients. Here, allelic loss of the SYK gene was explored in breast ductal carcinoma in situ (DCIS) using fluorescence in situ hybridization and pyrosequencing, respectively, and in infiltrating ductal carcinoma (IDC) using genomic data from The Cancer Genome Atlas (TCGA). Allelic loss was present in a subset of DCIS cases where adjacent IDC was present. SYK copy number loss was found in about 26% of 1002 total breast cancer cases and 30% of IDC cases. Quantitative immunofluorescence revealed Syk protein to be six-fold higher in infiltrating immune cells compared with epithelial cells. This difference distorted tumor cell mRNA and protein levels in extracts. 20% of 1002 IDC cases contained elevated immune cell infiltration as estimated by elevated immune-specific mRNAs. In cases without immune cell infiltration, loss of SYK copy number was associated with a significant reduction of SYK mRNA. Here we define a 55 Gene Set consisting of Syk interacting, motility- and invasion-related genes. We found that overall survival was significantly reduced in IDC and Luminal A+B cases where copy number and mutations of these 55 genes were affected (Kaplan-Meier, Logrank test p-value 0.007141 and Logrank test p-value 0.001198, respectively). We conclude that reduction in Syk expression and contributions of genomic instability to copy number and mutations in the 55 Syk interacting genes significantly contribute to poorer overall patient survival. A closer examination of the role of Syk interacting motility and invasion genes and their prognostic and/or causative association with metastatic disease and patient outcome is warranted.

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Characterization of the relationship between SYK copy number, mRNA, and protein in immune depleted cases from TCGA Provisional Study.801 of 1002 breast cancer cases were characterized as immune depleted (see methods) and were used for the following graphs. A. Putative SYK copy number (x-axis) for Diploid and Hetloss is plotted against SYK mRNA in a box plot. The blue arrow indicates the Hetloss group. B.SYK methylation (x-axis) is plotted against SYK mRNA (y-axis) for individual cases of HetLoss or Diploid. Blue circles indicate putative heterozygotic loss and black circles indicate diploid copy number. Dashed line indicates cutoff methylation level. C.SYK mRNA is plotted against Syk protein/phosphoprotein levels for Diploid and Hetloss cases.
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pone-0087610-g005: Characterization of the relationship between SYK copy number, mRNA, and protein in immune depleted cases from TCGA Provisional Study.801 of 1002 breast cancer cases were characterized as immune depleted (see methods) and were used for the following graphs. A. Putative SYK copy number (x-axis) for Diploid and Hetloss is plotted against SYK mRNA in a box plot. The blue arrow indicates the Hetloss group. B.SYK methylation (x-axis) is plotted against SYK mRNA (y-axis) for individual cases of HetLoss or Diploid. Blue circles indicate putative heterozygotic loss and black circles indicate diploid copy number. Dashed line indicates cutoff methylation level. C.SYK mRNA is plotted against Syk protein/phosphoprotein levels for Diploid and Hetloss cases.

Mentions: Beginning with a total 1002 invasive breast cancer cases from the TCGA, cases where immune cell infiltration was prominent were identified and removed (see Methods) for a final subset of 800 immune depleted cases. Using the immune depleted subset or using a subset of 696 IDC only cases, we found that only two mutations in SYK were present, one of which would likely have an effect on function, namely A146G [29], [30] (data not shown). The somatic mutation rate for SYK was 0.3% and the overall alteration including copy number (homozygotic deletions or amplifications) was 1.6% of IDC cases (696 cases). Putative copy number loss described as heterozygotic loss (HetLoss) occurs in 26.2% of the immune depleted cases (Figure 5A, 6B) and in 29.3% of IDC cases (Figure 6A). As described previously [6], [7], the SYK promoter is methylated in invasive breast cancers; and, methylation values were correlated with reduction in SYK mRNA levels in immune depleted cases (Figure 5B); similarly protein levels were positively associated with SYK mRNA levels (Figure 5C). In immune depleted cases, higher methylation values (> = 0.4) were found in about 11% of HetLoss cases but only in about 5% of diploid cases using either methylation array data (Figure 6C, HM450 or HM27).


SYK allelic loss and the role of Syk-regulated genes in breast cancer survival.

Blancato J, Graves A, Rashidi B, Moroni M, Tchobe L, Ozdemirli M, Kallakury B, Makambi KH, Marian C, Mueller SC - PLoS ONE (2014)

Characterization of the relationship between SYK copy number, mRNA, and protein in immune depleted cases from TCGA Provisional Study.801 of 1002 breast cancer cases were characterized as immune depleted (see methods) and were used for the following graphs. A. Putative SYK copy number (x-axis) for Diploid and Hetloss is plotted against SYK mRNA in a box plot. The blue arrow indicates the Hetloss group. B.SYK methylation (x-axis) is plotted against SYK mRNA (y-axis) for individual cases of HetLoss or Diploid. Blue circles indicate putative heterozygotic loss and black circles indicate diploid copy number. Dashed line indicates cutoff methylation level. C.SYK mRNA is plotted against Syk protein/phosphoprotein levels for Diploid and Hetloss cases.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3921124&req=5

pone-0087610-g005: Characterization of the relationship between SYK copy number, mRNA, and protein in immune depleted cases from TCGA Provisional Study.801 of 1002 breast cancer cases were characterized as immune depleted (see methods) and were used for the following graphs. A. Putative SYK copy number (x-axis) for Diploid and Hetloss is plotted against SYK mRNA in a box plot. The blue arrow indicates the Hetloss group. B.SYK methylation (x-axis) is plotted against SYK mRNA (y-axis) for individual cases of HetLoss or Diploid. Blue circles indicate putative heterozygotic loss and black circles indicate diploid copy number. Dashed line indicates cutoff methylation level. C.SYK mRNA is plotted against Syk protein/phosphoprotein levels for Diploid and Hetloss cases.
Mentions: Beginning with a total 1002 invasive breast cancer cases from the TCGA, cases where immune cell infiltration was prominent were identified and removed (see Methods) for a final subset of 800 immune depleted cases. Using the immune depleted subset or using a subset of 696 IDC only cases, we found that only two mutations in SYK were present, one of which would likely have an effect on function, namely A146G [29], [30] (data not shown). The somatic mutation rate for SYK was 0.3% and the overall alteration including copy number (homozygotic deletions or amplifications) was 1.6% of IDC cases (696 cases). Putative copy number loss described as heterozygotic loss (HetLoss) occurs in 26.2% of the immune depleted cases (Figure 5A, 6B) and in 29.3% of IDC cases (Figure 6A). As described previously [6], [7], the SYK promoter is methylated in invasive breast cancers; and, methylation values were correlated with reduction in SYK mRNA levels in immune depleted cases (Figure 5B); similarly protein levels were positively associated with SYK mRNA levels (Figure 5C). In immune depleted cases, higher methylation values (> = 0.4) were found in about 11% of HetLoss cases but only in about 5% of diploid cases using either methylation array data (Figure 6C, HM450 or HM27).

Bottom Line: In cases without immune cell infiltration, loss of SYK copy number was associated with a significant reduction of SYK mRNA.We found that overall survival was significantly reduced in IDC and Luminal A+B cases where copy number and mutations of these 55 genes were affected (Kaplan-Meier, Logrank test p-value 0.007141 and Logrank test p-value 0.001198, respectively).We conclude that reduction in Syk expression and contributions of genomic instability to copy number and mutations in the 55 Syk interacting genes significantly contribute to poorer overall patient survival.

View Article: PubMed Central - PubMed

Affiliation: Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D. C., United States of America.

ABSTRACT
Heterozygotic loss of SYK, a non-receptor tyrosine kinase, gives rise to mouse mammary tumor formation where Syk protein levels are reduced by about half; loss of SYK mRNA is correlated with invasive cell behavior in in vitro models; and SYK loss has been correlated with distant metastases in patients. Here, allelic loss of the SYK gene was explored in breast ductal carcinoma in situ (DCIS) using fluorescence in situ hybridization and pyrosequencing, respectively, and in infiltrating ductal carcinoma (IDC) using genomic data from The Cancer Genome Atlas (TCGA). Allelic loss was present in a subset of DCIS cases where adjacent IDC was present. SYK copy number loss was found in about 26% of 1002 total breast cancer cases and 30% of IDC cases. Quantitative immunofluorescence revealed Syk protein to be six-fold higher in infiltrating immune cells compared with epithelial cells. This difference distorted tumor cell mRNA and protein levels in extracts. 20% of 1002 IDC cases contained elevated immune cell infiltration as estimated by elevated immune-specific mRNAs. In cases without immune cell infiltration, loss of SYK copy number was associated with a significant reduction of SYK mRNA. Here we define a 55 Gene Set consisting of Syk interacting, motility- and invasion-related genes. We found that overall survival was significantly reduced in IDC and Luminal A+B cases where copy number and mutations of these 55 genes were affected (Kaplan-Meier, Logrank test p-value 0.007141 and Logrank test p-value 0.001198, respectively). We conclude that reduction in Syk expression and contributions of genomic instability to copy number and mutations in the 55 Syk interacting genes significantly contribute to poorer overall patient survival. A closer examination of the role of Syk interacting motility and invasion genes and their prognostic and/or causative association with metastatic disease and patient outcome is warranted.

Show MeSH
Related in: MedlinePlus