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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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SYK promoter methylation.The mean value for promoter methylation at 4 CpG islands was plotted for each case. DCIS cases are arranged by whether adjacent IDC was absent or present, and benign only cases are shown for comparison (mean 4.97+/−1.68 S.D., 2.91 S.E.). The dashed line indicates the mean of the benign cases plus 2 S.D. (8.3). Red arrows indicate cases where FISH identified allelic loss.
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pone-0087610-g002: SYK promoter methylation.The mean value for promoter methylation at 4 CpG islands was plotted for each case. DCIS cases are arranged by whether adjacent IDC was absent or present, and benign only cases are shown for comparison (mean 4.97+/−1.68 S.D., 2.91 S.E.). The dashed line indicates the mean of the benign cases plus 2 S.D. (8.3). Red arrows indicate cases where FISH identified allelic loss.

Mentions: Previously, it was reported that CpG islands in the SYK promoter were methylated resulting in gene silencing and that methylation of SYK was less than 5% in normal or benign tissues, and 47% in node-negative, and 40% in node positive IDC cases [6], [7]. Methylation in DCIS was found to be 45% [7]. We examined the promoter methylation status of SYK in DCIS for the present study using bisulphite pyrosequencing using a subset of cases that were available following the FISH study. In 5 benign cases, only three sections were available or yielded to pyrosequencing, only 6 of 8 DCIS only tissues produced results, and only 7 of 11 DCIS tissues from cases with adjacent IDC produced results (Table S2). If a cutoff of 8.3% methylation was set ( = benign only tissue mean +2 S.D., Figure 2, dashed line), 0 of 3 benign cases, 4 of 6 DCIS (only) cases, and 2 of 7 DCIS (with adjacent IDC) cases were considered positive for CpG island methylation (Table S2). Overall, DCIS tissue was positive in 46% of 13 total cases. When means of methylation were analyzed by tissue, benign, DCIS, or IDC, no overall significant differences were observed between them (Kruskal-Wallis, p = 0.48, data not shown). Taken together with the results revealing SYK allelic loss together with promoter methylation, Syk protein levels would likely be impacted.


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)

SYK promoter methylation.The mean value for promoter methylation at 4 CpG islands was plotted for each case. DCIS cases are arranged by whether adjacent IDC was absent or present, and benign only cases are shown for comparison (mean 4.97+/−1.68 S.D., 2.91 S.E.). The dashed line indicates the mean of the benign cases plus 2 S.D. (8.3). Red arrows indicate cases where FISH identified allelic loss.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0087610-g002: SYK promoter methylation.The mean value for promoter methylation at 4 CpG islands was plotted for each case. DCIS cases are arranged by whether adjacent IDC was absent or present, and benign only cases are shown for comparison (mean 4.97+/−1.68 S.D., 2.91 S.E.). The dashed line indicates the mean of the benign cases plus 2 S.D. (8.3). Red arrows indicate cases where FISH identified allelic loss.
Mentions: Previously, it was reported that CpG islands in the SYK promoter were methylated resulting in gene silencing and that methylation of SYK was less than 5% in normal or benign tissues, and 47% in node-negative, and 40% in node positive IDC cases [6], [7]. Methylation in DCIS was found to be 45% [7]. We examined the promoter methylation status of SYK in DCIS for the present study using bisulphite pyrosequencing using a subset of cases that were available following the FISH study. In 5 benign cases, only three sections were available or yielded to pyrosequencing, only 6 of 8 DCIS only tissues produced results, and only 7 of 11 DCIS tissues from cases with adjacent IDC produced results (Table S2). If a cutoff of 8.3% methylation was set ( = benign only tissue mean +2 S.D., Figure 2, dashed line), 0 of 3 benign cases, 4 of 6 DCIS (only) cases, and 2 of 7 DCIS (with adjacent IDC) cases were considered positive for CpG island methylation (Table S2). Overall, DCIS tissue was positive in 46% of 13 total cases. When means of methylation were analyzed by tissue, benign, DCIS, or IDC, no overall significant differences were observed between them (Kruskal-Wallis, p = 0.48, data not shown). Taken together with the results revealing SYK allelic loss together with promoter methylation, Syk protein levels would likely be impacted.

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