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, 14 (2), e0211507
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BAP1 Expression Is Prognostic in Breast and Uveal Melanoma but Not Colon Cancer and Is Highly Positively Correlated With RBM15B and USP19

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BAP1 Expression Is Prognostic in Breast and Uveal Melanoma but Not Colon Cancer and Is Highly Positively Correlated With RBM15B and USP19

Leili Shahriyari et al. PLoS One.

Abstract

BAP1 is a tumor suppressor gene important to the development and prognosis of many cancers, especially uveal melanoma (UM). Its role in more common cancers such as breast and colon cancer is largely unknown. We collected the transcriptome profiling data sets from the TCGA uveal melanoma (TCGA-UVM), breast cancer (TCGA-BRCA), and colon cancer (TCGA-COAD) projects to analyze the expression of BAP1. We found that patients with UM and breast cancer, but not colon cancer, who died had a lower level of BAP1 gene expression compared to surviving patients. Importantly, in breast cancer patients, the lowest BAP1 expression levels corresponded to the dead young patients (age at diagnosis < 46). Since the number of cases in TCGA-BRCA was much higher than TCGA-UVM, we obtained highly correlated genes with BAP1 in invasive breast carcinomas. Then, we tested if these genes are also highly correlated with BAP1 in UM and colon cancer. We found that BAP1 is highly positively correlated with RBM15B and USP19 expression in invasive breast carcinoma, UM, and colon adenocarcinoma. All three genes are located in close proximity on the 3p21 tumor suppressor region that is commonly altered in many cancers.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. BAP1 expression.
The left and right sub-figures respectively represent the density function and the values of BAP1 after normalizing the data set excluding genes with zero values. The size of circles represents the age at diagnosis.
Fig 2
Fig 2. Highly correlated genes with BAP1 in UVM.
The top sub-figure shows the scatter plot of the values of BAP1 and the gene, which has the maximum positive correlation with BAP1 in the entire UVM data set. The bottom sub-figure shows the scatter plot of the values of BAP1 and the gene, which has the maximum negative correlation with BAP1 in all patients with UVM. The right panel shows the exact same scatter plot as the left panel using n-normalization.
Fig 3
Fig 3. Highly correlated genes with BAP1 in BRCA sub-categories.
In each panel, the top sub-figures show the scatter plot of the values of BAP1 and the gene, which has the maximum positive correlation with BAP1 in the given BRCA sub-category. The bottom sub-figures shows the scatter plot of the values of BAP1 and the gene, which has the maximum negative correlation with BAP1 in the given sub-category.
Fig 4
Fig 4. Highly correlated genes with BAP1 in COAD.
The top sub-figure shows the scatter plot of the values of BAP1 and the gene, which has the maximum positive correlation with BAP1 in the entire colon cancer data set. The bottom sub-figure shows the scatter plot of the values of BAP1 and the gene, which has the maximum negative correlation with BAP1 in all patients with colon adenocarcinoma. The right panel shows the exact same scatter plot as the left panel using n-normalization.
Fig 5
Fig 5. Sorted correlation coefficients of genes with BAP1.
The left sub-figure shows the sorted correlation of all genes with BAP1 in the dataset including genes with zero-values. The right sub-figure shows the results after using n-normalization (excluding genes with zero-values in the entire dataset).
Fig 6
Fig 6. Regression analysis.
This figure shows the linear function that predicts the normalized expression value of USP19 and RBM15B from the normalized level of BAP1.

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