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Background: Accumulating evidence indicates tumor-promoting roles of synaptotagmin 13 (<i>SYT13</i>) in several cancers; however, no studies have investigated its expression in breast cancer (BC). This study aimed to clarify the significance of <i>SYT13</i> in BC. Methods: <i>SYT13</i> mRNA expression levels were evaluated in BC cell lines. Polymerase chain reaction (PCR) array analysis was conducted to determine the correlation between expression levels of <i>SYT13</i> and other tumor-associated genes. Then, the association of <i>SYT13</i> expression levels in the clinical BC specimens with patients’ clinicopathological factors was evaluated. These findings were subsequently validated using The Cancer Genome Atlas (TCGA) database. Results: Among 13 BC cell lines, estrogen receptor (ER)-positive cells showed higher <i>SYT13</i> mRNA levels than ER-negative cells. PCR array analysis revealed positive correlations between <i>SYT13</i> and several oncogenes predominantly expressed in ER-positive BC, such as <i>estrogen receptor 1</i>, <i>AKT serine/threonine kinase 1</i>, and <i>cyclin-dependent kinases 4</i>. In 165 patients, ER-positive specimens exhibited higher <i>SYT13</i> mRNA expression levels than ER-negative specimens. The TCGA database analysis confirmed that patients with ER-positive BC expressed higher <i>SYT13</i> levels than ER-negative patients. Conclusion: This study suggests that <i>SYT13</i> is highly expressed in ER-positive BC cells and clinical specimens, and there is a positive association of <i>SYT13</i> with the ER signaling pathways.