Purpose: Forkhead box Q1 (FOXQ1) has been shown to contribute to the development and progression of cancers, including ovarian and breast cancer (BC). However, research exploring FOXQ1 expression, copy number variation (CNV), and prognostic value across different BC subtypes is limited. Our purpose was to evaluate FOXQ1 mRNA expression, CNV, and prognostic value across BC subtypes. Materials and Methods: We determined FOXQ1 expression and CNV in BC patient tumors using RT-qPCR and qPCR, respectively. We also analyzed FOXQ1 expression and CNV in BC cell lines in the CCLE database using K-means clustering. The prognostic value of FOXQ1 expression in the TCGA-BRCA database was assessed using univariate and multivariate Cox's regression analysis as well as using the online tools OncoLnc, GEPIA, and UALCAN. Results: Our analyses reveal that FOXQ1 mRNA is differentially expressed between different subtypes of BC and is significantly decreased in luminal BC and HER2 patients when compared to normal breast tissue samples. Furthermore, analysis of BC cell lines showed that FOXQ1 mRNA expression was independent of CNV. Moreover, patients with low FOXQ1 mRNA expression had significantly poorer overall survival compared to those with high FOXQ1 mRNA expression. Finally, low FOXQ1 expression had a critical impact on the prognostic values of BC patients and was an independent predictor of overall survival when it was adjusted for BC subtypes and to two other FOX genes, FOXF2 and FOXM1. Conclusion: Our study reveals for the first time that FOXQ1 is differentially expressed across BC subtypes and that low expression of FOXQ1 is indicative of poor prognosis in patients with BC.

As a member of the forkhead box (FOX) superfamily of transcription factors, FOXQ1 plays a critical role in a wide range of biological processes, including angiogenesis, epithelial differentiation and smooth muscle differentiation. Emerging evidence also show FOXQ1 to play important roles in the development and progression of various cancers such as ovarian, pancreatic, and colorectal cancer. Particularly, FOXQ1 has been linked to facilitating tumor invasion and metastasis in breast cancer and has also been specifically associated with Triple Negative Basal‐like Breast Cancer (TN/BL BC). Furthermore, experimental studies have demonstrated FOXQ1 overexpression to promote/mediate epithelial to mesenchymal transition, invasion, stemness traits, and chemoresistance in breast cancer. These processes contribute substantially to poor prognosis in breast cancer patients, thus making FOXQ1 a potential target for the diagnosis and treatment of breast cancer tumors. In this study, we investigated the mechanisms leading to increased expression levels of FOXQ1 in BC through analysis of FOXQ1 copy number variation (CNV) and mRNA levels across BC patient subtypes and cell lines. Additionally, we assessed the prognostic significance of FOXQ1 in BC patients. Finally, K‐means clustering was conducted by using Python coding to identify unique clusters for FOXQ1 mRNA levels and CNV in BC cell lines. We report for the first time, that FOXQ1 mRNA is differentially expressed across BC patients. FOXQ1 mRNA is significantly down regulated in Luminal (ER+) BC patients (n=6) when compared to control samples (n=6). FOXQ1mRNA expression is significantly up regulated in TN/BL BC patients (n=6) compared to Her2 (n=6) and ER+ BC (n=6) respectively. We also found FOXQ1 significantly has more copies in TN/BL BC compared to control samples. K‐means clustering analysis was conducted on BC cell lines, with the purpose of identifying distinct subpopulations based on FOXQ1 mRNA expression and CNV. Our supervised and unsupervised clustering analyses identified 3 and 4 clusters, respectively, among BC cell lines for FOXQ1 mRNA compared to their CNV. However, we found FOXQ1 mRNA expression to be independent of its CNV. Moreover, FOXQ1 mRNA was found to be highly expressed in numerous TN/BL cell lines. Lastly and most importantly, by applying the bioinformatic online tool GEPIA, Kaplan‐Meier survival curve analysis identified two risk groups with high (n=524) and low (n=531) FOXQ1 mRNA expression levels. Our Kaplan‐Meier survival analysis also showed patients with low FOXQ1 mRNA expression to have shorter overall survival time than those with high FOXQ1 mRNA expression (HR=0.71, P=0.042). In accordance to these results, we propose that FOXQ1 can serve as an emerging new prognostic biomarker for BC. Understanding the mechanism(s) underlying FOXQ1’s activation in breast cancer could facilitate the development of improved therapies for BC patients. Support or Funding Information Women and Children Health Research Institute Faculty of Medicine and Dentistry, U...