“…This included genes such as PTK7 involved in the Wnt signaling pathway (fold change relative to control in WT HOTAIR=2.6, p=0.008; in A783U HOTAIR=-1.4, p=0.002); CDH11, a mesenchymal cadherin that is upregulated in invasive breast cancer cell lines (Pishvaian et al, 1999) (fold change in WT HOTAIR=2.0, p=0.01; in A783U HOTAIR=-1.6, p=0.02); and GRIN2A, an oncogenic glutamate receptor (fold change in WT HOTAIR=2.5, p=0.006; in A783U HOTAIR=-3.7, p=9.3E-05). Similarly, genes downregulated with WT HOTAIR were significantly increased with A783U HOTAIR, compared to the parental MDA-MB-231 control, including SEMA5A, a guidance cue protein that suppresses the proliferation and migration of lung adenocarcinoma cells (Ko et al, 2020) (fold change relative to control in WT HOTAIR=-3.5, p=0.0002; in A783U HOTAIR=2.8, p=0.01); SIRPA, a cell surface receptor that can act as a negative regulator of the phosphatidylinositol 3-kinase signaling and mitogenactivated protein kinase pathways (Takahashi, 2018) (fold change in WT HOTAIR=-1.6, p=0.03; in A783U HOTAIR=3.1, p=0.009); and TP53I11, a p53-interacting protein that suppresses migration and metastasis in MDA-MB-231 cells (Xiao et al, 2019) (fold change in WT HOTAIR=-1.7, p=0.03; in A783U HOTAIR=4.0, p=0.008) (Figure 2C). To further analyze differences in cells expressing A783U mutant HOTAIR, we performed a pairwise comparison with control MDA-MB-231 cells and identified 758 differentially expressed genes (Figure 2D).…”