PCMT1 knockdown attenuates malignant properties by globally regulating transcriptome profiles in triple-negative breast cancer cells
Breast cancer is the most frequently diagnosed cancer in women, and has high mortality and metastasis rate, especially triple-negative breast cancer (TNBC). As an oncogene, Protein-L-Isoaspartate (D-Aspartate) O-Methyltransferase (PCMT1) is a prognostic biomarker in breast cancer and is highly expressed, while the underlying mechanisms remain unknown. In this study, we silenced PCTM1 in TNBC MDA-MB-231 cells by short hairpin RNA (shPCMT1) to investigate its cellular functions using cell proliferation, apoptosis, migration, and invasion experiments. Following this, the transcriptome sequencing (RNA-seq) experiment was performed to identify the molecular targets of PCMT1, including differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs). We found that shPCMT1 inhibited the proliferation, migration, and invasion of MDA-MB-231 cells. We obtained 1084 DEGs and 2287 RASEs between shPCMT1 and negative control (NC) groups through RNA-seq. The DEGs were highly enriched in immune or inflammation response and cell adhesion-associated pathways, pathways associated with PCMT1 cellular function in cell migration. The RASE genes were enriched in cell cycle-associated pathways and were associated with the altered cell proliferation rate. We finally validated the changed expression and splicing levels of DEGs and RASEs. We found that 34 RNA binding protein (RBP) genes were dysregulated by shPCMT1, including NQO1, S100A4, EEF1A2, and RBMS2. The dysregulated RBP genes could partially explain how PCMT1 regulates the global transcriptome profiles. In conclusion, our study identified the molecular targets of PCMT1 in the TNBC cell line, expands our understanding of the regulatory mechanisms of PCMT1 in cancer progression, and provides novel insights into the progression of TNBC. The identified molecular targets are potential therapeutic targets for future TNBC treatment. Overall design: In this study, we silenced PCTM1 in TNBC MDA-MB-231 cells by short hairpin RNA (shPCMT1) to investigate its cellular functions using cell proliferation, apoptosis, migration, and invasion experiments. Following this, the transcriptome sequencing (RNA-seq) experiment was performed to identify the molecular targets of PCMT1, including differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs).