Abstract Advanced metastatic triple-negative breast cancer (TNBC) is a highly aggressive malignancy with limited treatment options. TNBCs are enriched in cancer stem cells (CSCs), which contribute to immune evasion and poor clinical outcomes. Approximately 22% of patients diagnosed with metastatic TNBC survive for 5 years, and the average duration of survival is only 3 years. Mucin 1 (MUC1) is a heterodimeric transmembrane glycoprotein that is aberrantly expressed in ∼90% of TNBCs. MUC1 consists of two subunits: (i) an extracellular N-terminal subunit (MUC1-N) with glycosylated tandem repeats that are characteristic of the mucin family and (ii) a transmembrane C-terminal oncogenic subunit (M1C). The M1C cytoplasmic domain consists of 72 amino acids (aa) that include a CQC motif adjacent to the transmembrane domain, which is necessary for the formation of homodimers and interactions with binding partners, such as MYC. M1C regulates epigenetic remodeling and cancer stem cell states, yet its role in RNA splicing remains poorly defined. We performed Rapid Immunoprecipitation Mass Spectrometry of Endogenous proteins (RIME) analysis of M1C-associated nuclear proteins in BT549 TNBC cells. Our results demonstrate that M1C associates with RNA processing proteins, including splicing factors. Transcriptomic profiling of BT-549 and SUM149 models using long-read RNA-seq revealed that both inducible and stable silencing of M1C downregulates spliceosome gene signatures and suppresses expression of the SRSF, hnRNP, and RBM families of core splicing regulators. Studies with inducible MYC silencing further demonstrated overlapping regulation of these factors, supporting involvement of the M1C/MYC axis. Alternative splicing analysis using rMATS revealed a consistent shift in splicing subtype usage, with increased intron retention and reduced skipped exons upon M1C silencing. Genes affected by intron retention included regulators of cell cycle, RNA metabolism, and immune signaling, whereas skipped exon events were enriched in transcripts linked to stemness and stress adaptation. In 3D spheroid cultures, M1C and MYC silencing reinforced context-specific splicing alterations. Importantly, combined pharmacologic disruption of M1C and splicing produced synergistic inhibition of TNBC cell viability and suppressed oncogenic isoform expression. Of clinical significance, high expression of MUC1/MYC regulated splicing factors was enriched in basal-like TNBC tumors and correlated with poor survival. Together, these findings define a M1C/MYC axis that drives alternative splicing reprogramming as a hallmark of TNBC biology. Thus, the M1C/MYC axis is a master regulator of alternative splicing in TNBC. Inhibition of M1C and the splicing machinery demonstrates synergistic effects, highlighting a novel therapeutic opportunity in aggressive breast cancers. Future studies will assess whether these splicing events generate immunogenic neoantigens, offering opportunities for biomarker development and translational targeting. Citation Format: A. Bhattacharya, L. Ding, N. Yamashita, S. Pitroda, D. W. Kufe. The M1C/MYC Axis Reprograms Alternative Splicing Networks in Triple Negative Breast Cancer abstract. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS2-13-06.
Bhattacharya et al. (Tue,) studied this question.
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