Primary-Tumor Transcriptomic Signatures Associated with Circulating Tumor Cells Status in Breast Cancer: From CTC-Negative Remodeling to CTC-Associated Metastatic Programs

Background/Objectives: Circulating tumor cells (CTCs) play a central role in metastasis by enabling tumor dissemination through the bloodstream. However, the molecular transition from CTC-negative (CTC−) to CTC-positive (CTC+) states and their associated systemic remodeling remain poorly understood. Methods: We performed a transcriptomic comparison between CTC+, CTC−, and healthy individuals using RNA-seq data and a bioinformatics pipeline. Differentially expressed genes (DEGs) were subjected to functional enrichment, protein–protein interaction (PPI) analysis, survival modeling, and drug perturbation prediction to delineate the molecular determinants of CTC emergence and persistence. Results: Primary tumors from CTC+ patients exhibited distinct transcriptomic profiles characterized by the upregulation of genes involved in PI3K-Akt signaling, extracellular matrix organization, and chromatin regulation (e.g., HDAC1, JUN, KLK10), alongside the downregulation of immune activation pathways, including complement, B-cell receptor (BCR), and T-cell receptor (TCR) signaling. Multi-gene survival models derived from upregulated (KLK10, MEOX2, IRS4, RND2) and downregulated (ALDH3A1, PPP2R2B, IGF1R) hub genes significantly stratified patient outcomes (HR = 1.74–2.44, p < 0.01). In contrast, primary tumors from CTC− patients displayed early systemic transcriptional alterations relative to healthy controls, with 1700+ DEGs linked to MAPK/ERK and receptor tyrosine kinase (RTK) signaling pathways, suggesting pre-metastatic immune reprogramming even before CTC detection. Drug repurposing analysis identified Trichostatin A, BX-795, and Alvocidib as candidate compounds capable of reversing the CTC+ transcriptional signature. Conclusions: Rather than supporting a strictly binary view of CTC status, our findings are consistent with a transcriptional continuum of distinct yet partially overlapping primary-tumor transcriptional states associated with CTC− and CTC+ status, highlighting a molecular shift from immune suppression to epigenetic adaptation that facilitates hematogenous dissemination. The identified multi-gene prognostic panels and small-molecule candidates provide a foundation for CTC-targeted therapeutic strategies and early detection biomarkers in breast cancer.