Primary-Tumor Transcriptomic Signatures Associated with Circulating Tumor Cells Status in Breast Cancer: From...

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.