Abstract:Objective To investigate the clinical imaging characteristics of benign and malignant breast calcifications and explore their underlying molecular mechanisms at the transcriptomic level. Methods A retrospective analysis was conducted on the clinical and pathological data of 1 051 breast cancer patients admitted to Nanjing Women and Children's Healthcare Hospital between January 2016 and February 2024. Patients were divided into a calcification group（n=534）and a non-calcification group（n=517）based on mammography findings. Concurrently，3 pairs of benign and malignant breast calcification tissues were collected for high-throughput RNA sequencing（RNA-seq）. Differentially expressed genes（DEGs）were identified using DESeq2，followed by Gene Ontology（GO）annotation and Gene Set Enrichment Analysis（GSEA）to uncover key hallmark pathways driving malignant calcification. Results Clinically，the proportions of ductal carcinoma in situ and microinvasive carcinoma were significantly higher in the calcification group（P<0.05）.Molecularly，compared with the non - calcification group，the calcification group had a higher proportion of estrogen receptor（ER）and progesterone receptor（PR）negativity，a higher proportion of human epidermal growth factor receptor 2（HER2）strong positivity，and a higher proportion of intermediate Ki-67 proliferation（P<0.05）. RNA-seq identified 1 686 DEGs，which were significantly enriched in biological processes such as calcium ion binding，angiogenesis，and extracellular matrix organization by GO analysis. GSEA further revealed the robust activation of classical oncogenic pathways—including mTORC1 signaling pathway，E2F target gene，G2/M checkpoint，and MYC target gene—which are closely associated with metabolic reprogramming and cell cycle dysregulation in malignant calcification tissues（false discovery rate q<0.01）. Conclusion Malignant breast calcification is not merely a macroscopic imaging sign of high tumor proliferation，but a consequential by product of extreme tumor cell proliferation and metabolic remodeling driven by pathways such as mTORC1 and MYC in the microenvironment. Integrating macroscopic imaging with microscopic transcriptomic features will facilitate early accurate warning and targeted intervention for breast cancer.