Clonal Dynamics and Molecular Heterogeneity of Metaplastic Breast Cancer: Focus on TP53 and PIK3CA Truncal Mutations

Rupei Ye,1,2,* Xinzhi Dai,3,* Zihan Yang,1,2 Dandan Zhang,1,2 Zhimin Hu,4 Yehui Liao,5 Zhihui Yang1,2 1Department of Pathology, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, People’s Republic of China; 2Precision Pathology Diagnosis for Serious Diseases Key Laboratory of LuZhou, Luzhou, Sichuan, 646000, People’s Republic of China; 3Department of Pathology, Ruijin Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People’s Republic of China; 4School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, 646000, People’s Republic of China; 5Department of Orthopedics, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, People’s Republic of China*These authors contributed equally to this workCorrespondence: Yehui Liao, Email [email protected] Zhihui Yang, Email [email protected]: Metaplastic breast carcinoma (MBC) is a rare and aggressive subtype of triple-negative breast cancer with distinct molecular features that remain incompletely characterized, hindering the development of effective therapies.Methods: We integrated clinicopathological data with next-generation sequencing (NGS) of 437 cancer-related genes performed on 25 tumor samples (16 primary, 8 lymph node metastases, 1 distant metastasis) from 17 MBC patients. Functional enrichment analysis was conducted to identify key signaling pathways.Results: Recurrent alterations were identified in TP53 (14/16, 87.5%), PIK3CA (9/16, 56.2%), and MCL1 (10/16, 62.5% amplified). TP53 mutations (primarily frameshift and missense) showed consistent variant types between primary and metastatic sites. PIK3CA hotspot mutations (eg, H1047R, E545K) persisted across metastases. In contrast, MCL1 amplification exhibited dynamic evolution, being lost in some primary tumors but acquired de novo in lymph node metastases. Functional enrichment analysis revealed the PI3K-Akt signaling pathway as the most significantly altered pathway in MBC.Conclusion: This study delineates the distinct mutational landscape and clonal evolution patterns of MBC, underpinned by truncal mutations in TP53 and PIK3CA alongside dynamic MCL1 amplification. The persistent activation of the PI3K-Akt pathway presents a key therapeutic vulnerability. Our findings emphasize the potential of PI3K-Akt inhibition and metastasis-specific targeting strategies for this aggressive disease.Keywords: metaplastic breast carcinoma, next-generation sequencing, clinicopathological characteristics, molecular characteristics, functional enrichment analysis, TP53, PIK3CA