Multiomics Profiling Identifies the Poor Prognostic Role of a Tumor Cluster with GNA15 Overexpression in Triple-Negative Breast Cancer

Guixin Wang¹Junming Cao¹Lu Chenglu²Yu Cao³Shuo Wang¹Ziyi Chen¹Zhaohui Chen¹Yingxi Li⁴Yue Yu^1*Yao Tian^5*Xin Wang^1*

• ¹Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
• ²Tangshan People's Hospital, Tangshan, China
• ³Affiliated Hospital of Zunyi Medical University, Zunyi, China
• ⁴Ningbo University, Ningbo, China
• ⁵Ningbo Medical Centre Lihuili Hospital, Ningbo, China

Abstract Background: Tumor heterogeneity impacts invasive behaviors, treatment response, and clinical outcomes in triple-negative breast cancer (TNBC). However, this heterogeneity remains incompletely characterized. This study aims to utilize multi-scale data to investigate inter-tumoral heterogeneity and identify potential TNBC biomarkers. Methods: Single-cell RNA expression profiles were analyzed using R packages. Specifically, infercnv, Pyscenic, GeneNMF, SCP, Vector, CellChat, and hdWGCNA packages were employed to identify malignant cells and characterize heterogeneity in transcription factors, metaprograms, lineage evolution, developmental trajectories, cell-cell interactions, and co-expression networks. Bulk RNA datasets were incorporated to assess the prognostic value of cell clusters and candidate genes. GNA15 expression was determined by RT-qPCR and immunohistochemistry. Cell functional assays were performed to evaluate proliferation, migration, and invasion capabilities. Results: We isolated 14,335 malignant cells from epithelial cells across 15 single-cell RNA samples. Six tumor cell clusters were identified, which exhibited distinct prognoses, biological functions, driver transcription factors, and co-expression networks. Notably, the S2 cluster demonstrated association with multiple malignancy-related pathways and inferior survival outcomes. G Protein Subunit Alpha 15 (GNA15) emerged as the S2 cluster hub gene. In vitro experiments confirmed that GNA15 knockdown significantly attenuated proliferation, migration, and invasion in TNBC cell lines. Conclusions: Our study comprehensively delineates TNBC tumor cell heterogeneity and establishes the critical role of GNA15 in TNBC progression. These findings enhance understanding of TNBC heterogeneity and provide a theoretical foundation for TNBC treatment.