Table 1_Multiomics profiling identifies the poor prognostic role of a tumor cluster with GNA15 overexpression in triple-negative breast cancer.xlsx

BackgroundTumor 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.
MethodsSingle-cell RNA expression profiles were analyzed using R packages. Specifically, the 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. G Protein Subunit Alpha 15 (GNA15) expression was determined via reverse transcription–quantitative PCR (RT–qPCR) and immunohistochemistry. Cell functional assays were performed to evaluate proliferation, migration, and invasion capabilities.
ResultsA total of 14,335 malignant cells were isolated 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. 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.
ConclusionsOur study comprehensively delineated TNBC tumor cell heterogeneity and established the critical role of GNA15 in TNBC progression. These findings enhance the understanding of TNBC heterogeneity and provide a theoretical foundation for TNBC treatment.

背景
肿瘤异质性会影响三阴性乳腺癌（triple-negative breast cancer, TNBC）的侵袭行为、治疗应答及临床结局，但目前对该异质性的解析仍不充分。本研究旨在利用多尺度数据探究肿瘤间异质性，并筛选潜在的TNBC生物标志物。
方法
本研究通过R软件包分析单细胞RNA表达谱。具体而言，使用infercnv、Pyscenic、GeneNMF、SCP、Vector、CellChat及hdWGCNA等软件包鉴定恶性细胞，并解析转录因子、元程序、谱系演化、发育轨迹、细胞间互作及共表达网络层面的异质性。纳入批量转录组数据集以评估细胞簇与候选基因的预后价值。通过逆转录定量聚合酶链反应（RT–qPCR）与免疫组化检测G蛋白亚基α15（G Protein Subunit Alpha 15, GNA15）的表达水平。开展细胞功能实验以评估细胞的增殖、迁移及侵袭能力。
结果
本研究从15个单细胞RNA样本的上皮细胞中分离得到14335个恶性细胞。共鉴定出6个肿瘤细胞簇，各细胞簇具有独特的预后特征、生物学功能、驱动转录因子及共表达网络。值得注意的是，S2细胞簇与多种恶性相关通路显著相关，且对应不良生存结局。GNA15被鉴定为S2细胞簇的核心基因。体外实验证实，敲低GNA15可显著抑制TNBC细胞系的增殖、迁移及侵袭能力。
结论
本研究全面阐明了TNBC的肿瘤细胞异质性，并确立了GNA15在TNBC进展中的关键作用。本研究结果加深了对TNBC异质性的认识，为TNBC的临床治疗提供了理论依据。