INTRODUCTION We analyzed transcriptional and mutational profile mainly focused on tumor mutation burden (TMB), immune checkpoint crosstalk, and radiosensitivity using scRNA-seq data derived from breast cancer and immune cells. MATERIALS AND METHODS scRNA-seq transcriptome data were acquired from the GEO database (GSE75688). The radiosensitivity index (RSI) was used to evaluate radiosensitivity of each cell. CD274 mRNA expression was used to surrogate PD-L1 expression status. A computational approach was utilized for the immune and tumor cell group (N = 492) to identify potential interactions between tumor and immune cells with respect to immune checkpoint ligand-receptor gene pairs. Mutation data was profiled from raw scRNA-seq data of tumor cells acquired from both primary tumor and metastatic lymph node (N = 317). TMB and mutational signatures were compared between radiosensitive (RS) and radioresistant (RR) tumor cells. RESULTS Most RR cells were a basal subtype and showed the higher rate of PD-L1 positivity. The patients with TNBC or HER2 subtype showed increased number of immune checkpoint ligand-receptor interactions between tumor and immune cells. PD-L1 ligand-receptor interactions between tumor cells and T cells were differentially increased in patients with the HER2 subtype compared to patients with the luminal subtype. Meanwhile, CTLA-4 ligand-receptor interactions were increased in patients with the TNBC subtype. TMB was significantly higher in RR cells than RS cells. Mutational signatures including microsatellite instability (MSI) and NRF2 pathway were altered in RR cells. CONCLUSIONS RR cells exhibited a basal subtype, high PD-L1 expression, and high TMB with mutational signature found in tumors having MSI. Differential crosstalk between tumor and immune cells was associated with the patient subtype of breast cancer. These findings could be useful to identify potential biomarker(s) and optimal combination strategies of immune checkpoint blockades and radiation therapy in the management of breast cancer.

中文翻译：

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乳腺癌单细胞RNA测序数据中的肿瘤突变负荷、免疫检查点串扰和放射敏感性

引言 我们使用来自乳腺癌和免疫细胞的 scRNA-seq 数据分析了主要集中在肿瘤突变负荷 (TMB)、免疫检查点串扰和放射敏感性的转录和突变谱。材料和方法 scRNA-seq 转录组数据从 GEO 数据库 (GSE75688) 中获得。放射敏感性指数（RSI）用于评估每个细胞的放射敏感性。CD274 mRNA 表达用于替代 PD-L1 表达状态。对免疫和肿瘤细胞组（N = 492）使用计算方法来确定肿瘤和免疫细胞之间关于免疫检查点配体-受体基因对的潜在相互作用。从原发肿瘤和转移淋巴结（N = 317）获得的肿瘤细胞的原始 scRNA-seq 数据分析突变数据。比较了放射敏感（RS）和放射抗性（RR）肿瘤细胞之间的 TMB 和突变特征。结果 大部分 RR 细胞为基础亚型，PD-L1 阳性率较高。TNBC 或 HER2 亚型患者的肿瘤和免疫细胞之间的免疫检查点配体-受体相互作用数量增加。与 luminal 亚型患者相比，HER2 亚型患者的肿瘤细胞和 T 细胞之间的 PD-L1 配体-受体相互作用有差异地增加。同时，TNBC 亚型患者的 CTLA-4 配体-受体相互作用增加。RR 细胞中的 TMB 显着高于 RS 细胞。包括微卫星不稳定性（MSI）和 NRF2 通路在内的突变特征在 RR 细胞中发生了改变。结论 RR 细胞表现出一种基础亚型，高 PD-L1 表达，在具有 MSI 的肿瘤中发现具有突变特征的高 TMB。肿瘤和免疫细胞之间的差异串扰与乳腺癌患者亚型有关。这些发现可能有助于确定潜在的生物标志物以及免疫检查点阻断和放射治疗在乳腺癌治疗中的最佳组合策略。