骨膜蛋白在雌激素受体阳性乳腺癌中的作用分析——基于单细胞RNA测序和批量RNA测序数据

doi:10.19586/j.2095-2341.2024.0123

生物技术进展 ›› 2024, Vol. 14 ›› Issue (6): 1055-1066.DOI: 10.19586/j.2095-2341.2024.0123

• 研究论文 • 上一篇

骨膜蛋白在雌激素受体阳性乳腺癌中的作用分析——基于单细胞RNA测序和批量RNA测序数据

布尔兰·叶尔肯别克(), 孙莉莉, 安外尔·约麦尔阿卜拉, 郭文佳()

新疆医科大学附属肿瘤医院，乌鲁木齐 830011

收稿日期:2024-07-03 接受日期:2024-10-14 出版日期:2024-11-25 发布日期:2024-12-27
通讯作者: 郭文佳
作者简介:布尔兰·叶尔肯别克 E-mail: burlinbk@163.com；
基金资助:
新疆维吾尔自治区重点研发任务专项(2022B03019-4);新疆维吾尔自治区天池英才(2022TCYCGWJ)

Comprehensive Analysis of POSTN in ER⁺ Breast Cancer——Based on Single-cell RNA and Bulk RNA-seq Sequencing

Yeerkenbieke BUERLAN(), Lili SUN, Yuemaierabola ANWAIER, Wenjia GUO()

Affiliated Cancer Hospital of Xinjiang Medical University，Urumqi 830011，China

Received:2024-07-03 Accepted:2024-10-14 Online:2024-11-25 Published:2024-12-27
Contact: Wenjia GUO

摘要/Abstract

摘要：

利用单细胞RNA测序（single-cell RNA-seq，scRNA-seq）和批量RNA测序（bulk RNA-seq）数据，探讨骨膜蛋白（periostin, POSTN）在雌激素受体阳性（estrogen receptor positive，ER⁺）乳腺癌中的表达特征及其临床相关性，为ER⁺乳腺癌患者的诊断、预后和个体化治疗提供理论建议。利用基因表达总库（gene expression omnibus，GEO）中的scRNA-seq数据鉴定ER⁺乳腺癌的细胞亚群和POSTN的表达特征。通过细胞轨迹和细胞通讯进一步分析POSTN和特异性高表达POSTN的癌症相关成纤维细胞（cancer-associated fibroblasts，CAFs）亚型。利用癌症基因组图谱（the cancer genome atlas，TCGA）数据库中的ER⁺乳腺癌数据，分析POSTN的表达水平、诊断和预后价值、通路富集、免疫治疗反应和药物敏感性。基于ER⁺乳腺癌的scRNA-seq数据，鉴定出一组高表达POSTN的CAFs，命名为POSTN⁺ CAFs。它们都处于分化的晚期阶段并对细胞间通讯至关重要；基于ER⁺乳腺癌bulk RNA-seq数据，发现POSTN在ER⁺乳腺癌中显著表达，并且与诊断和预后有相关性；根据功能富集分析，POSTN可能在血管生成、转移以及癌症的发生和进展中发挥作用；POSTN表达水平较低的个体可能从免疫治疗中获益；化疗药物对POSTN低表达的患者影响更大。基于scRNA-seq和bulk RNA-seq，全面分析了POSTN和POSTN⁺ CAFs在ER⁺乳腺癌中的生物学作用，并得出结论，POSTN可能是ER⁺乳腺癌诊断、预后、治疗反应和治疗靶点的生物标志物。

关键词: 骨膜蛋白, 乳腺癌, 单细胞测序, 免疫检查点, 药物敏感性

Abstract:

Using single-cell RNA-seq and bulk RNA-seq data， we investigated the expression characteristics and clinical relevance of periostin（POSTN） in estrogen receptor-positive （ER⁺） breast cancer and offered theoretical recommendations for the diagnosis， prognosis， and tailored treatment of ER⁺ breast cancer patients. scRNA-seq data in the gene expression omnibus （GEO） database were used to identify the cell subsets of ER⁺ breast cancer and the expression characteristics of POSTN. POSTN and cancer-associated fibroblasts （CAFs） subtypes with specifically high expression of POSTN were further analyzed by cell trajectory analysis and cell communication. Using the ER⁺ breast cancer data from TCGA-RBCA， the expression level， diagnostic and prognostic value， pathway enrichment， immunotherapy response， and drug sensitivity of POSTN were analyzed. We identified a subgroup of CAFs that strongly express POSTN， named POSTN⁺ CAFs， based on ER⁺ breast cancer scRNA-seq data. They were all in advanced stages of differentiation and were essential for intercellular communication. We found that POSTN is substantially expressed in patients with ER⁺ breast cancer and has diagnostic and prognostic relevance based on the bulk RNA-seq data of ER⁺ breast cancer. According to the functional enrichment analysis， POSTN may play a role in angiogenesis， metastasis and the onset and progression of cancer. Individuals who express lower levels of POSTN may benefit from immunotherapy. Based on scRNA-seq and bulk RNA-seq， this study offers a thorough examination of the biological roles of POSTN and POSTN⁺ CAFs in ER⁺breast cancer and concluded that POSTN may be a useful biomarker for ER⁺breast cancer diagnosis， prognosis， treatment response and therapeutic target.

Key words: POSTN, breast cancer, single-cell RNA sequencing, immunecheckpoint, chemotherapy drug sensitivity

中图分类号:

Q279

布尔兰·叶尔肯别克, 孙莉莉, 安外尔·约麦尔阿卜拉, 郭文佳. 骨膜蛋白在雌激素受体阳性乳腺癌中的作用分析——基于单细胞RNA测序和批量RNA测序数据[J]. 生物技术进展, 2024, 14(6): 1055-1066.

Yeerkenbieke BUERLAN, Lili SUN, Yuemaierabola ANWAIER, Wenjia GUO. Comprehensive Analysis of POSTN in ER⁺ Breast Cancer——Based on Single-cell RNA and Bulk RNA-seq Sequencing[J]. Current Biotechnology, 2024, 14(6): 1055-1066.

图/表 6

图1 单细胞RNA测序（scRNA-seq）数据鉴定ER+乳腺癌的细胞亚群及POSTN的表达特征A：UMAP 降维可视化114 457个单细胞被分为7种不同的细胞类型；B：每个簇中POSTN表达的特征图；C：热图显示了每个细胞群体的标志基因；D：UMAP图展示6种不同CAFs亚群；E：UMAP图展示POSTN的在CAFs亚群中的表达；F：小提琴图展示POSTN在CAFs亚型中的表达

Fig. 1 Single-cell RNA sequencing (scRNA-seq) data to identify cell subsets and POSTN expression profiles in ER+ breast cancer

图2 CAF亚型及POSTN的拟时序轨迹分析A：对所有CAF亚群的细胞轨迹进行拟时序分析，细胞分化的时间轴颜色越深，发育阶段越早；B：拟时间轨迹图CAFs轨迹图（按阶段分类），CAF有5种不同的分化状态，每一种用不同的颜色标记，右边的红色为分化最早的类型；C：CAFs每个细胞状态的位置；D：CAF各亚型树形结构轨迹图；E：POSTN的拟时分化表达趋势；F：右侧为拟时序Beam分析基因表达热图，左侧为相应的GO: BP注释

Fig. 2 Trajectory analysis of CAF subtypes and POSTN

图3 CAFs的细胞通讯分析A：CAFs细胞群之间互作数量和强度网络图。细胞间通信网络是一个加权有向图，左图为细胞间互作数量网络图，图中的节点表示不同细胞类型，节点圆圈越大表示该种细胞类型的细胞数目越多，线条越粗表示不同细胞类型之间检测到的互作数量越多，线条的颜色与配体细胞的颜色一致。右图为细胞间互作强度网络图，节点表示不同细胞类型，线条越粗表示细胞类型之间的互作强度越高，线条的颜色与配体细胞的颜色一致。B：分别展示每个簇的网络图。C：每种CAFs细胞类型的传入和传出相互作用强度。D：不同细胞类型的交互次数和作用强度。E：CAFs细胞发出的配体-受体相互作用。F：成纤维细胞之间几种肿瘤特异性通路的配体-受体对的点图。点的颜色反映的是通信概率，点的大小代表P值。空白意味着通信概率为零。P值是单边排列检验计算得到的。

Fig. 3 Inference of cell-cell communications in CAFs

图4 功能富集分析A：左上角为ER+和ER-乳腺癌组织中POSTN基因表达的分布。****表示差异在P<0.000 1水平有统计学意义，不同的颜色对应不同的组，横坐标表示不同样本组，纵坐标表示POSTN基因表达分布。采用Wilcox检验来确定显著性。B、C：通过POSTN水平的ROC曲线预测乳腺癌和ER+乳腺癌。D：以ER状态为“阳性“的亚组评价高、低POSTN组的预后。E~T：通路由得分与POSTN表达的Spearman关联分析。路径评分用图中的y轴表示，右侧的密度曲线表示路径评分的分布趋势，x轴显示基因表达，基因表达的分布趋势由上密度曲线表示，相关系数，用于确定相关性的方法，以及连接的P值（单个基因和通路得分）由最上面的值（轴内的蓝色曲线）表示。

Fig. 4 Functional enrichment analysis

图5 免疫治疗与POSTN表达的关系A：XCELL免疫细胞评分的热图显示了许多样本中不同色调的表达趋势；B：免疫评分XCELL纵坐标表示特定样品中免疫细胞含量的百分比，横坐标表示样品，不同颜色表示不同的免疫细胞类型。肿瘤浸润性免疫细胞在每个样本中的丰度百分比；C、D：POSTN高表达组和低表达组CIBERSORT免疫评分的分布;纵坐标表示免疫浸润评分在各组间的分布，横坐标表示免疫细胞浸润类型；E：免疫检查点基因在POSTN高、低表达组的表达分布;横坐标表示不同的样本分组，纵坐标表示不同分组的基因表达分布，用不同的颜色表示；F：采用IPS评分免疫表型评分IPS来评价免疫检查点抑制剂用药的反应；G：上图显示预测结果中两个组样本免疫反应的统计表，下图为免疫反应评分预测结果在各组间的分布。*P<0.05， **P<0.01， ***P<0.001，****P<0.000 1。Wilcox检验了这两个样本组的重要性。

Fig. 5 Relationship between immunotherapy and POSTN expression

图6 不同POSTN表达及化疗药物敏感性分析A~O：在POSTN低表达组中，他莫昔芬、吉非替尼、阿霉素、多西他赛、长春瑞滨、长春碱、顺铂、5-氟尿嘧啶、依托泊苷、艾替洛酮B、维利帕瑞、甲氨蝶呤、丝破霉素C、替莫唑胺、紫草素的IC50值均较低，说明该组患者对药物更敏感。两组之间的数字为P值。

Fig. 6 Analysis of different POSTN expressions and chemotherapeutic drug sensitivity

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骨膜蛋白在雌激素受体阳性乳腺癌中的作用分析——基于单细胞RNA测序和批量RNA测序数据

Comprehensive Analysis of POSTN in ER⁺ Breast Cancer——Based on Single-cell RNA and Bulk RNA-seq Sequencing

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