Zhao Zhe, Li Wenqi, Zhu LiMeng, Xu Bei, Jiang Yudong, Ma Nan, Liu LiQun, Qiu Jie, Zhang Min
Zhengzhou KingMed Center for Clinical Laboratory Co. Ltd., Zhengzhou, China.
Department of Newborn Infants, Children's Hospital of Nanjing Medical University, Nanjing, China.
Front Genet. 2022 Jul 14;13:908957. doi: 10.3389/fgene.2022.908957. eCollection 2022.
Traditionally, cancer-associated fibroblasts (CAFs), an essential component of tumor microenvironment, were exert a crucial part in colon cancer progression. In this study, single-cell RNA-sequencing (scRNA-seq) data from 23 and bulk RNA-seq data from 452 colon cancer patients were extracted from the GEO database and TCGA-COAD and GEO databases, respectively. From single-cell analysis, 825 differentially expressed genes (DEGs) in CAFs were identified between each pair of six newly defined CAFs, named enCAF, adCAF, vaCAF, meCAF, erCAF, and cyCAF. Cell communication analysis with the iTALK package showed communication relationship between CAFs, including cell autocrine, cytokine, and growth factor subtypes, such as receptor-ligand pairs of , and . Herein, we demonstrated the presence and prognostic value of adCAF and erCAF in colon cancer based on CIBERSORTx, combining single-cell marker genes and transcriptomics data. The prognostic significance of the enCAF and erCAF has been indirectly proved by both the correlation analysis with macrophages and CAFs, and the quantitative reverse transcription-polymerase chain reaction (qRT-PCR) experiment based on 20 paired tumor samples. A prognostic model was constructed with 10 DEGs using the LASSO Cox regression method. The model was validated using two testing datasets, indicate a significant survival accuracy ( < 0.0025). Correlation analyses between clinical information, such as age, gender, tumor stage and tumor features (tumor purity and immune score), and risk scores revealed our CAF-related model's robustness and excellent performance. Cell infiltration analysis by xCell revealed that the interaction between CAFs and multiple non-specific immune cells such as macrophages and the dendritic cell was a vital factor affecting immune score and prognosis. Finally, we analyzed how common anti-cancer drugs, including camptothecin, docetaxel and bortezomib, and immunotherapy, such as anti-PD-1 treatment, could be different in low-risk and high-risk patients inferred from our CAF-related model. In conclusion, the study utilized refined colon cancer fibroblast subsets and established the prognostic effects from the interaction with nonspecific immune cell.
传统上，癌症相关成纤维细胞（CAFs）是肿瘤微环境的重要组成部分，在结肠癌进展中发挥关键作用。在本研究中，分别从GEO数据库以及TCGA-COAD和GEO数据库中提取了23例患者的单细胞RNA测序（scRNA-seq）数据和452例结肠癌患者的批量RNA测序数据。通过单细胞分析，在六种新定义的CAFs（分别命名为enCAF、adCAF、vaCAF、meCAF、erCAF和cyCAF）的每一对之间鉴定出825个CAFs中的差异表达基因（DEGs）。使用iTALK软件包进行的细胞通讯分析显示了CAFs之间的通讯关系，包括细胞自分泌、细胞因子和生长因子亚型，如 、 和 的受体-配体对。在此，我们基于CIBERSORTx，结合单细胞标记基因和转录组学数据，证明了adCAF和erCAF在结肠癌中的存在及其预后价值。通过与巨噬细胞和CAFs的相关性分析以及基于20对肿瘤样本的定量逆转录-聚合酶链反应（qRT-PCR）实验，间接证明了enCAF和erCAF的预后意义。使用LASSO Cox回归方法，用10个DEGs构建了一个预后模型。该模型在两个测试数据集上得到验证，显示出显著的生存准确性（<0.0025）。年龄、性别、肿瘤分期和肿瘤特征（肿瘤纯度和免疫评分）等临床信息与风险评分之间的相关性分析揭示了我们的CAF相关模型的稳健性和优异性能。通过xCell进行的细胞浸润分析表明，CAFs与巨噬细胞和树突状细胞等多种非特异性免疫细胞之间的相互作用是影响免疫评分和预后的重要因素。最后，我们分析了包括喜树碱、多西他赛和硼替佐米在内的常见抗癌药物以及抗PD-1治疗等免疫疗法在从我们的CAF相关模型推断出的低风险和高风险患者中的差异。总之，该研究利用了精细的结肠癌成纤维细胞亚群，并确定了与非特异性免疫细胞相互作用的预后影响。
