Department of Gastrointestinal Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361102, China.
Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen 361102, China.
Int J Mol Sci. 2023 Aug 17;24(16):12890. doi: 10.3390/ijms241612890.
According to the World Health Organization (WHO), gastric cancer (GC) is the fourth leading cause of tumor-related mortality globally and one of the most prevalent malignant tumors. To better understand the role of tumor-infiltrating B cells (TIBs) in GC, this work used single-cell RNA sequencing (scRNA-Seq) and bulk RNA sequencing (bulk RNA-Seq) data to identify candidate hub genes. Both scRNA-Seq and bulk RNA-Seq data for stomach adenocarcinoma (STAD) were obtained from the GEO and TCGA databases, respectively. Using scRNA-seq data, the FindNeighbors and FindClusters tools were used to group the cells into distinct groups. Immune cell clusters were sought in the massive RNA-seq expression matrix using the single-sample gene set enrichment analysis (ssGSEA). The expression profiles were used in Weighted Gene Coexpression Network Analysis (WGCNA) to build TCGA's gene coexpression networks. Next, univariate Cox regression, LASSO regression, and Kaplan-Meier analyses were used to identify hub genes in scRNA-seq data from sequential B-cell analyses. Finally, we examined the correlation between the hub genes and TIBs utilizing the TISIDB database. We confirmed the immune-related markers in clinical validation samples using reverse transcriptase polymerase chain reaction (RT-PCR) and immunohistochemistry (IHC). 15 cell clusters were classified in the scRNA-seq database. According to the WGCNA findings, the green module is most associated with cancer and B cells. The intersection of 12 genes in two separate datasets (scRNA and bulk) was attained for further analysis. However, survival studies revealed that increased () expression was linked to worse overall survival. expression is correlated with active, immature, and memory B cells in STAD were identified. Finally, RT-PCR and IHC assays verified that in GC, is overexpressed, and its expression level correlates with TIBs. We used scRNA-Seq and bulk RNA-Seq to study STAD's cellular composition. We found that is highly expressed by TIBs in GC, suggesting that it may serve as a hub gene for these cells and a starting point for future research into the molecular mechanisms by which these immune cells gain access to tumors and potentially identify therapeutic targets.
根据世界卫生组织（WHO）的数据，胃癌（GC）是全球第四大肿瘤相关死亡原因，也是最常见的恶性肿瘤之一。为了更好地了解肿瘤浸润 B 细胞（TIBs）在 GC 中的作用，本研究使用单细胞 RNA 测序（scRNA-Seq）和批量 RNA 测序（bulk RNA-Seq）数据来鉴定候选的枢纽基因。胃腺癌（STAD）的 scRNA-Seq 和批量 RNA-Seq 数据分别从 GEO 和 TCGA 数据库中获得。使用 scRNA-seq 数据，使用 FindNeighbors 和 FindClusters 工具将细胞分为不同的组。使用单细胞基因集富集分析（ssGSEA）在大量 RNA-seq 表达矩阵中寻找免疫细胞簇。使用表达谱在 TCGA 的基因共表达网络分析（WGCNA）中构建基因共表达网络。接下来，使用单变量 Cox 回归、LASSO 回归和 Kaplan-Meier 分析在连续 B 细胞分析的 scRNA-seq 数据中识别枢纽基因。最后，我们利用 TISIDB 数据库研究了枢纽基因与 TIBs 的相关性。我们使用逆转录聚合酶链反应（RT-PCR）和免疫组织化学（IHC）在临床验证样本中验证了免疫相关标记物。在 scRNA-seq 数据库中对 15 个细胞簇进行了分类。根据 WGCNA 的研究结果，绿色模块与癌症和 B 细胞最相关。在两个独立数据集（scRNA 和 bulk）中，获取了 12 个基因的交集进行进一步分析。然而，生存研究表明，（）表达的增加与总体生存率的降低有关。在 STAD 中，鉴定出与活跃、未成熟和记忆 B 细胞相关的 表达。最后，RT-PCR 和 IHC 检测验证了在 GC 中，表达上调，其表达水平与 TIBs 相关。我们使用 scRNA-Seq 和批量 RNA-Seq 研究了 STAD 的细胞组成。我们发现，在 GC 中，TIBs 高度表达，这表明它可能作为这些细胞的枢纽基因，并为研究这些免疫细胞进入肿瘤的分子机制以及潜在的治疗靶点提供了起点。
