研究动态
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通过单细胞测序数据和TCGA数据分析鉴定和验证结直肠癌肝转移的关键基因。

Identification and Verification of Key Genes in Colorectal Cancer Liver Metastases Through Analysis of Single-Cell Sequencing Data and TCGA Data.

发表日期:2024 Oct 09
作者: Hui Zhang, Changhua Zhuo, Ruirong Lin, Fayong Ke, Ming Wang, Chunkang Yang
来源: ANNALS OF SURGICAL ONCOLOGY

摘要:

结直肠癌(CRC)在全球范围内非常流行,更多患者出现结直肠癌肝转移(CRLM)。本研究旨在通过单细胞测序数据再分析和实验验证来识别 CRLM 中的关键基因。该研究分析了来自基因表达综合 (GEO) 数据库的单细胞 RNA 测序 (scRNA-seq) 数据。使用基因本体论(GO)和京都基因和基因组百科全书(KEGG)进行基因功能富集分析。癌症基因组图谱 (TCGA) 数据支持批量 RNA 表达和生存预后分析。实时聚合酶链反应 (qPCR) 检测 mRNA 表达,而蛋白质印迹则确定蛋白质水平。细胞功能实验评估了 SPARC 对 CRC 细胞行为的影响。聚类分析显示 17 个 CRLM 样本中有 23 个类别,代表六种细胞类型。 GO 和 KEGG 分析确定白介素 1 β (IL1B)、CD2 分子 (CD2) 和 C-X-C 基序趋化因子配体 8 (CXCL8) 是 CRC 的重要预后因素。富含半胱氨酸的酸性分泌蛋白(SPARC)是组织干细胞中最重要的差异表达基因(DEG)之一,已在原发性和转移性病变中得到证实。转移性病灶中 SPARC 和含有 G 蛋白偶联受体 5 (LGR5) 的 CRC 干细胞标志物富含亮氨酸重复序列表达较高,且与 LGR5 表达显着正相关。 SPARC 的敲低降低了 CRC 细胞球和集落的形成、侵袭和迁移能力。 SPARC的过表达显着增加了CRC细胞的恶性程度。在CRLM过程中鉴定出了几个关键基因。在 CRLM 样本和 CRC 干细胞对应的样本中,SPARC 显着上调。在 CRLM 的治疗中,SPARC 可能是一个潜在的靶点。© 2024。作者。
Colorectal cancer (CRC) is highly prevalent worldwide, with more patients experiencing colorectal cancer liver metastases (CRLM). This study aimed to identify key genes in CRLM through single-cell sequencing data reanalysis and experimental validation.The study analyzed single-cell RNA-sequencing (scRNA-seq) data from the Gene Expression Omnibus (GEO) database. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for gene functional enrichment analysis. The Cancer Genome Atlas (TCGA) data enabled bulk-RNA expression and survival prognosis analysis. Real-time polymerase chain reaction (qPCR) detected mRNA expression, whereas Western blot determined protein levels. Cell function experiments assessed SPARC's impact on CRC cell behavior.Cluster analysis showed 23 classes among 17 CRLM samples, representing six cell types. A GO and KEGG analysis identified interleukin-1 beta (IL1B), CD2 molecule (CD2), and C-X-C motif chemokine ligand 8 (CXCL8) as significant prognostic factors in CRC. Secreted protein acidic and cysteine rich (SPARC) was one of the top differentially expressed genes (DEGs) in tissue stem cells, confirmed in primary and metastatic lesions. Metastatic lesions showed higher expression of SPARC and CRC stem cell marker leucine-rich repeat containing G protein-coupled receptor 5 (LGR5), which was significantly correlated positively with LGR5 expression. Knockdown of SPARC reduced CRC cell sphere- and colony-formation, invasion, and migration abilities. Overexpression of SPARC significantly increased the malignancy of CRC cells.Several key genes were identified in the process of CRLM. In CRLM samples and those corresponding to CRC stem cells, SPARC was significantly upregulated. In the therapy of CRLM, SPARC might be a potential target.© 2024. The Author(s).