Cai Linkun, Ke Chuanfeng, Lin Zikai, Huang Yalan, Wang Aling, Wang Shiying, Chen Chunhui, Zhong Cailing, Fu Lingyu, Hu Peixin, Chai Jiwei, Zhang Haiyan, Zhang Beiping
Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
Department of Gastrointestinal Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
J Gastrointest Oncol. 2022 Dec;13(6):2845-2862. doi: 10.21037/jgo-22-1092.
Because stomach adenocarcinoma (STAD) has a poor prognosis, it is necessary to explore new prognostic genes to stratify patients to guide existing individualized treatments.
Survival and clinical information, RNA-seq data and mutation data of STAD were acquired from The Cancer Genome Atlas (TCGA) database. Fifty-one nicotinamide adenine dinucleotide (NAD) metabolism-related genes (NMRGs) were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome databases. Differentially expressed NMRGs (DE-NMRGs) between STAD and normal samples were screened, and consistent clustering analysis of STAD patients was performed based on the DE-NMRGs. Survival analysis, Gene Set Enrichment Analysis (GSEA), mutation frequency analysis, immune microenvironment analysis and drug prediction were performed among different clusters. Additionally, the differentially expressed genes (DEGs) among different clusters were selected, and the intersections of DEGs and DE-NMRGs were selected as the prognostic genes. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) was performed on a human gastric mucosa epithelial cell line and cancer cell line to verify the expression of the prognostic genes.
A total of 27 DE-NMRGs and two clusters were selected. There was a difference in survival between clusters 1 and 2. Furthermore, 18 DE-NMRGs were significantly different between clusters 1 and 2. The different Gene Ontology (GO) biological processes and KEGG pathways between clusters 1 and 2 were mainly enriched in cyclic nucleotide mediated signaling, synaptic signaling and hedgehog signaling pathway, etc. The somatic mutation frequencies were different between the two clusters, and TTN was the highest mutated gene in the patients of the clusters 1 and 2. Additionally, eight immune cells, immune score, stromal score, and estimate score were different between clusters 1 and 2. The patients in cluster 2 were sensitive to CTLA4 inhibitor treatment. Furthermore, the top five drugs (AP.24534, BX.795, Midostaurin, WO2009093927 and CCT007093) were significantly higher in cluster 1 than in cluster 2. Finally, three genes (AOX1, NNMT and PTGIS) were acquired as prognostic, and their expressions were consistent with the results of bioinformatics analysis.
Three prognostic genes related to NAD metabolism in STAD were screened out, which provides a theoretical basis and reference value for future treatment and prognosis of STAD.
由于胃腺癌（STAD）预后较差，因此有必要探索新的预后基因对患者进行分层，以指导现有的个体化治疗。
从癌症基因组图谱（TCGA）数据库获取STAD的生存和临床信息、RNA测序数据及突变数据。从京都基因与基因组百科全书（KEGG）和Reactome数据库中获得51个烟酰胺腺嘌呤二核苷酸（NAD）代谢相关基因（NMRGs）。筛选出STAD与正常样本之间差异表达的NMRGs（DE-NMRGs），并基于DE-NMRGs对STAD患者进行一致性聚类分析。在不同聚类之间进行生存分析、基因集富集分析（GSEA）、突变频率分析、免疫微环境分析和药物预测。此外，选择不同聚类之间的差异表达基因（DEGs），并将DEGs与DE-NMRGs的交集作为预后基因。最后，在人胃黏膜上皮细胞系和癌细胞系上进行定量实时聚合酶链反应（qRT-PCR），以验证预后基因的表达。
共筛选出27个DE-NMRGs和两个聚类。聚类1和聚类2之间的生存存在差异。此外，聚类1和聚类2之间有18个DE-NMRGs存在显著差异。聚类1和聚类2之间不同的基因本体（GO）生物学过程和KEGG通路主要富集在环核苷酸介导的信号传导、突触信号传导和刺猬信号通路等。两个聚类之间的体细胞突变频率不同，TTN是聚类1和聚类2患者中突变最多的基因。此外，聚类1和聚类2之间的8种免疫细胞、免疫评分、基质评分和估计评分不同。聚类2中的患者对CTLA4抑制剂治疗敏感。此外，聚类1中前五种药物（AP.24534、BX.795、米哚妥林、WO2009093927和CCT007093）的含量显著高于聚类2。最后，获得了三个基因（AOX1、NNMT和PTGIS）作为预后基因，其表达与生物信息学分析结果一致。
筛选出了三个与STAD中NAD代谢相关的预后基因，为STAD未来的治疗和预后提供了理论依据和参考价值。
