PDE1B表达与胃癌预后和肿瘤微环境的生物信息学分析

doi:10.13481/j.1671-587X.20240620

摘要/Abstract

摘要：

目的通过生物信息学方法筛选胃癌中具有差异预后意义的调节性细胞死亡和衰老基因，分析磷酸二酯酶1（PDE1）B对胃癌患者生存预后的影响。方法自TCGA公共数据库下载胃癌基因表达数据和临床数据，本地数据库中随机抽取50例胃癌患者，收集其临床信息和石蜡样本，包括胃癌组织和癌旁正常组织。采用R软件“limma”程序包筛选差异表达基因（DEGs），单因素COX分析和Kaplan-Meier生存分析筛选有预测生存价值的DEGs，获取影响胃癌患者生存预后的交集基因，筛选与临床病理特征最具关联的基因PDE1B。TCGA数据库和Kaplan-Meier生存分析检测胃癌患者癌旁正常组织和胃癌组织中PDE1B mRNA表达水平及其与胃癌患者生存期的关系，采用基因本体论（GO）功能和京都基因与基因组百科全书（KEGG）信号通路富集分析PDE1B生物学功能，CIBERSORT算法、肿瘤免疫数据库（TISIDB）和GSCA在线网站分析PDE1B与肿瘤微环境、免疫特征分子和药物敏感性的相关性。实时荧光定量PCR（RT-qPCR）法检测胃癌患者胃癌组织和癌旁正常组织中PDE1B mRNA表达水平。结果共筛选716个DEGs，其中505个DEGs表达上调（P<0.05），211个DEGs表达下调（P<0.05），获得10个影响生存预后的交集基因，PDE1B mRNA表达水平与胃癌患者临床病理特征关系最为密切，其与年龄、肿瘤分级、肿瘤分期和肿瘤T、N及M期有关联（P<0.05）；与G1-G2、Stage Ⅰ、T1-T2、N0和M0期胃癌患者比较，G3-G4、StageⅡ-Ⅳ、T3-T4、N1-N3和M1分期胃癌患者胃癌组织中PDE1B mRNA表达水平均明显升高（P<0.05）。与癌旁正常组织比较，胃癌患者胃癌组织中PDE1B mRNA表达水平明显降低（P<0.05）；与PDE1B低表达胃癌患者比较，PDE1B高表达胃癌患者总体生存率明显降低（P<0.01）。PDE1B表达、年龄和肿瘤分期是胃癌患者预后的危险因素（P<0.05）。在调整了性别、年龄、肿瘤分级和肿瘤分期后，PDE1B表达是影响胃癌患者预后的独立危险因素（P<0.05）。PDE1B主要富集于免疫球蛋白产生、钙离子转运、第二信使介导的信号转导等生物过程（BP），T淋巴细胞受体复合体、细胞膜信号受体复合体和含胶原蛋白的细胞外基质等细胞成分（CC），抗原结合、糖胺聚糖结合和细胞外基质结构成分等分子功能（MF）；PDE1B主要参与了神经活性配体-受体相互作用、钙信号通路、环磷酸鸟苷（cGMP）-蛋白激酶G（PKG）信号通路及细胞因子-细胞因子受体的相互作用等途径。PDE1B与调节性T淋巴细胞（r=0.488）、髓源性抑制细胞（r=0.474）和巨噬细胞（r=0.617）呈正相关关系（P<0.01）；与PDE1B低表达胃癌患者比较，PDE1B高表达胃癌患者促进肿瘤的调节性T淋巴细胞、单核细胞和M2型巨噬细胞浸润均明显增加（P<0.05）。PDE1B mRNA表达水平与免疫抑制剂转化生长因子β（TGF-β）1（r=0.535）、集落刺激因子1受体（CSF1R）（r=0.519）、免疫激活剂外核苷三磷酸二磷酸水解酶1（ENTPD1）（r=0.593）和CXC趋化因子配体12（CXCL12）（r=0.646）呈正相关关系（P<0.01）。PDE1B高表达的胃癌组织对氟尿嘧啶（-0.3<r <-0.1）、甲氨蝶呤（-0.3<r <-0.1）和地西他滨（-0.3<r <-0.1）等药物较为敏感（P<0.05）。与癌旁正常组织比较，胃癌患者胃癌组织中PDE1B mRNA表达水平明显降低（P<0.01）；与PDE1B低表达胃癌患者比较，PDE1B高表达胃癌患者总体生存率明显降低（P<0.05）；与T1-T2期胃癌患者比较，肿瘤T3-T4期胃癌患者胃癌组织中PDE1B mRNA表达水平明显升高（P<0.01）。结论 PDE1B是胃癌患者预后的独立危险因素，可作为胃癌预后不良的有效指标。

关键词: 胃肿瘤, 生存预后, 磷酸二酯酶1B, 肿瘤微环境, 药物敏感性

Abstract:

Objective To screen for regulatory cell death and senescence genes with differential prognostic significances in the gastric cancer through bioinformatics methods， and to analyze the effect of phosphodiesterase 1B （PDE1B） on the survival prognosis of the gastric cancer patients. Methods The gastric cancer gene expression data and clinical data were downloaded from the TCGA Public Database.Fifty gastric cancer patients were randomly selected from the local database， and their clinical informations and paraffin samples， including gastric cancer tissue and adjacent normal tissue， were collected. The R software “limma” package was used to screen differentially expressed genes （DEGs）； univariate COX analysis and Kaplan-Meier survival analysis were used to screen DEGs with predictive survival value. The intersection genes affecting the survival prognosis of gastric cancer patients were obtained， and the gene most associated with clinical pathological features PDE1B was screened. The TCGA Database and Kaplan-Meier survival analysis were used to detect the expression levels of PDE1B mRNA in adjacent normal and gastric cancer tissues and their relationships with survival period of the gastric cancer patients. Gene Ontology （GO） functional and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analyses were used to enrich the biological functions of PDE1B. The CIBERSORT algorithm， Tumor Immunity Database （TISIDB）， and GSCA online website were used to analyze the correlation between PDE1B and tumor microenvironment， immune characteristic molecules， and drug sensitivity. The real-time fluorescence quantitative PCR （RT-qPCR） method was used to detect the PDE1B mRNA expression levels in gastric cancer tissue and adjacent normal tissue of the gastric cancer patients. Results A total of 716 DEGs were screened， among which 505 DEGs were upregulated （P<0.05）， and 211 DEGs were downregulated （P<0.05）. There were 10 intersection genes affecting survival prognosis.The PDE1B mRNA expression level was most closely related to the clinical pathological characteristics of the gastric cancer patients， being associated with age， tumor grade， tumor stage， and tumor T， N， and M stages （P<0.05）. Compared with G1-G2， StageⅠ， T1-T2， N0， and M0 stage gastric cancer patients，the PDE1B mRNA expression levels in G3-G4， StageⅡ-Ⅳ， T3-T4， N1-N3， and M1 stage gastric cancer patients were significantly increased （P<0.05）. Compared with adjacent normal tissue， the PDE1B mRNA expression level in gastric cancer tissue was significantly decreased （P<0.05）. Compared with the patients with low PDE1B expression， the patients with high PDE1B expression had a significantly lower overall survival rate （P<0.01）. PDE1B expression， age， and tumor stage were the risk factors for the prognosis of gastric cancer patients （P<0.05）. After adjusting for gender， age， tumor grade， and tumor stage， PDE1B expression was an independent risk factor affecting the prognosis of the gastric cancer patients （P<0.05）. PDE1B was mainly enriched in the biological process（BP）， such as immunoglobilin production， second-messenger， mediated signaling transduction and calcium ion transport， cellular component（CC）， such as Tlymplocytes receptor complex， plasma membrance signaling receptor complex and collagen-containing extracellular matrix， and molecular function（MF）， such as antigen binding， glycosaminoglycan binding， and extracellular matrix structural constituents. PDE1B was mainly involved in the pathways such as neuroactive ligand-receptor interaction， calcium signaling pathway， cGMP-PKG signaling pathway， and cytokine-cytokine receptor interaction. PDE1B was positively correlated with regulatory T lymphocytes （r=0.488）， myeloid-derived suppressor cells （r=0.474）， and macrophages （r=0.617）（P<0.01）. Compared with the patients with low PDE1B expression， the patients with high PDE1B expression promoted the significant increase of infiltration of regulatory T lymphocytes， monocytes， and M2 macrophages （P<0.05）. The PDE1B mRNA expression levels were positively correlated with the immunosuppressive agents transforming growth factor-β1 （TGF-β1）（r=0.535）， colony-stimulating factor 1 receptor （CSF1R）（r=0.519）， immune activator ectonucleoside triphosphate diphosphohydrolase 1 （ENTPD1）（r=0.593）， and CXC chemokine ligand 12 （CXCL12）（r=0.646）（P<0.01）. The gastric cancer tissue with high PDE1B expression was more sensitive to the drugs such as fluorouracil （-0.3<r <-0.1）， methotrexate （-0.3<r <-0.1）， and decitabine （-0.3<r <-0.1）（P<0.05）. Compared with adjacent normal tissue， the PDE1B mRNA expression levels in gastric cancer tissue were significantly decreased （P<0.01）. Compared with low PDE1B expression group， the overall survival rate patients in of the high PDE1B expression group had a significantly lower was decreased（P<0.05）.Compared with T1-T2 stage gastric cancer patients， the PDE1B mRNA expression level of the T3-T4 stage gastric cancer patients was significantly increased （P<0.01）. Conclusion PDE1B is an independent risk factor for the prognosis of the gastric cancer patients and can serve as an effective indicator of poor prognosis of gastric cancer.

Key words: Stomach neoplasm, Survival prognosis, Phosphodiesterase 1B, Tumor microenvironment, Drug sensitivity

中图分类号:

R735.2

杨希,袁琴,杨兰,张文杰. PDE1B表达与胃癌预后和肿瘤微环境的生物信息学分析[J]. 吉林大学学报(医学版), 2024, 50(6): 1664-1676.

Xi YANG,Qin YUAN,Lan YANG,Wenjie ZHANG. Bioinformatics analysis on PDE1B expression and prognosis of gastric cancer and tumor microenvironment[J]. Journal of Jilin University(Medicine Edition), 2024, 50(6): 1664-1676.

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ID	P value of gender	P value of age	P value of grade	P value of stage	P value of TNM			Significative number
ID	P value of gender	P value of age	P value of grade	P value of stage	T	N	M	Significative number
PDE1B	0.670 0	0.027 0	6.8E-07	0.002 6	0.008 2	0.007 6	0.042 0	6
AKAP12	0.390 0	0.047 0	4.4E-05	0.027 0	1.7E-05	0.040 0	0.650 0	5
GHR	0.350 0	0.001 3	4.1E-06	0.002 4	0.000 2	0.290 0	0.380 0	4
GGT5	0.480 0	0.022 0	6.4E-08	0.009 2	1.4E-07	0.130 0	0.530 0	4
CDO1	0.920 0	0.001 8	9.4E-08	0.010 0	1.2E-06	0.230 0	0.280 0	4
LOX	0.520 0	0.280 0	0.000 3	0.013 0	7.4E-07	0.390 0	0.290 0	3
PDGFRB	0.280 0	0.850 0	3.4E-05	0.004 1	1.8E-06	0.260 0	0.620 0	3
VCAN	0.750 0	0.800 0	0.000 5	0.018 0	2.1E-07	0.200 0	0.780 0	3
TMEM200A	0.078 0	0.100 0	0.230 0	0.017 0	0.002 0	0.240 0	0.820 0	2
SERPINE1	0.850 0	0.410 0	0.022 0	0.140 0	0.003 4	0.430 0	0.520 0	2

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