| Background and AimsGastric cancer(GC)is one of the most common malignant tumors which leads to the second incidence and third frequent tumor death in China and has severe impact in people's health.Although the 5-year survival rate is more than 90%for early stage GC patients who received radical surgery.However,because early diagnose is difficult,90%of patients are diagnosed at the advanced stage in China.For these patients,even after radical surgery and multiple courses of chemotherapy,most of them still experience recurrence and metastasis,the 5-year survival rate is less than 30%.So it is urgent to detect and diagnose in GC early stage.Although the tumor treatment has entered the era of precision medicine,the molecular mechanism underlying the development of gastric cancer has not been fully elucidated.Compared with other tumors,the research on the precise diagnosis and individualized treatment of gastric cancer is slow,and there is no ideal curative effect and prognostic indicators.And the development of targeted therapeutic drugs in gastric cancer has mostly ended in failure.At present,chemotherapy is still the main treatment for advanced gastric cancer,but its survival benefits are limited.Therefore,it is urgent to further reveal the mechanism of gastric cancer occurrence and development.Provide new prognostic indicators and treatment ideas for patients with gastric cancer.More and more studies have confirmed that non-coding RNA(ncRNA),especially microRNA/miRNA and long non-coding RNA(lncRNA)are involved in the occurrence?metastasis and various biological functions such as resistance to chemoradiotherapy and establishment of tumor microenvironment.Competing endogenous RNA(ceRNA)refers to various types of RNA transcripts through miRNAs response elements(MREs),which compete and combine with common miRNAs to achieve mutual regulation.Studies have found that various types of ceRNA,such as messenger RNA(mRNA),pseudogenes,lncRNA,and circular RNA(circRNA),can communicate with each other through the ceRNA network to regulate tumor cells and their microenvironment.It played an important role in the process of metastasis,which opened up a new field for studying the pathogenesis of gastric cancer.In addition,with the development and widespread application of gene chips and sequencing technologies,a large amount of biological information data has been generated,and various databases have emerged at the historic moment,such as The Cancer Genome Atlas(TCGA)?Gene Expression Omnibus GEO)and Oncomine database.The analysis of multiomics data has become an important tool for people to explore the mechanism of gastric cancer development.This study intends to select 5 patients undergoing radical gastrectomy for gastric cancer in our hospital with cancer and paired adjacent tissues and use biochip technology to determine gene expression profiling.The edgeR package in R language is used to screen for differential expression mRNA?lncRNA and miRNA of cancer and adjacent tissues.The GO biological process enrichment analysis and KEGG pathway enrichment analysis of differentially expressed DEmRNA were performed through the online bioinformatics analysis tool DAVID database.Apply online prediction tools miRTarBase?miRDB?star Base and DIANA-LncBase to predict DEmiRNA-DElncRNA?DEmiRNA-DEmRNA interactions.With the help of Cytoscape software,visualize the ceRNA network and screen out the hub gene,then use the OncoLnc database to screen out the correlation with gastric cancer prognosis.The gastric cancer-related ceRNA network constructed through this study can help to understand the molecular mechanisms involved in the occurrence and progression of gastric cancer,and thus help find potential biomarkers and therapeutic targets.Materials and Methods1.Fresh cancer tissues and corresponding paracancer tissues of gastric cancer patients receiving radical gastrectomy for gastric cancer in the first affiliated hospital of zhengzhou university were selected,among which the paracancer tissues were normal tissues more than 5cm away from the tumor.Fresh tissue samples were cut and quickly refrigerated in liquid nitrogen for later use.2.Agilent Human miRNA(8x60K)array chip and Agilent SurePrint G3 Human Gene Expression Microarray(8x60K)chip were used to operate according to the standard operating procedures provided by Agilent Expression profile chip and Agilent miRNA chip.The chip results were scanned by Agilent Microarray Scanner.The original data obtained from the chip scan was normalized by GeneSpring Software GX 11.0.3.The R language package was used to preprocess the chip data,and the differentially expressed genes were screened with log|FC|?0.58 and P<0.05.4.Using biological information annotation database DAVID carried out GO biological process enrichment analysis and KEGG pathway enrichment analysis for differentially expressed DEmRNA.5.In R language,UCSCXenaTools package was used to download the mRNA?miRNA and lncRNA data of gastric cancer and paracancer tissues in TCGA database to verify partial differentially expressed mRNAs,miRNAs and lncRNAs.6.The application of on-line forecasting tool miRTarBase(http://mirtarbase.mbc.nctu.edu.tw/),Target-Scan(http://www.targetscan.org/),miRDB(http://www.mirdb.org/miRDB/),the star Base(http://starbase.sysu.edu.cn/)to retrieve the miRNA Target mRNA.Overlapping genes were defined as DEmRNA targeted by DEmiRNA.DElncRNA-DEmiRNA interaction with DIANA-LncBase database(http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php).7.With the help of Cytoscape software,visualize the ceRNA network,calculate the connectivity in the ceRNA regulatory network,search for the hub genes with strong potential regulatory ability,and screen out the top 20 hub genes with high connectivity.8.The OncoLnc database(https://www.oncolnc.org/)was used to analyze the expression level of hub gene and survival rate of gastric cancer patients for kaplan-meier survival analysis and log-rank test,and the hub gene related to the prognosis of gastric cancer was screened out.Results1.Differential expressions of 10 DEmiRNA,766 DEmRNA and 110 delncrnas were screened,among which 3 miRNA were up-regulated and 7 miRNA were down-regulated;403 mRNA were up-regulated and 363 mRNA were down-regulated;42 lncRNA were up-regulated and 681 ncRNA were down-regulated.2.Mlk7-as1?SPP1?SULF1?hsa-mir-1307-3p were highly expressed in gastric cancer tissues,while MT2A?MT1X were low expressed in gastric cancer tissues.3.12 GO biological processes were significantly enriched in BP(biological process),and the KEGG pathway enriched by differential genes was mainly the mineral absorption pathway.4.The top 20 hub genes were identified,including 5 miRNA and 15 mRNA,which were miR-3180-5p?miR-183-5p?miR-873-5p?miR-1910-3p?miR-182-5p?MBNL1?CHST1?HSP90AA1?PRKCB?ZNF827?SPIN4?CA12?MEF2C?AKAP11?ERI2?BCL11A?ELK3?EPDR1?RAB30 and KIF2A respectively.5.CHST1 was negatively correlated with the survival of patients,and the higher the expression level,the shorter the survival time of patients;Mir-183-5p was positively correlated with the survival of patients,and the higher the expression level,the longer the survival time of patients.Conclusion1.Mlk7-as1?SPP1?SULF1?and hsa-mir-1307-3p are highly expressed in the biochip of gastric cancer tissues;while MT2AvMT1X are low expressed in gastric cancer tissue biochip.2.CHST1 and mir-183-5p are closely related to the prognosis of gastric cancer patients.CHST1 is negatively correlated with the survival of patients,the higher the expression level,the shorter the survival time of patients.while miR-183-5p is just the opposite.3.These genes may play a crucial role in the occurrence and development of gastric cancer,providing a new idea for basic research?early diagnosis?prognosis and targeted treatment. |
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