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bioinformatics analysis and Identification of Potential Genes Associated with Pathogenesis and Prognosis of Gastric Cancer

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Current Medical Science 2022年第2期42卷 357-372页

作者： Dan-wen WANG Fei SU Li-jie YANG Li-wen SHI Tie-cheng YANG Hua-qiao WANG Xuan-fei LI Mao-hui FENG Department of Gastrointestinal Surgery Zhongnan Hospital of Wuhan UniversityWuhan443071China Clinical Medical Research Center of Peritoneal Cancer of Wuhan Wuhan443071China Clinical Cancer Study Center of Hubei Provence Wuhan443071China Hubei Key Laboratory of Tumor Biological Behaviors Wuhan443071China Department of Oncology the First Hospital of Lanzhou UniversityLanzhou730000China

Objective Gastric cancer(GC)is a deadly cancer and a challenging public health problem *** study aimed to analyze potential genes associated with pathogenesis and prognosis of gastric *** This work selected the overlapping differentially expressed genes(DEGs)in GC from four datasets,the GSE29272,GSE29998,GSE54129 and GSE118916 Gene Expression Omnibus *** DEGs were used to carry out comprehensive bioinformatic analysis to analyze the related functions and pathways enriched,the relative expression levels and immune infiltrates,the prognostic characteristics and the interaction *** In total,55 DEGs increased while 98 decreased in their expression *** those DEGs with increased expression,they were mostly concentrated on“focal adhesion”and“ECM-receptor interaction”,whereas DEGs with decreased expression were mostly associated with“gastric acid secretion”and“drug metabolism cytochrome P450”.MCODE and ClueGO results were then integrated to screen 10 hub genes,which were FN1,COL1A1,COL3A1,BGN,TIMP1,COL1A2,LUM,VCAN,COL5A2 and *** analysis revealed that higher expression of the ten hub genes significantly predicted lower overall survival of GC ***1 was most significantly related to neutrophils,CD8+T cells,as well as dendritic cells,while LUM was most significantly related to *** Immunohistochemistry results and functional testing showed that the expression of COL5A2 was elevated in GC and that it might be a key gene in GC tumorigenesis.

关键词： gastric cancer differentially expressed genes bioinformatics analysis prognosis immune infiltrate

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bioinformatics analysis of human kallikrein 5 (KLK5) expression in metaplastic triple‐negative breast cancer

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Cancer Innovation 2023年第5期2卷 376-390页

作者： Yue Song Guiying Bai Xiaoqing Li Liyan Zhou Yiran Si Xiaohui Liu Yilin Deng Yehui Shi Department of Phase I Clinical Trial Tianjin Medical University Cancer Institute and HospitalTianjinChina Medical Oncology Department of Breast Cancer Tianjin Medical University Cancer Institute and HospitalTianjinChina National Clinical Research Center for Cancer TianjinChina

Background:Metaplastic breast carcinoma(MBC)is a rare breast cancer subtype;most cases are triple‐negative breast cancers(TNBCs)and are poorly responsive to conventional systemic *** potential diagnostic and prognostic markers for distinguishing between metaplastic TNBC and nonmetaplastic TNBC have been *** performed bioinformatic analysis to explore the underlying mechanism by which metaplastic TNBC differs from nonmetaplastic TNBC and provides potential pathogenic genes of metaplastic ***:Differentially expressed genes(DEGs)in metaplastic tumors and nonmetaplastic tumors from TNBC patients were screened using *** GSE76275 data set and The Cancer Genome Atlas(TCGA)database were used to screen DEGs in TNBC and non‐*** and DAVID were used for the Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis and Gene Ontology(GO)analysis of *** databases,including UALCAN,GEPIA,HPA,Breast Cancer Gene‐Expression Miner,and quantitative PCR and western blot,were used to examine KLK5 messenger RNA and protein expression in breast *** of KLK5‑associated genes was performed with TCGA data,and the LinkedOmics database was used to detect the genes co‐expressed with ***(Search Tool for the Retrieval of Interacting Genes)and Cytoscape were used to screen for hub ***‑Meier plotter was used for survival ***:KLK5 was identified among the DEGs in nonmetaplastic TNBC and metaplastic *** KLK5 gene was overexpressed in nonmetaplastic TNBC but downregulated in metaplastic *** and GO analyses revealed that epithelial‐to‐mesenchymal transition was a pathogenic mechanism in metaplastic TNBC and an important pathway by which KLK5 and its associated genes DSG1and DSG3 influence metaplastic TNBC progression. Prognosis analysis showedthat only low expression of KLK5 in metaplastic TNBC had clinical ***: Our research indicated that KLK5 may be a pivotal moleculewit

关键词： bioinformatics analysis differentially expressed genes EMT KLK5 metaplastic breast carcinoma

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Targeted gene sequencing and bioinformatics analysis of patients with gallbladder neuroendocrine carcinoma:A case report

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World Journal of Gastrointestinal Oncology 2025年第1期17卷 239-251页

作者： Yun-Chuan Yang Zhi-Tao Chen Da-Long Wan Hui Tang Mu-Lin Liu Department of Medical College Jinan UniversityGuangzhou 510000Guangdong ProvinceChina Department of General Surgery The First Affiliated Hospital of Bengbu Medical UniversityBengbu 233000Anhui ProvinceChina Department of Hepatobiliary Surgery Shulan(Hangzhou)Hospital Affiliated to Zhejiang Shuren University Shulan International Medical CollegeHangzhou 310022Zhejiang ProvinceChina Department of Hepatobiliary and Pancreatic Surgery The First Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou 310003Zhejiang ProvinceChina Department of Pathology The First Affiliated Hospital of Medical School of Zhejiang UniversityHangzhou 310000Zhejiang ProvinceChina

BACKGROUND Gallbladder neuroendocrine carcinoma(NEC)represents a subtype of gallbladder malignancies characterized by a low incidence,aggressive nature,and poor *** its clinical severity,the genetic alterations,mechanisms,and signaling pathways underlying gallbladder NEC remain *** SUMMARY This case study presents a rare instance of primary gallbladder NEC in a 73-year-old female patient,who underwent a radical cholecystectomy with hepatic hilar lymphadenectomy and resection of liver segments IV-B and *** gene sequencing and bioinformatics analysis tools,including STRING,GeneMANIA,Metascape,TRRUST,Sangerbox,cBioPortal and GSCA,were used to analyze the biological functions and features of mutated genes in gallbladder *** mutations(APC,ARID2,IFNA6,KEAP1,RB1,SMAD4,TP53,BTK,GATA1,GNAS,and PRDM3)were identified,and the tumor mutation burden was determined to be 9.52 muts/Mb via targeted gene sequencing.A protein-protein interaction network showed significant interactions among the twelve mutated *** Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to assess mutation functions and *** results revealed 40 tumor-related pathways.A key regulatory factor for gallbladder NEC-related genes was identified,and its biological functions and features were compared with those of gallbladder *** Gallbladder NEC requires standardized *** with other gallbladder carcinomas revealed clinical phenotypes,molecular alterations,functional characteristics,and enriched pathways.

关键词： Gallbladder neuroendocrine carcinoma Targeted-gene sequencing bioinformatics analysis case report Immunocytochemistry Case report

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Identification of ITGA3 as an Oncogene in Human Tongue Cancer via Integrated bioinformatics analysis

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Current Medical Science 2018年第4期38卷 714-720页

作者： Wan-li CHEN Xiao-kang WANG Wei WU Department of Oral and Maxillofacial Surgery State Key Laboratory of Military Stomatology School of Stomatologythe Fourth Military Medical University Xi 'an 710032 China Key Laboratory of Cancer Prevention and Therapy National Clinical Research Center for Cancer Tianjin Medical University Cancer Institute and Hospital Tianjin 300060 China

Human tongue cancer （TC） is an aggressive malignancy with a very poor prognosis. There is an urgent need to elucidate the underlying molecular mechanisms involved in TC progression, mRNA expression profiles play a vital role in the exploration of cancer-related genes. Therefore, the purpose of our study was to identify the progression associated candidate genes of TC by bioinformatics analysis. Five microarray datasets of TC samples were downloaded from the Gene Expression Onmibus （GEO） database and the data of 133 TC patients were screened from The Cancer Genome Atlas （TCGA） head and neck squamous cell carcinoma （HNSC） database. The integrated analysis of five microarray datasets and the RNA sequencing data of TC samples in TCGA-HNSC was performed to obtain 1023 overlapping differentially expressed genes （DEGs） in TC and adjacent normal tissue （ANT） samples. Next, Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway analysis was conducted to enrich the significant pathways of the 1023 DEGs and PI3K- Akt signaling pathway （P=0.011） was selected to be the candidate pathway. A total of 23 DEGs with ｜log2 fold change （FC）｜ ≥1.0 in phosphatidylinositol 3-kinase-serine/threonine kinase （PI3K-Akt） signaling pathway were subjected to survival analysis of 125 eligible TC samples in TCGA database, indicating increased integrin-α3 gene （ITGA3） expression was significantly associated with poorer prognosis. Taken together, our study suggested ITGA3 may facilitate the development of TC via activating PI3K-Akt signaling pathway.

关键词： integrin-α3 gene tongue cancer Gene Expression Omnibus database The Cancer Genome Atlas bioinformatics analysis

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Identification of key pathways and gene expression in the activation of mast cells via calcium flux using bioinformatics analysis

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BIOCELL 2021年第2期45卷 395-415页

作者： XIAOYU WANG TAKESHI YAMAMOTO MAKOTO KADOWAKI YIFU YANG Laboratory of Immunology and Virology Experiment Center for Science and TechnologyShanghai University of Traditional Chinese MedicineShanghai201203China Division of Gastrointestinal Pathophysiology Institute of Natural MedicineUniversity of ToyamaToyama9300194Japan

Mast cells are the main effector cells in IgE-associated allergic disorders,and we have reported that mucosal mast cells(MMCs)play a more important role in the development of food allergy(FA).IgE with antigen or calcium ionophore stimulation can lead to the activation of MMCs via a calcium-dependent *** purpose of the present study was to identify gene signatures with IgE/antigen(dinitrophenyl-bovine serum albumin,DNP-BSA)or calcium ionophore(A23187)on the activation of *** expressed genes between the two types of samples were identified with microarray *** ontology functional and pathway enrichment analyses of differentially expressed genes were performed using the database for annotation,visualization,and integrated discovery *** results showed that IgE/antigen and A23187 could induce degranulation,increase vacuoles,and elevate the cytosolic calcium concentration in ***,GeneChip analysis showed that the same 134 mRNAs were altered with IgE/DNP-BSA and A23187,suggesting that DNP-BSA/IgE and A23187 affect the same signal pathway partly in *** analysis showed that the data were enriched in NF-κB,TNF,MAPK,transcription factor activity,DNA binding,and nucleic acid binding,suggesting that activation of MMCs is a complex *** results provide new insights on MMCs activation.

关键词： Mucosal mast cell Antigen Calcium ion bioinformatics analysis

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Prognostic role of expression of angiogenesis markers in hepatocellular carcinoma:A bioinformatics analysis

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World Journal of Gastroenterology 2022年第30期28卷 4221-4226页

作者： Yan-Dong Miao Xiao-Long Tang Jiang-Tao Wang Deng-Hai Mi The First Clinical Medical College Lanzhou UniversityLanzhou 730000Gansu ProvinceChina Yantai Affiliated Hospital of Binzhou Medical University The Second Clinical Medical College of Binzhou Medical UniversityYantai 264000Shandong ProvinceChina Dean’s Office Gansu Academy of Traditional Chinese MedicineLanzhou 730000Gansu ProvinceChina

The expression of angiopoietin(ANGPT)1,ANGPT2,vascular endothelial growth factor(VEGF)A,VEGFB,VEGFC,VEGFD,and placental growth factor(PGF)is significantly higher in tumor tissues than in normal tissues in both unpaired and paired hepatocellular carcinoma(HCC)***2,VEGFB,VEGFC,and PGF are primarily involved in regulating the activation of the epithelialmesenchymal transition pathway;ANGPT1 is primarily involved in regulating the activation of the RAS/mitogen-activated protein kinase and receptor tyrosine kinase(RTK)pathways;VEGFA is engaged in regulating the RTK activation pathway;and VEGFD is mainly involved in regulating the activation of the tuberous sclerosis protein/mammalian target of rapamycin *** is a significant difference in overall survival between HCC patients with high and low expression of ANGPT2,PGF,VEGFA,and *** free survival(DFS)is significantly shorter in HCC patients with high ANGPT2,PGF,and VEGFA expression than in those with low ANGPT2,PGF,and VEGFA expression.

关键词： Hepatocellular carcinoma Angiogenesis Marker bioinformatics analysis Pathway

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Transcriptomic and bioinformatics analysis of the mechanism by which erythropoietin promotes recovery from traumatic brain injury in mice

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Neural Regeneration Research 2024年第1期19卷 171-179页

作者： Weilin Tan Jun Ma Jiayuanyuan Fu Biying Wu Ziyu Zhu Xuekang Huang Mengran Du Chenrui Wu Ehab Balawi Qiang Zhou Jie Zhang Zhengbu Liao Department of Neurosurgery The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina

Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain ***,the precise mechanism of action remains unclea *** this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive *** sequencing detected a total of 4065 differentially expressed RNAs,including 1059 mRNAs,92 microRNAs,799 long non-coding RNAs,and 2115circular *** Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding RNAs that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK *** competing endogenous RNA networks showed that regulatory relationship between the differentially expressed non-coding RNAs and *** the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was ***6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro *** findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway.

关键词： axon guidance bioinformatics analysis competing endogenous RNA erythropoietin Gene Ontology Kyoto Encyclopedia of Genes and Genomes non-coding RNA RNA sequencing transcriptomics traumatic brain injury

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bioinformatics analysis of the Relationship between Dilated Cardiomyopathy and Chronic Heart Failure

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Journal of Biosciences and Medicines 2024年第8期12卷 333-346页

作者： Lanqing Yu Haidong Zhou Bailu Deng Jiaochang Wei Mei Zhang Chongyao Xu Guiyun Wei Junxiu Zhou Jun Huang Qi Lu Shaowu Ye Graduate School Youjiang Medical University for Nationalities Baise China Clinical Medical College Affiliated Hospital of Youjiang Medical University for Nationalities Baise China Department of Internal Medicine The Peoples Hospital of Wuzhou Wuzhou China Pharmaceutical College Guangxi Medical University Nanning China Department of Pharmacy Guangxi Zhuang Autonomous Region Maternal and Child Health Hospital Nanning China Department of Pharmacy Baise Maternal and Child Hospital Baise China Orthopedic Trauma Napo Peoples Hospital Baise China Department of Internal Medicine Wuzhou Gongren Hospital Wuzhou China

Objective: To screen and analyze the differentially expressed genes between dilated cardiomyopathy (DCM) and chronic heart failure (CHF) based on bioinformatics methods. Methods: The Gene Expression Omnibus (GEO) database was used for data retrieval, and the chip data GSE3585 was downloaded, which was the original data of DCM and normal control group. At the same time, the chip data GSE76701 was downloaded, which was the original data of CHF and control group. Differentially expressed mRNAs (DEmRNAs) were screened by R language limma package, the data were standardized, and the common differentially expressed genes were screened. GO function and KEGG pathway enrichment analysis were performed on the common differentially expressed genes. String11.0 online tool was used for data analysis to obtain differentially expressed genes, and the results were imported into Cytoscape 3.9.1 software. The results were imported into Cytoscape 3.9.1 software, and the common expression gene module was obtained by MOCDE algorithm. Nine Hub genes were obtained by 10 algorithms such as MCC. Results: A total of 248 differentially expressed genes were screened. GO analysis showed that differentially expressed genes were mainly concentrated in 9 different physiological and pathological processes. KEGG analysis showed that the main signaling pathways involved in differentially expressed genes were 2, and 9 key differentially expressed genes were predicted: NPPB, NPPA, MYH6, FRZB, ASPN, SFRP4, RPS4Y1, DDX3Y. Conclusion: This study preliminarily explored the molecular mechanism of DCM and CHF, and obtained the common differentially expressed genes of the two diseases. Further experimental studies are needed to verify the correlation between gene expression and clinicopathological features. Provide new ideas for clinical drug treatment research.

关键词： Dilated Cardiomyopathy Chronic Heart Failure bioinformatics analysis Differentially Expressed Genes

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Identification of survival-associated biomarkers based on three datasets by bioinformatics analysis in gastric cancer

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World Journal of Clinical Cases 2023年第20期11卷 4763-4787页

作者： Long-Kuan Yin Hua-Yan Yuan Jian-Jun Liu Xiu-Lian Xu Wei Wang Xiang-Yu Bai Pan Wang Department of Gastrointestinal Surgery Affiliated Hospital of North Sichuan Medical CollegeNanchong 637000Sichuan ProvinceChina Sichuan Key Laboratory of Medical Imaging North Sichuan Medical CollegeNanchong 637000Sichuan ProvinceChina

BACKGROUND Gastric cancer(GC)is one of the most common malignant tumors with poor prognosis in terms of advanced ***,the survival-associated biomarkers for GC remains *** To investigate the potential biomarkers of the prognosis of patients with GC,so as to provide new methods and strategies for the treatment of *** RNA sequencing data from The Cancer Genome Atlas(TCGA)database of STAD tumors,and microarray data from Gene Expression Omnibus(GEO)database(GSE19826,GSE79973 and GSE29998)were *** differentially expressed genes(DEGs)between GC patients and health people were picked out using R software(x644.1.3).The intersections were underwent between the above obtained co-expression of differential genes(co-DEGs)and the DEGs of GC from Gene Expression Profiling Interactive analysis database,and Gene Ontology(GO)analysis,Kyoto Encyclopedia of Gene and Genome(KEGG)pathway analysis,Gene Set Enrichment analysis(GSEA),Protein-protein Interaction(PPI)analysis and Kaplan-Meier Plotter survival analysis were performed on these *** Immunohistochemistry(IHC)database of Human Protein Atlas(HPA),we verified the candidate Hub *** With DEGs analysis,there were 334 co-DEGs,including 133 up-regulated genes and 201 down-regulated *** enrichment analysis showed that the co-DEGs were involved in biological process,cell composition and molecular function *** enrichment analysis suggested the co-DEGs pathways were mainly enriched in ECM-receptor interaction,protein digestion and absorption pathways,*** pathway analysis showed that co-DEGs mainly concentrated in cell cycle progression,mitotic cell cycle and cell cycle pathways,*** analysis showed 84 nodes and 654 edges for the *** survival analysis illustrated 11 Hub genes with notable significance for prognosis of patients were ***,using IHC database of HPA,we confirmed the above candidate Hub genes,and 10 Hub genes that associated with prognos

关键词： Gastric cancer Survival-associated biomarkers bioinformatics analysis Hub genes

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Identification of key genes involved in post-traumatic stress disorder:Evidence from bioinformatics analysis

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World Journal of Psychiatry 2020年第12期10卷 286-298页

作者： Yao-Yao Bian Li-Li Yang Bin Zhang Wen Li Zheng-Jun Li Wen-Lin Li Li Zeng School of Nursing Nanjing University of Chinese MedicineNanjing 210023Jiangsu ProvinceChina School of First Clinical Medicine Nanjing University of Chinese MedicineNanjing 210023Jiangsu ProvinceChina Jingwen Library Nanjing University of Chinese MedicineNanjing 210023Jiangsu ProvinceChina Digestive Department Ningbo Hospital of Traditional Chinese MedicineNingbo 315200Zhejiang ProvinceChina School of Preclinical Medicine Guizhou University of Traditional Chinese MedicineGuiyang 550025Guizhou ProvinceChina Management School University of St AndrewsSt Andrews KY169AJUnited Kingdom College of Health Economics Management Nanjing University of Chinese MedicineNanjing 210023Jiangsu ProvinceChina

BACKGROUND Post-traumatic stress disorder(PTSD)is a serious stress-related *** To identify the key genes and pathways to uncover the potential mechanisms of PTSD using bioinformatics *** Gene expression profiles were obtained from the Gene Expression Omnibus *** differentially expressed genes(DEGs)were identified by using *** functional annotation and pathway enrichment were then *** gene-pathway network was constructed with Cytoscape *** real-time polymerase chain reaction(qRT-PCR)analysis was applied for validation,and text mining by Coremine Medical was used to confirm the connections among genes and *** We identified 973 DEGs including 358 upregulated genes and 615 downregulated genes in PTSD.A group of centrality hub genes and significantly enriched pathways(MAPK,Ras,and ErbB signaling pathways)were identified by using gene functional assignment and enrichment *** genes(KRAS,EGFR,NFKB1,FGF12,PRKCA,and RAF1)were selected to validate using *** results of text mining further confirmed the correlation among hub genes and the enriched *** indicated that these altered genes displayed functional roles in PTSD via these pathways,which might serve as key signatures in the pathogenesis of *** The current study identified a panel of candidate genes and important pathways,which might help us deepen our understanding of the underlying mechanism of PTSD at the molecular ***,further studies are warranted to discover the critical regulatory mechanism of these genes via relevant pathways in PTSD.

关键词： Post-traumatic stress disorder Differentially expressed genes Key pathway Gene-pathway co-expression bioinformatics analysis Microarray

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