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Matos TL, Souza PFN, de Moraes MEA, Rabenhorst SHB, Mesquita FP, Montenegro RC. Molecular characterization and biomarker discovery in gastric cancer progression through transcriptome meta-analysis. Comput Biol Med 2024; 183:109276. [PMID: 39447404 DOI: 10.1016/j.compbiomed.2024.109276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 09/26/2024] [Accepted: 10/14/2024] [Indexed: 10/26/2024]
Abstract
Gastric cancer (GC) is a leading cause of cancer-related deaths globally. It is a multifactorial, molecularly heterogeneous disease whose carcinogenic patterns are not yet well established, requiring the development of new tools for better understanding and identifying gastric carcinogenesis. From this point of view, this study aims to compare transcriptome profiles from The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD) and a human-merged dataset to identify potential biomarkers and therapeutic targets. Principal component analysis (PCA) revealed shared and distinct gene expression patterns between datasets. Differential expression analysis identified key genes with altered expression across non-malignant and malignant samples. Six genes, including SERPINE1 and CLDN9, were significantly associated with patient survival. The findings underscore the molecular diversity of GC and highlight novel biomarkers for early diagnosis and therapeutic strategies. Further validation in clinical specimens is necessary.
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Affiliation(s)
- Thiago Loreto Matos
- Pharmacogenetics Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, 60430-160, Brazil
| | - Pedro Filho Noronha Souza
- Pharmacogenetics Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, 60430-160, Brazil
| | - Maria Elisabete Amaral de Moraes
- Pharmacogenetics Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, 60430-160, Brazil
| | - Silvia Helena Barem Rabenhorst
- Molecular Genetics Laboratory, Department of Pathology and Legal Medicine, Federal University of Ceará, Fortaleza, 60430-160, Brazil
| | - Felipe Pantoja Mesquita
- Pharmacogenetics Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, 60430-160, Brazil.
| | - Raquel Carvalho Montenegro
- Pharmacogenetics Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, 60430-160, Brazil
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Akhtar A, Hameed Y, Ejaz S, Abdullah I. Identification of gastric cancer biomarkers through in-silico analysis of microarray based datasets. Biochem Biophys Rep 2024; 40:101880. [PMID: 39655267 PMCID: PMC11626535 DOI: 10.1016/j.bbrep.2024.101880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2024] [Revised: 11/02/2024] [Accepted: 11/18/2024] [Indexed: 12/12/2024] Open
Abstract
Gastric cancer is among the most prevalent cancers worldwide including in Pakistan. Late diagnosis of gastric cancer leads to reduced survival. The present study aimed to investigate biomarkers for early diagnosis and prognosis of gastric cancer. For this purpose, the ten microarray-based gene expression datasets (GSE54129, GSE79973, GSE161533, GSE103236, GSE33651, GSE19826, GSE118916, GSE112369, GSE13911, and GSE81948) were retrieved from GEO database and analyzed by GEO2R to identify differentially expressed genes. Datasets were arranged in subsets of different dataset combinations to identify common DEGs. The gene ontology and functional pathway enrichment analysis of common DEGs was performed by DAVID tool. Pan-cancer analysis was conducted by UALCAN database. Survival analysis of common DEGs was done by Kaplan-Meier plotter. A total of 71 common DEGs were identified in different combinations of datasets. Among them, only 5 DEGs namely ATP4B, ATP4A, CCKBR, KCNJ15, and KCNJ16 were detected to be common in all the datasets. The GO and pathway analysis represented that the identified DEGs are involved in gastric acid secretion and collecting duct acid secretion pathways. Further expression validation of these five genes using three additional datasets (GSE31811, GSE26899, and GSE26272) confirmed their differential expression in gastric cancer samples. The pan-cancer analysis also revealed aberrant expression of DEGs in various cancers. The survival analysis showed the association of these 5 DEGs with poor survival of gastric cancer patients. To conclude, this study revealed a panel of 5 genes, which can be employed as diagnostic and prognostic biomarkers of gastric cancer patients.
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Affiliation(s)
- Arbaz Akhtar
- Department of Biochemistry & Molecular Biology, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, (63100), Pakistan
| | - Yasir Hameed
- Department of Biotechnology & Molecular Biology, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, (63100), Pakistan
| | - Samina Ejaz
- Department of Biochemistry & Molecular Biology, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, (63100), Pakistan
| | - Iqra Abdullah
- Department of Biochemistry & Molecular Biology, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, (63100), Pakistan
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Zhan Z, Lin K, Wang T. Construction of oxidative phosphorylation-related prognostic risk score model in uveal melanoma. BMC Ophthalmol 2024; 24:204. [PMID: 38698303 PMCID: PMC11067154 DOI: 10.1186/s12886-024-03441-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/09/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Uveal melanoma (UVM) is a malignant intraocular tumor in adults. Targeting genes related to oxidative phosphorylation (OXPHOS) may play a role in anti-tumor therapy. However, the clinical significance of oxidative phosphorylation in UVM is unclear. METHOD The 134 OXPHOS-related genes were obtained from the KEGG pathway, the TCGA UVM dataset contained 80 samples, served as the training set, while GSE22138 and GSE39717 was used as the validation set. LASSO regression was carried out to identify OXPHOS-related prognostic genes. The coefficients obtained from Cox multivariate regression analysis were used to calculate a risk score, which facilitated the construction of a prognostic model. Kaplan-Meier survival analysis, logrank test and ROC curve using the time "timeROC" package were conducted. The immune cell frequency in low- and high-risk group was analyzed through Cibersort tool. The specific genomic alterations were analyzed by "maftools" R package. The differential expressed genes between low- or high-risk group were analyzed and performed Gene Ontology (GO) and GSEA. Finally, we verified the function of CYC1 in UVM by gene silencing in vitro. RESULTS A total of 9 OXPHOS-related prognostic genes were identified, including NDUFB1, NDUFB8, ATP12A, NDUFA3, CYC1, COX6B1, ATP6V1G2, ATP4B and NDUFB4. The UVM prognostic risk model was constructed based on the 9 OXPHOS-related prognostic genes. The prognosis of patients in the high-risk group was poorer than low-risk group. Besides, the ROC curve demonstrated that the area under the curve of the model for predicting the 1 to 5-year survival rate of UVM patients were all more than 0.88. External validation in GSE22138 and GSE39717 dataset revealed that these 9 genes could also be utilized to evaluate and predict the overall survival of patients with UVM. The risk score levels related to immune cell frequency and specific genomic alterations. The DEGs between the low- and high- risk group were enriched in tumor OXPHOS and immune related pathway. In vitro experiments, CYC1 silencing significantly inhibited UVM cell proliferation and invasion, induced cell apoptosis. CONCLUSION In sum, a prognostic risk score model based on oxidative phosphorylation-related genes in UVM was developed to enhance understanding of the disease. This prognostic risk score model may help to find potential therapeutic targets for UVM patients. CYC1 acts as an oncogene role in UVM.
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Affiliation(s)
- Zhiyun Zhan
- Ophthalmology Department, First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang District, 350004, Fuzhou, Fujian, China
| | - Kun Lin
- Department of Neurosurgery, Shengli Clinical Medical College of Fujian Medical University, 516 Jinrong South Road, 350001, Fuzhou, China
| | - Tingting Wang
- Ophthalmology Department, First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang District, 350004, Fuzhou, Fujian, China.
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Lamare FA, Khongsti S, Marthong L, Ghosh S, Chenkual S, Dkhar H, Maitra A, Ghosh S. Genome-wide DNA methylation profiling of stomach cancer in the ethnic population of Mizoram, North East India. Genomics 2022; 114:110478. [PMID: 36064073 DOI: 10.1016/j.ygeno.2022.110478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/10/2022] [Accepted: 08/31/2022] [Indexed: 12/01/2022]
Abstract
Stomach cancer is the fifth most common cancer in terms of prevalence and incidence and the fourth leading cause of mortality in men and women worldwide. It is well-established that aberrant DNA methylation in cells can lead to carcinogenesis. The primary objective of our study was to investigate the aberrant DNA methylation status of genes associated with stomach cancer with a particular reference to the ethnic population of Mizoram, North East India. The site-level analysis identified 2883 CpG sites differentially methylated, representing ~922 genes. Out of which 476 Differentially Methylated Positions (DMPs) were promoter-associated, 452 DMPs were hypermethylated, and 24 were hypomethylated. The region-level analysis identified 462 Differentially Methylated Regions (DMRs) corresponding to ~320 genes, of which ~281 genes were hypermethylated and ~ 40 genes were hypomethylated. TCGA analysis showed that some of the genes had been previously implicated in other cancers including stomach cancer. Five hypermethylated genes were selected as candidate genes for further investigations and they have shown to be novel and could serve as candidate hypermethylation biomarkers for stomach cancer in this particular ethnic group.
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Affiliation(s)
- F A Lamare
- Department of Zoology, North-Eastern Hill University (NEHU), Shillong, India
| | - S Khongsti
- Department of Zoology, North-Eastern Hill University (NEHU), Shillong, India
| | - L Marthong
- Department of Zoology, North-Eastern Hill University (NEHU), Shillong, India
| | - S Ghosh
- National Institute of Biomedical Genomics (NIBMG), Kalyani, West Bengal, India
| | | | - H Dkhar
- Nazareth Hospital, Shillong, India
| | - A Maitra
- National Institute of Biomedical Genomics (NIBMG), Kalyani, West Bengal, India
| | - S Ghosh
- Department of Zoology, North-Eastern Hill University (NEHU), Shillong, India.
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Sarma RJ, Subbarayan S, Zohmingthanga J, Chenkual S, Zomuana T, Lalruatfela ST, Pautu JL, Maitra A, Kumar NS. Transcriptome analysis reveals SALL4 as a prognostic key gene in gastric adenocarcinoma. J Egypt Natl Canc Inst 2022; 34:11. [PMID: 35284980 DOI: 10.1186/s43046-022-00108-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stomach adenocarcinoma (STAD) dominates 80-90% of gastric cancer (GC). Over the years, it has been realized that the identification of the genes responsible for gastric carcinogenesis is essential to understand the biomarker discovery. METHODS This study aims to identify candidate genes for biomarker discovery in STAD. RNA-Seq was performed on three paired tumor-normal and one unpaired tumor samples from four GC patients and investigated for differentially expressed genes (DEGs) using DESeq2. Gene set enrichment analysis were performed. The DEGs were compared with two STAD microarray datasets available on Gene Expression Omnibus (GEO) database. Survival study (OS) were performed using KM-Plotter on the common genes between all the datasets. RESULTS Totally, 148 DEGs were identified, wherein 55 genes were upregulated and 93 genes were downregulated with |log2foldchange| > 1 and Benjamini-Hochberg (BH) Adjusted P value < 0.01. Cell adhesion molecule (CAM) Pathway was found to be the most significant among the upregulated genes. Gastric acid secretion and mineral absorption pathways were the most significant pathways among the downregulated genes. Comparison with two GEO datasets followed by OS analysis revealed two upregulating genes, APOC1 and SALL4 with prognostic significance. CONCLUSION Upregulation of APOC1 is associated with marginal overall survival (OS) and SALL4 over-expression was associated with the poor OS using KM-Plotter during 5 years data period. Our study suggests that SALL4 could be a promising biomarker candidate in STAD.
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Affiliation(s)
- Ranjan Jyoti Sarma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796 004, India
| | | | | | - Saia Chenkual
- Department of Surgery, Civil Hospital Aizawl, Aizawl, Mizoram, 796 001, India
| | - Thomas Zomuana
- Department of Surgery, Civil Hospital Aizawl, Aizawl, Mizoram, 796 001, India
| | | | - Jeremy L Pautu
- Department of Medical Oncology, Mizoram State Cancer Institute, Aizawl, Mizoram, 796017, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics, Kalyani, West Bengal, 741251, India.
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Guo Z, Chen M, Fan Y, Song Y. A general adaptive ridge regression method for generalized linear models: an iterative re-weighting approach. COMMUN STAT-THEOR M 2022. [DOI: 10.1080/03610926.2022.2028841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Zijun Guo
- College of Science, University of Shanghai for Science and Technology, Shanghai, China
| | - Mengxing Chen
- College of Science, University of Shanghai for Science and Technology, Shanghai, China
| | - Yali Fan
- College of Science, University of Shanghai for Science and Technology, Shanghai, China
| | - Yan Song
- Department of Control Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
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Construction of miRNA-mRNA-TF Regulatory Network for Diagnosis of Gastric Cancer. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9121478. [PMID: 34840985 PMCID: PMC8616677 DOI: 10.1155/2021/9121478] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/27/2021] [Indexed: 12/30/2022]
Abstract
Gastric cancer (GC), as an epidemic cancer worldwide, has more than 1 million new cases and an estimated 769,000 deaths worldwide in 2020, ranking fifth and fourth in global morbidity and mortality. In mammals, both miRNAs and transcription factors (TFs) play a partial role in gene expression regulation. The mRNA expression profile and miRNA expression profile of GEO database were screened by GEO2R for differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs). Then, DAVID annotated the functions of DEGs to understand the functions played in biological processes. The prediction of potential target genes of miRNA and key TFs of mRNA was performed by mipathDB V2.0 and CHEA3, respectively, and the gene list comparison was performed to look for overlapping genes coregulated by key TFs and DEMs. Finally, the obtained miRNAs, TF, and overlapping genes were used to construct the miRNA-mRNA-TF regulatory network, which was verified by RT-qPCR. 76 upregulated DEGs, 199 downregulated DEGs, and 3 upregulated miRNAs (miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p) were identified from the expression profiles of mRNA (GSE26899, GSE29998, GSE51575, and GSE13911) and miRNA (GSE93415), respectively. Through database prediction and gene list comparison, it was found that among the 199 downregulated DEGs, 61, 71, and 69 genes were the potential targets of miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p, respectively. 199 downregulated DEGs were used as the gene list for the prediction of key TFs, and the results showed that RFX6 ranked the highest. The potential target overlap genes of miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p were 4 genes (SH3GL2, ATP4B, CTSE, and SORBS2), 7 genes (SLC7A8, RNASE4, ESRRG, PGC, MUC6, Fam3B, and FMO5), and 6 genes (CHGA, PDK4, TMPRSS2, CLIC6, GPX3, and PSCA), respectively. Finally, we constructed a miRNA-mRNA-TF regulatory network based on the above 17 mRNAs, 3 miRNAs, and 1 TF and verified by RT-qPCR and western blot results that the expression of RFX6 was downregulated in GC tissues. These identified miRNAs, mRNAs, and TF have a certain reference value for further exploration of the regulatory mechanism of GC.
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Proteomic Signatures of Diffuse and Intestinal Subtypes of Gastric Cancer. Cancers (Basel) 2021; 13:cancers13235930. [PMID: 34885041 PMCID: PMC8656738 DOI: 10.3390/cancers13235930] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer is a leading cause of death from cancer globally. Gastric cancer is classified into intestinal, diffuse and indeterminate subtypes based on histology according to the Laurén classification. The intestinal and diffuse subtypes, although different in histology, demographics and outcomes, are still treated in the same fashion. This study was designed to discover proteomic signatures of diffuse and intestinal subtypes. Mass spectrometry-based proteomics using tandem mass tags (TMT)-based multiplexed analysis was used to identify proteins in tumor tissues from patients with diffuse or intestinal gastric cancer with adjacent normal tissue control. A total of 7448 or 4846 proteins were identified from intestinal or diffuse subtype, respectively. This quantitative mass spectrometric analysis defined a proteomic signature of differential expression across the two subtypes, which included gremlin1 (GREM1), bcl-2-associated athanogene 2 (BAG2), olfactomedin 4 (OLFM4), thyroid hormone receptor interacting protein 6 (TRIP6) and melanoma-associated antigen 9 (MAGE-A9) proteins. Although GREM1, BAG2, OLFM4, TRIP6 and MAGE-A9 have all been previously implicated in tumor progression and metastasis, they have not been linked to intestinal or diffuse subtypes of gastric cancer. Using immunohistochemical labelling of a tissue microarray comprising of 124 cases of gastric cancer, we validated the proteomic signature obtained by mass spectrometry in the discovery cohort. Our findings should help investigate the pathogenesis of these gastric cancer subtypes and potentially lead to strategies for early diagnosis and treatment.
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Xu Y, Wang N, Liu R, Lv H, Li Z, Zhang F, Gai C, Tian Z. Epigenetic Study of Esophageal Carcinoma Based on Methylation, Gene Integration and Weighted Correlation Network Analysis. Onco Targets Ther 2021; 14:3133-3149. [PMID: 34012270 PMCID: PMC8128498 DOI: 10.2147/ott.s298620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/13/2021] [Indexed: 12/16/2022] Open
Abstract
Purpose Esophageal carcinoma is a common and highly metastatic malignant tumor of the digestive tract. The aim of the present study was to identify potential molecular markers of esophageal carcinoma that may help its diagnosis and treatment. Materials and Methods First, mRNA and DNA methylation data were downloaded from The Cancer Genome Atlas (TCGA) database for the identification of differentially expressed genes (DEGs) and DNA methylation analysis. Secondly, Weighted Gene Co-Expression Network Analysis (WGCNA) was used to identify important modules and hub genes. In addition, correlation analysis between DNA methylation genes and DEGs was performed. Thirdly, the GSE45670 dataset was used to validate the expression of the diagnostic and survival ability analysis of genes in TCGA data. Finally, reverse transcription-quantitative PCR and immunohistochemical analysis of genes were performed. Results A total of 2408 DEGs and 5134 differentially methylated sites were obtained. In the WGCNA analysis, the royal blue module was found to be the optimal module. In addition, hub genes in the module, including ESRRG, MFSD4, CCKBR, ATP4B, ESRRB, ATP4A, CCKAR and B3GAT1, were also differentially methylated genes and DEGs. It was found that CCKAR, MFSD4 and ESRRG may be diagnostic gene biomarkers for esophageal carcinoma. In addition, the high expression of MFSD4 was significantly correlated with patient survival. Immunohistochemistry analysis results showed that the gene expression levels of ATP4B, B3GAT1, CCKBR and ESRRG were decreased in esophageal carcinoma tissues, which was in line with the bioinformatics results. Conclusion Therefore, these identified molecular markers may be helpful in the diagnosis and treatment of esophageal carcinoma.
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Affiliation(s)
| | - Na Wang
- Department of Cancer Institute
| | - Rongfeng Liu
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, People's Republic of China
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Liu H, Qu Y, Zhou H, Zheng Z, Zhao J, Zhang J. Bioinformatic analysis of potential hub genes in gastric adenocarcinoma. Sci Prog 2021; 104:368504211004260. [PMID: 33788653 PMCID: PMC10454997 DOI: 10.1177/00368504211004260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gastric adenocarcinoma is the most common histologic type of gastric cancer; however, the pathogenic mechanisms remain unclear. To improve mechanistic understanding and identify new treatment targets or diagnostic biomarkers, we used bioinformatic tools to predict the hub genes related to the process of gastric adenocarcinoma development from public datasets, and explored their prognostic significance. We screened differentially expressed genes between gastric adenocarcinoma and normal gastric tissues in Gene Expression Omnibus datasets (GSE79973, GSE118916, and GSE29998) using the GEO2R tool, and their functions were annotated with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes signaling pathway enrichment analyses in the DAVID database. Hub genes were identified based on the protein-protein network constructed in the STRING database with Cytoscape software. A total of 10 hub genes were selected for further analysis, and their expression patterns in gastric adenocarcinoma patients were investigated using the Oncomine GEPIA database. The expression levels of ATP4A, CA9, FGA, ALDH1A1, and GHRL were reduced, whereas those of TIMP1, SPP1, CXCL8, THY1, and COL1A1 were increased in gastric adenocarcinoma. The Kaplan-Meier online plotter tool showed associations of all hub genes except for CA9 with prognosis in gastric adenocarcinoma patients; CXCL8 and ALDH1A1 were positively correlated with survival, and the other genes were negatively correlated with survival. These 10 hub genes may be involved in important processes in gastric adenocarcinoma development, providing new directions for research to clarify the role of these genes and offer insight for improved treatment.
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Affiliation(s)
- Hao Liu
- General Surgery Department, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yidan Qu
- Rheumatology and Immunology Department, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Hao Zhou
- General Surgery Department, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Ziwen Zheng
- General Surgery Department, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Junjiang Zhao
- General Surgery Department, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jian Zhang
- General Surgery Department, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
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Huang ZB, Zhang HT, Yu B, Yu DH. Cell-free DNA as a liquid biopsy for early detection of gastric cancer. Oncol Lett 2021; 21:3. [PMID: 33240409 PMCID: PMC7681206 DOI: 10.3892/ol.2020.12264] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/17/2020] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) is one of the most common malignant tumors with poor prognosis worldwide, mainly due to the lack of suitable modalities for population-based screening and early detection of this disease. Therefore, novel and less invasive tests with improved clinical utility are urgently required. The remarkable advances in genomics and proteomics, along with emerging new technologies for highly sensitive detection of genetic alterations, have shown the potential to map the genomic makeup of a tumor in liquid biopsies, in order to assist with early detection and clinical management. The present review summarize the current status in the identification and development of cell-free DNA (cfDNA)-based biomarkers in GC, and also discusses their potential utility and the technical challenges in developing practical cfDNA-based liquid biopsy for early detection of GC.
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Affiliation(s)
- Zheng-Bin Huang
- Department of Surgery, Hanchuan Renmin Hospital, Hanchuan, Hubei 431600, P.R. China
| | - Hai-Tao Zhang
- Department of Gastrointestinal Surgery, The Second People's Hospital of Shenzhen, Shenzhen, Guangdong 518037, P.R. China
| | - Benjamin Yu
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - De-Hua Yu
- Shenzhen USK Bioscience Co., Ltd., Shenzhen, Guangdong 518110, P.R. China
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Zhu J, Deng L, Chen B, Huang W, Lin X, Chen G, Tzeng CM, Ying M, Lu Z. Magnesium-dependent Phosphatase (MDP) 1 is a Potential Suppressor of Gastric Cancer. Curr Cancer Drug Targets 2020; 19:817-827. [PMID: 31218958 DOI: 10.2174/1568009619666190620112546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/19/2019] [Accepted: 04/15/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Recurrence is the leading cause of treatment failure and death in patients with gastric cancer (GC). However, the mechanism underlying GC recurrence remains unclear, and prognostic markers are still lacking. METHODS We analyzed DNA methylation profiles in gastric cancer cases with shorter survival (<1 year) or longer survival (> 3 years), and identified candidate genes associated with GC recurrence. Then, the biological effects of these genes on gastric cancer were studied. RESULTS A novel gene, magnesium-dependent phosphatase 1 (mdp1), was identified as a candidate gene whose DNA methylation was higher in GC samples from patients with shorter survival and lower in patients with longer survival. MDP1 protein was highly expressed in GC tissues with longer survival time, and also had a tendency to be expressed in highly differentiated GC samples. Forced expression of MDP1 in GC cell line BGC-823 inhibited cell proliferation, whereas the knockdown of MDP1 protein promoted cell growth. Overexpression of MDP1 in BGC-823 cells also enhanced cell senescence and apoptosis. Cytoplasmic kinase protein c-Jun N-terminal kinase (JNK) and signal transducer and activator of transcription 3 (Stat3) were found to mediate the biological function of MDP1. CONCLUSION These results suggest that MDP1 protein suppresses the survival of gastric cancer cells and loss of MDP expression may benefit the recurrence of gastric cancer.
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Affiliation(s)
- Jianbo Zhu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Lijuan Deng
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Baozhen Chen
- Department of Pathology, Fujian Provincial Tumor Hospital, 420 Fuma Road, Fuzhou, Fujian 350014, China
| | - Wenqing Huang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Xiandong Lin
- Department of Pathology, Fujian Provincial Tumor Hospital, 420 Fuma Road, Fuzhou, Fujian 350014, China
| | - Gang Chen
- Department of Pathology, Fujian Provincial Tumor Hospital, 420 Fuma Road, Fuzhou, Fujian 350014, China
| | - Chi-Meng Tzeng
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361005, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen, Fujian 361005, China
| | - Mingang Ying
- Department of Pathology, Fujian Provincial Tumor Hospital, 420 Fuma Road, Fuzhou, Fujian 350014, China
| | - Zhongxian Lu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361005, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen, Fujian 361005, China
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Identification of an Individualized Prognostic Signature Based on the RWSR Model in Early-Stage Bladder Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9186546. [PMID: 32596394 PMCID: PMC7293744 DOI: 10.1155/2020/9186546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/11/2020] [Indexed: 12/19/2022]
Abstract
Bladder cancer (BLCA) is the fourth common cancer among males in the United States, which is also the fourth leading cause of cancer-related death in old males. BLCA has a high recurrence rate, with over 50% of patients which has at least one recurrence within five years. Due to the complexity of the molecular mechanisms and heterogeneous cancer feature, BLCA clinicians find it hard to make an efficient management decision as they lack reliable assessment of mortality risk. Meanwhile, there is currently no screening suitable prognostic signature or method recommended for early detection, which is significantly important to early-stage detection and prognosis. In this study, a novel model, named the risk-weighted sparse regression (RWSR) model, is constructed to identify a robust signature for patients of early-stage BLCA. The 17-gene signature is generated and then validated as an independent prognostic factor in BLCA cohorts from GSE13507 and TCGA_BLCA datasets. Meanwhile, a risk score model is developed and validated among the 17-gene signature. The risk score is also considered an independent factor for prognosis prediction, which is confirmed through prognosis analysis. The Kaplan-Meier with the log-rank test is used to assess survival difference. Furthermore, the predictive capacity of the signature is proved through stratification analysis. Finally, an effective patient classification is completed by a combination of the 17-gene signature and stage information, which is for better survival prediction and treatment decisions. Besides, 11 genes in the signature, such as coiled-coil domain containing 73 (CCDC73) and protein kinase, DNA-activated, and catalytic subunit (PRKDC), are proved to be prognosis marker genes or strongly associated with prognosis and progress of other types of cancer in published literature already. As a result, this paper would more accurately predict a patient's prognosis and improve surveillance in the clinical setting, which may provide a quantitative and reliable decision-making basis for the treatment plan.
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14
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Cytotoxic potential of Artemisia absinthium extract loaded polymeric nanoparticles against breast cancer cells: Insight into the protein targets. Int J Pharm 2020; 586:119583. [PMID: 32603837 DOI: 10.1016/j.ijpharm.2020.119583] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/18/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
Targeted drug delivery system in the form of herbal based nano-formulations is the new ray of hope for minimizing the side effects related to the anti-cancer drugs as well as conventional drug delivery system. In view of this, the present study was designed to evaluate the cytotoxic potential of A. absinthium extract loaded polymeric nanoparticles (NVA-AA) against the breast cancer cell lines (MCF-7 and MDA MB-231) and to identify the protein targets for the caused cytotoxicity. The polymeric nanoparticles (PNPs) were prepared by free radical mechanism and loaded with the whole plant extract. The cytotoxicity of these NVA-AA were evaluated on the breast cancer cell lines via different cytotoxic parameters viz. MTT assay, CFSE proliferation assay, apoptosis assay, cell cycle study. The protein targets and the interaction among them were identified by nano-LCMS/MS analysis and STRING online tool respectively, which were further validated by qPCR and BLI. The LCMS/MS analysis suggests that the caused cytotoxicity was due to the alteration of proteins involved in vesicular trafficking, apoptosis, proliferation and metastasis. Further, interactome analysis identified UBA52 in MCF-7 and TIAL1, PPP1CC in MDA MB-231 cells as the central molecule in the vesicular trafficking and apoptosis networking connection.
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15
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McCormick CA, Samuels TL, Battle MA, Frolkis T, Blumin JH, Bock JM, Wells C, Yan K, Altman KW, Johnston N. H+/K+ATPase Expression in the Larynx of Laryngopharyngeal Reflux and Laryngeal Cancer Patients. Laryngoscope 2020; 131:130-135. [PMID: 32250454 DOI: 10.1002/lary.28643] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVES The gastric H+/K+ ATPase proton pump has previously been shown to be expressed in the human larynx, however its contribution to laryngopharyngeal reflux (LPR) signs, symptoms and associated diseases such as laryngeal cancer is unknown. Proton pump expression in the larynx of patients with LPR and laryngeal cancer was investigated herein. A human hypopharyngeal cell line expressing the proton pump was generated to investigate its effects. STUDY DESIGN In-vitro translational. METHODS Laryngeal biopsies were obtained from three LPR and eight LSCC patients. ATP4A, ATP4B and HRPT1 were assayed via qPCR. Human hypopharyngeal FaDu cell lines stably expressing proton pump were created using lentiviral transduction and examined via transmission electron microscopy and qPCR for genes associated with inflammation or laryngeal cancer. RESULTS Expression of ATP4A and ATP4B was detected in 3/3 LPR, 4/8 LSCC-tumor and 3/8 LSCC-adjacent specimens. Expression of ATP4A and ATP4B in FaDu elicited mitochondrial damage and expression of IL1B, PTGS2, and TNFA (P < .0001); expression of ATP4B alone did not. CONCLUSIONS Gastric proton pump subunits are expressed in the larynx of LPR and LSCC patients. Mitochondrial damage and changes in gene expression observed in cells expressing the full proton pump, absent in those expressing a single subunit, suggest that acid secretion by functional proton pumps expressed in upper airway mucosa may elicit local cell and molecular changes associated with inflammation and cancer. LEVEL OF EVIDENCE NA Laryngoscope, 131:130-135, 2021.
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Affiliation(s)
- Caroline A McCormick
- Department of Otolaryngology, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Tina L Samuels
- Department of Otolaryngology, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Michele A Battle
- Department of Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Talia Frolkis
- Department of Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Joel H Blumin
- Department of Otolaryngology, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Jonathan M Bock
- Department of Otolaryngology, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Clive Wells
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Ke Yan
- Department of Pediatrics Quantitative Health Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Kenneth W Altman
- Department of Otolaryngology, Geisinger Health System, Danville, California, U.S.A
| | - Nikki Johnston
- Department of Otolaryngology, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A.,Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
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16
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Cao D, Zhao D, Jia Z, Su T, Zhang Y, Wu Y, Wu M, Tsukamoto T, Oshima M, Jiang J, Cao X. Reactivation of Atp4a concomitant with intragenic DNA demethylation for cancer inhibition in a gastric cancer model. Life Sci 2019; 242:117214. [PMID: 31884095 DOI: 10.1016/j.lfs.2019.117214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/15/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022]
Abstract
Accumulating evidence suggests that aberrant DNA methylation and gene silencing of tumor suppressors are pervasive in gastric malignancies, supporting reactivation of tumor suppressors through DNA demethylation as a potential therapeutic opportunity. Atp4a is an important tumor suppressor gene, encoding H+, K+-ATPase, and mediating gastric acid secretion in the stomach. Using transgenic gastric cancer model K19-Wnt1/C2mE (Gan) mice, by combining the transcriptome and MeDIP (methylated DNA immunoprecipitation) sequencing, together with qRT-PCR, we showed that Atp4a was expressed at low levels in tumor tissues and multiple GC cells, while both 5-aza-CdR and 18β-glycyrrhetinic acid (GRA) pharmacological treatment triggered Atp4a activation with downregulation of DNMT1. In addition, CpG island (CGI) search showed that the CpG rich region is absent in the promoter region but present in exons 9-14 of Atp4a. Methylation specific PCR (MSP) indicated that Atp4a was fully or partly methylated in multiple GC cells. Further MassArray suggested that the demethylation in the CpG site 75, 183, 196, 262-268 might be responsible for the reactivation of Atp4a. Our research identified that GRA, a bioactive component found in abundance in Radix Glycyrrhiza, reactivated Atp4a expression and inhibited gastric tumorigenesis as a potential demethylation agent.
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Affiliation(s)
- Donghui Cao
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Dan Zhao
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Zhifang Jia
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Tongrong Su
- Department of Gastric and Colorectal Surgery, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yangyu Zhang
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yanhua Wu
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Menghui Wu
- Department of Gastric and Colorectal Surgery, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Tetsuya Tsukamoto
- Department of Diagnostic Pathology I, School of Medicine, Fujita Health University, Toyoake 470-1192, Japan
| | - Masanobu Oshima
- Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - Jing Jiang
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Xueyuan Cao
- Department of Gastric and Colorectal Surgery, First Hospital of Jilin University, Changchun, Jilin 130021, China.
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17
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Wang W, Wang S, Chu X, Liu H, Xiang M. Predicting the Lung Squamous Cell Carcinoma Diagnosis and Prognosis Markers by Unique DNA Methylation and Gene Expression Profiles. J Comput Biol 2019; 27:1041-1054. [PMID: 31710242 DOI: 10.1089/cmb.2019.0138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The early diagnosis of lung squamous cell carcinoma (LUSC) is difficult, causing an unsatisfactory prognosis. Therefore, the 5-year survival rate of LUSC is poor. This study aimed at screening the potential diagnostic and prognostic markers for LUSC. The data of LUSC gene expression profiles and DNA methylation were obtained from The Cancer Genome Atlas (TCGA) database; the differentially expressed genes (DEGs) and the differentially methylated genes (DMGs) were screened out by an independent t-test and Benjamini/Hochberg methods. Further, the classifiers of the gene expression and DNA methylation markers in LUSC were constructed. After that, diagnostic and prognostic markers in LUSC were analyzed by the protein-protein interaction (PPI) network. The DEGs and the DMGs from TCGA database of LUSC were screened out. After strict filtration, we identified three potential DMGs (POU domain, class 4, transcription factor 2 [POU4F2], EN1, single-minded homolog 1 [SIM1]) for early diagnosis and seven potential DEGs (G-protein coupled receptor 78 [GPR78], PCDHA5, myosin binding protein H [MYBPH], RTL3, KIAA0408, HSD3B2, PCDHA12) for prognosis of LUSC. The tumor-normal tissue classification model and prognosis model were validated in two independent datasets. In addition, the PPI network was constructed, including three DMGs and the five DEGs (GPR78, MYBPH, KIAA0408, HSD3B2, PCDHA12) of the seven DEGs. The potential DMGs (POU4F2, EN1, SIM1) and DEGs (GPR78, MYBPH, KIAA0408, HSD3B2, PCDHA12) for the diagnosis and prognosis of LUSC identified in this article are expected to be further applied in clinical practice of the treatment of LUSC.
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Affiliation(s)
- Weiqing Wang
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
| | - Shaohua Wang
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
| | - Xiao Chu
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
| | - Hui Liu
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
| | - Ming Xiang
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Shanghai, China
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18
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Zhang JG, Xu C, Zhang L, Zhu W, Shen H, Deng HW. Identify gene expression pattern change at transcriptional and post-transcriptional levels. Transcription 2019; 10:137-146. [PMID: 30696368 PMCID: PMC6602563 DOI: 10.1080/21541264.2019.1575159] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 12/15/2022] Open
Abstract
Gene transcription is regulated with distinct sets of regulatory factors at multiple levels. Transcriptional and post-transcriptional regulation constitute two major regulation modes of gene expression to either activate or repress the initiation of transcription and thereby control the number of proteins synthesized during translation. Disruptions of the proper regulation patterns at transcriptional and post-transcriptional levels are increasingly recognized as causes of human diseases. Consequently, identifying the differential gene expression at transcriptional and post-transcriptional levels respectively is vital to identify potential disease-associated and/or causal genes and understand their roles in the disease development. Here, we proposed a novel method with a linear mixed model that can identify a set of differentially expressed genes at transcriptional and post-transcriptional levels. The simulation and real data analysis showed our method could provide an accurate way to identify genes subject to aberrant transcriptional and post-transcriptional regulation and reveal the potential causal genes that contributed to the diseases.
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Affiliation(s)
- Ji-Gang Zhang
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
- Computational Science, The Jackson Laboratory, Bar Harbor, ME, USA
| | - Chao Xu
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Lan Zhang
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
| | - Wei Zhu
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
| | - Hui Shen
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
| | - Hong-Wen Deng
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
- School of Basic Medical Science, Central South University, Changsha, China
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19
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Li QW, Ma L, Qiu B, Yang H, Zhu YJ, Qiang MY, Liu SR, Chen NB, Guo JY, Cai LZ, Wang JY, Zhang X, Liu H. Differential expression profiles of long noncoding RNAs in synchronous multiple and solitary primary esophageal squamous cell carcinomas: A microarray analysis. J Cell Biochem 2019; 120:2439-2453. [PMID: 30324748 DOI: 10.1002/jcb.27536] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/07/2018] [Indexed: 01/24/2023]
Abstract
As a unique subtype of esophageal cancer, synchronous multiple primary esophageal squamous cell carcinomas (ESCCs) mostly occur in Asian patients with alcohol and/or tobacco abuse, or with a family history of cancer. Multiple ESCCs are associated with poor clinical outcomes. Growing evidence has addressed that long noncoding RNAs (lncRNAs) are involved in the carcinogenesis of various malignancies. We compared the lncRNA and messenger RNA (mRNA) profiles between solitary and multiple ESCC tissues through microarray analysis, aiming at studying their different mechanisms in tumor development. As a result, in multiple ESCCs, a total of 5257 lncRNAs and 3371 mRNAs were consistently differentially expressed compared with solitary ESCC, including 2986 upregulated and 2271 downregulated lncRNAs, and 2313 upregulated, and 1058 downregulated mRNAs. We validated the results in four differentially expressed lncRNAs using quantitative real-time polymerase chain reaction. There were 38 and 20 pathways significantly related to up- and downregulated transcripts. The pathways associated with mostly enriched up- and downregulated mRNAs were hsa01200 (carbon metabolism) and hsa05221 (acute myeloid leukemia- homo sapiens [human]). Gene ontology analysis suggested that upregulated and downregulated mRNAs were mainly enriched in bounding membrane of organelle involved in the cellular component and positive regulation of transport involved in the biological process. Further analysis identified 189 differentially expressed paired antisense lncRNAs and relative sense mRNA, as well as 2134 differentially expressed long intergenic noncoding RNAs and their adjacent mRNA pairs. In conclusion, the aberrantly expressed lncRNAs might play a role in the carcinogenesis of multiple ESCCs and could be candidates as diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Qi-Wen Li
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Li Ma
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, Guangdong, China
| | - Bo Qiu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Hong Yang
- Department of Thoracic Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yu-Jia Zhu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Meng-Yun Qiang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Song-Ran Liu
- Department of Pathology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Nai-Bin Chen
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Jin-Yu Guo
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Ling-Zhi Cai
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Jun-Ye Wang
- Department of Thoracic Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xu Zhang
- Department of Thoracic Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Hui Liu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.,Lung Cancer Research Center, Sun Yat-sen University, Guangzhou, Guangdong, China
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20
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Lin J, Wu YJ, Liang X, Ji M, Ying HM, Wang XY, Sun X, Shao CH, Zhan LX, Zhang Y. Network-based integration of mRNA and miRNA profiles reveals new target genes involved in pancreatic cancer. Mol Carcinog 2018; 58:206-218. [PMID: 30294829 DOI: 10.1002/mc.22920] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 08/31/2018] [Accepted: 10/03/2018] [Indexed: 12/30/2022]
Abstract
Pancreatic cancer is regarded as the most fatal and aggressive malignancy cancer due to its low 5-year survival rate and poor prognosis. The approaches of early diagnosis and treatment are limited, which makes it urgent to identify the complex mechanism of pancreatic oncogenesis. In this study, we used RNA-seq to investigate the transcriptomic (mRNA and miRNA) profiles of pancreatic cancer in paired tumor and normal pancreatic samples from ten patients. More than 1000 differentially expressed genes were identified, nearly half of which were also found to be differentially expressed in the majority of examined patients. Functional enrichment analysis revealed that these genes were significantly enriched in multicellular organismal and metabolic process, secretion, mineral transport, and intercellular communication. In addition, only 24 differentially expressed miRNAs were found, all of which have been reported to be associated with pancreatic cancer. Furthermore, an integrated miRNA-mRNA interaction network was generated using multiple resources. Based on the calculation of disease correlation scores developed here, several genes present in the largest connected subnetwork, such as albumin, ATPase H+ /K+ exchanging alpha polypeptide and carcinoembryonic antigen-related cell adhesion molecule 1, were considered as novel genes that play important roles in the development of pancreatic cancer. Overall, our data provide new insights into further understanding of key molecular mechanisms underlying pancreatic tumorigenesis.
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Affiliation(s)
- Jie Lin
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong Province, P. R. China.,Key Laboratory of Nutrition, Metabolism, and Food Safety, Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Yan-Jun Wu
- Key Laboratory of Nutrition, Metabolism, and Food Safety, Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Xing Liang
- Department of Pancreatic-Biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, P. R. China
| | - Meng Ji
- Department of Pancreatic-Biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, P. R. China
| | - Hui-Min Ying
- Department of Endocrinology, Hangzhou Xixi Hospital, Hangzhou, Zhejiang, P. R. China
| | - Xin-Yu Wang
- Key Laboratory of Nutrition, Metabolism, and Food Safety, Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Xia Sun
- Key Laboratory of Nutrition, Metabolism, and Food Safety, Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Cheng-Hao Shao
- Department of Pancreatic-Biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, P. R. China
| | - Li-Xing Zhan
- Key Laboratory of Nutrition, Metabolism, and Food Safety, Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Yan Zhang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong Province, P. R. China
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21
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Binato R, Santos EC, Boroni M, Demachki S, Assumpção P, Abdelhay E. A common molecular signature of intestinal-type gastric carcinoma indicates processes related to gastric carcinogenesis. Oncotarget 2018; 9:7359-7371. [PMID: 29484116 PMCID: PMC5800908 DOI: 10.18632/oncotarget.23670] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022] Open
Abstract
Gastric carcinoma (GC) is one of the most aggressive cancers and the second leading cause of cancer death in the world. According to the Lauren classification, this adenocarcinoma is divided into two subtypes, intestinal and diffuse, which differ in their clinical, epidemiological and molecular features. Several studies have attempted to delineate the molecular signature of gastric cancer to develop new and non-invasive screening tests that improve diagnosis and lead to new treatment strategies. However, a consensus signature has not yet been identified for each condition. Thus, this work aimed to analyze the gene expression profile of Brazilian intestinal-type GC tissues using microarrays and compare the results to those of non-tumor tissue samples. Moreover, we compared our intestinal-type gastric carcinoma profile with those obtained from populations worldwide to assess their similarity. The results identified a molecular signature for intestinal-type GC and revealed that 38 genes differentially expressed in Brazilian intestinal-type gastric carcinoma samples can successfully distinguish gastric tumors from non-tumor tissue in the global population. These differentially expressed genes participate in biological processes important to cell homeostasis. Furthermore, Kaplan-Meier analysis suggested that 7 of these genes could individually be able to predict overall survival in intestinal-type gastric cancer patients.
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Affiliation(s)
- Renata Binato
- Laboratório de Célula tronco, Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Ciência e Tecnologia Para o Controle do Câncer (INCT), Rio de Janeiro, RJ, Brazil
| | - Everton Cruz Santos
- Laboratório de Célula tronco, Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Ciência e Tecnologia Para o Controle do Câncer (INCT), Rio de Janeiro, RJ, Brazil
| | - Mariana Boroni
- Laboratório de Bioinformática e Biologia Computacional, Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
| | - Samia Demachki
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará (UFPA), Belém, PA, Brazil
| | - Paulo Assumpção
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará (UFPA), Belém, PA, Brazil
| | - Eliana Abdelhay
- Laboratório de Célula tronco, Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Ciência e Tecnologia Para o Controle do Câncer (INCT), Rio de Janeiro, RJ, Brazil
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22
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Fei HJ, Chen SC, Zhang JY, Li SY, Zhang LL, Chen YY, Chang CX, Xu CM. Identification of significant biomarkers and pathways associated with gastric carcinogenesis by whole genome-wide expression profiling analysis. Int J Oncol 2018; 52:955-966. [PMID: 29328368 DOI: 10.3892/ijo.2018.4243] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/04/2018] [Indexed: 12/11/2022] Open
Abstract
The incidence of gastric cancer (GC) is extremely high in East Asia. GC is also one of the most common and lethal forms of cancer from a global perspective. However, to date, we have not been able to determine one or several genes as biomarkers in the diagnosis of GC and have also been unable to identify the genes which are important in the therapy of GC. In this study, we analyzed all genome-wide expression profiling arrays uploaded onto the Gene Expression Omnibus (GEO) database to filtrate the differentially expressed genes (DEGs) between normal stomach tissues and GC tissues. GSE13911, GSE19826 and GSE79973 were based on the GPL570 platform, and GSE29272 was based on the GPL96 platform. We screened out the DEGs from the two platforms and by selecting the intersection of these two platforms, we identified the common DEGs in the sequencing data from different laboratories. Finally, we obtained 3 upregulated and 34 downregulated DEGs in GC from 384 samples. As the number of downregulated DEGs was greater than that of the upregulated DEGs, functional analysis and pathway enrichment analysis were performed on the downregulated DEGs. Through our analysis, we identified the most significant genes associated with GC, such as secreted phosphoprotein 1 (SPP1), sulfatase 1 (SULF1), thrombospondin 2 (THBS2), ATPase H+/K+ transporting beta subunit (ATP4B), gastric intrinsic factor (GIF) and gastrokine 1 (GKN1). The prognostic power of these genes was corroborated in the Oncomine database and by Kaplan-Meier plotter (KM-plotter) analysis. Moreover, gastric acid secretion, collecting duct acid secretion, nitrogen metabolism and drug metabolism were significantly related to GC. Thus, these genes and pathways may be potential targets for improving the diagnosis and clinical effects in patients with GC.
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Affiliation(s)
- Hong-Jun Fei
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R. China
| | - Song-Chang Chen
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R. China
| | - Jun-Yu Zhang
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R. China
| | - Shu-Yuan Li
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R. China
| | - Lan-Lan Zhang
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R. China
| | - Yi-Yao Chen
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R. China
| | - Chun-Xin Chang
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R. China
| | - Chen-Ming Xu
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R. China
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Qamra A, Xing M, Padmanabhan N, Kwok JJT, Zhang S, Xu C, Leong YS, Lee Lim AP, Tang Q, Ooi WF, Suling Lin J, Nandi T, Yao X, Ong X, Lee M, Tay ST, Keng ATL, Gondo Santoso E, Ng CCY, Ng A, Jusakul A, Smoot D, Ashktorab H, Rha SY, Yeoh KG, Peng Yong W, Chow PK, Chan WH, Ong HS, Soo KC, Kim KM, Wong WK, Rozen SG, Teh BT, Kappei D, Lee J, Connolly J, Tan P. Epigenomic Promoter Alterations Amplify Gene Isoform and Immunogenic Diversity in Gastric Adenocarcinoma. Cancer Discov 2017; 7:630-651. [DOI: 10.1158/2159-8290.cd-16-1022] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/27/2016] [Accepted: 03/16/2017] [Indexed: 01/08/2023]
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Lin S, Lin B, Wang X, Pan Y, Xu Q, He JS, Gong W, Xing R, He Y, Guo L, Lu Y, Wang JM, Huang J. Silencing of ATP4B of ATPase H +/K + Transporting Beta Subunit by Intragenic Epigenetic Alteration in Human Gastric Cancer Cells. Oncol Res 2017; 25:317-329. [PMID: 28281974 PMCID: PMC7840950 DOI: 10.3727/096504016x14734735156265] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ATPase H+/K+ Transporting Beta Subunit (ATP4B) encodes the β subunit of the gastric H+, K+-ATPase, which controls gastric acid secretion and is therefore a target for acid reduction. Downregulation of ATP4B was recently observed in human gastric cancer (GC) without known mechanisms. In the present study, we demonstrated that ATP4B expression was decreased in human GC tissues and cell lines associated with DNA hypermethylation and histone hypoacetylation of histone H3 lysine 9 at its intragenic region close to the transcriptional start site. The expression of ATP4B was restored in GC cell lines by treatment with the DNA methyltransferase inhibitor, 5-aza-2'-deoxycytidine (5-AZA), or histone deacetylase inhibitor, trichostatin A (TSA), with further enhancement by combined treatment with both drugs. In contrast, 5-AZA had no effect on ATP4B expression in human hepatocellular carcinoma (HCC) and pancreatic cancer cell lines, in which ATP4B was silenced and accompanied by intragenic methylation. Chromatin immunoprecipitation (ChIP) showed that, in BGC823 GC cells, histone H3 lysine 9 acetylation (H3K9ac) was enhanced in the intragenic region of ATP4B upon TSA treatment, whereas 5-AZA showed a minimal effect. Additionally, ATP4B expression enhanced the inhibitory effects of chemotherapeutic mediation docetaxel on GC cell growth. Thus, as opposed to HCC and pancreatic cancer cells, the silencing of ATP4B in GC cells is attributable to the interplay between intragenic DNA methylation and histone acetylation of ATP4B, the restoration of which is associated with a favorable anticancer effect of docetaxel. These results have implications for targeting epigenetic alteration at the intragenic region of ATP4B in GC cells to benefit diagnosis and treatment of GC.
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Affiliation(s)
- Shuye Lin
- *College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, P.R. China
- †Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Bonan Lin
- *College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, P.R. China
| | - Xiaoyue Wang
- *College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, P.R. China
| | - Yuanming Pan
- ‡Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital/Institute, Beijing, P.R. China
| | - Qing Xu
- *College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, P.R. China
| | - Jin-Shen He
- *College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, P.R. China
| | - Wanghua Gong
- §Basic Research Program, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Rui Xing
- ‡Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital/Institute, Beijing, P.R. China
| | - Yuqi He
- ¶Department of Gastroenterology, PLA Army General Hospital, Beijing, P.R. China
| | - Lihua Guo
- *College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, P.R. China
| | - Youyong Lu
- ‡Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital/Institute, Beijing, P.R. China
| | - Ji Ming Wang
- †Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jiaqiang Huang
- *College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, P.R. China
- †Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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25
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Liu X, Chang X. Identifying module biomarkers from gastric cancer by differential correlation network. Onco Targets Ther 2016; 9:5701-5711. [PMID: 27703371 PMCID: PMC5036598 DOI: 10.2147/ott.s113281] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Gastric cancer (stomach cancer) is a severe disease caused by dysregulation of many functionally correlated genes or pathways instead of the mutation of individual genes. Systematic identification of gastric cancer biomarkers can provide insights into the mechanisms underlying this deadly disease and help in the development of new drugs. In this paper, we present a novel network-based approach to predict module biomarkers of gastric cancer that can effectively distinguish the disease from normal samples. Specifically, by assuming that gastric cancer has mainly resulted from dysfunction of biomolecular networks rather than individual genes in an organism, the genes in the module biomarkers are potentially related to gastric cancer. Finally, we identified a module biomarker with 27 genes, and by comparing the module biomarker with known gastric cancer biomarkers, we found that our module biomarker exhibited a greater ability to diagnose the samples with gastric cancer.
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Affiliation(s)
- Xiaoping Liu
- College of Statistics and Applied Mathematics, Anhui University of Finance and Economics, Bengbu, Anhui Province, People's Republic of China; Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China; Collaborative Research Center for Innovative Mathematical Modeling, Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - Xiao Chang
- College of Statistics and Applied Mathematics, Anhui University of Finance and Economics, Bengbu, Anhui Province, People's Republic of China; Collaborative Research Center for Innovative Mathematical Modeling, Institute of Industrial Science, University of Tokyo, Tokyo, Japan
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26
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Lin YL, Deng QK, Wang YH, Fu XL, Ma JG, Li WP. Aberrant Protocadherin17 (PCDH17) Methylation in Serum is a Potential Predictor for Recurrence of Early-Stage Prostate Cancer Patients After Radical Prostatectomy. Med Sci Monit 2015; 21:3955-690. [PMID: 26683656 PMCID: PMC4689382 DOI: 10.12659/msm.896763] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background Prostate cancer is a one of the most common malignant diseases in men worldwide. Now it is a challenge to identify patients at higher risk for relapse and progression after surgery, and more novel prognostic biomarkers are needed. The aim of this study was to investigate the clinical significance of protocadherin17 (PCDH17) methylation in serum and its predictive value for biochemical recurrence (BCR) after radical prostatectomy. Material/Methods We evaluated the methylation status of PCDH17 in serum samples of 167 early-stage prostate cancer patients and 44 patients with benign prostatic hyperplasia (BPH) using methylation-specific PCR (MSP), and then evaluated the relationship between PCDH17 methylation and clinicopathologic features. Kaplan-Meier survival analysis and Cox analysis were used to evaluate its predictive value for BCR. Results The ratio of PCDH17 methylation in prostate cancer patients was higher than in patients with BPH. Moreover, PCDH17 methylation was significantly associated with advanced pathological stage, higher Gleason score, higher preoperative PSA levels, and BCR. Kaplan-Meier survival analysis indicated that patients with methylated PCDH17 had shorter BCR-free survival time compared to patients with unmethylated PCDH17. Cox regression analysis indicated that PCDH17 methylation was an independent predictive factor for the BCR of patients after radical prostatectomy. Conclusions PCDH17 methylation in serum is a frequent event in early-stage prostate cancer, and it is an independent predictor of BCR after radical prostatectomy.
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Affiliation(s)
- Ying-Li Lin
- Department of Urology, Xuzhou Cancer Hospital, Affiliated Xuzhou Hospital of Jiangsu University, Xuzhou, Jiangsu, China (mainland)
| | - Qiu-Kui Deng
- Department of Orthopaedics, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Yu-Hao Wang
- Department of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China (mainland)
| | - Xing-Li Fu
- Health Science Center, Jiangsu University, Zhenjiang, Jiangsu, China (mainland)
| | - Jian-Guo Ma
- Department of Urology, Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China (mainland)
| | - Wen-Ping Li
- Department of Urology, Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China (mainland)
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27
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Aarthy R, Mani S, Velusami S, Sundarsingh S, Rajkumar T. Role of Circulating Cell-Free DNA in Cancers. Mol Diagn Ther 2015; 19:339-50. [PMID: 26400814 DOI: 10.1007/s40291-015-0167-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Liquid biopsy is a term used to describe non-invasive tests, which provide information about disease conditions through analysis of circulating cell-free DNA and circulating tumor cells from peripheral blood samples. In patients with cancer, the concentration of cell-free DNA increases, and structural, sequence, and epigenetic changes to DNA can be observed through the disease process and during therapy. Furthermore, cell-free DNA released by the tumor contains the same variants as those in the tumor cells. Therefore, cell-free DNA allows non-invasive assessment of cancer in real time. This review summarizes the origin of cell-free DNA, recent advancements in the detection of cell-free DNA, a possible role in metastasis, and its importance as a non-invasive diagnostic assay for cancer.
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Affiliation(s)
- Raghu Aarthy
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India
| | - Samson Mani
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India
| | - Sridevi Velusami
- Department of Surgical Oncology, Cancer Institute (WIA), Chennai, India
| | | | - Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India.
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28
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Ge P, Yu X, Wang ZC, Lin J. Aberrant Methylation of the 1p36 Tumor Suppressor Gene RIZ1 in Renal Cell Carcinoma. Asian Pac J Cancer Prev 2015; 16:4071-5. [DOI: 10.7314/apjcp.2015.16.9.4071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Kong SC, Giannuzzo A, Gianuzzo A, Novak I, Pedersen SF. Acid-base transport in pancreatic cancer: molecular mechanisms and clinical potential. Biochem Cell Biol 2014; 92:449-59. [PMID: 25372771 DOI: 10.1139/bcb-2014-0078] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Solid tumors are characterized by a microenvironment that is highly acidic, while intracellular pH (pHi) is normal or even elevated. This is the result of elevated metabolic rates in the highly proliferative cancer cells, in conjunction with often greatly increased rates of net cellular acid extrusion. Studies in various cancers have suggested that while the acid extrusion mechanisms employed are generally the same as those in healthy cells, the specific transporters upregulated vary with the cancer type. The main such transporters include Na(+)/H(+) exchangers, various HCO3(-) transporters, H(+) pumps, and lactate-H(+) cotransporters. The mechanisms leading to their dysregulation in cancer are incompletely understood but include changes in transporter expression levels, trafficking and membrane localization, and posttranslational modifications. In turn, accumulating evidence has revealed that in addition to supporting their elevated metabolic rate, their increased acid efflux capacity endows the cancer cells with increased capacity for invasiveness, proliferation, and chemotherapy resistance. The pancreatic duct exhibits an enormous capacity for acid-base transport, rendering pHi dysregulation a potentially very important topic in pancreatic ductal adenocarcinoma (PDAC). PDAC - accounting for about 90% of all pancreatic cancers - has one of the highest cancer mortality rates known, and new diagnostic and treatment options are highly needed. However, very little is known about whether pH regulation is altered in PDAC and, if so, the possible role of this in cancer development. Here, we review current models for pancreatic acid-base transport and pH homeostasis and summarize current views on acid-base dysregulation in cancer, focusing where possible on the few studies to date in PDAC. Finally, we present new data-mining analyses of acid-base transporter expression changes in PDAC and discuss essential directions for future work.
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Affiliation(s)
- Su Chii Kong
- a Section for Cell and Developmental Biology, Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen, Denmark
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30
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Lin F, Tan HJ, Guan JS, Lim YP. Divide and conquer: subproteomic approaches toward gastric cancer biomarker and drug target discovery. Expert Rev Proteomics 2014; 11:515-30. [PMID: 24684179 DOI: 10.1586/14789450.2014.904751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The discovery of biomarkers for early detection and treatment for gastric cancer are two important gaps that proteomics have the potential to fill. Advancements in mass spectrometry, sample preparation and separation strategies are crucial to proteomics-based discoveries and subsequent translations from bench to bedside. A great number of studies exploiting various subproteomic approaches have emerged for higher-resolution analysis (compared with shotgun proteomics) that permit interrogation of different post-translational and subcellular compartmentalized forms of the same proteins as determinants of disease phenotypes. This is a unique and key strength of proteomics over genomics. In this review, the salient features, competitive edges and pitfalls of various subproteomic approaches are discussed. We also highlight valuable insights from several subproteomic studies that have increased our understanding of the molecular etiology of gastric cancer and the findings that led to the discovery of potential biomarkers/drug targets that were otherwise not revealed by conventional shotgun expression proteomics.
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Affiliation(s)
- Fan Lin
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD4, level 1, 5 Science Drive 2, Singapore
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31
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Intragenic DNA methylation in transcriptional regulation, normal differentiation and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1161-74. [PMID: 23938249 DOI: 10.1016/j.bbagrm.2013.08.001] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 02/06/2023]
Abstract
Ever since the discovery of DNA methylation at cytosine residues, the role of this so called fifth base has been extensively studied and debated. Until recently, the majority of DNA methylation studies focused on the analysis of CpG islands associated to promoter regions. However, with the upcoming possibilities to study DNA methylation in a genome-wide context, this epigenetic mark can now be studied in an unbiased manner. As a result, recent studies have shown that not only promoters but also intragenic and intergenic regions are widely modulated during physiological processes and disease. In particular, it is becoming increasingly clear that DNA methylation in the gene body is not just a passive witness of gene transcription but it seems to be actively involved in multiple gene regulation processes. In this review we discuss the potential role of intragenic DNA methylation in alternative promoter usage, regulation of short and long non-coding RNAs, alternative RNA processing, as well as enhancer activity. Furthermore, we summarize how the intragenic DNA methylome is modified both during normal cell differentiation and neoplastic transformation.
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