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Petővári G, Tóth G, Turiák L, L. Kiss A, Pálóczi K, Sebestyén A, Pesti A, Kiss A, Baghy K, Dezső K, Füle T, Tátrai P, Kovalszky I, Reszegi A. Dynamic Interplay in Tumor Ecosystems: Communication between Hepatoma Cells and Fibroblasts. Int J Mol Sci 2023; 24:13996. [PMID: 37762298 PMCID: PMC10530979 DOI: 10.3390/ijms241813996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Tumors are intricate ecosystems where cancer cells and non-malignant stromal cells, including cancer-associated fibroblasts (CAFs), engage in complex communication. In this study, we investigated the interaction between poorly (HLE) and well-differentiated (HuH7) hepatoma cells and LX2 fibroblasts. We explored various communication channels, including soluble factors, metabolites, extracellular vesicles (EVs), and miRNAs. Co-culture with HLE cells induced LX2 to produce higher levels of laminin β1, type IV collagen, and CD44, with pronounced syndecan-1 shedding. Conversely, in HuH7/LX2 co-culture, fibronectin, thrombospondin-1, type IV collagen, and cell surface syndecan-1 were dominant matrix components. Integrins α6β4 and α6β1 were upregulated in HLE, while α5β1 and αVβ1 were increased in HuH7. HLE-stimulated LX2 produced excess MMP-2 and 9, whereas HuH7-stimulated LX2 produced excess MMP-1. LX2 activated MAPK and Wnt signaling in hepatoma cells, and conversely, hepatoma-derived EVs upregulated MAPK and Wnt in LX2 cells. LX2-derived EVs induced over tenfold upregulation of SPOCK1/testican-1 in hepatoma EV cargo. We also identified liver cancer-specific miRNAs in hepatoma EVs, with potential implications for early diagnosis. In summary, our study reveals tumor type-dependent communication between hepatoma cells and fibroblasts, shedding light on potential implications for tumor progression. However, the clinical relevance of liver cancer-specific miRNAs requires further investigation.
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Affiliation(s)
- Gábor Petővári
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, H-1085 Budapest, Hungary
| | - Gábor Tóth
- MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - Anna L. Kiss
- Department of Human Morphology and Developmental Biology, Semmelweis University, Tűzoltó u. 58, H-1094 Budapest, Hungary
| | - Krisztina Pálóczi
- Department of Genetics, Cell and Immunobiology, Semmelweis University, H-1085 Budapest, Hungary
| | - Anna Sebestyén
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, H-1085 Budapest, Hungary
| | - Adrián Pesti
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Üllői út 93, H-1091 Budapest, Hungary
| | - András Kiss
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Üllői út 93, H-1091 Budapest, Hungary
| | - Kornélia Baghy
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, H-1085 Budapest, Hungary
| | - Katalin Dezső
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, H-1085 Budapest, Hungary
| | - Tibor Füle
- Thermo Fisher Scientific Inc., Váci út. 41-43, H-1134 Budapest, Hungary
| | - Péter Tátrai
- Charles River Laboratories Hungary, Irinyi József utca 4-20, H-1117 Budapest, Hungary
| | - Ilona Kovalszky
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, H-1085 Budapest, Hungary
| | - Andrea Reszegi
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, H-1085 Budapest, Hungary
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Üllői út 93, H-1091 Budapest, Hungary
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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Mosharaf MP, Kibria MK, Hossen MB, Islam MA, Reza MS, Mahumud RA, Alam K, Gow J, Mollah MNH. Meta-Data Analysis to Explore the Hub of the Hub-Genes That Influence SARS-CoV-2 Infections Highlighting Their Pathogenetic Processes and Drugs Repurposing. Vaccines (Basel) 2022; 10:vaccines10081248. [PMID: 36016137 PMCID: PMC9415433 DOI: 10.3390/vaccines10081248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 01/09/2023] Open
Abstract
The pandemic of SARS-CoV-2 infections is a severe threat to human life and the world economic condition. Although vaccination has reduced the outspread, but still the situation is not under control because of the instability of RNA sequence patterns of SARS-CoV-2, which requires effective drugs. Several studies have suggested that the SARS-CoV-2 infection causing hub differentially expressed genes (Hub-DEGs). However, we observed that there was not any common hub gene (Hub-DEGs) in our analyses. Therefore, it may be difficult to take a common treatment plan against SARS-CoV-2 infections globally. The goal of this study was to examine if more representative Hub-DEGs from published studies by means of hub of Hub-DEGs (hHub-DEGs) and associated potential candidate drugs. In this study, we reviewed 41 articles on transcriptomic data analysis of SARS-CoV-2 and found 370 unique hub genes or studied genes in total. Then, we selected 14 more representative Hub-DEGs (AKT1, APP, CXCL8, EGFR, IL6, INS, JUN, MAPK1, STAT3, TNF, TP53, UBA52, UBC, VEGFA) as hHub-DEGs by their protein-protein interaction analysis. Their associated biological functional processes, transcriptional, and post-transcriptional regulatory factors. Then we detected hHub-DEGs guided top-ranked nine candidate drug agents (Digoxin, Avermectin, Simeprevir, Nelfinavir Mesylate, Proscillaridin, Linifanib, Withaferin, Amuvatinib, Atazanavir) by molecular docking and cross-validation for treatment of SARS-CoV-2 infections. Therefore, the findings of this study could be useful in formulating a common treatment plan against SARS-CoV-2 infections globally.
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Affiliation(s)
- Md. Parvez Mosharaf
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
- School of Business, Faculty of Business, Education, Law and Arts, University of Southern Queensland, Toowoomba, QLD 4350, Australia; (K.A.); (J.G.)
| | - Md. Kaderi Kibria
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
| | - Md. Bayazid Hossen
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
| | - Md. Ariful Islam
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
| | - Md. Selim Reza
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
| | - Rashidul Alam Mahumud
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia;
| | - Khorshed Alam
- School of Business, Faculty of Business, Education, Law and Arts, University of Southern Queensland, Toowoomba, QLD 4350, Australia; (K.A.); (J.G.)
| | - Jeff Gow
- School of Business, Faculty of Business, Education, Law and Arts, University of Southern Queensland, Toowoomba, QLD 4350, Australia; (K.A.); (J.G.)
- School of Accounting, Economics and Finance, University of KwaZulu Natal, Durban 4001, South Africa
| | - Md. Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
- Correspondence:
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Abstract
Objectives: Gastric cancer (GC) is a disease with high mortality, poor prognosis and numerous risk factors. GC has an asymptomatic nature in early stages of the diseases, making timely diagnosis complicated using common conventional approaches, namely pathological examinations and imaging tests. Recently, molecular profiling of GC using next generation sequencing (NGS) has opened new doors to efficient prognostic, diagnostic, and therapeutic strategies. The current review aims to thoroughly discuss and compare the current NGS techniques and commercial platforms utilized for GC diagnosis and treatment, highlighting the most recent NGS-based GC studies. Furthermore, this review addresses the challenges of clinical implementation of NGS in GC.Materials and methods: This review was conducted according to the eligible studies identified via search of Web of Science, PubMed, Scopus, Embase and the Cochrane Library. In the present study, data on gastric cancer patients and NGS methods used to diagnose the disease were reviewed.Conclusion: Given the ever-rising advancements in NGS technologies, bioinformatics, healthcare guidelines and refined classifications, it is hoped that these technologies can actualize their advantages and optimize GC patients' experience.
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Affiliation(s)
- Narges Moradi
- Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Siamak Heidarzadeh
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
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Luo W, Nagaria TS, Sun H, Ma J, Lombardo JL, Bassett R, Cao AC, Tan D. Expression and Potential Prognostic Value of SOX9, MCL-1 and SPOCK1 in Gastric Adenocarcinoma. Pathol Oncol Res 2022; 28:1610293. [PMID: 35221802 PMCID: PMC8863590 DOI: 10.3389/pore.2022.1610293] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 01/19/2022] [Indexed: 11/21/2022]
Abstract
Gastric cancer is a common malignancy and remains one of the leading causes of cancer-related deaths, though its incidence is in decline in most developed countries. One of the major challenges of treating gastric cancer is tumor heterogeneity, which portends a high degree of prognostic variance and the necessity for different treatment modalities. Tumor heterogeneity is at least in part due to divergent differentiation of tumor cells to clones harboring different molecular alterations. Here we studied the expression of emerging prognostic markers SOX9, MCL-1, and SPOCK1 (Testican-1) in a cohort of gastric cancer by immunohistochemistry and investigated how individual biomarkers and their combinations predict disease prognosis. We found frequent expression of SPOCK1 (in both nuclei and cytoplasm), MCL-1 and SOX9 in gastric cancer. In univariate analysis, nuclear SPOCK1 expression and pathologic TNM stage were negative prognostic markers in this cohort. In multivariate analysis, SOX9 expression stood out as a predictor of poor prognosis. Further subgroup analysis suggested prognostic value of SOX9 expression in poorly differentiated gastric adenocarcinoma. MCL-1 showed no prognostic role in this cohort.
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Affiliation(s)
- Wenyi Luo
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Department of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Teddy S Nagaria
- Department of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Pathology, McGill University, Montreal, QC, Canada
| | - Hongxia Sun
- Department of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Pathology and Laboratory Medicine, University of Texas McGovern Medical School at Houston, Houston, TX, United States
| | - Junsheng Ma
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jamie L Lombardo
- Department of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Pathology, Walter Reed National Military Medical Center, Bethesda, MD, United States
| | - Roland Bassett
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Austin C Cao
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Dongfeng Tan
- Department of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
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Mosharaf MP, Reza MS, Kibria MK, Ahmed FF, Kabir MH, Hasan S, Mollah MNH. Computational identification of host genomic biomarkers highlighting their functions, pathways and regulators that influence SARS-CoV-2 infections and drug repurposing. Sci Rep 2022; 12:4279. [PMID: 35277538 DOI: 10.1038/s41598-022-08073-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 02/15/2022] [Indexed: 12/13/2022] Open
Abstract
The pandemic threat of COVID-19 has severely destroyed human life as well as the economy around the world. Although, the vaccination has reduced the outspread, but people are still suffering due to the unstable RNA sequence patterns of SARS-CoV-2 which demands supplementary drugs. To explore novel drug target proteins, in this study, a transcriptomics RNA-Seq data generated from SARS-CoV-2 infection and control samples were analyzed. We identified 109 differentially expressed genes (DEGs) that were utilized to identify 10 hub-genes/proteins (TLR2, USP53, GUCY1A2, SNRPD2, NEDD9, IGF2, CXCL2, KLF6, PAG1 and ZFP36) by the protein–protein interaction (PPI) network analysis. The GO functional and KEGG pathway enrichment analyses of hub-DEGs revealed some important functions and signaling pathways that are significantly associated with SARS-CoV-2 infections. The interaction network analysis identified 5 TFs proteins and 6 miRNAs as the key regulators of hub-DEGs. Considering 10 hub-proteins and 5 key TFs-proteins as drug target receptors, we performed their docking analysis with the SARS-CoV-2 3CL protease-guided top listed 90 FDA approved drugs. We found Torin-2, Rapamycin, Radotinib, Ivermectin, Thiostrepton, Tacrolimus and Daclatasvir as the top ranked seven candidate drugs. We investigated their resistance performance against the already published COVID-19 causing top-ranked 11 independent and 8 protonated receptor proteins by molecular docking analysis and found their strong binding affinities, which indicates that the proposed drugs are effective against the state-of-the-arts alternatives independent receptor proteins also. Finally, we investigated the stability of top three drugs (Torin-2, Rapamycin and Radotinib) by using 100 ns MD-based MM-PBSA simulations with the two top-ranked proposed receptors (TLR2, USP53) and independent receptors (IRF7, STAT1), and observed their stable performance. Therefore, the proposed drugs might play a vital role for the treatment against different variants of SARS-CoV-2 infections.
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Abstract
SPOCK1, 2 and 3 are considered as matricellular proteoglycans without structural role. Their functions are only partly elucidated. SPOCK1 was detected in the brain as a member of the neural synapses, then in the neuromuscular junctions. It plays a role in the regulation of blood-brain barrier. Its best characterized activity was its oncogenic potential discovered in 2012. Its deleterious effect on tumor progression was detected on 36 different types of tumors by the end of 2020. However, its mode of actions is still not completely understood. Furthermore, even less was discovered about its physiological function. The fact that it was found to localize in the mitochondria and interfered with the lipid metabolism indicated, that the full discovery of SPOCK1 still waiting for us.
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Affiliation(s)
- Lóránd Váncza
- Semmelweis University 1st Department of Pathology and Experimental Cancer Research, Budapest, Hungary
| | | | - Andrea Reszegi
- Semmelweis University 1st Department of Pathology and Experimental Cancer Research, Budapest, Hungary
| | - Kornelia Baghy
- Semmelweis University 1st Department of Pathology and Experimental Cancer Research, Budapest, Hungary
| | - Ilona Kovalszky
- Semmelweis University 1st Department of Pathology and Experimental Cancer Research, Budapest, Hungary
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7
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Váncza L, Karászi K, Péterfia B, Turiák L, Dezső K, Sebestyén A, Reszegi A, Petővári G, Kiss A, Schaff Z, Baghy K, Kovalszky I. SPOCK1 Promotes the Development of Hepatocellular Carcinoma. Front Oncol 2022; 12:819883. [PMID: 35186754 PMCID: PMC8853618 DOI: 10.3389/fonc.2022.819883] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
The extracellular matrix proteoglycan SPOCK1 is increasingly recognized as a contributor to the development and progression of cancers. Here, we study how SPOCK1, which is present in non-tumorous hepatocytes at low concentrations, promotes the development and progression of malignant hepatocellular tumors. Although SPOCK1 is an extracellular matrix proteoglycan, its concentration increases in the cytoplasm of hepatocytes starting with very low expression in the normal cells and then appearing in much higher quantities in cells of cirrhotic human liver and hepatocellular carcinoma. This observation is similar to that observed after diethylnitrosamine induction of mouse hepatocarcinogenesis. Furthermore, syndecan-1, the major proteoglycan of the liver, and SPOCK1 are in inverse correlation in the course of these events. In hepatoma cell lines, the cytoplasmic SPOCK1 colocalized with mitochondrial markers, such as MitoTracker and TOMM20, a characteristic protein of the outer membrane of the mitochondrion and could be detected in the cell nucleus. SPOCK1 downregulation of hepatoma cell lines by siRNA inhibited cell proliferation, upregulated p21 and p27, and interfered with pAkt and CDK4 expression. A tyrosine kinase array revealed that inhibition of SPOCK1 in the liver cancer cells altered MAPK signaling and downregulated several members of the Sarc family, all related to the aggressivity of the hepatoma cell lines. These studies support the idea that SPOCK1 enhancement in the liver is an active contributor to human and rodent hepatocarcinogenesis and cancer progression. However, its mitochondrial localization raises the possibility that it has a currently unidentified physiological function in normal hepatocytes.
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Affiliation(s)
- Lóránd Váncza
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Katalin Karászi
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Bálint Péterfia
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Budapest, Hungary
| | - Katalin Dezső
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Anna Sebestyén
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Andrea Reszegi
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Gábor Petővári
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - András Kiss
- 2 Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Zsuzsanna Schaff
- 2 Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Kornélia Baghy
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Ilona Kovalszky
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
- *Correspondence: Ilona Kovalszky, ;
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Zhao C, Mo L, Lei T, Yan Y, Han S, Miao J, Gao Y, Wang X, Zhao W, Huang C. miR-5701 promoted apoptosis of clear cell renal cell carcinoma cells by targeting phosphodiesterase-1B. Anticancer Drugs 2021; 32:855-863. [PMID: 33929990 DOI: 10.1097/cad.0000000000001078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Increasing evidence has demonstrated that microRNAs play critical roles in malignant biological behaviors, including cancerogenesis, cancer progression and metastasis, through the regulation of target genes expression. As miR-5701 has recently been identified to play roles as tumor suppressor miRNA in the development of some kinds of cancers, in this study we sought to investigate the role of miR-5701 in clear cell renal cell carcinoma (ccRCC). Colony formation, cell apoptosis and proliferation assays were employed, and the results showed that miR-5701 inhibited proliferation and promoted apoptosis of ccRCC cells. Western blotting and dual-luciferase reporter assays were used to confirm that PDE1B is a new direct target of miR-5701. Furthermore, overexpression of PDE1B attenuated the effects of miR-5701, indicating that miR-5701 inhibited proliferation and promoted apoptosis of ccRCC cells via targeting PDE1B. Taken together, the data presented here indicate that t miR-5701 is a tumor suppressor in ccRCC and PDE1B is a new target of miR-5701.
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Affiliation(s)
- Changan Zhao
- Department of Pathology, School of Basic Medical Sciences
- Institute of Genetics and Developmental Biology, Xi'an Jiaotong University Health Science Center
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an Jiaotong University
| | - Liping Mo
- Department of Pathology, School of Basic Medical Sciences
| | - Ting Lei
- Department of Pathology, School of Basic Medical Sciences
| | - Yan Yan
- Department of Pathology, The First Hospital of Xi'an
| | - Shuiping Han
- Department of Pathology, School of Basic Medical Sciences
| | - Jiyu Miao
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an Jiaotong University
| | - Yi Gao
- Department of Cell Biology and Genetics, Medical College of Yan'an University, Yan'an
| | - Xiaofei Wang
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an Jiaotong University
| | - Wenbao Zhao
- Department of Pathology, School of Basic Medical Sciences
| | - Chen Huang
- Institute of Genetics and Developmental Biology, Xi'an Jiaotong University Health Science Center
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an Jiaotong University
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
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9
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Kołat D, Kałuzińska Ż, Orzechowska M, Bednarek AK, Płuciennik E. Functional genomics of AP-2α and AP-2γ in cancers: in silico study. BMC Med Genomics 2020; 13:174. [PMID: 33213447 PMCID: PMC7678100 DOI: 10.1186/s12920-020-00823-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/12/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Among all causes of death, cancer is the most prevalent and is only outpaced by cardiovascular diseases. Molecular theory of carcinogenesis states that apoptosis and proliferation are regulated by groups of tumor suppressors or oncogenes. Transcription factors are example of proteins comprising representatives of both cancer-related groups. Exemplary family of transcription factors which exhibits dualism of function is Activating enhancer-binding Protein 2 (AP-2). Scientific reports concerning their function in carcinogenesis depend on particular family member and/or tumor type which proves the issue to be unsolved. Therefore, the present study examines role of the best-described AP-2 representatives, AP-2α and AP-2γ, through ontological analysis of their target genes and investigation what processes are differentially regulated in 21 cancers using samples deposited in Genomic Data Analysis Center (GDAC) Firehose. METHODS Expression data with clinical annotation was collected from TCGA-dedicated repository GDAC Firehose. Transcription factor targets were obtained from Gene Transcription Regulation Database (GTRD), TRANScription FACtor database (TRANSFAC) and Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining (TRRUST). Monocle3 R package was used for global samples profiling while Protein ANalysis THrough Evolutionary Relationships (PANTHER) tool was used to perform gene ontology analysis. RESULTS With RNA-seq data and Monocle3 or PANTHER tools we outlined differences in many processes and signaling pathways, separating tumor from normal tissues or tumors from each other. Unexpectedly, a number of alterations in basal-like breast cancer were identified that distinguished it from other subtypes, which could bring future clinical benefits. CONCLUSIONS Our findings indicate that while the AP-2α/γ role remains ambiguous, their activity is based on processes that underlie the cancer hallmarks and their expression could have potential in diagnosis of selected tumors.
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Affiliation(s)
- Damian Kołat
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland.
| | - Żaneta Kałuzińska
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
| | - Magdalena Orzechowska
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
| | - Andrzej K Bednarek
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
| | - Elżbieta Płuciennik
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
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10
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Yin X, Zhang F, Guo Z, Kong W, Wang Y. Integrative analysis of miRNA and mRNA expression profiles reveals a novel mRNA/miRNA signature to improve risk classification for patients with gastric cancer. Oncol Lett 2019; 18:2330-2339. [PMID: 31402938 PMCID: PMC6676680 DOI: 10.3892/ol.2019.10536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 05/25/2019] [Indexed: 02/03/2023] Open
Abstract
Gastric cancer (GC) is one of the most common types of malignant cancer and is associated with poor prognosis. Although the prognosis of patients with GC is associated with grade, stage and lymph node metastases, these traditional clinical features are inadequate to predict the outcome of GC. Therefore, there has been an increased focus on identifying novel molecular biomarkers for early diagnosis and prognosis, in order to improve outcomes in GC. In the present study, an integrative analysis of microRNA (miRNA) expression profiles, mRNA expression profiles and clinical characteristics was performed in a large cohort of patients with GC in order to identify an integrative prognostic model for improving postoperative risk classification. An integrative mRNA/miRNA signature (IMMIS), comprised of three miRNAs and one mRNA, was identified from a large number of differentially expressed miRNAs and mRNAs using univariate and multivariate Cox regression analysis. The prognostic value of the IMMIS was validated in the discovery cohort, testing cohort and The Cancer Genome Atlas (TCGA) cohort. The present results suggested that the identified signature had a reliable predictive performance and could classify the patients into high- and low-risk groups with significantly different overall survival times. In the discovery cohort, the hazard ratio (HR) was 2.805 with a 95% CI=1.722–4.567 (P<0.001). The median overall survival time as 1.49 vs. 3.85 years. In the testing cohort, the HR was 1.625 with a 95% CI=1.004–2.638 (P=0.039) and the median overall survival time was 2.17 vs. 4.62 years. In the TCGA cohort, the HR was 2.139 with a 95% CI=1.519–3.012 (P<0.001) and the median overall survival time was 1.53 vs. 4.62 years. The IMMIS constituted a reliable independent prognostic factor compared with clinical covariates, including age, sex, grade and stage, as indicated by multivariate and stratified analyses. Furthermore, comparative analysis revealed that the predictive value of the IMMIS was superior to the mRNA-based signature alone. The present results suggested the potential value of the IMMIS as a promising novel biomarker for improving the clinical management of patients with GC.
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Affiliation(s)
- Xiang Yin
- Department of Minimally Invasive Tumor Surgery, Daqing Oilfield General Hospital, Daqing, Heilongjiang 163453, P.R. China
| | - Fumin Zhang
- Department of Minimally Invasive Tumor Surgery, Daqing Oilfield General Hospital, Daqing, Heilongjiang 163453, P.R. China
| | - Zhongwu Guo
- Department of Minimally Invasive Tumor Surgery, Daqing Oilfield General Hospital, Daqing, Heilongjiang 163453, P.R. China
| | - Weiyuan Kong
- Department of Minimally Invasive Tumor Surgery, Daqing Oilfield General Hospital, Daqing, Heilongjiang 163453, P.R. China
| | - Yuanyuan Wang
- Department of Gastroenterology, Daqing Long Nan Hospital, Daqing, Heilongjiang 163453, P.R. China
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11
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Lin M, Li X, Guo H, Ji F, Ye L, Ma X, Cheng W. Identification of Bone Metastasis-associated Genes of Gastric Cancer by Genome-wide Transcriptional Profiling. Curr Bioinform 2018. [DOI: 10.2174/1574893612666171121154017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background:Gastric cancer is one of the leading causes of cancer-related mortality worldwide. Genome-wide transcriptional profiling has provided valuable insights into the molecular basis underlying processes involved in gastric cancer initiation and progression. </P><P> Objective: To understand the pathological and biological mechanisms of gastric cancer metastasis in a genome-wide context. </P><P> Method: In this study, we constructed libraries from blood of gastric cancer patients with, and without, bone metastasis. High-throughput sequencing combined with differential expression analysis was used to investigate transcriptional changes.Results:We identified a total of 425 significantly differentially expressed genes. Protein-protein interaction network analysis suggested that most of these genes are involved in DNA replication, DNA damage response, collagen homeostasis and cell adhesion. Furthermore, our data suggested that NFkappaB and DNA damage response pathways were the key regulators of the bone metastasis associated with gastric cancer. Finally, most of these target genes were involved in pathways such as extracellular matrix organization and extracellular structure organization as revealed by gene set enrichment assay.Conclusion:Our study provides a comprehensive analysis of the transcriptional alterations involved in gastric cancer bone metastasis, which provides greater insights into the complexity of regulatory changes during tumorigenesis and offers novel diagnostic as well as therapeutic avenues.
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Affiliation(s)
- Mingzhe Lin
- Qinghai University Affiliated Hospital, Xining, 810001, Qinghai, China
| | - Xin Li
- Qinghai University Affiliated Hospital, Xining, 810001, Qinghai, China
| | - Haizhou Guo
- Qinghai University Affiliated Hospital, Xining, 810001, Qinghai, China
| | - Faxiang Ji
- Qinghai University Affiliated Hospital, Xining, 810001, Qinghai, China
| | - Linhan Ye
- Qinghai University Affiliated Hospital, Xining, 810001, Qinghai, China
| | - Xuemei Ma
- Qinghai University Affiliated Hospital, Xining, 810001, Qinghai, China
| | - Wen Cheng
- Qinghai University Affiliated Hospital, Xining, 810001, Qinghai, China
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12
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Theocharis AD, Karamanos NK. Proteoglycans remodeling in cancer: Underlying molecular mechanisms. Matrix Biol 2017; 75-76:220-259. [PMID: 29128506 DOI: 10.1016/j.matbio.2017.10.008] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 02/07/2023]
Abstract
Extracellular matrix is a highly dynamic macromolecular network. Proteoglycans are major components of extracellular matrix playing key roles in its structural organization and cell signaling contributing to the control of numerous normal and pathological processes. As multifunctional molecules, proteoglycans participate in various cell functions during morphogenesis, wound healing, inflammation and tumorigenesis. Their interactions with matrix effectors, cell surface receptors and enzymes enable them with unique properties. In malignancy, extensive remodeling of tumor stroma is associated with marked alterations in proteoglycans' expression and structural variability. Proteoglycans exert diverse functions in tumor stroma in a cell-specific and context-specific manner and they mainly contribute to the formation of a permissive provisional matrix for tumor growth affecting tissue organization, cell-cell and cell-matrix interactions and tumor cell signaling. Proteoglycans also modulate cancer cell phenotype and properties, the development of drug resistance and tumor stroma angiogenesis. This review summarizes the proteoglycans remodeling and their novel biological roles in malignancies with particular emphasis to the underlying molecular mechanisms.
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Affiliation(s)
- Achilleas D Theocharis
- Biochemistry, Biochemical Analysis & Matrix Pathobiochemistry Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, 26500 Patras, Greece.
| | - Nikos K Karamanos
- Biochemistry, Biochemical Analysis & Matrix Pathobiochemistry Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, 26500 Patras, Greece.
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13
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Chen D, Zhou H, Liu G, Zhao Y, Cao G, Liu Q. SPOCK1 promotes the invasion and metastasis of gastric cancer through Slug-induced epithelial-mesenchymal transition. J Cell Mol Med 2017; 22:797-807. [PMID: 28940639 PMCID: PMC5783867 DOI: 10.1111/jcmm.13357] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/20/2017] [Indexed: 01/05/2023] Open
Abstract
Metastasis is a crucial impediment to the successful treatment for gastric cancer. SPOCK1 has been demonstrated to facilitate cancer metastasis in certain types of cancers; however, the role of SPOCK1 in the invasion and metastasis of gastric cancer remains elusive. SPOCK1 and epithelial-mesenchymal transition (EMT)-related biomarkers were detected by immunohistochemistry and Western blot in gastric cancer specimens. Other methods including stably transfected against SPOCK1 into gastric cancer cells, Western blot, migration and invasion assays in vitro and metastasis assay in vivo were also performed. The elevated expression of SPOCK1 correlates with EMT-related markers in human gastric cancer tissue, clinical metastasis and a poor prognosis in patients with gastric cancer. In addition, knockdown of SPOCK1 expression significantly inhibits the invasion and metastasis of gastric cancer cells in vitro and in vivo, inversely, SPOCK1 overexpression results in the opposite effect. Interestingly, SPOCK1 expression has no effect on cell proliferation in vitro and in vivo. Regarding the mechanism(s) of SPOCK1-induced cells invasion and metastasis, we prove that Slug-induced EMT is involved in SPOCK1-facilitating gastric cancer cells invasion and metastasis. The elevated SPOCK1 expression is closely correlated with cancer metastasis and patient survival, and SPOCK1 promotes the invasion and metastasis of gastric cancer through Slug-mediated EMT, thereby possibly providing a novel therapeutic target for gastric cancer.
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Affiliation(s)
- Dehu Chen
- Department of General Surgery, Taizhou People's Hospital, The Fifth Affiliated Hospital of Nantong University, Taizhou, Jiangsu, China
| | - Haihua Zhou
- Department of General Surgery, Taizhou People's Hospital, The Fifth Affiliated Hospital of Nantong University, Taizhou, Jiangsu, China
| | - Guiyuan Liu
- Department of General Surgery, Taizhou People's Hospital, The Fifth Affiliated Hospital of Nantong University, Taizhou, Jiangsu, China
| | - Yinghai Zhao
- Department of General Surgery, Taizhou People's Hospital, The Fifth Affiliated Hospital of Nantong University, Taizhou, Jiangsu, China
| | - Gan Cao
- Department of General Surgery, Taizhou People's Hospital, The Fifth Affiliated Hospital of Nantong University, Taizhou, Jiangsu, China
| | - Qinghong Liu
- Department of General Surgery, Taizhou People's Hospital, The Fifth Affiliated Hospital of Nantong University, Taizhou, Jiangsu, China
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14
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Zhang F, Chen X, Wei K, Liu D, Xu X, Zhang X, Shi H. Identification of Key Transcription Factors Associated with Lung Squamous Cell Carcinoma. Med Sci Monit 2017; 23:172-206. [PMID: 28081052 PMCID: PMC5248564 DOI: 10.12659/msm.898297] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Lung squamous cell carcinoma (lung SCC) is a common type of lung cancer, but its mechanism of pathogenesis is unclear. The aim of this study was to identify key transcription factors in lung SCC and elucidate its mechanism. Material/Methods Six published microarray datasets of lung SCC were downloaded from Gene Expression Omnibus (GEO) for integrated bioinformatics analysis. Significance analysis of microarrays was used to identify differentially expressed genes (DEGs) between lung SCC and normal controls. The biological functions and signaling pathways of DEGs were mapped in the Gene Otology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, respectively. A transcription factor gene regulatory network was used to obtain insights into the functions of DEGs. Results A total of 1,011 genes, including 539 upregulated genes and 462 downregulated genes, were filtered as DEGs between lung SCC and normal controls. DEGs were significantly enriched in cell cycle, DNA replication, p53 signaling pathway, pathways in cancer, adherens junction, and cell adhesion molecules signaling pathways. There were 57 transcription factors identified, which were used to construct a regulatory network. The network consisted of 736 interactions between 49 transcription factors and 486 DEGs. NFIC, BRCA1, and NFATC2 were the top 3 transcription factors that had the highest connectivity with DEGs and that regulated 83, 82, and 75 DEGs in the network, respectively. Conclusions NFIC, BRCA1, and NFATC2 might be the key transcription factors in the development of lung SCC by regulating the genes involved in cell cycle and DNA replication pathways.
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Affiliation(s)
- Feng Zhang
- Department of Oncology, Linyi People's Hospital of Shandong Province, Linyi, Shandong, China (mainland)
| | - Xia Chen
- The Second Ward, Taian Disabled Soldiers Hospital of Shandong Province, Taian, Shandong, China (mainland)
| | - Ke Wei
- The Third Ward, Taian Disabled Soldiers Hospital of Shandong Province, Taian, Shandong, China (mainland)
| | - Daoming Liu
- Department of Respiratory Medicine, Taian City Central Hospital of Shandong Province, Taian, Shandong, China (mainland)
| | - Xiaodong Xu
- Department of Internal Medicine, Taian City Central Hospital of Shandong Province, Taian, Shandong, China (mainland)
| | - Xing Zhang
- The Second Ward, Taian Disabled Soldiers Hospital of Shandong Province, Taian, Shandong, China (mainland)
| | - Hong Shi
- Department of Respiratory Medicine, Taian City Central Hospital of Shandong Province, Taian, Shandong, China (mainland)
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15
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Subbannayya Y, Syed N, Barbhuiya MA, Raja R, Marimuthu A, Sahasrabuddhe N, Pinto SM, Manda SS, Renuse S, Manju HC, Zameer MAL, Sharma J, Brait M, Srikumar K, Roa JC, Vijaya Kumar M, Kumar KVV, Prasad TSK, Ramaswamy G, Kumar RV, Pandey A, Gowda H, Chatterjee A. Calcium calmodulin dependent kinase kinase 2 - a novel therapeutic target for gastric adenocarcinoma. Cancer Biol Ther 2015; 16:336-45. [PMID: 25756516 DOI: 10.4161/15384047.2014.972264] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer is one of the most common gastrointestinal malignancies and is associated with poor prognosis. Exploring alterations in the proteomic landscape of gastric cancer is likely to provide potential biomarkers for early detection and molecules for targeted therapeutic intervention. Using iTRAQ-based quantitative proteomic analysis, we identified 22 proteins that were overexpressed and 17 proteins that were downregulated in gastric tumor tissues as compared to the adjacent normal tissue. Calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) was found to be 7-fold overexpressed in gastric tumor tissues. Immunohistochemical labeling of tumor tissue microarrays for validation of CAMKK2 overexpression revealed that it was indeed overexpressed in 94% (92 of 98) of gastric cancer cases. Silencing of CAMKK2 using siRNA significantly reduced cell proliferation, colony formation and invasion of gastric cancer cells. Our results demonstrate that CAMKK2 signals in gastric cancer through AMPK activation and suggest that CAMKK2 could be a novel therapeutic target in gastric cancer.
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16
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Rui Q, Xu Z, Yang P, He Z. Long noncoding RNA expression patterns in lymph node metastasis in colorectal cancer by microarray. Biomed Pharmacother 2015; 75:12-8. [DOI: 10.1016/j.biopha.2015.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 08/02/2015] [Indexed: 01/06/2023] Open
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17
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Kim BC, Jeong HO, Park D, Kim CH, Lee EK, Kim DH, Im E, Kim ND, Lee S, Yu BP, Bhak J, Chung HY. Profiling age-related epigenetic markers of stomach adenocarcinoma in young and old subjects. Cancer Inform 2015; 14:47-54. [PMID: 25983541 PMCID: PMC4406278 DOI: 10.4137/cin.s16912] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 08/19/2014] [Accepted: 08/19/2014] [Indexed: 02/04/2023] Open
Abstract
The purpose of our study is to identify epigenetic markers that are differently expressed in the stomach adenocarcinoma (STAD) condition. Based on data from The Cancer Genome Atlas (TCGA), we were able to detect an age-related difference in methylation patterns and changes in gene and miRNA expression levels in young (n = 14) and old (n = 70) STAD subjects. Our analysis identified 323 upregulated and 653 downregulated genes in old STAD subjects. We also found 76 miRNAs with age-related expression patterns and 113 differentially methylated genes (DMGs), respectively. Our further analysis revealed that significant upregulated genes (n = 35) were assigned to the cell cycle, while the muscle system process (n = 27) and cell adhesion-related genes (n = 57) were downregulated. In addition, by comparing gene and miRNA expression with methylation change, we identified that three upregulated genes (ELF3, IL1β, and MMP13) known to be involved in inflammatory responses and cell growth were significantly hypomethylated in the promoter region. We further detected target candidates for age-related, downregulated miRNAs (hsa-mir-124–3, hsa-mir-204, and hsa-mir-125b-2) in old STAD subjects. This is the first report of the results from a study exploring age-related epigenetic biomarkers of STAD using high-throughput data and provides evidence for a complex clinicopathological condition expressed by the age-related STAD progression.
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Affiliation(s)
- Byoung-Chul Kim
- Molecular Inflammation Research Center for Aging Intervention, Pusan National University, Busan, Republic of Korea. ; Interdisciplinary Research Program of Bioinformatics and Longevity Science, Pusan National University, Busan, Republic of Korea
| | - Hyoung Oh Jeong
- Molecular Inflammation Research Center for Aging Intervention, Pusan National University, Busan, Republic of Korea. ; Interdisciplinary Research Program of Bioinformatics and Longevity Science, Pusan National University, Busan, Republic of Korea
| | - Daeui Park
- Molecular Inflammation Research Center for Aging Intervention, Pusan National University, Busan, Republic of Korea. ; Interdisciplinary Research Program of Bioinformatics and Longevity Science, Pusan National University, Busan, Republic of Korea
| | - Chul-Hong Kim
- Genomictree Inc., Yuseong-gu, Daejeon, Republic of Korea
| | - Eun Kyeong Lee
- Molecular Inflammation Research Center for Aging Intervention, Pusan National University, Busan, Republic of Korea
| | - Dae Hyun Kim
- Molecular Inflammation Research Center for Aging Intervention, Pusan National University, Busan, Republic of Korea
| | - Eunok Im
- Molecular Inflammation Research Center for Aging Intervention, Pusan National University, Busan, Republic of Korea. ; Interdisciplinary Research Program of Bioinformatics and Longevity Science, Pusan National University, Busan, Republic of Korea
| | - Nam Deuk Kim
- Molecular Inflammation Research Center for Aging Intervention, Pusan National University, Busan, Republic of Korea. ; Interdisciplinary Research Program of Bioinformatics and Longevity Science, Pusan National University, Busan, Republic of Korea
| | - Sunghoon Lee
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. ; BioMedical Engineering, UNIST, Ulsan, Republic of Korea
| | - Byung Pal Yu
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jong Bhak
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. ; BioMedical Engineering, UNIST, Ulsan, Republic of Korea
| | - Hae Young Chung
- Molecular Inflammation Research Center for Aging Intervention, Pusan National University, Busan, Republic of Korea. ; Interdisciplinary Research Program of Bioinformatics and Longevity Science, Pusan National University, Busan, Republic of Korea
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18
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Puttamallesh VN, Sreenivasamurthy SK, Singh PK, Harsha HC, Ganjiwale A, Broor S, Pandey A, Narayana J, Prasad TSK. Proteomic profiling of serum samples from chikungunya-infected patients provides insights into host response. Clin Proteomics 2013; 10:14. [PMID: 24124767 PMCID: PMC3879382 DOI: 10.1186/1559-0275-10-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 09/17/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Chikungunya is a highly debilitating febrile illness caused by Chikungunya virus, a single-stranded RNA virus, which is transmitted by Aedes aegypti or Aedes albopictus mosquito species. The pathogenesis and host responses in individuals infected with the chikungunya virus are not well understood at the molecular level. We carried out proteomic profiling of serum samples from chikungunya patients in order to identify molecules associated with the host response to infection by this virus. RESULTS Proteomic profiling of serum obtained from the infected individuals resulted in identification of 569 proteins. Of these, 63 proteins were found to be differentially expressed (≥ 2-fold) in patient as compared to control sera. These differentially expressed proteins were involved in various processes such as lipid metabolism, immune response, transport, signal transduction and apoptosis. CONCLUSIONS This is the first report providing a global proteomic profile of serum samples from individuals infected with the chikungunya virus. Our data provide an insight into the proteins that are involved as host response factors during an infection. These proteins include clusterin, apolipoproteins and S100A family of proteins.
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Affiliation(s)
- Vinuth N Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | | | - Pradeep Kumar Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - H C Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Anjali Ganjiwale
- Microtest Innovations Pvt. Limited, International Technology Park, Bangalore 560 066, India
| | - Shobha Broor
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
| | - Jayasuryan Narayana
- Microtest Innovations Pvt. Limited, International Technology Park, Bangalore 560 066, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
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