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Corlett R, Button C, Scheel S, Agrawal S, Rai V, Nandipati KC. miRNA profiling of esophageal adenocarcinoma using transcriptome analysis. Cancer Biomark 2024; 39:245-264. [PMID: 38250763 DOI: 10.3233/cbm-230170] [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] [Indexed: 01/23/2024]
Abstract
Esophageal adenocarcinoma (EAC) occurs following a series of histological changes through epithelial-mesenchymal transition (EMT). A variable expression of normal and aberrant genes in the tissue can contribute to the development of EAC through the activation or inhibition of critical molecular signaling pathways. Gene expression is regulated by various regulatory factors, including transcription factors and microRNAs (miRs). The exact profile of miRs associated with the pathogenesis of EAC is largely unknown, though some candidate miRNAs have been reported in the literature. To identify the unique miR profile associated with EAC, we compared normal esophageal tissue to EAC tissue using bulk RNA sequencing. RNA sequence data was verified using qPCR of 18 selected genes. Fourteen were confirmed as being upregulated, which include CDH11, PCOLCE, SULF1, GJA4, LUM, CDH6, GNA12, F2RL2, CTSZ, TYROBP, and KDELR3 as well as the downregulation of UGT1A1. We then conducted Ingenuity Pathway Analysis (IPA) to analyze for novel miR-gene relationships through Causal Network Analysis and Upstream Regulator Analysis. We identified 46 miRs that were aberrantly expressed in EAC compared to control tissues. In EAC tissues, seven miRs were associated with activated networks, while 39 miRs were associated with inhibited networks. The miR-gene relationships identified provide novel insights into potentially oncogenic molecular pathways and genes associated with carcinogenesis in esophageal tissue. Our results revealed a distinct miR profile associated with dysregulated genes. The miRs and genes identified in this study may be used in the future as biomarkers and serve as potential therapeutic targets in EAC.
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Affiliation(s)
- Ryan Corlett
- Department of Surgery, Creighton University School of Medicine, Omaha, NE, USA
- Department of Surgery, Creighton University School of Medicine, Omaha, NE, USA
| | - Charles Button
- Department of Surgery, Creighton University School of Medicine, Omaha, NE, USA
- Department of Surgery, Creighton University School of Medicine, Omaha, NE, USA
| | - Sydney Scheel
- Department of Surgery, Creighton University School of Medicine, Omaha, NE, USA
- Department of Surgery, Creighton University School of Medicine, Omaha, NE, USA
| | - Swati Agrawal
- Department of Surgery, Creighton University School of Medicine, Omaha, NE, USA
| | - Vikrant Rai
- Department of Translational Research, Western University of Health Sciences, Pomona, CA, USA
- Department of Translational Research, Western University of Health Sciences, Pomona, CA, USA
| | - Kalyana C Nandipati
- Department of Surgery, Creighton University School of Medicine, Omaha, NE, USA
- Department of Translational Research, Western University of Health Sciences, Pomona, CA, USA
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Santos-Silva MA, Sousa N, Majar M, Machado M, Reis J, Sousa JC. Pattern recognition of hematological profiles of tumors of the digestive tract: an exploratory study. Front Med (Lausanne) 2023; 10:1208022. [PMID: 37663664 PMCID: PMC10469010 DOI: 10.3389/fmed.2023.1208022] [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: 04/18/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Aims In this study, we aimed to apply laboratory blood analysis to identify the hematological (based on hemoglobin concentration, erythrocytes, hematocrit, and RDW count) profiles associated with the most prevalent forms of digestive tract malignancies. Furthermore, we aimed to evaluate how these profiles contributed to distinguishing these tumors at diagnosis. Methods We collected data from the date of ICD-10 diagnostic coding for C15 esophagus, C16 stomach, C18 colon, and C19 rectum tumors of 184 individuals. The statistical analysis and data visualization approaches, notably the heat map and principal component analysis (PCA), allowed for creating a summary hematological profile and identifying the most associated parameters for each pathologic state. Univariate and multivariate data modeling and ROC analysis were performed in both SPSS and Python. Results Our data reveal unique patterns based on tumor development anatomical location, clustering the C18 colon and C19 rectum from the C15 esophagus and C16 stomach. We found a significant difference between C16 stomach carcinoma and the other tumors, which substantially correlated with raised RDW in conjunction with low hemoglobin concentration, erythrocytes, and hematocrit counts. In contrast, C18 colon carcinoma had the higher red blood cell count, allowing for the best classification metrics in the test set of the binary logistic regression (LR) model, accounting for an AUC of 0.77 with 94% sensitivity and 52% specificity. Conclusion This study emphasizes the significance of adding hematological patterns in diagnosing these malignancies, which could path further investigations regarding profiling and monitoring at the point of care.
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Affiliation(s)
- Miguel A. Santos-Silva
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Nuno Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga/Guimarães, Portugal
- Clinical Academic Center-Braga (2CA), Braga, Portugal
- Association P5 Digital Medical Center (ACMP5), Braga, Portugal
| | - Marina Majar
- Clinical Pathology Department, Hospital de Braga, Braga, Portugal
| | - Miguel Machado
- Clinical Pathology Department, Hospital de Braga, Braga, Portugal
| | - Joana Reis
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga/Guimarães, Portugal
- Clinical Academic Center-Braga (2CA), Braga, Portugal
| | - Joao C. Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga/Guimarães, Portugal
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Snoderly-Foster LJ, Olivas WM. Regulation of Parkinson's disease-associated genes by Pumilio proteins and microRNAs in SH-SY5Y neuronal cells. PLoS One 2022; 17:e0275235. [PMID: 36174040 PMCID: PMC9522289 DOI: 10.1371/journal.pone.0275235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Parkinson's disease is the second most common age-related, neurodegenerative disease. A small collection of genes has been linked to Parkinson's disease including LRRK2, SAT1, and SNCA, the latter of which encodes the protein alpha-synuclein that aggregates in Lewy bodies as a hallmark of the disease. Overexpression of even wild-type versions of these genes can lead to pathogenesis, yet the regulatory mechanisms that control protein production of the genes are not fully understood. Pumilio proteins belong to the highly conserved PUF family of eukaryotic RNA-binding proteins that post-transcriptionally regulate gene expression through binding conserved motifs in the 3' untranslated region (UTR) of mRNA targets known as PUF Recognition Elements (PREs). The 3'UTRs of LRRK2, SNCA and SAT1 each contain multiple putative PREs. Knockdown (KD) of the two human Pumilio homologs (Pumilio 1 and Pumilio 2) in a neurodegenerative model cell line, SH-SY5Y, resulted in increased SNCA and LRRK2 mRNA, as well as alpha-synuclein levels, suggesting these genes are normally repressed by the Pumilio proteins. Some studies have indicated a relationship between Pumilio and microRNA activities on the same target, especially when their binding sites are close together. LRRK2, SNCA, and SAT1 each contain several putative microRNA-binding sites within the 3'UTR, some of which reside near PREs. Small RNA-seq and microRNA qPCR assays were performed in both wild type and Pumilio KD SH-SY5Y cells to analyze global and differential microRNA expression. One thousand four hundred and four microRNAs were detected across wild type and Pumilio KD cells. Twenty-one microRNAs were differentially expressed between treatments, six of which were previously established to be altered in Parkinson's disease patient samples or research models. Expression of ten miRs predicted to target LRRK2 and SNCA was verified by RT-qPCR. Collectively, our results demonstrate that Pumilios and microRNAs play a multi-faceted role in regulating Parkinson's disease-associated genes.
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Affiliation(s)
- Lisa J. Snoderly-Foster
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, United States of America
| | - Wendy M. Olivas
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, United States of America
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Xu Z, Chen Z, Peng M, Zhang Z, Luo W, Shi R, Wang L, Hong Y. MicroRNA MiR-490-5p suppresses pancreatic cancer through regulating epithelial-mesenchymal transition via targeting MAGI2 antisense RNA 3. Bioengineered 2022; 13:2673-2685. [PMID: 35043728 PMCID: PMC8974041 DOI: 10.1080/21655979.2021.2024653] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pancreatic cancer with about 5% five-year overall survival rate remains a challenge. Invasion and migration of pancreatic cancer cells are the main factors leading to poor prognosis. MicroRNA-490-5p (miR-490-5p) has anti-cancer effects in a variety of tumors, but its role in pancreatic cancer has not been reported. The mRNA expressions of miR-490-5p, MAGI2 antisense RNA 3 (MAGI2-AS3), Matrix metalloproteinase (MMP)2, MMP9, N-cadherin, and E-cadherin were detected by quantitative real-time PCR, while the protein expressions of these genes except miR-490-5p were measured by Western blot analysis. The cell viability, apoptosis, migration and invasion were detected by cell counting kit-8 (CCK-8), apoptosis and transwell assays. MiR-490-5p was abnormally low-expressed in pancreatic cancer, whose down-regulation generated enhanced effects on viability, migration and invasion in pancreatic cancer cells, as well as MAGI2-AS3 expression. MiR-490-5p mimic exerted the opposite effect on cells, which also down-regulated MMP2, MMP9, and N-cadherin protein expressions, while up-regulating E-cadherin protein expression. MAGI2-AS3, which was the targeted binding site of miR-490-5p, promoted viability, migration and invasion, and inhibited apoptosis of cancer cells. More importantly, miR-490-5p played an anti-cancer role in pancreatic cancer by targeting MAGI2-AS3 and regulating epithelial-mesenchymal transition (EMT), which was partially offset by MAGI2-AS3.
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Affiliation(s)
- Zhenglei Xu
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Guangdong, China
| | - Zeming Chen
- The Second Clinical Medical College, Jinan University, Guangdong, China
| | - Minsi Peng
- The Second Clinical Medical College, Jinan University, Guangdong, China
| | - Zhuliang Zhang
- The Second Clinical Medical College, Jinan University, Guangdong, China
| | - Weixiang Luo
- Department of Nursing, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Guangdong, China
| | - Ruiyue Shi
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Guangdong, China
| | - Lisheng Wang
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Guangdong, China
| | - Yingcai Hong
- Department of Thoracic Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Guangdong, China
- CONTACT Yingcai Hong Department of Thoracic Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Guangdong, China
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MiR-490-5p Restrains Progression of Gastric cancer through DTL Repression. Gastroenterol Res Pract 2021; 2021:2894117. [PMID: 34594374 PMCID: PMC8478551 DOI: 10.1155/2021/2894117] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022] Open
Abstract
Gastric cancer (GC) accounts for a main cause of cancer-related deaths. This study sought for molecular mechanism of miR-490-5p/DTL axis in affecting GC progression, thus bringing new hope for treatment of GC. Expression data of differentially expressed miRNAs and mRNAs in GC tissue from TCGA database were analyzed. MiR-490-5p and DTL mRNA expression levels in GC were evaluated with qRT-PCR. Cell viability was confirmed with CCK-8 method. Cell cycle distribution and apoptosis were analyzed with flow cytometry. Cell migratory and invasive potential was proved with Transwell assay. The targeted relationship between DTL and miR-490-5p was analyzed with dual-luciferase assay. The results indicated a decreased miR-490-5p level in GC cells. MiR-490-5p upregulation hampered proliferation, migration, invasion and promote cell apoptosis. DTL was the target of and inversely associated with miR-490-5p, and it could remarkably induce the carcinogenesis of GC. MiR-490-5p mediated GC cell progression by DTL repression. In conclusion, miR-490-5p and DTL may be valuable in diagnosis and treatment for GC.
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Jakob M, Mattes LM, Unger K, Kueffer S, Hess J, Canis M, Schirmer M, Spiegel JL, Haubner F, Ihler F, Weiss BG, Kitz J. Human microRNA-182-5p and kinectin 1: Potential biomarkers for prognosis in oral squamous cell carcinoma. Head Neck 2021; 43:3707-3719. [PMID: 34591354 DOI: 10.1002/hed.26857] [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: 03/08/2021] [Revised: 07/08/2021] [Accepted: 08/12/2021] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND The prognostic impact of hsa-miRNA-182-5p in oral cancer remains unexplored. Therefore, the aim of this study was to investigate the prognostic value of hsa-miRNA-182-5p and its predicted target kinectin 1 (KTN1) in oral squamous cell carcinoma (OSCC). METHOD Expression level of hsa-miRNA-182-5p was analyzed in tumor tissue (n = 36) and healthy oral mucosal tissue (n = 17) using quantitative real-time polymerase chain reaction. Protein level of the predicted target KTN1 was detected via immunohistochemistry. Results were validated in a cohort of The Cancer Genome Atlas (TCGA). RESULTS After dividing the data into a subgroup with high and low hsa-miRNA-182-5p expression level, a significant better overall (p = 0.016), recurrence-free (p = 0.009), and progression-free survival (p = 0.004) was observed in an upregulation of hsa-miRNA-182-5p. Staining intensity of KTN1 showed a reciprocal impact on the prognosis. Validation in a TCGA cohort confirmed these results. CONCLUSION Our results indicate hsa-miRNA-182-5p and KTN1 as potential biomarkers for OSCC.
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Affiliation(s)
- Mark Jakob
- Department of Otorhinolaryngology, University Hospital, LMU Munich, Munich, Germany.,Department of Otorhinolaryngology, Pan Klinik am Neumarkt Köln, Cologne, Germany
| | - Lena M Mattes
- Department of Otorhinolaryngology, University Medical Center Göttingen, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Research Center for Environmental Health (GmbH), Munich, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Stefan Kueffer
- Institute of Pathology, University Medical Center Göttingen, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Research Center for Environmental Health (GmbH), Munich, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Martin Canis
- Department of Otorhinolaryngology, University Hospital, LMU Munich, Munich, Germany
| | - Markus Schirmer
- Department of Radiation Oncology, University Medical Center Göttingen, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Jennifer L Spiegel
- Department of Otorhinolaryngology, University Hospital, LMU Munich, Munich, Germany
| | - Frank Haubner
- Department of Otorhinolaryngology, University Hospital, LMU Munich, Munich, Germany
| | - Friedrich Ihler
- Department of Otorhinolaryngology, University Hospital, LMU Munich, Munich, Germany.,German Center for Vertigo and Balance Disorders (DSGZ), University Hospital, LMU Munich, Munich, Germany
| | - Bernhard G Weiss
- Department of Otorhinolaryngology, University Hospital, LMU Munich, Munich, Germany
| | - Julia Kitz
- Institute of Pathology, University Medical Center Göttingen, Georg-August-Universität Göttingen, Göttingen, Germany
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The oncogenic role of HIF-1α/miR-182-5p/ZFP36L1 signaling pathway in nasopharyngeal carcinoma. Cancer Cell Int 2021; 21:462. [PMID: 34465330 PMCID: PMC8406720 DOI: 10.1186/s12935-021-02177-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Accumulating evidence indicates that dysregulation of miR-182-5p can serve as diagnostic and prognostic biomarkers for some cancers, whereas the role of miR-182-5p has not been explored in nasopharyngeal carcinoma (NPC). Our study aims to elucidate the biological function of miR-182-5p in NPC and the potential molecular mechanism involved. Methods Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to determine miR-182-5p expression in NPC primary tissues and cell lines. Immunohistochemistry (IHC) for ZFP36L1 was conducted in NPC samples. Western blot was used to evaluate protein expression in cell lines. A series of functional assays were carried out to evaluate the roles of miR-182-5p and ZFP36L1 in tumor development and progression of NPC. Bioinformatics tools and luciferase reporter assays were utilized to identify the potential mechanisms of action. Moreover, rescue experiments were applied to explore whether ZFP36L1 mediated the effects of miR-182-5p in NPC. Results Up-regulation of miR-182-5p was significantly associated with tumor development and poor prognosis in patients with NPC. Functional study demonstrated that miR-182-5p overexpression enhanced, whereas suppression of miR-182-5p impeded NPC cell proliferation, migration, tumorigenesis and metastasis. Mechanistically, miR-182-5p interacted with ZFP36L1 at two sites in its 3′ un-translated region (UTR) and repressed ZFP36L1 expression in NPC. Consistently, an inverse correlation was observed between the expression levels of miR-182-5p and ZFP36L1 using clinical NPC tissues, and down-regulation of ZFP36L1 in NPC predicts poor survival. Furthermore, overexpression of miR-182-5p in NPC was partly attributable to the transcriptional activation effect induced by hypoxia-inducible factor 1α (HIF-1α). Conclusions Our data suggests that miR-182-5p facilitates cell proliferation and migration in NPC through its ability to down-regulate ZFP36L1 expression, and that the HIF-1α/miR-182-5p/ZFP36L1 axis may serve as a novel therapeutic target in the management of NPC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02177-3.
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Xia X, Zhang H, Xia P, Zhu Y, Liu J, Xu K, Yuan Y. Identification of Glycolysis-Related lncRNAs and the Novel lncRNA WAC-AS1 Promotes Glycolysis and Tumor Progression in Hepatocellular Carcinoma. Front Oncol 2021; 11:733595. [PMID: 34527595 PMCID: PMC8437343 DOI: 10.3389/fonc.2021.733595] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/12/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND High glycolysis efficiency in tumor cells can promote tumor growth. lncRNAs play an important role in the proliferation, metabolism and migration of cancer cells, but their regulation of tumor glycolysis is currently not well researched. METHODS We analyzed the co-expression of glycolysis-related genes and lncRNAs in The Cancer Genome Atlas (TCGA) database to screen glycolysis-related lncRNAs. Further prognostic analysis and differential expression analysis were performed. We further analyzed the relationship between lncRNAs and tumor immune infiltration. Since WAC antisense RNA 1 (WAC-AS1) had the greatest effect on the prognosis among all screened lncRNAs and had a larger coefficient in the prognostic model, we chose WAC-AS1 for further verification experiments and investigated the function and mechanism of action of WAC-AS1 in hepatocellular carcinoma. RESULTS We screened 502 lncRNAs that have co-expression relationships with glycolytic genes based on co-expression analysis. Among them, 112 lncRNAs were abnormally expressed in liver cancer, and 40 lncRNAs were related to the prognosis of patients. Eight lncRNAs (WAC-AS1, SNHG3, SNHG12, MSC-AS1, MIR210HG, PTOV1-AS1, AC145207.5 and AL031985.3) were used to established a prognostic model. Independent prognostic analysis (P<0.001), survival analysis (P<0.001), receiver operating characteristic (ROC) curve analysis (AUC=0.779) and clinical correlation analysis (P<0.001) all indicated that the prognostic model has good predictive power and that the risk score can be used as an independent prognostic factor (P<0.001). The risk score and lncRNAs in the model were found to be related to a variety of immune cell infiltration and immune functions. WAC-AS1 was found to affect glycolysis and promote tumor proliferation (P<0.01). WAC-AS1 affected the expression of several glycolysis-related genes (cAMP regulated phosphoprotein 19 (ARPP19), CHST12, MED24 and KIF2A) (P<0.01). Under hypoxic conditions, WAC-AS1 regulated ARPP19 by sponging miR-320d to promote glucose uptake and lactate production (P<0.01). CONCLUSION We constructed a model based on glycolysis-related lncRNAs to evaluate the prognostic risk of patients. The risk score and lncRNAs in the model were related to immune cell infiltration. WAC-AS1 can regulate ARPP19 to promote glycolysis and proliferation by sponging miR-320d.
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Affiliation(s)
- Xigang Xia
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, China
| | - Hao Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, China
| | - Peng Xia
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, China
| | - Yimin Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, China
| | - Jie Liu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, China
| | - Kequan Xu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, China
| | - Yufeng Yuan
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, China
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Mathew R, Mattei V, Al Hashmi M, Tomei S. Updates on the Current Technologies for microRNA Profiling. Microrna 2021; 9:17-24. [PMID: 31264553 DOI: 10.2174/2211536608666190628112722] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/16/2019] [Accepted: 05/31/2019] [Indexed: 12/21/2022]
Abstract
MicroRNAs are RNA molecules of ~22 nt length that regulate gene expression posttranscriptionally. The role of miRNAs has been reported in many cellular processes including apoptosis, cell differentiation, development and proliferation. The dysregulated expression of miRNAs has been proposed as a biomarker for the diagnosis, onset and prognosis of human diseases. The utility of miRNA profiles to identify and discriminate patients from healthy individuals is highly dependent on the sensitivity and specificity of the technologies used for their detection and the quantity and quality of starting material. In this review, we present an update of the current technologies for the extraction, QC assessment and detection of miRNAs with special focus to the most recent methods, discussing their advantages as well as their shortcomings.
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Affiliation(s)
- Rebecca Mathew
- Omics Core and Biorepository, Sidra Medicine, Out Patient Clinic, Doha, Qatar
| | - Valentina Mattei
- Omics Core and Biorepository, Sidra Medicine, Out Patient Clinic, Doha, Qatar
| | - Muna Al Hashmi
- Omics Core and Biorepository, Sidra Medicine, Out Patient Clinic, Doha, Qatar
| | - Sara Tomei
- Omics Core and Biorepository, Sidra Medicine, Out Patient Clinic, Doha, Qatar
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Woo Y, Behrendt CE, Yang A, Hahn M, Goel A, Li H, Yuan YC, Fong Y. Tumor Epigenetic Signature and Survival in Resected Gastric Cancer Patients. J Am Coll Surg 2021; 232:483-491.e1. [PMID: 33465468 DOI: 10.1016/j.jamcollsurg.2020.12.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Precision oncology can identify patient-specific molecular signatures to better inform the prognosis and management of surgical cancer patients. Specifically, microRNAs (miRs) hold promise as prognostic biomarkers because dysregulation of individual miRs is implicated in tumorigenesis, progression, and metastases of various malignancies, including gastric adenocarcinoma (GC). STUDY DESIGN To identify miRs prognostic of survival after radical gastrectomy, we studied GC patients within The Cancer Genome Atlas (TCGA) who had undergone R0 or R1 resection and had data on clinical characteristics, overall survival (OS), and tumor miR expression. The miRs expressed by at least 15% of tumors were eligible for study. From 10 replicate samples, each with 80% of patients, miRs were selected using age-adjusted proportional hazards regression with stepwise selection. Cross-validated miRs (selected by multiple replicates) were retained if they optimized an accelerated failure-time model of OS using all patients. RESULTS In this GC cohort (n = 270), half (916/1,870) of miRs screened met our criteria for evaluation. Cross-validation identified 20 miRs as prognostic, of which 14 (miR-129-1, miR-373, miR-490, miR-597, miR-1185-2, miR-3943, miR-4756, miR-5683, miR-6510, miR-6733, miR-6808, miR-6855, miR-6882, miR-8072) were independently informative. The age-adjusted 14-miRNA panel remained significantly associated with OS after adjustment for pathologic prognostic factors (number of lymph nodes examined, number of positive lymph nodes) and other clinical covariates (TNM stage, residual tumor, tumor microsatellite instability, targeted molecular therapy, sex, race, ethnicity). Panel-predicted survival estimates below the upper tertile cut-off were associated with worse outcome (30% vs 74% OS at 3 years, p < 0.0001). CONCLUSIONS In surgically resected GC patients, an epigenetic signature of miRs associated with survival has the potential to improve prognostication.
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Affiliation(s)
- Yanghee Woo
- Division of Surgical Oncology, Department of Surgery, City of Hope National Medical Center, Beckman Research Institute of City of Hope, Duarte, CA; Cancer Immunotherapeutics Program, Beckman Research Institute of City of Hope, Duarte, CA.
| | - Carolyn E Behrendt
- Division of Biostatistics, Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA
| | - Annie Yang
- Division of Surgical Oncology, Department of Surgery, City of Hope National Medical Center, Beckman Research Institute of City of Hope, Duarte, CA
| | - Maria Hahn
- Division of Surgical Oncology, Department of Surgery, City of Hope National Medical Center, Beckman Research Institute of City of Hope, Duarte, CA
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA
| | - Haiqing Li
- Department of Computational Quantitative Medicine, Center for Informatics, Beckman Research Institute of City of Hope, Duarte, CA
| | - Yate-Ching Yuan
- Department of Computational Quantitative Medicine, Center for Informatics, Beckman Research Institute of City of Hope, Duarte, CA
| | - Yuman Fong
- Division of Surgical Oncology, Department of Surgery, City of Hope National Medical Center, Beckman Research Institute of City of Hope, Duarte, CA
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11
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Study on miRNAs in Pan-Cancer of the Digestive Tract Based on the Illumina HiSeq System Data Sequencing. BIOMED RESEARCH INTERNATIONAL 2019; 2019:8016120. [PMID: 31737678 PMCID: PMC6817930 DOI: 10.1155/2019/8016120] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 08/16/2019] [Accepted: 09/06/2019] [Indexed: 02/08/2023]
Abstract
Objective miRNA has gained attention as a therapeutic target in various malignancies. The proposal of this study was to investigate the biological functions of key miRNAs and target genes in cancers of the digestive tract which include esophageal carcinoma (ESCA), gastric adenocarcinoma (GAC), colon adenocarcinoma (COAD), and rectal adenocarcinoma (READ). Materials and Methods After screening differentially expressed miRNAs (DEMIs) and differentially expressed mRNAs (DEMs) in four digestive cancers from The Cancer Genome Atlas (TCGA) database, the diagnostic value of above DEMIs was evaluated by receiver-operating characteristic (ROC) curve analysis. Then, corresponding DEMIs' target genes were predicted by miRWalk 2.0. Intersection of predicted target genes and DEMs was taken as the target genes of DEMIs, and miRNA-mRNA regulatory networks between DEMIs and target genes were constructed. Meanwhile, the univariate Cox risk regression model was used to screen miRNAs with distinct prognostic value, and Kaplan-Meier analysis was used to determine their significance of prognosis. Furthermore, we performed bioinformatics methods including protein-protein interaction (PPI) networks, gene ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and gene group RIDA analysis by Gene-Cloud of Biotechnology Information (GCBI) to explore the function and molecular mechanisms of DEMIs and predicted target genes in tumor development. Results Eventually, 3 DEMIs (miR-7-3, miR-328, and miR-323a) with significant prognostic value were obtained. In addition, 3 DEMIs (miR-490-3p, miR-133a-3p, and miR-552-3p) and 281 target genes were identified, and the 3 DEMIs showed high diagnostic value in READ and moderate diagnostic value in ESCA, GAC, and COAD. Also, the miRNA-mRNA regulatory network with 3 DEMIs and 281 overlapping genes was successfully established. Functional enrichment analysis showed that 281 overlapping genes were mainly related to regulation of cell proliferation, cell migration, and PI3K-Akt signaling pathway. Conclusion The diagnostic value and prognostic value of significant DEMIs in cancers of the digestive tract were identified, which may provide a novel direction for treatment and prognosis improvement of cancers of the digestive tract.
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12
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Machackova T, Prochazka V, Kala Z, Slaby O. Translational Potential of MicroRNAs for Preoperative Staging and Prediction of Chemoradiotherapy Response in Rectal Cancer. Cancers (Basel) 2019; 11:cancers11101545. [PMID: 31614848 PMCID: PMC6827048 DOI: 10.3390/cancers11101545] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer is the third most common cancer and the second cause of cancer-related deaths. Rectal cancer presents roughly one-third of all colorectal cancer cases and differs from it on both anatomical and molecular levels. While standard treatment of colon cancer patients is radical surgery, rectal cancer is usually treated with pre-operative chemoradiotherapy followed by total mesorectal excision, which requires precise estimation of TNM staging. Unfortunately, stage evaluation is based solely on imaging modalities, and they often do not correlate with postoperative pathological findings. Moreover, approximately half of rectal cancer patients do not respond to such pre-operative therapy, so they are exposed to its toxic effects without any clinical benefit. Thus, biomarkers that could precisely predict pre-operative TNM staging, and especially response to therapy, would significantly advance rectal cancer treatment—but till now, no such biomarker has been identified. In cancer research, microRNAs are emerging biomarkers due to their connection with carcinogenesis and exceptional stability. Circulating miRNAs are promising non-invasive biomarkers that could allow monitoring of a patient throughout the whole therapeutic process. This mini-review aims to summarize the current knowledge on miRNAs and circulating miRNAs involved in the prediction of response to treatment and pre-operative staging in rectal cancer patients.
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Affiliation(s)
- Tana Machackova
- Department of Molecular Medicine, European Institute of Technology, 625 00 Brno, Czech Republic.
| | - Vladimir Prochazka
- Department of Surgery, University Hospital Brno, 625 00 Brno, Czech Republic.
| | - Zdenek Kala
- Department of Surgery, University Hospital Brno, 625 00 Brno, Czech Republic.
| | - Ondrej Slaby
- Department of Molecular Medicine, European Institute of Technology, 625 00 Brno, Czech Republic.
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13
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Klinge CM, Piell KM, Tooley CS, Rouchka EC. HNRNPA2/B1 is upregulated in endocrine-resistant LCC9 breast cancer cells and alters the miRNA transcriptome when overexpressed in MCF-7 cells. Sci Rep 2019; 9:9430. [PMID: 31263129 PMCID: PMC6603045 DOI: 10.1038/s41598-019-45636-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/10/2019] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs are dysregulated in breast cancer. Heterogeneous Nuclear Ribonucleoprotein A2/B1 (HNRNPA2/B1) is a reader of the N(6)-methyladenosine (m6A) mark in primary-miRNAs (pri-miRNAs) and promotes DROSHA processing to precursor-miRNAs (pre-miRNAs). We examined the expression of writers, readers, and erasers of m6A and report that HNRNPA2/B1 expression is higher in tamoxifen-resistant LCC9 breast cancer cells as compared to parental, tamoxifen-sensitive MCF-7 cells. To examine how increased expression of HNRNPA2/B1 affects miRNA expression, HNRNPA2/B1 was transiently overexpressed (~5.4-fold) in MCF-7 cells for whole genome miRNA profiling (miRNA-seq). 148 and 88 miRNAs were up- and down-regulated, respectively, 48 h after transfection and 177 and 172 up- and down-regulated, respectively, 72 h after transfection. MetaCore Enrichment analysis identified progesterone receptor action and transforming growth factor β (TGFβ) signaling via miRNA in breast cancer as pathways downstream of the upregulated miRNAs and TGFβ signaling via SMADs and Notch signaling as pathways of the downregulated miRNAs. GO biological processes for mRNA targets of HNRNPA2/B1-regulated miRNAs included response to estradiol and cell-substrate adhesion. qPCR confirmed HNRNPA2B1 downregulation of miR-29a-3p, miR-29b-3p, and miR-222 and upregulation of miR-1266-5p, miR-1268a, miR-671-3p. Transient overexpression of HNRNPA2/B1 reduced MCF-7 sensitivity to 4-hydroxytamoxifen and fulvestrant, suggesting a role for HNRNPA2/B1 in endocrine-resistance.
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Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40292, USA.
| | - Kellianne M Piell
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40292, USA
| | - Christine Schaner Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, 14203, USA
| | - Eric C Rouchka
- Bioinformatics and Biomedical Computing Laboratory, Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, 40292, USA
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14
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Mjelle R, Sjursen W, Thommesen L, Sætrom P, Hofsli E. Small RNA expression from viruses, bacteria and human miRNAs in colon cancer tissue and its association with microsatellite instability and tumor location. BMC Cancer 2019; 19:161. [PMID: 30786859 PMCID: PMC6381638 DOI: 10.1186/s12885-019-5330-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/29/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNA) and other small RNAs are frequently dysregulated in cancer and are promising biomarkers for colon cancer. Here we profile human, virus and bacteria small RNAs in normal and tumor tissue from early stage colon cancer and correlate the expression with clinical parameters. METHODS Small RNAs from colon cancer tissue and adjacent normal mucosa of 48 patients were sequenced using Illumina high-throughput sequencing. Clinical parameters were correlated with the small RNA expression data using linear models. We performed a meta-analysis by comparing publicly available small RNA sequencing datasets with our original sequencing data to confirm the main findings. RESULTS We identified 331 differentially expressed miRNAs between tumor and normal samples. We found that the major changes in miRNA expression between left and right colon are due to miRNAs located within the Hox-developmental genes, including miR-10b, miR-196b and miR-615. Further, we identified new miRNAs associated with microsatellite instability (MSI), including miR-335, miR-26 and miR-625. We performed a meta-analysis on all publicly available miRNA-seq datasets and identified 117 common miRNAs that were differentially expressed between tumor and normal tissue. The miRNAs miR-135b and miR-31 were the most significant upregulated miRNA in tumor across all datasets. The miRNA miR-133a was the most strongly downregulated miRNA in our dataset and also showed consistent downregulation in the other datasets. The miRNAs associated with MSI and tumor location in our data showed similar changes in the other datasets. Finally, we show that small RNAs from Epstein-Barr virus and Fusobacterium nucleatum are differentially expressed between tumor and normal adjacent tissue. CONCLUSIONS Small RNA profiling in colon cancer tissue revealed novel RNAs associated with MSI and tumor location. We show that Fusobacterium nucleatum are detectable at the RNA-level in colon tissue, and that both Fusobacterium nucleatum and Epstein-Barr virus separate tumor and normal tissue.
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Affiliation(s)
- Robin Mjelle
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.
| | - Wenche Sjursen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,Department of Medical Genetics, St Olavs Hospital, Trondheim Norway, Erling Skjalgssons gt 1, 7030, Trondheim, Norway
| | - Liv Thommesen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,Department of Biomedical Laboratory Science, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,Department of Computer and Information Science, Norwegian University of Science and Technology, NTNU, Sem Sælandsvei 9, 7491, Trondheim, Norway.,Bioinformatics core facility-BioCore, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Eva Hofsli
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,The Cancer Clinic, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
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15
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Molecular Diagnostics in the Neoplasms of the Pancreas, Liver, Gallbladder, and Extrahepatic Biliary Tract: 2018 Update. Clin Lab Med 2019; 38:367-384. [PMID: 29776636 DOI: 10.1016/j.cll.2018.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Pancreatic neoplasms, including ductal adenocarcinoma, solid pseudopapillary neoplasm, pancreatic endocrine neoplasms, acinar cell carcinoma, and pancreatoblastoma, are associated with different genetic abnormalities. Hepatic adenomas with beta-catenin exon 3 mutation are associated with a high risk of malignancy. Hepatic adenoma with arginosuccinate synthetase 1 expression or sonic hedgehog mutations are associated with a risk of bleeding. Hepatocellular carcinoma and choangiocarcinoma display heterogeneity at both morphologic and molecular levels Cholangiocellular carcinoma is most commonly associated with IDH 1/2 mutations.
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16
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Liu J, Huang Y, Wang H, Wu D. MiR-106a-5p promotes 5-FU resistance and the metastasis of colorectal cancer by targeting TGFβR2. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:5622-5634. [PMID: 31949649 PMCID: PMC6963073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 10/26/2018] [Indexed: 06/10/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is the third leading cause of cancer-related deaths. 5-Fluorouracil (5-FU)-based chemotherapy has always been the first-line treatment. However, development of 5-FU resistance seriously affects its curative effect. The aim of this study was to elucidate the molecular mechanisms of 5-FU resistance through miR-106a-5p in CRC. METHODS Colorectal cancer tissues were collected to analyze miR-106a-5p and TGFβR2 expressions by qPCR. Functional experiments for evaluating cell survival and metastasis were conducted to observe the biological effects of miR-106a-5p and TGFβR2. The cell survival rate was calculated using an MTT assay; the metastasis was confirmed with a Transwell invasion assay and Western blotting, which we used to measure the expression levels of the epithelial-mesenchymal transition (EMT) markers E-cadherin and vimentin. The combination of miR-106a to TGFβR2 was predicted using Targetscan, and confirmed through the construction of the luciferase reporter plasmid pGL3-basic. The interplay between miR-106a-5p and TGFβR2 was tested with qPCR and Western blotting. A Spearman rank analysis was employed to verify the correlation of miR-106a-5p and TGFβR2 expressions. RESULTS MiR-106a-5p was up-regulated and TGFβR2 was down-regulated in 5-FU resistant CRC tissues and HT-29 cells. MiR-106a-5p promoted cell survival and suppressed the apoptosis rate and caspase 3 activity. Additionally, cell invasion was promoted by miR-106a-5p overexpression in the HT-29 cells and was inhibited by miR-106a-5p knockdown in the 5-FU resistant HT-29 cells; miR-106a-5p overexpression contributed to migration by increasing vimentin expression and by decreasing E-cadherin expression in the HT-29 cells; miR-106a-5p functioned by directly binding to TGFβR2. The TGFβR2 knockdown conferred chemoresistance of 5-FU and metastasis in 5-FU resistant HT-29 cells, and TGFβR2 overexpression reduced cell survival, invasion numbers, vimentin expression, and increased the cell apoptosis rate and caspase 3 activity in 5-FU resistant HT-29 cells. Also, miR-106a-5p negatively regulated TGFβR2 in a linear correlation way in the CRC tissues. CONCLUSION The up-regulation of miR-106a-5p contributes to the pathomechanism of colorectal cancer by promoting 5-FU resistance and metastasis via inhibiting target TGFβR2. Our findings provide new promising ways for the clinical application of the TGFβR2-miR-106a axis in clinical chemotherapy for 5-FU resistant colorectal cancer.
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Affiliation(s)
- Jian Liu
- Department of General Surgery, The Second Affiliated Hospital of Zhejiang Chinese Medical University (Xinhua Hospital of Zhejiang Province)Hangzhou, China
| | - Yanqin Huang
- Cancer Institute, Second Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
| | - Hongqian Wang
- Department of General Surgery, The Second Affiliated Hospital of Zhejiang Chinese Medical University (Xinhua Hospital of Zhejiang Province)Hangzhou, China
| | - Denghai Wu
- Department of General Surgery, The Second Affiliated Hospital of Zhejiang Chinese Medical University (Xinhua Hospital of Zhejiang Province)Hangzhou, China
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17
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Gao P, Wang H, Yu J, Zhang J, Yang Z, Liu M, Niu Y, Wei X, Wang W, Li H, Wang Y, Sun G. miR-3607-3p suppresses non-small cell lung cancer (NSCLC) by targeting TGFBR1 and CCNE2. PLoS Genet 2018; 14:e1007790. [PMID: 30557355 PMCID: PMC6312350 DOI: 10.1371/journal.pgen.1007790] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 12/31/2018] [Accepted: 10/25/2018] [Indexed: 01/07/2023] Open
Abstract
Accumulating evidence indicates that miRNAs can be promising diagnostic and/or prognostic markers for various cancers. In this study, we identified a novel miRNA, miR-3607-3p, and its targets in non-small cell lung cancer (NSCLC). The expression of miR-3607-3p was measured and its correlation with patient prognosis was determined. Ectopic expression in NSCLC cells, xenografts, and metastasis models was used to evaluate the effects of miR-3607-3p on proliferation and migration of NSCLC. Luciferase assay and western blotting were performed to validate the potential targets of miR-3607-3p after preliminary screening by microarray analysis and computer-aided algorithms. We demonstrated that miR-3607-3p was downregulated in NSCLC tissues and that miR-3607-3p might act as an independent predictor for overall survival in NSCLC. Moreover, serum miR-3607-3p may be a novel and stable marker for NSCLC. We found that overexpression of miR-3607-3p inhibited cell proliferation, colony formation, migration and invasion, and hampered the cell cycle of NSCLC cell lines in vitro. Our results suggested that miR-3607-3p directly targets TGFBR1 and CCNE2. In accordance with in vitro studies, we confirmed that miR-3607-3p functions as a potent suppressor miRNA of NSCLC. We showed that miR-3607-3p agomir could reduce tumor growth and inhibit TGFBR1 and CCNE2 protein expression. Taken together, our findings indicate that miR-3607-3p can inhibit NSCLC cell growth and metastasis by targeting TGFBR1 and CCNE2 protein expression, and provide new evidence of miR-3607-3p as a potential non-invasive biomarker and therapeutic target for NSCLC.
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MESH Headings
- Aged
- Animals
- Biomarkers, Tumor/antagonists & inhibitors
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/therapy
- Cell Cycle/genetics
- Cell Line, Tumor
- Cell Movement/genetics
- Cell Proliferation/genetics
- Cyclins/antagonists & inhibitors
- Cyclins/genetics
- Down-Regulation
- Female
- Gene Knockdown Techniques
- Humans
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Lung Neoplasms/therapy
- Male
- Mice
- Mice, Nude
- Middle Aged
- Neoplasm Invasiveness/genetics
- Neoplasm Invasiveness/prevention & control
- Neoplasm Metastasis
- Prognosis
- RNA, Small Nucleolar/antagonists & inhibitors
- RNA, Small Nucleolar/blood
- RNA, Small Nucleolar/genetics
- Receptor, Transforming Growth Factor-beta Type I/antagonists & inhibitors
- Receptor, Transforming Growth Factor-beta Type I/genetics
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Affiliation(s)
- Peng Gao
- Department of Radiation Oncology, North China University of Science and Technology Affiliated People’s Hospital, Tangshan, China
| | - Huan Wang
- Department of Radiation Oncology, North China University of Science and Technology Affiliated People’s Hospital, Tangshan, China
| | - Jiarui Yu
- Department of Radiation Oncology, North China University of Science and Technology Affiliated People’s Hospital, Tangshan, China
| | - Jie Zhang
- Department of pathology, North China University of Science and Technology Affiliated People’s Hospital, Tangshan, China
| | - Zhao Yang
- Department of Radiation Oncology, North China University of Science and Technology Affiliated People’s Hospital, Tangshan, China
| | - Meiyue Liu
- Department of Radiation Oncology, North China University of Science and Technology Affiliated People’s Hospital, Tangshan, China
| | - Yi Niu
- Department of Radiation Oncology, North China University of Science and Technology Affiliated People’s Hospital, Tangshan, China
| | - Xiaomei Wei
- Department of Radiation Oncology, North China University of Science and Technology Affiliated People’s Hospital, Tangshan, China
| | - Wei Wang
- Department of Radiation Oncology, North China University of Science and Technology Affiliated People’s Hospital, Tangshan, China
| | - Hongmin Li
- Department of pathology, North China University of Science and Technology Affiliated People’s Hospital, Tangshan, China
| | - Yadi Wang
- Department of Radiation Oncology, PLA Army General Hospital, Beijing, China
| | - Guogui Sun
- Department of Radiation Oncology, North China University of Science and Technology Affiliated People’s Hospital, Tangshan, China
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18
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Chen F, Zhou H, Wu C, Yan H. Identification of miRNA profiling in prediction of tumor recurrence and progress and bioinformatics analysis for patients with primary esophageal cancer: Study based on TCGA database. Pathol Res Pract 2018; 214:2081-2086. [PMID: 30477645 DOI: 10.1016/j.prp.2018.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 09/13/2018] [Accepted: 10/17/2018] [Indexed: 02/07/2023]
Abstract
OBJECT This study focused on the identification of prognostic miRNAs for the prediction of tumor recurrence and progress in esophageal cancer. METHODS MiRNA profiling and clinical characteristics of esophageal cancer patients was downloaded from the TCGA database. Univariate analysis was performed to select potential prognostic miRNAs and covariates. LASSO based logistic regression was conducted to identify the prognostic miRNAs given covariates. Bioinformatics analysis including gene ontology, disease ontology and pathway enrichment analysis were performed. A nomogram was generated based on multivariate logistic regression to illustrate the association between the identified miRNAs and the risk of tumor recurrence and progress. RESULTS A total of 1881 miRNAs and 10 clinical characteristics were obtained from TCGA database. 18 miRNAs were finally identified in which 6 miRNAs were identified for the first time to be associated with the tumor recurrence and progress of esophageal cancer given covariates. Bioinformatics analysis suggested that the identified miRNAs were associated with the tumor recurrence and progress of esophageal cancer. The association between identified miRNAs and risk of tumor recurrence and progress were presented in a nomogram. CONCLUSION The 6 newly identified miRNAs may be potential biomarkers for the prediction of tumor recurrence and progress of esophageal cancer.
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Affiliation(s)
- Fangyao Chen
- Department of Epidemiology and Health Statistics, School of Public Health, Xi'an Jiaotong University Health Science Center, 76 Yanta Xilu Road, Xi'an, Shaanxi, 710061, China
| | - Hui Zhou
- Department of Pharmacy, First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta Xilu Road, Xi'an, Shaanxi, 710061, China
| | - Chenqiuzi Wu
- First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta Xilu Road, Xi'an, Shaanxi, 710061, China
| | - Hong Yan
- Department of Epidemiology and Health Statistics, School of Public Health, Xi'an Jiaotong University Health Science Center, 76 Yanta Xilu Road, Xi'an, Shaanxi, 710061, China.
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19
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Chiam K, Mayne GC, Watson DI, Woodman RJ, Bright TF, Michael MZ, Karapetis CS, Irvine T, Phillips WA, Hummel R, Wang T, Pimlott LK, Marri S, Astill DS, Ruszkiewicz AR, Thompson SK, Hussey DJ. Identification of microRNA Biomarkers of Response to Neoadjuvant Chemoradiotherapy in Esophageal Adenocarcinoma Using Next Generation Sequencing. Ann Surg Oncol 2018; 25:2731-2738. [PMID: 29987600 DOI: 10.1245/s10434-018-6626-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Clinical trials report improved overall survival following neoadjuvant chemoradiotherapy in patients undergoing surgery for esophageal adenocarcinoma, with a 10-15% survival improvement. MicroRNAs (miRNAs) are small noncoding RNAs that are known to direct the behavior of cancers, including response to treatment. We investigated the ability of miRNAs to predict outcomes after neoadjuvant chemoradiotherapy. METHODS Endoscopic biopsies from esophageal adenocarcinomas were obtained before neoadjuvant chemoradiotherapy and esophagectomy. miRNA levels were measured in the biopsies using next generation sequencing and compared with pathological response in the surgical resection, and subsequent survival. miRNA ratios that predicted pathological response were identified by Lasso regression and leave-one-out cross-validation. Association between miRNA ratio candidates and relapse-free survival was assessed using Kaplan-Meier analysis. Cox regression and Harrell's C analyses were performed to assess the predictive performance of the miRNAs. RESULTS Two miRNA ratios (miR-4521/miR-340-5p and miR-101-3p/miR-451a) that predicted the pathological response to neoadjuvant chemoradiotherapy were found to be associated with relapse-free survival. Pretreatment expression of these two miRNA ratios, pretreatment tumor differentiation, posttreatment AJCC histopathological tumor regression grading, and posttreatment tumor clearance/margins were significant factors associated with survival in Cox regression analysis. Multivariate analysis of the two ratios together with pretherapy factors resulted in a risk prediction accuracy of 85% (Harrell's C), which was comparable with the prediction accuracy of the AJCC treatment response grading (77%). CONCLUSIONS miRNA-ratio biomarkers identified using next generation sequencing can be used to predict disease free survival following neoadjuvant chemoradiotherapy and esophagectomy in patients with esophageal adenocarcinoma.
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Affiliation(s)
- Karen Chiam
- Cancer Research Division, Cancer Council New South Wales, Sydney, Australia.,Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia
| | - George C Mayne
- Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - David I Watson
- Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Richard J Woodman
- Flinders Centre for Epidemiology and Biostatistics, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Tim F Bright
- Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Michael Z Michael
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Christos S Karapetis
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Tanya Irvine
- Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Wayne A Phillips
- Cancer Biology and Surgical Oncology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Richard Hummel
- Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia.,Department of Surgery, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Tingting Wang
- Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Letitia K Pimlott
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Shashikanth Marri
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - David StJ Astill
- Department of Anatomical Pathology, Flinders Medical Centre, Adelaide, SA, Australia
| | - Andrew R Ruszkiewicz
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Sarah K Thompson
- Department of Surgery, University of Adelaide, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Damian J Hussey
- Discipline of Surgery, College of Medicine and Public Health, Flinders University of South Australia, Adelaide, SA, Australia. .,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia.
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20
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Fang ZQ, Li MC, Zhang YQ, Liu XG. MiR-490-5p inhibits the metastasis of hepatocellular carcinoma by down-regulating E2F2 and ECT2. J Cell Biochem 2018; 119:8317-8324. [PMID: 29932246 DOI: 10.1002/jcb.26876] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/21/2018] [Indexed: 01/07/2023]
Abstract
We intended to evaluate miR-490-5p expression in hepatocellular carcinoma (HCC) tissues and detect the potential targets of miR-490-5p. In vitro experiments were conducted to further investigate the biological function of miR-490-5p on HCC cell metastasis. We investigated the abnormally expressed miRNAs in HCC tissues, and the miR-490-5p expression level was detected by qRT-PCR. E2F2 and ECT2 were proved to be the potential targets of miR-490-5p by luciferase reporter assay. The expression levels of E2F2 and ECT2 were determined using Western blot. Transwell assay was used to analyse the impact of miR-490-5p on metastasis of HCC cells. Four high-expressed miRNAs, and seven low-expressed miRNAs, including miR-490-5p, were detected in HCC tissues. The expression level of miR-490-5p was connected with the tumor size, tumor node metastasis (TNM) stage, and survival ratio of HCC patients. E2F2 and ECT2 were the targets of miR-490-5p, and miR-490-5p inhibited HCC cell metastasis through down-regulating the expressions of E2F2 and ECT2. The over-expressed miR-490-5p could restrain the metastasis of HCC cells by down-regulating E2F2 and ECT2 expression levels.
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Affiliation(s)
- Zheng-Qing Fang
- School of Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Mao-Chun Li
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yu-Qin Zhang
- Department of Medicine, Anhui No. 2 Provincial People's Hospital, Hefei, Anhui, China
| | - Xiang-Guo Liu
- College of Chinese and Western Medicine (School of Life Science), Anhui University of Chinese Medicine, Hefei, Anhui, China
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21
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Brown RAM, Epis MR, Horsham JL, Kabir TD, Richardson KL, Leedman PJ. Total RNA extraction from tissues for microRNA and target gene expression analysis: not all kits are created equal. BMC Biotechnol 2018; 18:16. [PMID: 29548320 PMCID: PMC5857145 DOI: 10.1186/s12896-018-0421-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 02/28/2018] [Indexed: 01/10/2023] Open
Abstract
Background microRNAs (miRNAs) are short non-coding RNAs that fine-tune gene expression. The aberrant expression of miRNAs is associated with many diseases and they have both therapeutic and biomarker potential. However, our understanding of their usefulness is dependent on the tools we have to study them. Previous studies have identified the need to optimise and standardise RNA extraction methods in order to avoid biased results. Herein, we extracted RNA from murine lung, liver and brain tissues using five commercially available total RNA extraction methods. These included either: phenol: chloroform extraction followed by alcohol precipitation (TRIzol), phenol:chloroform followed by solid-phase extraction (column-based; miRVana and miRNeasy) and solid-phase separation with/without affinity resin (Norgen total and Isolate II). We then evaluated each extraction method for the quality and quantity of RNA recovered, and the expression of miRNAs and target genes. Results We identified differences between each of the RNA extraction methods in the quantity and quality of RNA samples, and in the analysis of miRNA and target gene expression. For the purposes of consistency in quantity, quality and high recovery of miRNAs from tissues, we identified that Phenol:chloroform phase separation combined with silica column-based solid extraction method was preferable (miRVana microRNA isolation). We also identified a method that is not appropriate for miRNA analysis from tissue samples (Bioline Isolate II). For target gene expression any of the kits could be used to analyse mRNA, but if interested in analysing mRNA and miRNA from the same RNA samples some methods should be avoided. Conclusions Different methods used to isolate miRNAs will yield different results and therefore a robust RNA isolation method is required for reproducibility. Researchers should optimise these methods for their specific application and keep in mind that “total RNA” extraction methods do not isolate all types of RNA equally. Electronic supplementary material The online version of this article (10.1186/s12896-018-0421-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rikki A M Brown
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, University of Western Australia, Centre for Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, WA, 6009, Australia
| | - Michael R Epis
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, University of Western Australia, Centre for Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, WA, 6009, Australia
| | - Jessica L Horsham
- School of Medicine and Pharmacology, the University of Western Australia, Nedlands, WA, 6009, Australia.
| | - Tasnuva D Kabir
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, University of Western Australia, Centre for Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, WA, 6009, Australia
| | - Kirsty L Richardson
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, University of Western Australia, Centre for Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, WA, 6009, Australia
| | - Peter J Leedman
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, University of Western Australia, Centre for Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, WA, 6009, Australia. .,School of Medicine and Pharmacology, the University of Western Australia, Nedlands, WA, 6009, Australia.
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22
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Zhang L, Zhang Y, Wong SH, Law PTY, Zhao S, Yu J, Chan MTV, Wu WKK. Common Deregulation of Seven Biological Processes by MicroRNAs in Gastrointestinal Cancers. Sci Rep 2018; 8:3287. [PMID: 29459716 PMCID: PMC5818544 DOI: 10.1038/s41598-018-21573-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/07/2018] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs are frequently dysregulated in human neoplasms, including gastrointestinal cancers. Nevertheless, the global influence of microRNA dysregulation on cellular signaling is still unknown. Here we sought to elucidate cellular signaling dysregulation by microRNAs in gastrointestinal cancers at the systems biology level followed by experimental validation. Signature dysregulated microRNAs in gastric, colorectal and liver cancers were defined based on our previous studies. Targets of signature dysregulated miRNAs were predicted using multiple computer algorithms followed by gene enrichment analysis to identify biological processes perturbed by dysregulated microRNAs. Effects of microRNAs on endocytosis were measured by epidermal growth factor (EGF) internalization assay. Our analysis revealed that, aside from well-established cancer-related signaling pathways, several novel pathways, including axon guidance, neurotrophin/nerve growth factor signaling, and endocytosis, were found to be involved in the pathogenesis of gastrointestinal cancers. The regulation of EGF receptor (EGFR) endocytosis by two predicted miRNAs, namely miR-17 and miR-145, was confirmed experimentally. Functionally, miR-145, which blocked EGFR endocytosis, prolonged EGFR membrane signaling and altered responsiveness of colon cancer cells to EGFR-targeting drugs. In conclusion, our analysis depicts a comprehensive picture of cellular signaling dysregulation, including endocytosis, by microRNAs in gastrointestinal cancers.
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Affiliation(s)
- Lin Zhang
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuchen Zhang
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny H Wong
- Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Priscilla T Y Law
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Shan Zhao
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China.
| | - William K K Wu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China. .,Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.
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23
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Li X, Xu W, Kang W, Wong SH, Wang M, Zhou Y, Fang X, Zhang X, Yang H, Wong CH, To KF, Chan SL, Chan MTV, Sung JJY, Wu WKK, Yu J. Genomic analysis of liver cancer unveils novel driver genes and distinct prognostic features. Theranostics 2018; 8:1740-1751. [PMID: 29556353 PMCID: PMC5858179 DOI: 10.7150/thno.22010] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/12/2017] [Indexed: 01/04/2023] Open
Abstract
Objective: Hepatocellular carcinoma (HCC) is a highly heterogeneous disease with a dismal prognosis. However, driver genes and prognostic markers in HCC remain to be identified. It is hoped that in-depth analysis of HCC genomes in relation to available clinicopathological information will give rise to novel molecular prognostic markers. Methods: We collected genomic data of 1,061 HCC patients from previous studies, and performed integrative analysis to identify significantly mutated genes and molecular prognosticators. We employed three MutSig algorithms (MutSigCV, MutSigCL and MutSigFN) to identify significantly mutated genes. The GISTIC2 algorithm was used to delineate focally amplified and deleted genomic regions. Nonnegative matrix factorization (NMF) was utilized to decipher mutational signatures. Kaplan-Meier survival and Cox regression analyses were used to associate gene mutation and copy number alteration with survival outcome. Logistic regression model was applied to test association between gene mutation and mutational signatures. Results: We discovered 11 novel driver genes, including RNF213, VAV3 and TNRC6B, with mutational prevalence ranging from 1% to 3%. Seven mutational signatures were also identified in HCC, some of which were associated with mutations of classical driver genes (e.g., TP53, TERT) as well as alcohol consumption. Focal amplifications of TERT and other druggable targets, including AURKA, were also revealed. Targeting AURKA by a small-molecule inhibitor potently induced apoptosis in HCC cells. We further demonstrated that HCC patients with TERT amplification displayed shortened overall survival independent of other clinicopathological parameters. In conclusion, our study identified novel cancer driver genes and prognostic markers in HCC, reiterating the translational importance of omics data in the precision medicine era.
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Affiliation(s)
- Xiangchun Li
- Institute of Digestive Diseases and Department of Medicine & Therapeutics, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
- Public Laboratory, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, People's Republic of China
| | - Weiqi Xu
- Institute of Digestive Diseases and Department of Medicine & Therapeutics, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong
| | - Sunny H Wong
- Institute of Digestive Diseases and Department of Medicine & Therapeutics, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Mengyao Wang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, Guangdong, People's Republic of China
| | - Yong Zhou
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, Guangdong, People's Republic of China
| | - Xiaodong Fang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, Guangdong, People's Republic of China
| | - Xiuqing Zhang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, Guangdong, People's Republic of China
| | - Huanming Yang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, Guangdong, People's Republic of China
- James D. Watson Institute of Genome Sciences, 310058, Hangzhou, People's Republic of China
| | - Chi H Wong
- Department of Clinical Oncology, State Key Laboratory in Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
| | - Ka F To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong
| | - Stephen L Chan
- Department of Clinical Oncology, State Key Laboratory in Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong
| | - Joseph J Y Sung
- Institute of Digestive Diseases and Department of Medicine & Therapeutics, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - William K K Wu
- Institute of Digestive Diseases and Department of Medicine & Therapeutics, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong
| | - Jun Yu
- Institute of Digestive Diseases and Department of Medicine & Therapeutics, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
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24
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Grassi A, Perilli L, Albertoni L, Tessarollo S, Mescoli C, Urso EDL, Fassan M, Rugge M, Zanovello P. A coordinate deregulation of microRNAs expressed in mucosa adjacent to tumor predicts relapse after resection in localized colon cancer. Mol Cancer 2018; 17:17. [PMID: 29386021 PMCID: PMC5791208 DOI: 10.1186/s12943-018-0770-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/19/2018] [Indexed: 12/11/2022] Open
Abstract
Up to 20% of colorectal cancer (CRC) node-negative patients develop loco-regional or distant recurrences within 5 years from surgery. No predictive biomarker able to identify the node-negative subjects at high risk of relapse after curative treatment is presently available.Forty-eight localized (i.e. stage I-II) colon cancer patients who underwent radical tumor resection were considered. The expression of five miRNAs, involved in CRC progression, was investigated by qRT-PCR in both tumor tissue and matched normal colon mucosa.Interestingly, we found that the coordinate deregulation of four miRNAs (i.e. miR-18a, miR-21, miR-182 and miR-183), evaluated in the normal mucosa adjacent to tumor, is predictive of relapse within 55 months from curative surgery.Our results, if confirmed in independent studies, may help to identify high-risk patients who could benefit most from adjuvant therapy. Moreover, this work highlights the importance of extending the search for tissue biomarkers also to the tumor-adjacent mucosa.
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Affiliation(s)
- Angela Grassi
- Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy.
| | - Lisa Perilli
- Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy. .,Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy.
| | - Laura Albertoni
- Surgical Pathology and Cytopathology Unit, Department of Medicine DIMED, University of Padova, Padova, Italy
| | - Sofia Tessarollo
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Claudia Mescoli
- Surgical Pathology and Cytopathology Unit, Department of Medicine DIMED, University of Padova, Padova, Italy
| | | | - Matteo Fassan
- Surgical Pathology and Cytopathology Unit, Department of Medicine DIMED, University of Padova, Padova, Italy
| | - Massimo Rugge
- Surgical Pathology and Cytopathology Unit, Department of Medicine DIMED, University of Padova, Padova, Italy
| | - Paola Zanovello
- Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy. .,Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy.
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25
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Abstract
MicroRNA (miRNA) is the noncoding gene: therefore, the miRNA gene inheritably controls protein gene expression through transcriptional and post-transcriptional levels. Aberrant expression of miRNA genes causes various human diseases, especially cancers. Although cancer is a complex disease, cancer/miRNA implication has yet been grasped from the perspective of miRNA profile in bed side. Since miRNA is the mobile genetic element, the clinical verification of miRNA in microvesicle of blood is too much straggle to predict potential cancer/miRNA associations without bioinformatical computing. Further, experimental investigation of miRNA/cancer pathways is expensive and time-consuming. While the accumulated data (big data) of miRNA profiles has been on line as the databases in cancers, using the database algorithms for miRNA target prediction have reduced required time for conventional experiments and have cut the cost. Computational prediction of miRNA/target mRNA has shown numerous significant outcomes that are unobtainable only by experimental approaches. However, ID of miRNA in the annotation is an arbitrary number and the ID is not related with miRNA its functions. Therefore, it has not been physicochemically shown why multiple miRNAs in blood or tissues are useful for diagnosis and porgnosis of human diseases or why function of single miRNA in cancer is rendered to oncomir or tumopr suppressor. In addition, it is less cleared why environmental factors, such as temperature, radiation, therapeutic anti-cancer immune or chemical agents can alter the expression of miRNAs in the cell. The ceRNA theory would not be enough for the investigation of such subjects. Given miRNA/target prediction tools, to elucidate such issues with computer simulation we have previously introduced the quantum miRNA/miRNA interaction as a new scoring using big database. The quantum score was implicated in miRNA synergisms in cancer and participated in the miRNA/target interaction on human diseases. On the other hand, ribosomal RNA (rRNA) is the dominant RNA species of the cells. It is well known that ribosomopathies, such as Diamond-Blackfan anemia, dyskeratiosis congenital, Shwachman-Diamond syndrome, 5q-myelodysplastic syndrome, Treacher Collins syndrome, cartilage-hair hypoplasia, North American Indian childhood cirrhosis, isolated congenital asplenia, Bowen-Conradi syndrome and cancer are caused by altered expression of ribosomal proteins or rRNA genes. We have proposed the hypothesis that the interaction among miRNAs from rRNA and/or other cellular miRNAs would be involved into cancer as the ribosomopathy. Subsequently, we found rRNA-derived miRNAs (rmiRNAs) by using the sequence homology search (miPS) with miRNA database (miRBase). Further, the pathway related with cancer between rmiRNA/target protein gene was predicted by miRNA entangling target sorting (METS) algorithm. In this chapter, we describe about the usage of in silico miRNA identification program, miRNA/target prediction search through the database and quantum language of miRNA by the METS, and the ontology analysis. In particular, the METS algorithm according to the quantum value would be useful simulator to discover a new therapeutic target aganist cancer. It may also partly contribute to the elucidation of complex mechanisms and development of agents of anti-cancer.
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Affiliation(s)
- Yoichi Robertus Fujii
- Retroviral Genetics Group, Pharmaco-MicroRNA Genomics, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan.
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26
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Amin M, Islam F, Gopalan V, Lam AK. Detection and Quantification of MicroRNAs in Esophageal Adenocarcinoma. Methods Mol Biol 2018; 1756:257-268. [PMID: 29600376 DOI: 10.1007/978-1-4939-7734-5_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
MicroRNAs (miRNAs) are a class of small, noncoding RNAs that have been emerging as novel regulators in esophageal adenocarcinoma. Their role has been established in various aspects of esophageal adenocarcinoma including carcinogenesis, progression, treatment, and prognosis. Therefore, miRNA detection, profiling, and quantification have become extremely important for scientists and clinicians. As miRNAs are small, their detection can be challenging. There have been various methods developed to detect and/or quantify miRNAs. This chapter aims to introduce the fundamentals and methods of the most commonly used approaches including miRNA microarrays and quantitative real-time polymerase chain reaction (RT-qPCR) to detect and quantify miRNAs in esophageal adenocarcinoma.
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Affiliation(s)
- Moein Amin
- Cancer Molecular Pathology of School of Medicine, Griffith University, Gold Coast, Australia
| | - Farhadul Islam
- Cancer Molecular Pathology of School of Medicine, Griffith University, Gold Coast, Australia
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Vinod Gopalan
- Cancer Molecular Pathology of School of Medicine, Griffith University, Gold Coast, Australia
| | - Alfred K Lam
- Cancer Molecular Pathology of School of Medicine, Griffith University, Gold Coast, Australia.
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27
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Yang X, Pang YY, He RQ, Lin P, Cen JM, Yang H, Ma J, Chen G. Diagnostic value of strand-specific miRNA-101-3p and miRNA-101-5p for hepatocellular carcinoma and a bioinformatic analysis of their possible mechanism of action. FEBS Open Bio 2017; 8:64-84. [PMID: 29321958 PMCID: PMC5757177 DOI: 10.1002/2211-5463.12349] [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: 03/19/2017] [Revised: 05/08/2017] [Accepted: 11/08/2017] [Indexed: 02/06/2023] Open
Abstract
There is accumulating evidence that miRNA might serve as potential diagnostic and prognostic markers for various types of cancer. Hepatocellular carcinoma (HCC) is the most common type of malignant lesion but the significance of miRNAs in HCC remains largely unknown. The present study aimed to establish the diagnostic value of miR-101-3p/5p in HCC and then further investigate the prospective molecular mechanism via a bioinformatic analysis. First, the miR-101 expression profiles and parallel clinical parameters from 362 HCC patients and 50 adjacent non-HCC tissue samples were downloaded from The Cancer Genome Atlas (TCGA). Second, we aggregated all miR-101-3p/5p expression profiles collected from published literature and the Gene Expression Omnibus and TCGA databases. Subsequently, target genes of miR-101-3p and miR-101-5p were predicted by using the miRWalk database and then overlapped with the differentially expressed genes of HCC identified by natural language processing. Finally, bioinformatic analyses were conducted with the overlapping genes. The level of miR-101 was significantly lower in HCC tissues compared with adjacent non-HCC tissues (P < 0.001), and the area under the curve of the low miR-101 level for HCC diagnosis was 0.925 (P < 0.001). The pooled summary receiver operator characteristic (SROC) of miR-101-3p was 0.86, and the combined SROC curve of miR-101-5p was 0.80. Bioinformatic analysis showed that the target genes of both miR-101-3p and miR-101-5p are involved in several pathways that are associated with HCC. The hub genes for miR-101-3p and miR-101-5p were also found. Our results suggested that both miR-101-3p and miR-101-5p might be potential diagnostic markers in HCC, and that they exert their functions via targeting various prospective genes in the same pathways.
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Affiliation(s)
- Xia Yang
- Department of Pathology First Affiliated Hospital of Guangxi Medical University Nanning China
| | - Yu-Yan Pang
- Department of Pathology First Affiliated Hospital of Guangxi Medical University Nanning China
| | - Rong-Quan He
- Department of Medical Oncology First Affiliated Hospital of Guangxi Medical University Nanning China
| | - Peng Lin
- Department of Ultrasonography First Affiliated Hospital of Guangxi Medical University Nanning China
| | - Jie-Mei Cen
- Department of Medical Oncology First Affiliated Hospital of Guangxi Medical University Nanning China
| | - Hong Yang
- Department of Ultrasonography First Affiliated Hospital of Guangxi Medical University Nanning China
| | - Jie Ma
- Department of Medical Oncology First Affiliated Hospital of Guangxi Medical University Nanning China
| | - Gang Chen
- Department of Pathology First Affiliated Hospital of Guangxi Medical University Nanning China
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28
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Stool- and Blood-Based Molecular Tests in Screening for Colorectal Cancer: Ready for Prime Time? CURRENT COLORECTAL CANCER REPORTS 2017. [DOI: 10.1007/s11888-017-0383-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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29
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Bijlsma MF, Sadanandam A, Tan P, Vermeulen L. Molecular subtypes in cancers of the gastrointestinal tract. Nat Rev Gastroenterol Hepatol 2017; 14:333-342. [PMID: 28400627 DOI: 10.1038/nrgastro.2017.33] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Malignancies of the gastrointestinal tract are among the most common human cancers. The distinct tissues of origin give rise to a diverse set of diseases, such as colorectal cancer, pancreatic carcinoma and gastric cancers, with each associating with specific clinical features. Genomic and transcriptomic analyses have further defined the heterogeneity that occurs within these cancers by identifying so-called molecular subtypes. These subtypes are characterized by specific genetic aberrations and expression signatures that suggest important biological differences. Although at first sight this subdivision of organ-specific cancers might increase the complexity of classification, closer analysis suggests that the subtypes detected in the various malignancies are recurring. For example, nearly all gastrointestinal cancers appear to present with subtypes that are either characterized by a mesenchymal gene expression signatures, extensive immune infiltration or metabolic dysregulation. Additionally, in each of the gastrointestinal malignancies, a 'canonical' subtype is recognized that retains characteristic features of the epithelial tissue of origin. These common themes can enhance our collective understanding of these malignancies, and could perhaps be therapeutically exploited. In this Review, the identification of subtypes in the various gastrointestinal cancer types are discussed along with how they could be incorporated into clinical practice.
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Affiliation(s)
- Maarten F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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30
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Youns M, Abdel Halim Hegazy W. The Natural Flavonoid Fisetin Inhibits Cellular Proliferation of Hepatic, Colorectal, and Pancreatic Cancer Cells through Modulation of Multiple Signaling Pathways. PLoS One 2017; 12:e0169335. [PMID: 28052097 PMCID: PMC5215656 DOI: 10.1371/journal.pone.0169335] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/15/2016] [Indexed: 02/06/2023] Open
Abstract
Digestive cancers are major causes of mortality and morbidity worldwide. Fisetin, a naturally occurring flavonoid, has been previously shown anti-proliferative, anti-cancer, neuroprotective, and antioxidant activities. In our study, the anti-tumor activities in addition to regulatory effects of fisetin on some cancer cell lines were investigated. Data presented here showed that fisetin induces growth inhibition, and apoptosis in hepatic (HepG-2), colorectal (Caco-2) and pancreatic (Suit-2) cancer cell lines. Gene expression results showed that 1307 genes were significantly regulated in their expression in hepatic and pancreatic cell lines. 350 genes were commonly up-regulated and 353 genes were commonly down-regulated. Additionally, 604 genes were oppositely expressed in both tumor cells. CDK5 signaling, NRF2-mediated oxidative stress response, glucocorticoid signaling, and ERK/MAPK signaling were among most prominent signaling pathways modulating the growth inhibitory effects of fisetin on hepatic and pancreatic cancer cells. The present analysis showed, for the first time, that the anti-tumor effect of fisetin was mediated mainly through modulation of multiple signaling pathways and via activation of CDKN1A, SEMA3E, GADD45B and GADD45A and down-regulation of TOP2A, KIF20A, CCNB2 and CCNB1 genes.
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Affiliation(s)
- Mаhmoud Youns
- Department of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
- * E-mail:
| | - Wael Abdel Halim Hegazy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Al-Sharqia, Egypt
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31
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Cheng Y, Yang B, Xi Y, Chen X. RAD51B as a potential biomarker for early detection and poor prognostic evaluation contributes to tumorigenesis of gastric cancer. Tumour Biol 2016; 37:14969-14978. [PMID: 27651161 DOI: 10.1007/s13277-016-5340-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/06/2016] [Indexed: 01/30/2023] Open
Abstract
Gastric cancer (GC) is a common and deadly disease worldwide. Outcomes of patients are poor largely due to chemoresistance or recurrence. Thus, identifying novel biomarkers to predict response to therapy and/or prognosis are urgently needed. RAD51B, a key player in DNA repair/recombination, has the potential to be a candidate oncogene and biomarker for cancer diagnosis and prognosis. However, its relationship with GC remains unclear. To evaluate clinicopathological and prognostic significance of RAD51B in GC, we examined messenger RNA (mRNA) and protein expression via quantitative real-time polymerase chain reaction (qRT-PCR) from 69 and tissue microarray from 144 GC patients, respectively. Our results showed that RAD51B mRNA expression was significantly up-regulated in tumors compared to that of matched noncancerous tissues (P < 0.001). In parallel, RAD51B protein showed a mainly nucleus-staining pattern, and the positive rate in tumors and stomach atypical hyperplasia was significantly higher than that in matched noncancerous tissues (P = 0.015). Moreover, high level of RAD51B protein was correlated with advanced stage (P = 0.009), aggressive differentiation (P = 0.022), and lymph node metastasis (P = 0.001). Further, Kaplan-Meier analysis indicated that patients with high level of RAD51B expression exhibited worse overall survival compared to patients with low level (P = 0.040). A multivariate Cox regression analysis suggested that RAD51B may be an independent prognostic factor for GC patients in Chinese population (P = 0.004). Additionally, functional studies indicated that over-expression of RAD51B promoted cell proliferation, aneuploidy, and drug resistance, while RAD51B knockdown led to G1 arrest and sensitized cells to 5-fluorouracil (5-FU). In conclusion, RAD51B may act as an oncogene during GC progression, and its hyper-expression may be a potential biomarker for early detection and poor prognosis of GC.
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Affiliation(s)
- Yikun Cheng
- Beijing New Oriental Foreign Language School at Yangzhou, Yangzhou, Jiangsu, 225006, China
| | - Bin Yang
- Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi, 030001, People's Republic of China
| | - Yanfeng Xi
- Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi, 030001, People's Republic of China.
| | - Xing Chen
- Department of Endoscopy, Shanxi Cancer Hospital, Taiyuan, Shanxi, 030001, China.
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