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Weng KQ, Liu JY, Li H, She LL, Qiu JL, Qi H, Qi HY, Li YS, Dai YB. Identification of Treg-related prognostic molecular subtypes and individualized characteristics in clear cell renal cell carcinoma through single-cell transcriptomes and bulk RNA sequencing. Int Immunopharmacol 2024; 130:111746. [PMID: 38442575 DOI: 10.1016/j.intimp.2024.111746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND In clear cell renal cell carcinoma (ccRCC), the role of Regulatory T cells (Treg cells) as prognostic and immunotherapy response predictors is not fully explored. METHODS Analyzing renal clear cell carcinoma datasets from TISCH, TCGA, and GEO, we focused on 8 prognostic Treg genes to study patient subtypes in ccRCC. We assessed Treg subtypes in relation to patient prognosis, tumor microenvironment, metabolism. Using Cox regression and principal component analysis, we devised Treg scores for individual patient characterization and explored the molecular role of C1QL1, a critical gene in the Treg model, through in vivo and in vitro studies. RESULTS Eight Treg-associated prognostic genes were identified, classifying ccRCC patients into cluster A and B. Cluster A patients showed poorer prognosis with distinct clinical and molecular profiles, potentially benefiting more from immunotherapy. Low Treg scores correlated with worse outcomes and clinical progression. Low scores also suggested that patients might respond better to immunotherapy and targeted therapies. In ccRCC, C1QL1 knockdown reduced tumor proliferation and invasion via NF-kb-EMT pathways and decreased Treg cell infiltration, enhancing immune efficacy. CONCLUSIONS The molecular subtype and Treg score in ccRCC, based on Treg cell marker genes, are crucial in personalizing ccRCC treatment and underscore C1QL1's potential as a tumor biomarker and target for immunotherapy.
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Affiliation(s)
- Kang Qiang Weng
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China.
| | - Jin Yu Liu
- The Affiliated Hospital of Putian University, 999 DongZhen East Rd, Putian 351100, Fujian, China.
| | - Hu Li
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China.
| | - Lin Lu She
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China.
| | - Jun Liang Qiu
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China.
| | - Hao Qi
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China.
| | - Hui Yue Qi
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China.
| | - Yong Sheng Li
- Department of Urology, Fujian Province, Fujian Medical University Union Hospital, Gulou District, 29 Xin-quan Road, Fuzhou, China.
| | - Ying Bo Dai
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China.
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Wang J, Luo LZ, Liang DM, Guo C, Huang ZH, Sun GY, Wen J. Progress in the research of cuproptosis and possible targets for cancer therapy. World J Clin Oncol 2023; 14:324-334. [PMID: 37771632 PMCID: PMC10523190 DOI: 10.5306/wjco.v14.i9.324] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/05/2023] [Accepted: 09/04/2023] [Indexed: 09/20/2023] Open
Abstract
Developing novel cancer therapies that exploit programmed cell death pathways holds promise for advancing cancer treatment. According to a recently published study in Science, copper death (cuproptosis) occurs when intracellular copper is overloaded, triggering aggregation of lipidated mitochondrial proteins and Fe-S cluster proteins. This intriguing phenomenon is triggered by the instability of copper ions. Understanding the molecular mechanisms behind cuproptosis and its associated genes, as identified by Tsvetkov, including ferredoxin 1, lipoic acid synthase, lipoyltransferase 1, dihydrolipid amide dehydrogenase, dihydrolipoamide transacetylase, pyruvate dehydrogenase α1, pyruvate dehydrogenase β, metallothionein, glutaminase, and cyclin-dependent kinase inhibitor 2A, may open new avenues for cancer therapy. Here, we provide a new understanding of the role of copper death and related genes in cancer.
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Affiliation(s)
- Jiang Wang
- Children Medical Center, Hunan Provincial People’s Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha 410013, Hunan Province, China
| | - Lan-Zhu Luo
- Children Medical Center, Hunan Provincial People’s Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha 410013, Hunan Province, China
| | - Dao-Miao Liang
- Department of Hepatobiliary Surgery, Hunan Provincial People’s Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha 410013, Hunan Province, China
| | - Chao Guo
- Department of Hepatobiliary Surgery, Hunan Provincial People’s Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha 410013, Hunan Province, China
| | - Zhi-Hong Huang
- Children Medical Center, Hunan Provincial People’s Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha 410013, Hunan Province, China
| | - Guo-Ying Sun
- Department of Histology and Embryology, Hunan Normal University School of Medicine, Changsha 410013, Hunan Province, China
| | - Jie Wen
- Department of Pediatric Orthopedics, Hunan Provincial People’s Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha 410013, Hunan Province, China
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Feng L, Shu HP, Sun LL, Tu YC, Liao QQ, Yao LJ. Role of the SLIT-ROBO signaling pathway in renal pathophysiology and various renal diseases. Front Physiol 2023; 14:1226341. [PMID: 37497439 PMCID: PMC10366692 DOI: 10.3389/fphys.2023.1226341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 06/30/2023] [Indexed: 07/28/2023] Open
Abstract
SLIT ligand and its receptor ROBO were initially recognized for their role in axon guidance in central nervous system development. In recent years, as research has advanced, the role of the SLIT-ROBO signaling pathway has gradually expanded from axonal repulsion to cell migration, tumor development, angiogenesis, and bone metabolism. As a secreted protein, SLIT regulates various pathophysiological processes in the kidney, such as proinflammatory responses and fibrosis progression. Many studies have shown that SLIT-ROBO is extensively involved in various aspects of kidney development and maintenance of structure and function. The SLIT-ROBO signaling pathway also plays an important role in different types of kidney disease. This article reviews the advances in the study of the SLIT-ROBO pathway in various renal pathophysiological and kidney disorders and proposes new directions for further research in this field.
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Zhu M, Yan T, Zhu S, Weng F, Zhu K, Wang C, Guo C. Identification and verification of FN1, P4HA1 and CREBBP as potential biomarkers in human atrial fibrillation. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:6947-6965. [PMID: 37161136 DOI: 10.3934/mbe.2023300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
BACKGROUND Atrial fibrillation (AF) is a common arrhythmia that can lead to cardiac complications. The mechanisms involved in AF remain elusive. We aimed to explore the potential biomarkers and mechanisms underpinning AF. METHODS An independent dataset, GSE2240, was obtained from the Gene Expression Omnibus database. The R package, "limma", was used to screen for differentially expressed genes (DEGs) in individuals with AF and normal sinus rhythm (SR). Weighted gene co-expression network analysis (WGCNA) was applied to cluster DEGs into different modules based on functional disparities. Enrichment analyses were performed using the Database for Annotation, Visualization and Integrated Discovery. A protein-protein interaction network was constructed, and hub genes were identified using cytoHubba. Quantitative reverse-transcription PCR was used to validate mRNA expression in individuals with AF and SR. RESULTS We identified 2, 589 DEGs clustered into 10 modules using WGCNA. Gene Ontology analysis showed specific clustered genes significantly enriched in pathways associated with the extracellular matrix and collagen organization. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the target genes were mainly enriched for proteoglycans in cancer, extracellular matrix-receptor interaction, focal adhesion, and the PI3K-Akt signaling pathway. Three hub genes, FN1, P4HA1 and CREBBP, were identified, which were highly correlated with AF endogenesis. mRNA expression of hub genes in patients with AF were higher than in individuals with normal SR, consistent with the results of bioinformatics analysis. CONCLUSIONS FN1, P4HA1, and CREBBP may play critical roles in AF. Using bioinformatics, we found that expression of these genes was significantly elevated in patients with AF than in individuals with normal SR. Furthermore, these genes were elevated at core positions in the mRNA interaction network. These genes should be further explored as novel biomarkers and target candidates for AF therapy.
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Affiliation(s)
- Miao Zhu
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Tao Yan
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Shijie Zhu
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Fan Weng
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Kai Zhu
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Chunsheng Wang
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Changfa Guo
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
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Molina-Cerrillo J, Santoni M, Ruiz Á, Massari F, Pozas J, Ortego I, Gómez V, Grande E, Alonso-Gordoa T. Epigenetics in advanced renal cell carcinoma: Potential new targets. Crit Rev Oncol Hematol 2022; 180:103857. [DOI: 10.1016/j.critrevonc.2022.103857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/06/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
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Li X, Sun X, Kan C, Chen B, Qu N, Hou N, Liu Y, Han F. COL1A1: A novel oncogenic gene and therapeutic target in malignancies. Pathol Res Pract 2022; 236:154013. [PMID: 35816922 DOI: 10.1016/j.prp.2022.154013] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 02/07/2023]
Abstract
Collagen type I alpha 1 (COL1A1), a member of the collagen family, is involved in epithelial-mesenchymal transition, which is closely linked to malignant tumorigenesis. COL1A1 is highly expressed in various cancers and regulates various cellular processes, including cell proliferation, metastasis, apoptosis, and cisplatin resistance. COL1A1 is also associated with cancer progression and prognosis; elevated COL1A1 expression is associated with poor prognosis in cancer patients. However, the main role of COL1A as a cancer-promoting factor in specific tumors has not been reported. Additionally, the protein levels and mechanisms of action of this protein differ among tumor types. This review discusses current research progress concerning COL1A1 in different tumor types, and then summarizes its contributions to cancer progression, thus providing a basis for follow-up research and potential targets for cancer treatment.
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Affiliation(s)
- Xue Li
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang, China; Department of Pathology, Affiliated Hospital of Weifang Medical University, Weifang, China; Branch of Shandong Provincial Clinical Research Center for Diabetes and Metabolic Diseases, and Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Xiaodong Sun
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang, China; Branch of Shandong Provincial Clinical Research Center for Diabetes and Metabolic Diseases, and Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Chengxia Kan
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang, China; Branch of Shandong Provincial Clinical Research Center for Diabetes and Metabolic Diseases, and Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Bing Chen
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang, China; Department of Pathology, Affiliated Hospital of Weifang Medical University, Weifang, China; Branch of Shandong Provincial Clinical Research Center for Diabetes and Metabolic Diseases, and Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Na Qu
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang, China; Department of Pathology, Affiliated Hospital of Weifang Medical University, Weifang, China; Branch of Shandong Provincial Clinical Research Center for Diabetes and Metabolic Diseases, and Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Ningning Hou
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang, China; Branch of Shandong Provincial Clinical Research Center for Diabetes and Metabolic Diseases, and Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Yongping Liu
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang, China; Branch of Shandong Provincial Clinical Research Center for Diabetes and Metabolic Diseases, and Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China.
| | - Fang Han
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang, China; Department of Pathology, Affiliated Hospital of Weifang Medical University, Weifang, China; Branch of Shandong Provincial Clinical Research Center for Diabetes and Metabolic Diseases, and Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China.
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MALDI-MSI: A Powerful Approach to Understand Primary Pancreatic Ductal Adenocarcinoma and Metastases. Molecules 2022; 27:molecules27154811. [PMID: 35956764 PMCID: PMC9369872 DOI: 10.3390/molecules27154811] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022] Open
Abstract
Cancer-related deaths are very commonly attributed to complications from metastases to neighboring as well as distant organs. Dissociate response in the treatment of pancreatic adenocarcinoma is one of the main causes of low treatment success and low survival rates. This behavior could not be explained by transcriptomics or genomics; however, differences in the composition at the protein level could be observed. We have characterized the proteomic composition of primary pancreatic adenocarcinoma and distant metastasis directly in human tissue samples, utilizing mass spectrometry imaging. The mass spectrometry data was used to train and validate machine learning models that could distinguish both tissue entities with an accuracy above 90%. Model validation on samples from another collection yielded a correct classification of both entities. Tentative identification of the discriminative molecular features showed that collagen fragments (COL1A1, COL1A2, and COL3A1) play a fundamental role in tumor development. From the analysis of the receiver operating characteristic, we could further advance some potential targets, such as histone and histone variations, that could provide a better understanding of tumor development, and consequently, more effective treatments.
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8
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Identification of COL1A1 associated with immune infiltration in brain lower grade glioma. PLoS One 2022; 17:e0269533. [PMID: 35789341 PMCID: PMC9255759 DOI: 10.1371/journal.pone.0269533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 05/23/2022] [Indexed: 11/19/2022] Open
Abstract
Brain low grade gliomas (LGG) often give serious clinical symptoms due to the invasion towards nervous system, affecting the life quality of patients. Collagen type I alpha 1(COL1A1) is the main component of type I collagen. Although there are many reports about abnormal expression of COL1A1 in various tumors, specific role and clinical significance of COL1A1 in LGG have not yet been elucidated. In this work, Tumor Immune Estimation Resource database was used for detecting the expression level of COL1A1 in cancer and normal tissues, and aimed to explore the relationship between COL1A1 and tumor immune infiltration. We applied Kaplan-Meier to analyze the role of COL1A1 in clinical prognosis. Univariate survival rate and multivariate Cox analysis were used to compare clinical characteristics and survival rate. The relativity between the expression of COL1A1 and the tumor microenvironment was evaluated using ESTIMATE algorithm. Finally, the relationship between expression level of COL1A1 and gene marker sets of immune cell infiltration was investigated via TIMER. According to TCGA, COL1A1 overexpression was correlated with overall survival (OS), progression free interval (PFI) and disease specific survival (DSS) of multiple tumors, especially in LGG. Multivariate analysis showed that COL1A1 expression was an independent prognostic factor for LGG. The expression of COL1A1 was positively correlated with the infiltration of CD4 + T and CD8 + T cells, neutrophils, macrophages and dendritic cells in LGG. In addition, there was a strong correlation between expression of COL1A1 and different immune marker sets in LGG. The results suggest that COL1A1 is related with tumor immune infiltration of LGG.
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Yang F, Lian M, Ma H, Feng L, Shen X, Chen J, Fang J. Identification of key genes associated with papillary thyroid microcarcinoma characteristics by integrating transcriptome sequencing and weighted gene co-expression network analysis. Gene 2022; 811:146086. [PMID: 34856364 DOI: 10.1016/j.gene.2021.146086] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/01/2021] [Accepted: 11/23/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Papillary thyroid microcarcinoma (PTMC) is the most prevalent histological type of thyroid carcinoma. Despite the overall favorable prognosis of PTMC, some cases exhibit aggressive phenotypes. The identification of robust biomarkers may improve early PTMC diagnosis. In this study, we integrated high-throughput transcriptome sequencing, bioinformatic analyses and experimental validation to identify key genes associated with the malignant characteristics of PTMC. METHODS Total RNA was extracted from 24 PTMC samples and 7 non-malignant thyroid tissue samples, followed by RNA sequencing. The differentially expressed genes (DEGs) were identified and used to construct co-expression networks by weighted gene co-expression network analysis (WGCNA). Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed, and protein-protein interaction networks were constructed. Key modules and hub genes showing a strong correlation with the malignant characteristics of PTMC were identified and validated. RESULTS The green-yellow and turquoise modules generated by WGCNA were strongly associated with the malignant characteristics of PTMC. Functional enrichment analysis revealed that genes in the green-yellow module participated in cell motility and metabolism, whereas those in the turquoise module participated in several oncogenic biological processes. Nine real hub genes (FHL1, NDRG2, NEXN, SYNM, COL1A1, FN1, LAMC2, POSTN, and TGFBI) were identified and validated at the transcriptional and translational levels. Our preliminary results indicated their diagnostic potentials in PTMC. CONCLUSIONS In this study, we identified key co-expression modules and nine malignancy-related genes with potential diagnostic value in PTMC.
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Affiliation(s)
- Fan Yang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, China, 100029.
| | - Meng Lian
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Hongzhi Ma
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Ling Feng
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Xixi Shen
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Jiaming Chen
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Jugao Fang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730; Department of Thyroid Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730.
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Yao ZY, Xing C, Liu YW, Xing XL. Identification of Two Immune Related Genes Correlated With Aberrant Methylations as Prognosis Signatures for Renal Clear Cell Carcinoma. Front Genet 2021; 12:750997. [PMID: 34925447 PMCID: PMC8674690 DOI: 10.3389/fgene.2021.750997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
Almost 75% of renal cancers are renal clear cell carcinomas (KIRC). Accumulative evidence indicates that epigenetic dysregulations are closely related to the development of KIRC. Cancer immunotherapy is an effective treatment for cancers. The aim of this study was to identify immune-related differentially expressed genes (IR-DEGs) associated with aberrant methylations and construct a risk assessment model using these IR-DEGs to predict the prognosis of KIRC. Two IR-DEGs (SLC11A1 and TNFSF14) were identified by differential expression, correlation analysis, and Cox regression analysis, and risk assessment models were established. The area under the receiver operating characteristic (ROC) curve (AUC) was 0.6907. In addition, we found that risk scores were significantly associated with 31 immune cells and factors. Our present study not only shows that two IR-DEGs can be used as prognosis signatures for KIRC, but also provides a strategy for the screening of suitable prognosis signatures associated with aberrant methylation in other cancers.
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Affiliation(s)
- Zhi-Yong Yao
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua, China.,The First Affiliated Hospital of Hunan University of Medicine, Huaihua, China
| | - Chaoqung Xing
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua, China
| | - Yuan-Wu Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China
| | - Xiao-Liang Xing
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua, China.,The First Affiliated Hospital of Hunan University of Medicine, Huaihua, China
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11
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Mohamed AA, Abo-Amer YEE, Aalkhalegy A, Fathalla LA, Elmaghraby MB, Elhoseeny MM, Mostafa SM, El-Abgeegy M, Khattab RA, El-damasy DA, Salah W, Salem AM, Elmashad WM, Elbahnasawy M, Abd-Elsalam S. COL1A1 Gene Expression in Hepatitis B Virus (HBV) Related Hepatocellular Carcinoma (HCC) Egyptian's Patients. THE OPEN BIOMARKERS JOURNAL 2021; 11:108-114. [DOI: 10.2174/1875318302111010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/28/2021] [Accepted: 08/26/2021] [Indexed: 09/01/2023]
Abstract
Introduction:
Collagens are the most abundant proteins in the human body, accounting for one-third of total proteins. Over the last few years, accumulated evidence have indicated that some collagens are differentially expressed in cancer. The aim of the study was to assess COL1A1 gene expression as a novel marker for the progression of hepatitis B cirrhosis into hepatocellular carcinoma.
Methods:
This cohort study included 348 subjects and was conducted between May 2018 and June 2019. Subjects were divided into 4 groups: group1 included HBV positive hepatocellular carcinoma patients “HCC” (n= 87), group II included HBV positive patients with liver cirrhosis “LC” (n = 87), group III included chronic hepatitis B patients with neither HCC nor cirrhosis “ C-HBV” (n = 87) and group IV consisted of healthy volunteers as controls (n = 87). Fasting venous blood samples (10 ml) were collected from each participant in this study and were used for assessment of aspartate aminotransferase (AST), alanine aminotransferase (ALT), total bilirubin, albumin and alfa-fetoprotein (AFP). Another portion of blood was collected in 2 vacutainer tubes containing EDTA, one for Complete blood count and the other for gene expression of COL1A1.
Results:
The gene expression of collagen was 6.9 ± 8.8 in group 1 (HBV positive hepatocellular carcinoma patients) and this was a significant increase in comparison with the other groups. In group 2 (HBV positive patients with liver cirrhosis), the gene expression (collagen) was 3.7±1.5 and it was significantly increased when compared with group 4 (healthy volunteers).
Conclusion:
COL1A1 gene expression can be used as an indicator of the progression of hepatitis B cirrhosis into hepatocellular carcinoma.
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Ren T, Xue X, Wang X, Zhou X, Dang S. Bioinformatic and experimental analyses of key biomarkers in pancreatic cancer. Exp Ther Med 2021; 22:1359. [PMID: 34659505 PMCID: PMC8515505 DOI: 10.3892/etm.2021.10794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 09/15/2020] [Indexed: 12/18/2022] Open
Abstract
The present study aimed to screen the key genes in pancreatic cancer and to explore the pathogenesis of pancreatic cancer. A total of three expression profiling datasets (GSE28735, GSE16515 and GSE15471) associated with pancreatic cancer were retrieved from the public gene chip database. The differentially expressed genes (DEGs) were screened by GEO2R and subjected to Gene Ontology (GO) and signaling pathway enrichment analysis. Furthermore, a protein interaction network was constructed. The GEPIA online database was used to screen for genes that affect the prognosis of pancreatic cancer. Finally, cell functional experiments were performed on the selected key genes. A total of 72 DEGs were identified, including 52 upregulated and 20 downregulated genes. Enrichment analysis revealed roles of the DEGs in endodermal cell differentiation, cell adhesion, extracellular matrix-receptor interaction and PI3K-Akt signaling pathway. In total, 10 key nodal genes were identified, including integrin subunit α 2 (ITGA2), ITGB6 and collagen α 1 chain 1. Through survival analysis, two genes with an impact on the prognosis of pancreatic cancer were identified, namely ITGA2 and ITGB6. Silencing of ITGB6 in a pancreatic cancer cell line significantly suppressed cell proliferation and induced cell cycle arrest at G2/M phase. The identified key genes and signaling pathways may help to deepen the understanding of the molecular mechanisms involved in pancreatic cancer and provide a theoretical basis to develop novel therapies.
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Affiliation(s)
- Tianyu Ren
- Department of General Surgery, The Affiliated Hospital, Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
| | - Xiaofei Xue
- Department of General Surgery, Pucheng Hospital, Weinan, Shaanxi 715500, P.R. China
| | - Xiaogang Wang
- Department of General Surgery, Pucheng Hospital, Weinan, Shaanxi 715500, P.R. China
| | - Xingtong Zhou
- Department of General Surgery, The Affiliated Hospital, Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
| | - Shengchun Dang
- Department of General Surgery, The Affiliated Hospital, Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China.,Department of General Surgery, Pucheng Hospital, Weinan, Shaanxi 715500, P.R. China
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Zhu M, Gong J, Zhan M, Xi C, Shen G, Shen H. Transcriptome analysis reveals the molecular mechanism of long-term exposure of Eriocheir sinensis to low concentration of trichlorfon. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100916. [PMID: 34601228 DOI: 10.1016/j.cbd.2021.100916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022]
Abstract
Trichlorphon, a common organophosphorus pesticide (OPs), is widely used in aquaculture to prevent aquatic insects from infecting cultured objects as well as to control the excessive proliferation of plankton in water bodies. However, its repeated use time can contaminate water bodies and impart direct/indirect toxicity to beneficial aquatic species. However, the underlying mechanism regarding toxicity and cellular metabolism remains unclear. Understanding the mechanism would enable the standardized use and management of OPs and their use in the aquatic environment. Here, low concentration of trichlorphon (5 × 10-5 g/L) was used to construct a hepatopancreatic transcriptional library 30 d, 60 d and 90 d after exposure using RNA-Seq. We detected 649, 148, and 2949 DEGs in the hepatopancreas of E. sinensis for the Tri01 vs. Ctr01, Tri02 vs. Ctr02 and Tri03 vs. Ctr03 library, respectively. The results of KEGG pathway enrichment analysis showed that DEGs were mainly enriched in signal transduction, carbohydrate metabolism, transport and catabolism, endocrine system, and digestive system. Also, under trichlorfon stress, DEGs of E. sinensis were enriched in thyroid hormone signaling pathways, protein digestion and absorption, cancer pathways, etc. The significant DEGs were mainly related to metabolism and the apoptosis and autophagy pathways. This study lays a foundation for further revealing the effects of long-term trichlorfon stress on E. sinensis as well as the potential physiological toxicity. The relevant transcriptome data could provide a reference for the molecular toxicological evaluation of trichlorfon in aquaculture.
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Affiliation(s)
- Mengru Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jie Gong
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Ming Zhan
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Changjun Xi
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Guoqing Shen
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Huaishun Shen
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
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14
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Fan Y, Dai F, Yuan M, Wang F, Wu N, Xu M, Bai Y, Liu Y. A construction and comprehensive analysis of ceRNA networks and infiltrating immune cells in papillary renal cell carcinoma. Cancer Med 2021; 10:8192-8209. [PMID: 34598322 PMCID: PMC8607257 DOI: 10.1002/cam4.4309] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 08/16/2021] [Accepted: 09/05/2021] [Indexed: 12/13/2022] Open
Abstract
Background As the second most common malignancy in adults, papillary renal cell carcinoma (PRCC) has shown an increasing trend in both incidence and mortality. Effective treatment for advanced metastatic PRCC is still lacking. In this study, we aimed to establish competitive endogenous RNA (ceRNA) networks related to PRCC tumorigenesis, and analyze the specific role of differentially expressed ceRNA components and infiltrating immune cells in tumorigenesis. Methods CeRNA networks were established to identify the key ceRNAs related to PRCC tumorigenesis based on the 318 samples from The Cancer Genome Atlas database (TCGA), including 285 PRCC and 33 normal control samples. The R package, “CIBERSORT,” was used to evaluate the infiltration of 22 types of immune cells. Then we identified the significant ceRNAs and immune cells, based on which two nomograms were obtained for predicting the prognosis in PRCC patients. Finally, we investigated the co‐expression of PRCC‐specific immune cells and core ceRNAs via Pearson correlation test. Results COL1A1, H19, ITPKB, LDLR, TCF4, and WNK3 were identified as hub genes in ceRNA networks. Four prognostic‐related tumor‐infiltrating immune cells, including T cells CD4 memory resting, Macrophages M1, and Macrophages M2 were revealed. Pearson correlation test indicated that Macrophage M1 was negatively related with COL1A1 (p < 0.01) and LDLR (p < 0.01), while Macrophage M2 was positively related with COL1A1 (p < 0.01), TCF4 (p < 0.01), and H19 (p = 0.032). Two nomograms were conducted with favorable accuracies (area under curve of 1‐year survival: 0.935 and 0.877; 3‐year survival: 0.849 and 0.841; and 5‐year survival: 0.818 and 0.775, respectively). Conclusion The study constructed two nomograms suited for PRCC prognosis predicting. Moreover, we concluded that H19‐miR‐29c‐3p‐COL1A1 axis might promote the polarization of M2 macrophages and inhibit M1 macrophage activation through Wnt signaling pathway, collaborating to promote PRCC tumorigenesis and lead to poor overall survival of PRCC patients.
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Affiliation(s)
- Yaqi Fan
- Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fangfang Dai
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Mengqin Yuan
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Feiyan Wang
- Shanghai Skin Disease Clinical College of Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, China
| | - Nanhui Wu
- Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, China
| | - Mingyuan Xu
- Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yun Bai
- Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yeqiang Liu
- Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, China
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15
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Soto JA, Rodríguez-Antolín C, Vera O, Pernía O, Esteban-Rodríguez I, Dolores Diestro M, Benitez J, Sánchez-Cabo F, Alvarez R, De Castro J, Ibanez de Cáceres I. Transcriptional epigenetic regulation of Fkbp1/Pax9 genes is associated with impaired sensitivity to platinum treatment in ovarian cancer. Clin Epigenetics 2021; 13:167. [PMID: 34454589 PMCID: PMC8401184 DOI: 10.1186/s13148-021-01149-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 08/09/2021] [Indexed: 12/31/2022] Open
Abstract
Background In an effort to contribute to overcoming the platinum resistance exhibited by most solid tumors, we performed an array of epigenetic approaches, integrating next-generation methodologies and public clinical data to identify new potential epi-biomarkers in ovarian cancer, which is considered the most devastating of gynecological malignancies.
Methods We cross-analyzed data from methylome assessments and restoration of gene expression through microarray expression in a panel of four paired cisplatin-sensitive/cisplatin-resistant ovarian cancer cell lines, along with publicly available clinical data from selected individuals representing the state of chemoresistance. We validated the methylation state and expression levels of candidate genes in each cellular phenotype through Sanger sequencing and reverse transcription polymerase chain reaction, respectively. We tested the biological role of selected targets using an ectopic expression plasmid assay in the sensitive/resistant tumor cell lines, assessing the cell viability in the transfected groups. Epigenetic features were also assessed in 189 primary samples obtained from ovarian tumors and controls. Results We identified PAX9 and FKBP1B as potential candidate genes, which exhibited epigenetic patterns of expression regulation in the experimental approach. Re-establishment of FKBP1B expression in the resistant OVCAR3 phenotype in which this gene is hypermethylated and inhibited allowed it to achieve a degree of platinum sensitivity similar to the sensitive phenotype. The evaluation of these genes at a translational level revealed that PAX9 hypermethylation leads to a poorer prognosis in terms of overall survival. We also set a precedent for establishing a common epigenetic signature in which the validation of a single candidate, MEST, proved the accuracy of our computational pipelines. Conclusions Epigenetic regulation of PAX9 and FKBP1B genes shows that methylation in non-promoter areas has the potential to control gene expression and thus biological consequences, such as the loss of platinum sensitivity. At the translational level, PAX9 behaves as a predictor of chemotherapy response to platinum in patients with ovarian cancer. This study revealed the importance of the transcript-specific study of each gene under potential epigenetic regulation, which would favor the identification of new markers capable of predicting each patient’s progression and therapeutic response. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01149-8.
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Affiliation(s)
- Javier Andrés Soto
- Universidad de Santander, School of Medical and Health Sciences, Masira Research Institute, Bucaramanga, Colombia. .,Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Paseo de la Castellana 261, 28046, Madrid, Spain.
| | - Carlos Rodríguez-Antolín
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Paseo de la Castellana 261, 28046, Madrid, Spain.,Biomarkers and Experimental Therapeutics in Cancer, Calle de Pedro Rico, 6, 28029, IdiPAZMadrid, Spain
| | - Olga Vera
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Paseo de la Castellana 261, 28046, Madrid, Spain.,Biomarkers and Experimental Therapeutics in Cancer, Calle de Pedro Rico, 6, 28029, IdiPAZMadrid, Spain
| | - Olga Pernía
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Paseo de la Castellana 261, 28046, Madrid, Spain.,Biomarkers and Experimental Therapeutics in Cancer, Calle de Pedro Rico, 6, 28029, IdiPAZMadrid, Spain
| | - Isabel Esteban-Rodríguez
- Biomarkers and Experimental Therapeutics in Cancer, Calle de Pedro Rico, 6, 28029, IdiPAZMadrid, Spain.,Department of Pathology, La Paz University Hospital, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Maria Dolores Diestro
- Gynecologic Oncology Unit, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Javier Benitez
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Calle de Melchor Fernández Almagro, 3, 28029, Madrid, Spain.,Spanish Network On Rare Diseases (CIBERER), Av. Monforte de Lemos, 3-5. Pabellón 11. Planta 0, 28029, Madrid, Spain
| | - Fátima Sánchez-Cabo
- Spanish National Center for Cardiovascular Research Center (CNIC), Calle de Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Rafael Alvarez
- Hospital Universitario HM Sanchinarro, Calle de Oña, 10, 28050, Sanchinarro, Madrid, Spain
| | - Javier De Castro
- Biomarkers and Experimental Therapeutics in Cancer, Calle de Pedro Rico, 6, 28029, IdiPAZMadrid, Spain
| | - Inmaculada Ibanez de Cáceres
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Paseo de la Castellana 261, 28046, Madrid, Spain. .,Biomarkers and Experimental Therapeutics in Cancer, Calle de Pedro Rico, 6, 28029, IdiPAZMadrid, Spain.
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16
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The Role of Epigenetics in the Progression of Clear Cell Renal Cell Carcinoma and the Basis for Future Epigenetic Treatments. Cancers (Basel) 2021; 13:cancers13092071. [PMID: 33922974 PMCID: PMC8123355 DOI: 10.3390/cancers13092071] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The accumulated evidence on the role of epigenetic markers of prognosis in clear cell renal cell carcinoma (ccRCC) is reviewed, as well as state of the art on epigenetic treatments for this malignancy. Several epigenetic markers are likely candidates for clinical use, but still have not passed the test of prospective validation. Development of epigenetic therapies, either alone or in combination with tyrosine-kinase inhibitors of immune-checkpoint inhibitors, are still in their infancy. Abstract Clear cell renal cell carcinoma (ccRCC) is curable when diagnosed at an early stage, but when disease is non-confined it is the urologic cancer with worst prognosis. Antiangiogenic treatment and immune checkpoint inhibition therapy constitute a very promising combined therapy for advanced and metastatic disease. Many exploratory studies have identified epigenetic markers based on DNA methylation, histone modification, and ncRNA expression that epigenetically regulate gene expression in ccRCC. Additionally, epigenetic modifiers genes have been proposed as promising biomarkers for ccRCC. We review and discuss the current understanding of how epigenetic changes determine the main molecular pathways of ccRCC initiation and progression, and also its clinical implications. Despite the extensive research performed, candidate epigenetic biomarkers are not used in clinical practice for several reasons. However, the accumulated body of evidence of developing epigenetically-based biomarkers will likely allow the identification of ccRCC at a higher risk of progression. That will facilitate the establishment of firmer therapeutic decisions in a changing landscape and also monitor active surveillance in the aging population. What is more, a better knowledge of the activities of chromatin modifiers may serve to develop new therapeutic opportunities. Interesting clinical trials on epigenetic treatments for ccRCC associated with well established antiangiogenic treatments and immune checkpoint inhibitors are revisited.
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17
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Rosas-Alonso R, Colmenarejo-Fernandez J, Pernia O, Rodriguez-Antolín C, Esteban I, Ghanem I, Sanchez-Cabrero D, Losantos-Garcia I, Palacios-Zambrano S, Moreno-Bueno G, de Castro J, Martinez-Marin V, Ibanez-de-Caceres I. Clinical validation of a novel quantitative assay for the detection of MGMT methylation in glioblastoma patients. Clin Epigenetics 2021; 13:52. [PMID: 33750464 PMCID: PMC7941980 DOI: 10.1186/s13148-021-01044-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/28/2021] [Indexed: 12/03/2022] Open
Abstract
Background The promoter hypermethylation of the methylguanine-DNA methyltransferase gene is a frequently used biomarker in daily clinical practice as it is associated with a favorable prognosis in glioblastoma patients treated with temozolamide. Due to the absence of adequately standardized techniques, international harmonization of the MGMT methylation biomarker is still an unmet clinical need for the diagnosis and treatment of glioblastoma patients. Results In this study we carried out a clinical validation of a quantitative assay for MGMT methylation detection by comparing a novel quantitative MSP using double-probe (dp_qMSP) with the conventional MSP in 100 FFPE glioblastoma samples. We performed both technologies and established the best cutoff for the identification of positive-methylated samples using the quantitative data obtained from dp_qMSP. Kaplan–Meier curves and ROC time dependent curves were employed for the comparison of both methodologies. Conclusions We obtained similar results using both assays in the same cohort of patients, in terms of progression free survival and overall survival according to Kaplan–Meier curves. In addition, the results of ROC(t) curves showed that dp_qMSP increases the area under curve time-dependent in comparison with MSP for predicting progression free survival and overall survival over time. We concluded that dp_qMSP is an alternative methodology compatible with the results obtained with the conventional MSP. Our assay will improve the therapeutic management of glioblastoma patients, being a more sensitive and competitive alternative methodology that ensures the standardization of the MGMT-biomarker making it reliable and suitable for clinical use. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01044-2.
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Affiliation(s)
- Rocio Rosas-Alonso
- Epigenetics Laboratory. INGEMM, Paseo La Castellana 261. Edificio Bloque Quirúrgico Planta -2. University Hospital La Paz, 28046, Madrid, Spain. .,Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ, Madrid, Spain.
| | - Julian Colmenarejo-Fernandez
- Epigenetics Laboratory. INGEMM, Paseo La Castellana 261. Edificio Bloque Quirúrgico Planta -2. University Hospital La Paz, 28046, Madrid, Spain.,Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ, Madrid, Spain
| | - Olga Pernia
- Epigenetics Laboratory. INGEMM, Paseo La Castellana 261. Edificio Bloque Quirúrgico Planta -2. University Hospital La Paz, 28046, Madrid, Spain.,Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ, Madrid, Spain
| | - Carlos Rodriguez-Antolín
- Epigenetics Laboratory. INGEMM, Paseo La Castellana 261. Edificio Bloque Quirúrgico Planta -2. University Hospital La Paz, 28046, Madrid, Spain.,Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ, Madrid, Spain
| | - Isabel Esteban
- Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ, Madrid, Spain.,Pathology Department, La Paz University Hospital, Madrid, Spain
| | - Ismael Ghanem
- Medical Oncology Department, La Paz University Hospital, Madrid, Spain
| | | | | | | | - Gema Moreno-Bueno
- MD Anderson Cancer Center, Madrid, Spain.,Biochemistry Department, UAM/ IIBm (CSIC-UAM), IdiPaz, Fundación MD Anderson Internacional, Madrid, Spain.,CIBERONC, Madrid, Spain
| | - Javier de Castro
- Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ, Madrid, Spain.,Medical Oncology Department, La Paz University Hospital, Madrid, Spain
| | | | - Inmaculada Ibanez-de-Caceres
- Epigenetics Laboratory. INGEMM, Paseo La Castellana 261. Edificio Bloque Quirúrgico Planta -2. University Hospital La Paz, 28046, Madrid, Spain. .,Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ, Madrid, Spain.
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18
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Gómez-González C, Rosas-Alonso R, Rodríguez-Antolín C, García-Guede A, Ibáñez de Caceres I, Sanguino J, Pascual SI, Esteban I, Pozo AD, Mori MÁ, Torres RJ, Prior C. Symptomatic heterozygous X-Linked myotubular myopathy female patient with a large deletion at Xq28 and decrease expression of normal allele. Eur J Med Genet 2021; 64:104170. [PMID: 33618039 DOI: 10.1016/j.ejmg.2021.104170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/04/2021] [Accepted: 02/16/2021] [Indexed: 11/28/2022]
Abstract
X-linked myotubular myopathy (XLMTM; OMIM 310400) is a centronuclear congenital muscular disorder of X-linked recessive inheritance. Although female carriers are typically asymptomatic, affected heterozygous females have been described. Here, we describe the case of a sporadic female patient with suspicion of centronuclear myopathy and a heterozygous large deletion at Xq28 encompassing the MAMLD1, MTM1, MTMR1, CD99L2, and HMGB3 genes. The deletion was first detected using a custom next generation sequencing (NGS)-based multigene panel and finally characterized by comparative genomic hybridization array and multiplex ligation probe assay techniques. In this patient we have confirmed, by MTM1 mRNA quantification, a MTM1 gene expression less than the expected 50 percent in patient muscle. The significant 20% reduction in MTM1 mRNA expression in muscle, precludes low level of the normal myotubularin protein as the cause of the phenotype in this heterozygous female. We have also found that BIN1 expression in patient muscle biopsy was significantly increased, and postulate that BIN1 expression will be increased in XLMTM patient muscle as an attempt to maintain muscle function.
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Affiliation(s)
| | - Rocío Rosas-Alonso
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPaz, Madrid, Spain
| | - Carlos Rodríguez-Antolín
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPaz, Madrid, Spain
| | - Alvaro García-Guede
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPaz, Madrid, Spain
| | - Inmaculada Ibáñez de Caceres
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPaz, Madrid, Spain
| | - Javier Sanguino
- Department of Genetics, INGEMM, La Paz University Hospital, Madrid, Spain
| | - Samuel I Pascual
- Department of Pediatric Neurology. La Paz University Hospital, Madrid, Spain
| | - Isabel Esteban
- Department of Anatomical Pathology. La Paz University Hospital, Madrid, Spain
| | - Angela Del Pozo
- Department of Bioinformatics, INGEMM, La Paz University Hospital, Madrid, Spain
| | - María Ángeles Mori
- Department of Genetics, INGEMM, La Paz University Hospital, Madrid, Spain
| | - Rosa J Torres
- La Paz University Hospital Health Research Institute (FIBHULP), IdiPaz, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Spain.
| | - Carmen Prior
- Department of Genetics, INGEMM, La Paz University Hospital, Madrid, Spain
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Li G, Jiang W, Kang Y, Yu X, Zhang C, Feng Y. High expression of collagen 1A2 promotes the proliferation and metastasis of esophageal cancer cells. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1672. [PMID: 33490184 PMCID: PMC7812173 DOI: 10.21037/atm-20-7867] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background To undertake a bioinformatics analysis to identify abnormally expressed genes [also referred to as differentially expressed genes (DEGs)] and their functions in esophageal carcinoma (ESCA). Methods DEGs (i.e., GSE100942, GSE17351, GSE26886, and GSE77861) were obtained from a gene expression omnibus database. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using online tools from the Database for Annotation, Visualization and Integrated Discovery. A protein-protein interaction network was then constructed based on the Search Tool for the Retrieval of Interacting Genes website. Cytoscape software was used to identify the top 20 DEGs located in the central region of the network. For the overall survival analysis, a Kaplan-Meier analysis was conducted of the Gene Expression Profiling Interactive Analysis website, and collagen (COL) 1A2 was selected to detect the molecular mechanism of COL1A2-small interfering ribonucleic acid (siRNA) in the following ESCA cell lines: Eca109 and TE-1. Next, the expression of COL1A2-messanger ribonucleic acid was determined using real-time quantitative polymerase chain reaction. The expression of COL1A2 was also verified by Western blot. Cell proliferation was measured by colony-forming and MTT assays, and migration and invasion by the transwell assay. Results Based on the GEO database and screening out the hub gene, we identified that COL1A2 was abnormally expressed in ESCA. With a series of in vitro experiments, the expression of COL1A2 was defined as higher in Eca109 and TE-1. Conclusions COL1A2 was highly expressed in ESCA tissue samples. Additionally, the proliferation and metastasis of Eca109 and TE-1 cell lines were significantly attenuated by siRNA-COL1A2-mediated small interference. Notably, the expression level of COL1A2 was obviously related to the Akt and epithelial-mesenchymal transition (EMT) pathways.
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Affiliation(s)
- Guangbin Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Wei Jiang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yunteng Kang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaojun Yu
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chengpeng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yu Feng
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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20
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Methylation of MGMT promoter does not predict response to temozolomide in patients with glioblastoma in Donostia Hospital. Sci Rep 2020; 10:18445. [PMID: 33116181 PMCID: PMC7595088 DOI: 10.1038/s41598-020-75477-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status has been considered a prognostic factor in newly diagnosed glioblastoma (GBM). In this study, we evaluated the prognostic and predictive value of MGMT promoter methylation in patients with glioblastoma in Donostia Hospital. Surprisingly, methylation of MGMT promoter did not predict response to temozolomide in patients with glioblastoma in Donostia Hospital. Specifically, overall survival (OS) and progression-free survival (PFS) did not differ significantly by MGMT methylation status in our cohort. In contrast, both were longer in patients who received treatment, received more TMZ cycles, had a better general status and perform at least a partial resection. No association was detected between methylation of MGMT promoter and molecular markers such as ATRX, IDH, p53 and Ki67. These results indicate that MGMT methylation did not influence in patient survival in our cohort.
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21
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Zhao W, Jiang X, Yang S. lncRNA TUG1 Promotes Cell Proliferation, Migration, and Invasion in Hepatocellular Carcinoma via Regulating miR-29c-3p/ COL1A1 Axis. Cancer Manag Res 2020; 12:6837-6847. [PMID: 32821161 PMCID: PMC7425090 DOI: 10.2147/cmar.s256624] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/14/2020] [Indexed: 12/18/2022] Open
Abstract
Background Taurine upregulated gene 1 (TUG1) has been recognized as a novel oncogenic gene. The current study was established to explore the function and regulatory mechanism of TUG1 in hepatocellular carcinoma (HCC). Methods Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression of TUG1, miR-29c-3p, and COL1A1 in tissues and cell lines. MTT assay, wound-healing and transwell assay were utilized for the detection of cell viability, migration and invasion, respectively. The interactions between miR-29c-3p and TUG1/COL1A1 were predicted by starBase v2.0 (http://starbase.sysu.edu.cn/) and verified by the dual-luciferase reporter or RNA immunoprecipitation assay. Western blot assay was performed to determine the protein levels of COL1A1, cyclin D1, E-cadherin, N-cadherin, Bcl-2, and Bax. Results Dramatically increased expression of TUG1 was noticed in HCC tissues and cell lines. TUG1 knockdown restrained the proliferation, migration, and invasion, and promoted the apoptosis of HCC cells. TUG1 targeted miR-29c-3p and inhibited miR-29c-3p expression. Overexpression of miR-29c-3p inhibited the proliferation, migration and invasion of HCC cells. MiR-29c-3p directly targeted COL1A1 and down-regulated COL1A1 expression. In addition, downregulation of miR-29c-3p and upregulation of COL1A1 both reversed the effects of TUG1 knockdown on the proliferation, apoptosis, migration, and invasion of HCC cells. Conclusion TUG1 could promote the proliferation, migration and invasion of HCC cells through regulating miR-29c-3p/COL1A1 axis. This novel finding might provide a latent target for the treatment of HCC.
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Affiliation(s)
- Wei Zhao
- Department of Functional Examination, The Sixth People's Hospital of Qingdao, Qingdao City, Shandong Province 266033, People's Republic of China
| | - Xue Jiang
- Health Examination Center, The Sixth People's Hospital of Qingdao, Qingdao City, Shandong Province 266033, People's Republic of China
| | - Shuxia Yang
- Health Examination Center, The Sixth People's Hospital of Qingdao, Qingdao City, Shandong Province 266033, People's Republic of China
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Jin L, Shen F, Weinfeld M, Sergi C. Insulin Growth Factor Binding Protein 7 (IGFBP7)-Related Cancer and IGFBP3 and IGFBP7 Crosstalk. Front Oncol 2020; 10:727. [PMID: 32500027 PMCID: PMC7242731 DOI: 10.3389/fonc.2020.00727] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/16/2020] [Indexed: 12/17/2022] Open
Abstract
The insulin/insulin-like growth factors (IGFs) have crucial tasks in the growth, differentiation, and proliferation of healthy and pernicious cells. They are involved in coordinated complexes, including receptors, ligands, binding proteins, and proteases. However, the systems can become dysregulated in tumorigenesis. Insulin-like growth factor-binding protein 7 (IGFBP7) is a protein belonging to the IGFBP superfamily (also termed GFBP-related proteins). Numerous studies have provided evidence that IGFBP3 and IGFBP7 are involved in a variety of cancers, including hepatocellular carcinoma (HCC), breast cancer, gastroesophageal cancer, colon cancer, prostate cancer, among many others. Still, very few suggest an interaction between these two molecules. In studying several cancer types in our laboratories, we found that both proteins share some crucial signaling pathways. The objective of this review is to present a comprehensive overview of the relationship between IGFBP7 and cancer, as well as highlighting IGFBP3 crosstalk with IGFBP7 reported in recent studies.
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Affiliation(s)
- Li Jin
- Department of Laboratory Medicine, Shiyan Taihe Hospital, College of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Fan Shen
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Michael Weinfeld
- Division of Experimental Oncology, Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
| | - Consolato Sergi
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.,Department of Orthopedics, Tianyou Hospital, Wuhan University of Science and Technology, Wuhan, China.,Key Laboratory of Fermentation Engineering, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Stollery Children's Hospital, University Alberta Hospital, Edmonton, AB, Canada
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23
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A Novel Role for the Tumor Suppressor Gene ITF2 in Tumorigenesis and Chemotherapy Response. Cancers (Basel) 2020; 12:cancers12040786. [PMID: 32224864 PMCID: PMC7226299 DOI: 10.3390/cancers12040786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/22/2020] [Accepted: 03/24/2020] [Indexed: 11/18/2022] Open
Abstract
Despite often leading to platinum resistance, platinum-based chemotherapy continues to be the standard treatment for many epithelial tumors. In this study we analyzed and validated the cytogenetic alterations that arise after treatment in four lung and ovarian paired cisplatin-sensitive/resistant cell lines by 1-million microarray-based comparative genomic hybridization (array-CGH) and qRT-PCR methodologies. RNA-sequencing, functional transfection assays, and gene-pathway activity analysis were used to identify genes with a potential role in the development of this malignancy. The results were further explored in 55 lung and ovarian primary tumors and control samples, and in two extensive in silico databases. Long-term cell exposure to platinum induces the frequent deletion of ITF2 gene. Its expression re-sensitized tumor cells to platinum and recovered the levels of Wnt/β-catenin transcriptional activity. ITF2 expression was also frequently downregulated in epithelial tumors, predicting a worse overall survival. We also identified an inverse correlation between ITF2 and HOXD9 expression, revealing that Non-small cell lung cancer (NSCLC) patients with lower expression of HOXD9 had a better overall survival rate. We defined the implication of ITF2 as a molecular mechanism behind the development of cisplatin resistance probably through the activation of the Wnt-signaling pathway. This data highlights the possible role of ITF2 and HOXD9 as novel therapeutic targets for platinum resistant tumors.
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Singh NP, Vinod PK. Integrative analysis of DNA methylation and gene expression in papillary renal cell carcinoma. Mol Genet Genomics 2020; 295:807-824. [PMID: 32185457 DOI: 10.1007/s00438-020-01664-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 03/03/2020] [Indexed: 12/18/2022]
Abstract
Patterns of DNA methylation are significantly altered in cancers. Interpreting the functional consequences of DNA methylation requires the integration of multiple forms of data. The recent advancement in the next-generation sequencing can help to decode this relationship and in biomarker discovery. In this study, we investigated the methylation patterns of papillary renal cell carcinoma (PRCC) and its relationship with the gene expression using The Cancer Genome Atlas (TCGA) multi-omics data. We found that the promoter and body of tumor suppressor genes, microRNAs and gene clusters and families, including cadherins, protocadherins, claudins and collagens, are hypermethylated in PRCC. Hypomethylated genes in PRCC are associated with the immune function. The gene expression of several novel candidate genes, including interleukin receptor IL17RE and immune checkpoint genes HHLA2, SIRPA and HAVCR2, shows a significant correlation with DNA methylation. We also developed machine learning models using features extracted from single and multi-omics data to distinguish early and late stages of PRCC. A comparative study of different feature selection algorithms, predictive models, data integration techniques and representations of methylation data was performed. Integration of both gene expression and DNA methylation features improved the performance of models in distinguishing tumor stages. In summary, our study identifies PRCC driver genes and proposes predictive models based on both DNA methylation and gene expression. These results on PRCC will aid in targeted experiments and provide a strategy to improve the classification accuracy of tumor stages.
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Affiliation(s)
- Noor Pratap Singh
- Center for Computational Natural Sciences and Bioinformatics, IIIT Hyderabad, Hyderabad, 500032, India
| | - P K Vinod
- Center for Computational Natural Sciences and Bioinformatics, IIIT Hyderabad, Hyderabad, 500032, India.
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25
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Hypertonicity-Affected Genes Are Differentially Expressed in Clear Cell Renal Cell Carcinoma and Correlate with Cancer-Specific Survival. Cancers (Basel) 2019; 12:cancers12010006. [PMID: 31861377 PMCID: PMC7017076 DOI: 10.3390/cancers12010006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 02/07/2023] Open
Abstract
The heterogeneity of renal cell carcinoma (RCC) subtypes reflects the cell type of origin in the nephron, with consequences for therapy and prognosis. The transcriptional cues that determine segment-specific gene expression patterns are poorly understood. We recently showed that hypertonicity in the renal medulla regulates nephron-specific gene expression. Here, we analyzed a set of 223 genes, which were identified in the present study by RNA-Seq to be differentially expressed by hypertonicity, for the prediction of cancer-specific survival (CSS). Cluster analyses of these genes showed discrimination between tumor and non-tumor samples of clear cell RCC (ccRCC). Refinement of this gene signature to a four-gene score (OSM score) through statistical analyses enabled prediction of CSS in ccRCC patients of The Cancer Genome Atlas (TCGA) (n = 436) in univariate (HR = 4.1; 95% CI: 2.78−6.07; p = 4.39 × 10−13), and multivariate analyses including primary tumor (T); regional lymph node (N); distant metastasis (M); grading (G)(p = 2.3 × 10−5). The OSM score could be validated in an independent ccRCC study (n = 52) in univariate (HR = 1.29; 95% CI = 1.05–1.59; p = 0.011) and multivariate analyses (p = 0.016). Cell culture experiments using RCC cell lines demonstrated that the expression of the tumor suppressor ELF5 could be restored by hypertonicity. The innovation of our novel gene signature is that these genes are physiologically regulated only by hypertonicity, thereby providing the possibility to be targeted for therapy.
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26
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Wu W, Yang Z, Long F, Luo L, Deng Q, Wu J, Ouyang S, Tang D. COL1A1 and MZB1 as the hub genes influenced the proliferation, invasion, migration and apoptosis of rectum adenocarcinoma cells by weighted correlation network analysis. Bioorg Chem 2019; 95:103457. [PMID: 31901757 DOI: 10.1016/j.bioorg.2019.103457] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 10/15/2019] [Accepted: 11/19/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVES The influences of COL1A1 and MZB1 on the proliferation, migration, invasion and apoptosis abilities of rectum adenocarcinoma was aimed to explore in this study. METHODS Gene expression levels in rectum adenocarcinoma and adjacent tissues were analyzed by differential analysis. Weighted gene correlation network analysis (WGCNA) was employed to investigate rectal adenocarcinoma (READ) hub genes. MCODE was performed to screen the modules of protein-protein interaction network in Cytoscape software. Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool is considered to be the most effective tool in gene ontology (GO) enrichment and Kyoto Gene and Genomics Encyclopedia (KEGG) pathway analysis. Survival analysis was performed using READ patient information from TCGA-READ project database. Quantitative Real-time Polymerase Chain Reaction (qRT-PCR) and western blot were employedto examinemRNA and protein expressions of COL1A1 and MZB1 in tumor tissues and cell lines. After transfecting various interference sequences by liposome-mediated transfection, the influence of COL1A1 and MZB1 on the proliferation, apoptosis, migration and invasion of rectal cancer cells were observed by plate clone formation assay, flow cytometry, wound healing assay and transwell assay respectively. Moreover, xenograft tumor growth assay in vivo validated the results. RESULTS Higher expression levels of COL1A1 and lower expression levels of MZB1 were discovered in tumor tissues of patients with colorectal adenocarcinoma. Overexpression of MZB1 and silencing COL1A1 significantly inhibited proliferation, migration and invasion, while cell apoptosis was promoted. Overexpression of MZB1 and silencing COL1A1 inhibited the orthotopic growth of tumor in vivo. CONCLUSION COL1A1 promoted proliferation, migration and invasion but inhibited apoptosis of rectal adenocarcinoma cells while MZB1 was totally on the contrary.
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Affiliation(s)
- Wenyu Wu
- Department of Oncology, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang 550001, Guizhou, China
| | - Zhu Yang
- Party Committee Office, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, China
| | - Fengxi Long
- Graduate School, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, China
| | - Li Luo
- Department of Oncology, Guihang Guiyang Hospital, Guiyang 550009, Guizhou, China
| | - Qian Deng
- Graduate School, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, China
| | - Jinlin Wu
- Graduate School, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, China
| | - Silu Ouyang
- Graduate School, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, China
| | - Dongxin Tang
- Department of Science and Education, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang 550001, Guizhou, China.
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Collagen 1A1 (COL1A1) Is a Reliable Biomarker and Putative Therapeutic Target for Hepatocellular Carcinogenesis and Metastasis. Cancers (Basel) 2019; 11:cancers11060786. [PMID: 31181620 PMCID: PMC6627889 DOI: 10.3390/cancers11060786] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/27/2019] [Accepted: 06/01/2019] [Indexed: 12/12/2022] Open
Abstract
Increasing evidence shows that hepatocellular carcinoma (HCC) is a principal cause of cancer-related mortality globally, especially among Asian and African populations. Collagen type I α1 (COL1A1) is the major component of type I collagen. While aberrant expression of COL1A1 and COL1A2 is implicated in numerous cancers, the differential role of COL1A1 in malignant, premalignant and normal tissues remains unclear, and its clinical significance in HCC has not been elucidated. In this study, using bioinformatics analysis of publicly-available HCC microarray data from Gene Expression Omnibus (GEO) and RNAseq data from The Cancer Genome Atlas (TCGA) database, we determined that COL1A1 is significantly upregulated in HCC tumor tissues in comparison to normal tissues. Our analysis also revealed that COL1A1 confers survival advantage and enhanced oncogenicity on HCC cells. Interestingly, the siRNA-mediated silencing of COL1A1 expression (siCOLIA1) suppressed HCC cells clonogenicity, motility, invasiveness and tumorsphere formation. Concomitantly, siCOL1A1 abrogated Slug-dependent epithelial-to-mesenchymal transition (EMT) and HCC stemness gene-signature, by attenuating expression of stemness markers SOX2, OCT4 and CD133. The present study provides some mechanistic insight into COL1A1 activity in HCC and highlights its putative role as an important diagnostic biomarker and potential therapeutic target in early development and metastasis of HCC.
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28
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Borys AM, Seweryn M, Gołąbek T, Bełch Ł, Klimkowska A, Totoń-Żurańska J, Machlowska J, Chłosta P, Okoń K, Wołkow PP. Patterns of gene expression characterize T1 and T3 clear cell renal cell carcinoma subtypes. PLoS One 2019; 14:e0216793. [PMID: 31150395 PMCID: PMC6544217 DOI: 10.1371/journal.pone.0216793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 04/29/2019] [Indexed: 12/21/2022] Open
Abstract
Renal carcinoma is the 20th most common cancer worldwide. Clear cell renal cell carcinoma is the most frequent type of renal cancer. Even in patients diagnosed at an early stage, characteristics of disease progression remain heterogeneous. Up-to-date molecular classifications stratify the ccRCC samples into two clusters. We analyzed gene expression in 23 T1 or T3 ccRCC samples. Unsupervised clustering divided this group into three clusters, two of them contained pure T1 or T3 samples while one contained a mixed group. We defined a group of 36 genes that discriminate the mixed cluster. This gene set could be associated with tumor classification into a higher stage and it contained significant number of genes coding for molecular transporters, channel and transmembrane proteins. External data from TCGA used to test our findings confirmed that the expression levels of those 36 genes varied significantly between T1 and T3 tumors. In conclusion, we found a clustering pattern of gene expression, informative for heterogeneity among T1 and T3 tumors of clear cell renal cell carcinoma.
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Affiliation(s)
- Agnieszka M Borys
- Center for Medical Genomics OMICRON, Medical Faculty, Jagiellonian University Medical College, Krakow, Poland
| | - Michał Seweryn
- Center for Medical Genomics OMICRON, Medical Faculty, Jagiellonian University Medical College, Krakow, Poland
| | - Tomasz Gołąbek
- Chair and Department of Urology, Medical Faculty, Jagiellonian University Medical College, Krakow, Poland
| | - Łukasz Bełch
- Chair and Department of Urology, Medical Faculty, Jagiellonian University Medical College, Krakow, Poland
| | - Agnieszka Klimkowska
- Chair of Pathomorphology, Medical Faculty, Jagiellonian University Medical College, Krakow, Poland
| | - Justyna Totoń-Żurańska
- Center for Medical Genomics OMICRON, Medical Faculty, Jagiellonian University Medical College, Krakow, Poland
| | - Julita Machlowska
- Center for Medical Genomics OMICRON, Medical Faculty, Jagiellonian University Medical College, Krakow, Poland
| | - Piotr Chłosta
- Chair and Department of Urology, Medical Faculty, Jagiellonian University Medical College, Krakow, Poland
| | - Krzysztof Okoń
- Chair of Pathomorphology, Medical Faculty, Jagiellonian University Medical College, Krakow, Poland
| | - Paweł P Wołkow
- Center for Medical Genomics OMICRON, Medical Faculty, Jagiellonian University Medical College, Krakow, Poland
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29
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杨 万, 潘 云, 管 沛, 李 雪, 尤 崇. [Bioinformatics analysis of COL1A1 regulated by miR-129-5p as a potential therapeutic target for gastric cancer]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2019; 39:540-546. [PMID: 31140417 PMCID: PMC6743932 DOI: 10.12122/j.issn.1673-4254.2019.05.07] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Indexed: 01/25/2023]
Abstract
OBJECTIVE To explore the pathogenesis of gastric cancer through a bioinformatic approach to provide evidence for the prevention and treatment of gastric cancer. METHODS The differentially expressed genes (DEGs) in gastric cancer and normal gastric mucosa in GSE79973 dataset were analyzed using GEO2R online tool. GO analysis and KEGG pathway enrichment analysis of the DEGs in DAVID database were performed. The protein interaction network was constructed using STRING database, and the key genes (Hub genes) were screened and their functional modules were analyzed using Cytoscape software. The GEPIA database was used to validate the Hub genes, and the Target Scan database was used to predict the microRNAs that regulate the target genes; OncomiR was used to analyze the expressions of the microRNAs in gastric cancer tissues and their relationship with the survival outcomes of the patients. RESULTS A total of 181 DEGs were identified in gastric cancer, and 10 hub genes were screened by the protein- protein interaction network. Functional analysis showed that these DEGs were involved mainly in protein digestion and absorption, PI3K-Akt signaling pathway, ECM-receptor interaction and platelet activation signal pathway. GEPIA database validation showed that COL1A1 was highly expressed in gastric cancer tissues and was associated with a poor prognosis of patients with gastric cancer. MiR-129-5p was found to bind to the 3'UTR of COL1A1 mRNA, and compared with that in normal tissues, miR-129-5p expression was obviously down-regulated in gastric cancer tissues, and was correlated with the prognosis of the patients. CONCLUSIONS COL1A1 under regulation by MiR-129-5p is a potential therapeutic target for gastric cancer.
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Affiliation(s)
- 万霞 杨
- />兰州大学第二医院检验医学中心,甘肃 兰州 730030Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou 730030, China
| | - 云燕 潘
- />兰州大学第二医院检验医学中心,甘肃 兰州 730030Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou 730030, China
| | - 沛文 管
- />兰州大学第二医院检验医学中心,甘肃 兰州 730030Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou 730030, China
| | - 雪 李
- />兰州大学第二医院检验医学中心,甘肃 兰州 730030Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou 730030, China
| | - 崇革 尤
- />兰州大学第二医院检验医学中心,甘肃 兰州 730030Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou 730030, China
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30
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Yang W, Ma J, Zhou W, Li Z, Zhou X, Cao B, Zhang Y, Liu J, Yang Z, Zhang H, Zhao Q, Hong L, Fan D. Identification of hub genes and outcome in colon cancer based on bioinformatics analysis. Cancer Manag Res 2018; 11:323-338. [PMID: 30643458 PMCID: PMC6312054 DOI: 10.2147/cmar.s173240] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background Colon cancer is one of the leading malignant neoplasms worldwide. Until now, the concrete mechanisms of colonic cancerogenesis are largely unknown; identification of driven genes and pathways is, therefore, of great importance for monitoring and conquering this disease. This study aims to explore the potential biomarkers and therapeutic targets for colon cancer treatment. Methods The gene expression profile of GSE44076 from Gene Expression Omnibus database, including 98 primary colon cancers and 98 normal distant colon mucosa, was deeply analyzed. GEO2R tool was used to screen the differentially expressed genes (DEGs) between colon cancer tissues and normal samples. Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed for screening DEGs using Database for Annotation, Visualization and Integrated Discovery database and Panther database. Moreover, Search Tool for the Retrieval of Interacting Genes, Cytoscape software, and Molecular Complex Detection plug-in were used to visualize the protein-protein interaction of these DEGs. Results A total of 497 DEGs were obtained, including 129 upregulated genes mainly enriched in Hippo signaling pathway, Wnt signaling pathway, and cytokine-cytokine receptor interaction and 368 downregulated genes enriched in retinol metabolism, steroid hormone biosynthesis, drug metabolism, and chemical carcinogenesis. Using Molecular Complex Detection software, three important modules were selected from the protein-protein interaction network. Moreover, 20 hub genes with high degree of connectivity were selected, including COL1A1, CXCL5, GNG4, TIMP1, and so on. The Kaplan-Meier analysis for overall survival and correlation analysis were applied among the hub genes. Conclusion Taken together, DEGs, especially the hub genes such as COL1A1, might be the driven genes in colon cancer progression. More importantly, they might be the novel biomarkers for diagnosis and guiding therapeutic strategies of colon cancer.
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Affiliation(s)
- Wanli Yang
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, China,
| | - Jiaojiao Ma
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, China,
| | - Wei Zhou
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, China,
| | - Zichao Li
- The First Brigade of Student, Air Force Military Medical University, Xi'an, China
| | - Xin Zhou
- The First Brigade of Student, Air Force Military Medical University, Xi'an, China
| | - Bo Cao
- The First Brigade of Student, Air Force Military Medical University, Xi'an, China
| | - Yujie Zhang
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, China,
| | - Jinqiang Liu
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, China,
| | - Zhiping Yang
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, China,
| | - Hongwei Zhang
- Department of Digestive Surgery, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Qingchuan Zhao
- Department of Digestive Surgery, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Liu Hong
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, China,
| | - Daiming Fan
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, China,
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31
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Yang Z, Liu B, Lin T, Zhang Y, Zhang L, Wang M. Multiomics analysis on DNA methylation and the expression of both messenger RNA and microRNA in lung adenocarcinoma. J Cell Physiol 2018; 234:7579-7586. [PMID: 30370535 DOI: 10.1002/jcp.27520] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 09/10/2018] [Indexed: 02/03/2023]
Abstract
Lung adenocarcinoma (LUAD) poses a significant threat to public health worldwide, while the genetic and epigenetic abnormalities involved in the oncogenesis of LUAD remains unknown. This study aimed to identify and validate key genes during the development and progression of LUAD by multiomics analysis. First, Empirical Analysis of Digital Gene Expression Data in R (EdgeR) was used to identify differentially regulated genes between normal samples and LUAD samples. Then significance analysis of microarrays (SAM) was used to identify differentially methylated genes and regulated microRNAs (miRNAs) between normal samples and LUAD samples. Following that, Kyoto Encyclopedia of Genes and Genomes (KEGG)-enrichment analysis was used to analyze the function that these genes enriched in. A total of 4,816 genes, 419 miRNAs, and 4,476 methylated genes that were significantly differentially expressed corresponding to the normal tissues in LUAD were obtained, and some of the pathways these genes enriched in were the same. Moreover, 255 genes differentially methylated and expressed at the same time were also found, and these 255 genes were the target genes of the miRNAs differentially expressed in LUAD. Finally, nine genes (BRCA1, COL1A1, ESR1, FGFR2, HNF4A, IGFBP3, MET, MMP3, and PAK1) network analysis, and two of which were found to be related to the survival of LUAD patients. In summary, a total of nine genes that may play important roles in the development of LUAD were identified, and two (PAK1 and FGFR2) of them can be served as prognostic biomarkers for LUAD patients. The genes found in this study played different roles in the tumor progression of LUAD, indicating these genes may be considered as potential target genes for LUAD treatment.
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Affiliation(s)
- Zhaoyang Yang
- Department of Respiratory Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Bao Liu
- Department of Respiratory Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Tie Lin
- Department of Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yingli Zhang
- Department of Internal Medicine, Harbin Red Cross Center Hospital, Harbin, China
| | - Limin Zhang
- Department of Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Meng Wang
- Department of Respiratory Medicine, Harbin Medical University Cancer Hospital, Harbin, China
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32
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Vera-Puente O, Rodriguez-Antolin C, Salgado-Figueroa A, Michalska P, Pernia O, Reid BM, Rosas R, Garcia-Guede A, SacristÁn S, Jimenez J, Esteban-Rodriguez I, Martin ME, Sellers TA, León R, Gonzalez VÍM, De Castro J, Ibanez de Caceres I. MAFG is a potential therapeutic target to restore chemosensitivity in cisplatin-resistant cancer cells by increasing reactive oxygen species. Transl Res 2018; 200:1-17. [PMID: 30053382 PMCID: PMC7787305 DOI: 10.1016/j.trsl.2018.06.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/06/2018] [Accepted: 06/17/2018] [Indexed: 02/05/2023]
Abstract
Adjuvant chemotherapy for solid tumors based on platinum-derived compounds such as cisplatin is the treatment of choice in most cases. Cisplatin triggers signaling pathways that lead to cell death, but it also induces changes in tumor cells that modify the therapeutic response, thereby leading to cisplatin resistance. We have recently reported that microRNA-7 is silenced by DNA methylation and is involved in the resistance to platinum in cancer cells through the action of the musculoaponeurotic fibrosarcoma oncogene family, protein G (MAFG). In the present study, we first confirm the miR-7 epigenetic regulation of MAFG in 44 normal- and/or tumor-paired samples in non-small-cell lung cancer (NSCLC). We also provide translational evidence of the role of MAFG and the clinical outcome in NSCLC by the interrogation of two extensive in silico databases of 2019 patients. Moreover, we propose that MAFG-mediated resistance could be conferred due to lower reactive oxygen species production after cisplatin exposure. We developed specifically selected aptamers against MAFG, with high sensitivity to detect the protein at a nuclear level probed by aptacytochemistry and histochemistry analyses. The inhibition of MAFG activity through the action of the specific aptamer apMAFG6F increased the levels of reactive oxygen species production and the sensitivity to cisplatin. We report first the specific nuclear identification of MAFG as a novel detection method for diagnosis in NSCLC, and then we report that MAFG modulates the redox response and confers cell protection against free radicals generated after platinum administration, thus also being a promising therapeutic target.
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MESH Headings
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/genetics
- Aptamers, Nucleotide/pharmacology
- Carcinoma, Non-Small-Cell Lung/diagnosis
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Cell Line, Tumor
- Cisplatin/therapeutic use
- Cloning, Molecular
- DNA Methylation
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/physiology
- Epigenesis, Genetic/genetics
- Gene Expression
- Gene Silencing
- HEK293 Cells
- Humans
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- MafG Transcription Factor/antagonists & inhibitors
- MafG Transcription Factor/genetics
- MafG Transcription Factor/physiology
- MicroRNAs/genetics
- MicroRNAs/physiology
- Oxidation-Reduction
- Prognosis
- Reactive Oxygen Species/metabolism
- Repressor Proteins/antagonists & inhibitors
- Repressor Proteins/genetics
- Repressor Proteins/physiology
- Sequence Analysis, DNA
- Transfection
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Affiliation(s)
- Olga Vera-Puente
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Carlos Rodriguez-Antolin
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Ana Salgado-Figueroa
- Department of Biochemistry Research, Laboratory of Aptamers, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Patrycja Michalska
- Biomedical Research Foundation of University Hospital La Princesa, Madrid, Spain; Institute Teófilo Hernando and Department of Pharmacology and Therapeutics, Autonomous University of Madrid, Madrid, Spain
| | - Olga Pernia
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Brett M Reid
- Department of Cancer Epidemiology, MOFFITT Cancer Center, Tampa, Florida
| | - RocÍo Rosas
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Alvaro Garcia-Guede
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Silvia SacristÁn
- Department of Biochemistry Research, Laboratory of Aptamers, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Julia Jimenez
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Isabel Esteban-Rodriguez
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain; Department of Pathology, La Paz University Hospital, Madrid, Spain
| | - M Elena Martin
- Department of Biochemistry Research, Laboratory of Aptamers, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Thomas A Sellers
- Department of Cancer Epidemiology, MOFFITT Cancer Center, Tampa, Florida
| | - Rafael León
- Biomedical Research Foundation of University Hospital La Princesa, Madrid, Spain; Institute Teófilo Hernando and Department of Pharmacology and Therapeutics, Autonomous University of Madrid, Madrid, Spain
| | - VÍctor M Gonzalez
- Department of Biochemistry Research, Laboratory of Aptamers, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Javier De Castro
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Inmaculada Ibanez de Caceres
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain.
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Abstract
OBJECTIVE To identify novel clinically relevant genes in papillary thyroid carcinoma from public databases. METHODS Four original microarray datasets, GSE3678, GSE3467, GSE33630 and GSE58545, were downloaded. Differentially expressed genes (DEGs) were filtered from integrated data. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed, followed by protein-protein interaction (PPI) network construction. The CentiScape pug-in was performed to scale degree. The genes at the top of the degree distribution (≥ 95% percentile) in the significantly perturbed networks were defined as central genes. UALCAN and The Cancer Genome Atlas Clinical Explorer were used to verify clinically relevant genes and perform survival analysis. RESULT 225 commonly changed DEGs (111 up-regulated and 114 down-regulated) were identified. The DEGs were classified into three groups by GO terms. KEGG pathway enrichment analysis showed DEGs mainly enriched in the PI3K-Akt signaling pathway, pathways in cancer, focal adhesion and proteoglycans in cancer. DEGs' protein-protein interaction (PPI) network complex was developed; six central genes (BCL2, CCND1, FN1, IRS1, COL1A1, CXCL12) were identified. Among them, BCL2, CCND1 and COL1A1 were identified as clinically relevant genes. CONCLUSION BCL2, CCND1 and COL1A1 may be key genes for papillary thyroid carcinoma. Further molecular biological experiments are required to confirm the function of the identified genes.
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Affiliation(s)
- W Liang
- Department of Endocrinology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, People's Republic of China.
| | - F Sun
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, 310009, People's Republic of China
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Vera O, Rodriguez-Antolin C, de Castro J, Karreth FA, Sellers TA, Ibanez de Caceres I. An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells. Epigenetics 2018; 13:251-263. [PMID: 29436261 PMCID: PMC5997141 DOI: 10.1080/15592294.2018.1436364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are critical regulators of cell biology whose alteration can lead to the development of diseases such as cancer. The potential role of lncRNAs and their epigenetic regulation in response to platinum treatment are largely unknown. We analyzed four paired cisplatin-sensitive/resistant non-small cell lung cancer and ovarian cancer cell lines. The epigenetic landscape of overlapping and cis-acting lncRNAs was determined by combining human microarray data on 30,586 lncRNAs and 20,109 protein coding mRNAs with whole-genome bisulfite sequencing. Selected candidate lncRNAs were further characterized by PCR, gene-ontology analysis, and targeted bisulfite sequencing. Differential expression in response to therapy was observed more frequently in cis-acting than in overlapping lncRNAs (78% vs. 22%, fold change ≥1.5), while significantly altered methylation profiles were more commonly associated with overlapping lncRNAs (29% vs. 8%; P value <0.001). Moreover, overlapping lncRNAs contain more CpG islands (CGIs) (25% vs. 17%) and the majority of CGI-containing overlapping lncRNAs share these CGIs with their associated coding genes (84%). The differences in expression between sensitive and resistant cell lines were replicated in 87% of the selected candidates (P<0.05), while our bioinformatics approach identifying differential methylation was confirmed in all of the selected lncRNAs (100%). Five lncRNAs under epigenetic regulation appear to be involved in cisplatin resistance (AC091814.2, AC141928.1, RP11-65J3.1-002, BX641110, and AF198444). These novel findings provide new insights into epigenetic mechanisms and acquired resistance to cisplatin that highlight specific lncRNAs, some with unknown function, that may signal strategies in epigenetic therapies.
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Affiliation(s)
- Olga Vera
- a Cancer Epigenetics Laboratory, INGEMM , La Paz University Hospital , Madrid , Spain.,b Biomarkers and Experimental Therapeutics in Cancer , IdiPAZ , Madrid , Spain
| | - Carlos Rodriguez-Antolin
- a Cancer Epigenetics Laboratory, INGEMM , La Paz University Hospital , Madrid , Spain.,b Biomarkers and Experimental Therapeutics in Cancer , IdiPAZ , Madrid , Spain
| | - Javier de Castro
- a Cancer Epigenetics Laboratory, INGEMM , La Paz University Hospital , Madrid , Spain.,b Biomarkers and Experimental Therapeutics in Cancer , IdiPAZ , Madrid , Spain
| | - Florian A Karreth
- c Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , Tampa , USA
| | - Thomas A Sellers
- d Department of Cancer Epidemiology , H. Lee Moffitt Cancer Center and Research Institute , Tampa , USA
| | - Inmaculada Ibanez de Caceres
- a Cancer Epigenetics Laboratory, INGEMM , La Paz University Hospital , Madrid , Spain.,b Biomarkers and Experimental Therapeutics in Cancer , IdiPAZ , Madrid , Spain
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Seelan RS, Mukhopadhyay P, Pisano MM, Greene RM. Effects of 5-Aza-2'-deoxycytidine (decitabine) on gene expression. Drug Metab Rev 2018; 50:193-207. [PMID: 29455551 DOI: 10.1080/03602532.2018.1437446] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
5-Aza-2'-deoxycytidine (AzaD), also known as Decitabine, is a deoxycytidine analog that is typically used to activate methylated and silenced genes by promoter demethylation. However, a survey of the scientific literature indicates that promoter demethylation may not be the only (or, indeed, the major) mechanism by which AzaD affects gene expression. Regulation of gene expression by AzaD can occur in several ways, including some that are independent of DNA demethylation. Results from several studies indicate that the effect of AzaD on gene expression is highly context-dependent and can differ for the same gene under different environmental settings. This may, in part, be due to the nature of the silencing mechanism(s) involved - DNA methylation, repressive histone modifications, or a combination of both. The varied effects of AzaD on such context-dependent regulation of gene expression may underlie some of the diverse responses exhibited by patients undergoing AzaD therapy. In this review, we describe the salient properties of AzaD with particular emphasis on its diverse effects on gene expression, aspects that have barely been discussed in most reviews of this interesting drug.
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Affiliation(s)
- Ratnam S Seelan
- a Department of Surgical and Hospital Dentistry, Division of Craniofacial Development and Anomalies , ULSD, University of Louisville , Louisville , KY , USA
| | - Partha Mukhopadhyay
- a Department of Surgical and Hospital Dentistry, Division of Craniofacial Development and Anomalies , ULSD, University of Louisville , Louisville , KY , USA
| | - M Michele Pisano
- a Department of Surgical and Hospital Dentistry, Division of Craniofacial Development and Anomalies , ULSD, University of Louisville , Louisville , KY , USA
| | - Robert M Greene
- a Department of Surgical and Hospital Dentistry, Division of Craniofacial Development and Anomalies , ULSD, University of Louisville , Louisville , KY , USA
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Angulo JC, López JI, Ropero S. DNA Methylation and Urological Cancer, a Step Towards Personalized Medicine: Current and Future Prospects. Mol Diagn Ther 2017; 20:531-549. [PMID: 27501813 DOI: 10.1007/s40291-016-0231-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Urologic malignancies are some of the commonest tumors often curable when diagnosed at early stage. However, accurate diagnostic markers and faithful predictors of prognosis are needed to avoid over-diagnosis leading to overtreatment. Many promising exploratory studies have identified epigenetic markers in urinary malignancies based on DNA methylation, histone modification and non-coding ribonucleic acid (ncRNA) expression that epigenetically regulate gene expression. We review and discuss the current state of development and the future potential of epigenetic biomarkers for more accurate and less invasive detection of urological cancer, tumor recurrence and progression of disease serving to establish diagnosis and monitor treatment efficacies. The specific clinical implications of such methylation tests on therapeutic decisions and patient outcome and current limitations are also discussed.
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Affiliation(s)
- Javier C Angulo
- Servicio de Urología, Hospital Universitario de Getafe, Departamento Clínico, Facultad de Ciencias Biomédicas, Universidad Europea de Madrid, Laureate Universities, Hospital Universitario de Getafe, Carretera de Toledo Km 12.5, Getafe, 28905, Madrid, Spain.
| | - Jose I López
- Servicio de Anatomía Patológica, Hospital Universitario de Cruces, Instituto BioCruces,Universidad del País Vasco (UPV-EHU), Bilbao, Spain
| | - Santiago Ropero
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
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Vera O, Jimenez J, Pernia O, Rodriguez-Antolin C, Rodriguez C, Sanchez Cabo F, Soto J, Rosas R, Lopez-Magallon S, Esteban Rodriguez I, Dopazo A, Rojo F, Belda C, Alvarez R, Valentin J, Benitez J, Perona R, De Castro J, Ibanez de Caceres I. DNA Methylation of miR-7 is a Mechanism Involved in Platinum Response through MAFG Overexpression in Cancer Cells. Am J Cancer Res 2017; 7:4118-4134. [PMID: 29158814 PMCID: PMC5695001 DOI: 10.7150/thno.20112] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/04/2017] [Indexed: 11/16/2022] Open
Abstract
One of the major limitations associated with platinum use is the resistance that almost invariably develops in different tumor types. In the current study, we sought to identify epigenetically regulated microRNAs as novel biomarkers of platinum resistance in lung and ovarian cancers, the ones with highest ratios of associated chemo-resistance. Methods: We combined transcriptomic data from microRNA and mRNA under the influence of an epigenetic reactivation treatment in a panel of four paired cisplatin -sensitive and -resistant cell lines, followed by real-time expression and epigenetic validations for accurate candidate selection in 19 human cancer cell lines. To identify specific candidate genes under miRNA regulation, we assembled “in silico” miRNAs and mRNAs sequences by using ten different algorithms followed by qRT-PCR validation. Functional assays of site-directed mutagenesis and luciferase activity, miRNAs precursor overexpression, silencing by antago-miR and cell viability were performed to confirm their specificity in gene regulation. Results were further explored in 187 primary samples obtained from ovarian tumors and controls. Results: We identified 4 candidates, miR-7, miR-132, miR-335 and miR-148a, which deregulation seems to be a common event in the development of resistance to cisplatin in both tumor types. miR-7 presented specific methylation in resistant cell lines, and was associated with poorer prognosis in ovarian cancer patients. Our experimental results strongly support the direct regulation of MAFG through miR-7 and their involvement in the development of CDDP resistance in human tumor cells. Conclusion: The basal methylation status of miR-7 before treatment may be a potential clinical epigenetic biomarker, predictor of the chemotherapy outcome to CDDP in ovarian cancer patients. To the best of our knowledge, this is the first report linking the regulation of MAFG by miRNA-7 and its role in chemotherapy response to CDDP. Furthermore, this data highlights the possible role of MAFG as a novel therapeutic target for platinum resistant tumors.
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Pires-Luís AS, Costa-Pinheiro P, Ferreira MJ, Antunes L, Lobo F, Oliveira J, Henrique R, Jerónimo C. Identification of clear cell renal cell carcinoma and oncocytoma using a three-gene promoter methylation panel. J Transl Med 2017; 15:149. [PMID: 28662726 PMCID: PMC5492907 DOI: 10.1186/s12967-017-1248-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/21/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Promoter methylation has emerged as a promising class of epigenetic biomarkers for diagnosis and prognosis of renal cell tumors (RCTs). Although differential gene promoter methylation patterns have been reported for the major subtypes (clear cell, papillary and chromophobe renal cell carcinoma, and oncocytoma), validation of diagnostic performance in independent series have been seldom performed. Herein, we aimed at assessing the diagnostic performance of genes previously shown to be hypermethylated in RCTs in different clinical settings. METHODS Promoter methylation levels of HOXA9 and OXR1 were assessed by quantitative methylation specific PCR. ROC curves were generated for OXR1, OXR1 combined with MST1R and HOXA9. Sensitivity, specificity, positive predictive value, negative predictive value and accuracy were computed, maximizing specificity. Methylation levels were also correlated with clinical and pathological relevant parameters. RESULTS HOXA9 and OXR1 promoter methylation was disclosed in 73 and 87% of RCTs, respectively. A two-gene methylation panel comprising OXR1 and MST1R identified malignancy with 98% sensitivity and 100% specificity, and clear cell renal cell carcinoma with 90% sensitivity and 98% specificity. HOXA9 promoter methylation allowed for discrimination between oncocytoma and both papillary and chromophobe renal cell carcinoma but only with 77% sensitivity and 73% specificity. Significantly higher OXR1 promoter methylation levels (p = 0.005) were associated with high nuclear grade in ccRCC. CONCLUSIONS A panel including OXR1 and MST1R promoter methylation allows specific and sensitive identification of renal cell tumors, and, especially, of clear cell renal cell carcinoma. Moreover, higher OXR1 promoter methylation levels associate with clear cell renal cell carcinoma nuclear grade, a surrogate for tumor aggressiveness. Thus, gene promoter methylation analysis might a useful ancillary tool in diagnostic management of renal masses.
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Affiliation(s)
- Ana Sílvia Pires-Luís
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Pedro Costa-Pinheiro
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Maria João Ferreira
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Luís Antunes
- Department of Epidemiology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Francisco Lobo
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Jorge Oliveira
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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Gene expression profile of renal cell carcinomas after neoadjuvant treatment with sunitinib: new pathways revealed. Int J Biol Markers 2017; 32:e210-e217. [PMID: 27834463 DOI: 10.5301/jbm.5000234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2016] [Indexed: 01/03/2023]
Abstract
BACKGROUND In renal cell carcinoma (RCC) of the clear cell type, inactivity of the VHL gene induces overexpression of HIF1 α and its targets, the tyrosine kinase receptors, promoting RCC development and progression. The discovery of tyrosine kinase inhibitors (TKIs) changed the treatment of these tumors. Other molecular pathways involved in the TKI mechanisms of action have not been described in the literature. The aim of our study was to elucidate alternative mechanisms of action of sunitinib in tumor tissue after neoadjuvant treatment of RCC. METHODS The gene expression profile was accessed using microarray (Affymetrix Human Genome U133 Plus 2.0 platform) and frozen RCC tissues collected from 5 patients with locally advanced non-metastatic tumors who underwent nephrectomy after being treated with 2 cycles of neoadjuvant sunitinib. The results were compared with matched controls comprising 6 patients with no neoadjuvant intervention. RESULTS There was underexpression of the majority of genes after sunitinib treatment. The lower expression levels of IGFBP1, CCL20, CXCL6 and FGB were confirmed by qRT-PCR in all cases. The downregulation of gene expression leads us to search for methylation as a mechanism of action of the TKI. IGFBP1 was shown to be methylated by methylation-sensitive high-resolution melting technique. CONCLUSIONS The ultimate genetic effects of sunitinib may explain its actions as an antitumor drug that apparently suppresses the expression of important genes related to cell survival, adhesion, invasion and immunomodulation. The methylation of gene promoters was shown to be part of the mechanism of action of this class of drugs.
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Li J, Ding Y, Li A. Identification of COL1A1 and COL1A2 as candidate prognostic factors in gastric cancer. World J Surg Oncol 2016; 14:297. [PMID: 27894325 PMCID: PMC5126984 DOI: 10.1186/s12957-016-1056-5] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 11/22/2016] [Indexed: 11/17/2022] Open
Abstract
Background The role of type I collagen, composed of collagen type I alpha 1 (COL1A1) and collagen type I alpha 2 (COL1A2), has been studied in several cancers. However, the expression of COL1A1 and COL1A2 in malignant, premalignant, and normal gastric tissues and their clinical significances in gastric cancer have not been elucidated. Methods Real-time quantitative PCR was performed in 55 malignant, 27 premalignant, and 19 normal tissues to measure COL1A1 and COL1A2 messenger RNA (mRNA) expression, and the correlations between COL1A1 and COL1A2 expression and clinicopathological parameters and patients’ survival rate were analyzed. Results We found that COL1A1 mRNA expression was significantly upregulated in premalignant and malignant tissues than in normal tissues, whereas COL1A2 mRNA expression was significantly higher in malignant tissues than in premalignant and normal tissues. Moreover, COL1A1 expression was unrelated to clinicopathological parameters, while COL1A2 expression was positively related to tumor size and depth of invasion. Besides, higher COL1A1 and COL1A2 expression levels were related to lower overall survival. Conclusions We find that COL1A1 might have its potential as a monitoring factor to screen early gastric cancer, and COL1A1 and COL1A2 might predict poor clinical outcomes in gastric cancer patients.
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Affiliation(s)
- Jun Li
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University, 3 East Qingchun Road, Hangzhou, Zhejiang, China
| | - Yuemin Ding
- School of Medicine, Zhejiang University City College, 51 Huzhoujie, Hangzhou, Zhejiang, China
| | - Aiqing Li
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University, 3 East Qingchun Road, Hangzhou, Zhejiang, China.
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Abstract
The majority of kidney cancers are associated with mutations in the von Hippel-Lindau gene and a small proportion are associated with infrequent mutations in other well characterized tumour-suppressor genes. In the past 15 years, efforts to uncover other key genes involved in renal cancer have identified many genes that are dysregulated or silenced via epigenetic mechanisms, mainly through methylation of promoter CpG islands or dysregulation of specific microRNAs. In addition, the advent of next-generation sequencing has led to the identification of several novel genes that are mutated in renal cancer, such as PBRM1, BAP1 and SETD2, which are all involved in histone modification and nucleosome and chromatin remodelling. In this Review, we discuss how altered DNA methylation, microRNA dysregulation and mutations in histone-modifying enzymes disrupt cellular pathways in renal cancers.
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Affiliation(s)
- Mark R Morris
- Brain Tumour Research Centre, Wolverhampton School of Sciences, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK
| | - Farida Latif
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Tezval H, Dubrowinskaja N, Peters I, Reese C, Serth K, Atschekzei F, Hennenlotter J, Stenzl A, Kuczyk MA, Serth J. Tumor Specific Epigenetic Silencing of Corticotropin Releasing Hormone -Binding Protein in Renal Cell Carcinoma: Association of Hypermethylation and Metastasis. PLoS One 2016; 11:e0163873. [PMID: 27695045 PMCID: PMC5047469 DOI: 10.1371/journal.pone.0163873] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 09/15/2016] [Indexed: 02/03/2023] Open
Abstract
The relevance of Corticotropin Releasing Hormone (CRH)-system in human malignancies is a question of growing interest. Here we investigated hypermethylation and epigenetic silencing of the CRH-Binding Protein (CRHBP) gene in clear cell renal cell cancer (ccRCC). Relative methylation of the CRHBP CpG island (CGI) was determined in 17 tumor cell lines as well as 86 ccRCC samples and 66 paired normal tissues using pyrosequencing and quantitative methylation specific PCR of bisulfite converted DNA. Results were statistically compared with relative mRNA expression levels of CRHBP and clinicopathological parameters of patients. Re-expression of CRHBP following 5-aza-2´-deoxycytidine treatment was investigated by quantitative mRNA expression analysis. Real-time impedance analysis was applied for analysis of invasiveness of renal tumor cells following si-RNA knockdown of CRHBP expression or ectopic expression of CRHBP. We found the CRHBP CGI to be frequently methylated in tumor cell lines of renal, prostatic, and bladder cancer. Comparison of methylation in normal and paired renal cancer tissue specimens revealed hypermethylation of the CRHBP CGI in tumors (p<1*10−12). DNA methylation and decreased mRNA expression were correlated (R = 0.83, p<1*10−12). Tumor cell lines showed 5-aza-2´-deoxycytidine dependent reduction of methylation and re-expression of CRHBP was associated with altered cellular invasiveness of renal cancer cells in real-time impedance invasion assays. Hypermethylation and inverse relationship with mRNA expression were validated in silico using the TCGA network data. We describe for the first time tumor specific epigenetic silencing of CRHBP and statistical association with aggressive tumors thus suggesting the CRH system to contribute to the development of kidney cancer.
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Affiliation(s)
- Hossein Tezval
- Department of Urology and Urological Oncology, Hannover Medical School, Hannover, Germany
| | - Natalia Dubrowinskaja
- Department of Urology and Urological Oncology, Hannover Medical School, Hannover, Germany
| | - Inga Peters
- Department of Urology and Urological Oncology, Hannover Medical School, Hannover, Germany
| | - Christel Reese
- Department of Urology and Urological Oncology, Hannover Medical School, Hannover, Germany
| | - Katrin Serth
- Department of Molecular Biology, Hannover Medical School, Hannover, Germany
| | - Faranaz Atschekzei
- Department of Urology and Urological Oncology, Hannover Medical School, Hannover, Germany
| | - Jörg Hennenlotter
- Department of Urology, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Arnulf Stenzl
- Department of Urology, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Markus A. Kuczyk
- Department of Urology and Urological Oncology, Hannover Medical School, Hannover, Germany
| | - Jürgen Serth
- Department of Urology and Urological Oncology, Hannover Medical School, Hannover, Germany
- * E-mail:
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Soto J, Rodriguez-Antolin C, Vallespín E, de Castro Carpeño J, Ibanez de Caceres I. The impact of next-generation sequencing on the DNA methylation-based translational cancer research. Transl Res 2016; 169:1-18.e1. [PMID: 26687736 DOI: 10.1016/j.trsl.2015.11.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/29/2015] [Accepted: 11/14/2015] [Indexed: 01/08/2023]
Abstract
Epigenetics is currently in an exponential phase of growth, constituting one of the most promising fields in science, particularly in cancer research. Impaired epigenetic processes can lead to abnormal gene activity or inactivity, causing cellular disorders that are closely associated with tumor initiation and progression. Thus, there is a pivotal role of massive sequencing techniques for epigenetics, which aim to find novel biomarkers, factors of prognosis and prediction, and targets for achieving personalized treatments. We present a brief description of the evolution of next-generation sequencing technologies and its coupling with DNA methylation analysis techniques, highlighting its future in translational medicine and presenting significant findings in several malignancies. We also expose critical topics related to the implementation of these approaches, which is expected to be affordable for most research centers in the near future.
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Affiliation(s)
- Javier Soto
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Carlos Rodriguez-Antolin
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Elena Vallespín
- Structural and Functional Genomics, INGEMM-IdiPAZ-CIBERER, La Paz University Hospital, Madrid, Spain
| | | | - Inmaculada Ibanez de Caceres
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain.
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Ragone R, Sallustio F, Piccinonna S, Rutigliano M, Vanessa G, Palazzo S, Lucarelli G, Ditonno P, Battaglia M, Fanizzi FP, Schena FP. Renal Cell Carcinoma: A Study through NMR-Based Metabolomics Combined with Transcriptomics. Diseases 2016; 4:diseases4010007. [PMID: 28933387 PMCID: PMC5456302 DOI: 10.3390/diseases4010007] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/15/2015] [Accepted: 01/15/2016] [Indexed: 12/13/2022] Open
Abstract
Renal cell carcinoma (RCC) is a heterogeneous cancer often showing late symptoms. Until now, some candidate protein markers have been proposed for its diagnosis. Metabolomics approaches have been applied, predominantly using Mass Spectrometry (MS), while Nuclear Magnetic Resonance (NMR)-based studies remain limited. There is no study about RCC integrating NMR-based metabolomics with transcriptomics. In this work, 1H-NMR spectroscopy combined with multivariate statistics was applied on urine samples, collected from 40 patients with clear cell RCC (ccRCC) before nephrectomy and 29 healthy controls; nine out of 40 patients also provided samples one-month after nephrectomy. We observed increases of creatine, alanine, lactate and pyruvate, and decreases of hippurate, citrate, and betaine in all ccRCC patients. A network analysis connected most of these metabolites with glomerular injury, renal inflammation and renal necrosis/cell death. Interestingly, intersecting metabolites with transcriptomic data from CD133+/CD24+ tumoral renal stem cells isolated from ccRCC patients, we found that both genes and metabolites differentially regulated in ccRCC patients belonged to HIF-α signaling, methionine and choline degradation, and acetyl-CoA biosynthesis. Moreover, when comparing urinary metabolome of ccRCC patients after nephrectomy, some processes, such as the glomerular injury, renal hypertrophy, renal necrosis/cell death and renal proliferation, were no more represented.
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Affiliation(s)
- Rosa Ragone
- Consorzio C.A.R.S.O., Centro di Addestramento e Ricerca Scientifica in Oncologia, Strada Provinciale Casamassima Km 3, Valenzano (Bari) 70010, Italy.
| | - Fabio Sallustio
- Consorzio C.A.R.S.O., Centro di Addestramento e Ricerca Scientifica in Oncologia, Strada Provinciale Casamassima Km 3, Valenzano (Bari) 70010, Italy.
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, Lecce 73100, Italy.
| | - Sara Piccinonna
- Consorzio C.A.R.S.O., Centro di Addestramento e Ricerca Scientifica in Oncologia, Strada Provinciale Casamassima Km 3, Valenzano (Bari) 70010, Italy.
| | - Monica Rutigliano
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
| | - Galleggiante Vanessa
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
| | - Silvano Palazzo
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
| | - Giuseppe Lucarelli
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
| | - Pasquale Ditonno
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
| | - Michele Battaglia
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
| | - Francesco Paolo Fanizzi
- Consorzio C.A.R.S.O., Centro di Addestramento e Ricerca Scientifica in Oncologia, Strada Provinciale Casamassima Km 3, Valenzano (Bari) 70010, Italy.
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, Lecce 73100, Italy.
| | - Francesco Paolo Schena
- Consorzio C.A.R.S.O., Centro di Addestramento e Ricerca Scientifica in Oncologia, Strada Provinciale Casamassima Km 3, Valenzano (Bari) 70010, Italy.
- Department of Emergency and Organ Transplantation, University of Bari, Bari 70124, Italy.
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, Lecce 73100, Italy.
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Singh V, Singh LC, Vasudevan M, Chattopadhyay I, Borthakar BB, Rai AK, Phukan RK, Sharma J, Mahanta J, Kataki AC, Kapur S, Saxena S. Esophageal Cancer Epigenomics and Integrome Analysis of Genome-Wide Methylation and Expression in High Risk Northeast Indian Population. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:688-99. [DOI: 10.1089/omi.2015.0121] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Virendra Singh
- National Institute of Pathology (ICMR), New Delhi, India
| | | | | | | | | | | | - Rup Kumar Phukan
- Regional Medical Research Centre (RMRC), Dibrugadh, Assam, India
| | | | - Jagadish Mahanta
- Regional Medical Research Centre (RMRC), Dibrugadh, Assam, India
| | | | - Sujala Kapur
- National Institute of Pathology (ICMR), New Delhi, India
| | - Sunita Saxena
- National Institute of Pathology (ICMR), New Delhi, India
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Klar AS, Gopinadh J, Kleber S, Wadle A, Renner C. Treatment with 5-Aza-2'-Deoxycytidine Induces Expression of NY-ESO-1 and Facilitates Cytotoxic T Lymphocyte-Mediated Tumor Cell Killing. PLoS One 2015; 10:e0139221. [PMID: 26447882 PMCID: PMC4598131 DOI: 10.1371/journal.pone.0139221] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 09/10/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND NY-ESO-1 belongs to the cancer/testis antigen (CTA) family and represents an attractive target for cancer immunotherapy. Its expression is induced in a variety of solid tumors via DNA demethylation of the promoter of CpG islands. However, NY-ESO-1 expression is usually very low or absent in some tumors such as breast cancer or multiple myeloma. Therefore, we established an optimized in vitro treatment protocol for up-regulation of NY-ESO-1 expression by tumor cells using the hypomethylating agent 5-aza-2'-deoxycytidine (DAC). METHODOLOGY/PRINCIPAL FINDINGS We demonstrated de novo induction of NY-ESO-1 in MCF7 breast cancer cells and significantly increased expression in U266 multiple myeloma cells. This effect was time- and dose-dependent with the highest expression of NY-ESO-1 mRNA achieved by the incubation of 10 μM DAC for 72 hours. NY-ESO-1 activation was also confirmed at the protein level as shown by Western blot, flow cytometry, and immunofluorescence staining. The detection and quantification of single NY-ESO-1 peptides presented at the tumor cell surface in the context of HLA-A*0201 molecules revealed an increase of 100% and 50% for MCF7 and U266 cells, respectively. Moreover, the enhanced expression of NY-ESO-1 derived peptides at the cell surface was accompanied by an increased specific lysis of MCF7 and U266 cells by HLA-A*0201/NY-ESO-1(157-165) peptide specific chimeric antigen receptor (CAR) CD8+ T cells. In addition, the killing activity of CAR T cells correlated with the secretion of higher IFN-gamma levels. CONCLUSIONS/SIGNIFICANCE These results indicate that NY-ESO-1 directed immunotherapy with specific CAR T cells might benefit from concomitant DAC treatment.
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Affiliation(s)
- Agnes S. Klar
- Tissue Biology Research Unit, Department of Surgery, University Children’s Hospital Zurich, Zurich, Switzerland
- Children’s Research Center, University Children’s Hospital Zurich, Zurich, Switzerland
| | - Jakka Gopinadh
- Department of Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Sascha Kleber
- Department of Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Andreas Wadle
- Department of Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Christoph Renner
- Department of Oncology, University Hospital Basel, Basel, Switzerland
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Solarek W, Czarnecka AM, Escudier B, Bielecka ZF, Lian F, Szczylik C. Insulin and IGFs in renal cancer risk and progression. Endocr Relat Cancer 2015; 22:R253-64. [PMID: 26330483 DOI: 10.1530/erc-15-0135] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Insulin and IGFs play a significant role in cancer development and progression, including renal cell carcinoma (RCC). RCC is the most frequent type of kidney cancer in adults and the tenth most common malignancy worldwide. Insulin is normally associated with metabolism control, whereas IGFs are defined as proliferation regulators. Today, there is convincing evidence of an association between obesity and the risk of RCC. Indicated risk factors together with type 2 diabetes are irreversibly connected with circulating insulin and IGF levels. The interplay between these molecules, their receptors, and IGF-binding proteins might be crucial for RCC cell biology and RCC progression. Given the potent activity IGF/IGF receptor 1 (IGF1R) inhibitors demonstrate against RCC in basic research, some type of combination therapy may prove to be beneficial clinically in the management of RCC. This review addresses not only molecular but also clinical associations between insulin and IGF1 signaling pathways and both RCC biology and clinical course. Revealing these interactions may improve our understanding of basic molecular oncology processes in RCC and improve treatment strategies.
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Affiliation(s)
- W Solarek
- Laboratory of Molecular Oncology Department of Oncology, Military Institute of Medicine, Szaserow 128, 04-141 Warsaw, Poland School of Molecular Medicine Medical University of Warsaw, Warsaw, Poland Institut Gustave Roussy 114 rue Edouard Vaillant, 94805 Villejuif, France Emory University School of Medicine Atlanta, Georgia, USA Laboratory of Molecular Oncology Department of Oncology, Military Institute of Medicine, Szaserow 128, 04-141 Warsaw, Poland School of Molecular Medicine Medical University of Warsaw, Warsaw, Poland Institut Gustave Roussy 114 rue Edouard Vaillant, 94805 Villejuif, France Emory University School of Medicine Atlanta, Georgia, USA
| | - A M Czarnecka
- Laboratory of Molecular Oncology Department of Oncology, Military Institute of Medicine, Szaserow 128, 04-141 Warsaw, Poland School of Molecular Medicine Medical University of Warsaw, Warsaw, Poland Institut Gustave Roussy 114 rue Edouard Vaillant, 94805 Villejuif, France Emory University School of Medicine Atlanta, Georgia, USA
| | - B Escudier
- Laboratory of Molecular Oncology Department of Oncology, Military Institute of Medicine, Szaserow 128, 04-141 Warsaw, Poland School of Molecular Medicine Medical University of Warsaw, Warsaw, Poland Institut Gustave Roussy 114 rue Edouard Vaillant, 94805 Villejuif, France Emory University School of Medicine Atlanta, Georgia, USA
| | - Z F Bielecka
- Laboratory of Molecular Oncology Department of Oncology, Military Institute of Medicine, Szaserow 128, 04-141 Warsaw, Poland School of Molecular Medicine Medical University of Warsaw, Warsaw, Poland Institut Gustave Roussy 114 rue Edouard Vaillant, 94805 Villejuif, France Emory University School of Medicine Atlanta, Georgia, USA Laboratory of Molecular Oncology Department of Oncology, Military Institute of Medicine, Szaserow 128, 04-141 Warsaw, Poland School of Molecular Medicine Medical University of Warsaw, Warsaw, Poland Institut Gustave Roussy 114 rue Edouard Vaillant, 94805 Villejuif, France Emory University School of Medicine Atlanta, Georgia, USA
| | - F Lian
- Laboratory of Molecular Oncology Department of Oncology, Military Institute of Medicine, Szaserow 128, 04-141 Warsaw, Poland School of Molecular Medicine Medical University of Warsaw, Warsaw, Poland Institut Gustave Roussy 114 rue Edouard Vaillant, 94805 Villejuif, France Emory University School of Medicine Atlanta, Georgia, USA
| | - C Szczylik
- Laboratory of Molecular Oncology Department of Oncology, Military Institute of Medicine, Szaserow 128, 04-141 Warsaw, Poland School of Molecular Medicine Medical University of Warsaw, Warsaw, Poland Institut Gustave Roussy 114 rue Edouard Vaillant, 94805 Villejuif, France Emory University School of Medicine Atlanta, Georgia, USA
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Han JJ, Xue DW, Han QR, Liang XH, Xie L, Li S, Wu HY, Song B. Induction of apoptosis by IGFBP3 overexpression in hepatocellular carcinoma cells. Asian Pac J Cancer Prev 2015; 15:10085-9. [PMID: 25556430 DOI: 10.7314/apjcp.2014.15.23.10085] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The insulin-like growth factor (IGF) system comprises a group of proteins that play key roles in regulating cell growth, differentiation, and apoptosis in a variety of cellular systems. The aim of this study was to investigate the role of insulin-like growth factor binding protein 3 (IGFBP3) in hepatocellular carcinoma. MATERIALS AND METHODS Expression of IGF2, IGFBP3, and PTEN was analyzed by qRT-PCR. Lentivirus vectors were used to overexpress IGFBP3 in hepatocellular carcinoma cell (HCC) lines. The effect of IGFBP3 on proliferation was investigated by MTT and colony formation assays. RESULTS Expression of IGF2, IGFBP3, and PTEN in several HCC cell lines was lower than in normal cell lines. After 5-aza-2'-deoxycytidine/trichostatin A treatment, significant demethylation of the promoter region of IGFBP3 was observed in HCC cells. Overexpression of IGFBP3 induced apoptosis and reduced colony formation in HUH7 cells. CONCLUSIONS Expression of IGF2, IGFBP3, and PTEN in several HCC cell lines was lower than in normal cell lines. After 5-aza-2'-deoxycytidine/ trichostatin A treatment, significant demethylation of the promoter region of IGFBP3 was observed in HCC cells. Overexpression of IGFBP3 induced apoptosis and reduced colony formation in HUH7 cells.
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Affiliation(s)
- Jian-Jun Han
- Department of Cancer Intervention Treatment Center, Shandong Cancer Hospital and Institute, Jinan, China E-mail :
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Pernía O, Belda-Iniesta C, Pulido V, Cortes-Sempere M, Rodriguez C, Vera O, Soto J, Jiménez J, Taus A, Rojo F, Arriola E, Rovira A, Albanell J, Macías MT, de Castro J, Perona R, Ibañez de Caceres I. Methylation status of IGFBP-3 as a useful clinical tool for deciding on a concomitant radiotherapy. Epigenetics 2015; 9:1446-53. [PMID: 25482372 PMCID: PMC4622698 DOI: 10.4161/15592294.2014.971626] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The methylation status of the IGFBP-3 gene is strongly associated with cisplatin sensitivity in patients with non-small cell lung cancer (NSCLC). In this study, we found in vitro evidence that linked the presence of an unmethylated promoter with poor response to radiation. Our data also indicate that radiation might sensitize chemotherapy-resistant cells by reactivating IGFBP-3-expression through promoter demethylation, inactivating the PI3K/AKT pathway. We also explored the IGFBP-3 methylation effect on overall survival (OS) in a population of 40 NSCLC patients who received adjuvant therapy after R0 surgery. Our results indicate that patients harboring an unmethylated promoter could benefit more from a chemotherapy schedule alone than from a multimodality therapy involving radiotherapy and platinum-based treatments, increasing their OS by 2.5 y (p = .03). Our findings discard this epi-marker as a prognostic factor in a patient population without adjuvant therapy, indicating that radiotherapy does not improve survival for patients harboring an unmethylated IGFBP-3 promoter.
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Affiliation(s)
- Olga Pernía
- a Cancer Epigenetics Laboratory, INGEMM ; University Hospital La Paz ; Madrid , Spain
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Braga EA, Khodyrev DS, Loginov VI, Pronina IV, Senchenko VN, Dmitriev AA, Kubatiev AA, Kushlinskii NE. Methylation in the regulation of the expression of chromosome 3 and microRNA genes in clear-cell renal cell carcinomas. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415050026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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