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Badr EAE, El Sayed IE, Gabber MKR, Ghobashy EAE, Al-Sehemi AG, Algarni H, Elghobashy YAS. Are Antisense Long Non-Coding RNA Related to COVID-19? Biomedicines 2022; 10:2770. [PMID: 36359290 PMCID: PMC9687826 DOI: 10.3390/biomedicines10112770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/10/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Fighting external pathogens relies on the tight regulation of the gene expression of the immune system. Ferroptosis, which is a distinct form of programmed cell death driven by iron, is involved in the enhancement of follicular helper T cell function during infection. The regulation of RNA is a key step in final gene expression. The present study aimed to identify the expression level of antisense lncRNAs (A2M-AS1, DBH-AS1, FLVCR1-DT, and NCBP2AS2-1) and FLVCR1 in COVID-19 patients and its relation to the severity of the disease. COVID-19 patients as well as age and gender-matched healthy controls were enrolled in this study. The expression level of the antisense lncRNAs was measured by RT-PCR. Results revealed the decreased expression of A2M-AS1 and FLVCR1 in COVID-19 patients. Additionally, they showed the increased expression of DBH-AS1, FLVCR1-DT, and NCBP2AS2. Both FLVCR1-DT and NCBP2AS2 showed a positive correlation with interleukin-6 (IL-6). DBH-AS1 and FLVCR1-DT had a significant association with mortality, complications, and mechanical ventilation. A significant negative correlation was found between A2M-AS1 and NCBP2AS2-1 and between FLVCR1 and FLVCR1-DT. The study confirmed that the expression level of the antisense lncRNAs was deregulated in COVID-19 patients and correlated with the severity of COVID-19, and that it may have possible roles in the pathogenesis of this disease.
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Affiliation(s)
- Eman A E Badr
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Menoufia University, Shebeen El-Kom 32511, Egypt
| | | | | | | | - Abdullah G. Al-Sehemi
- Research Centre for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Chemistry, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Hamed Algarni
- Research Centre for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Physics, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Yasser AS Elghobashy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Menoufia University, Shebeen El-Kom 32511, Egypt
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2
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Azad P, Caldwell AB, Ramachandran S, Spann NJ, Akbari A, Villafuerte FC, Bermudez D, Zhao H, Poulsen O, Zhou D, Bafna V, Subramaniam S, Haddad GG. ARID1B, a molecular suppressor of erythropoiesis, is essential for the prevention of Monge's disease. Exp Mol Med 2022; 54:777-787. [PMID: 35672450 PMCID: PMC9256584 DOI: 10.1038/s12276-022-00769-1] [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: 09/29/2021] [Revised: 01/10/2022] [Accepted: 02/14/2022] [Indexed: 11/09/2022] Open
Abstract
At high altitude Andean region, hypoxia-induced excessive erythrocytosis (EE) is the defining feature of Monge's disease or chronic mountain sickness (CMS). At the same altitude, resides a population that has developed adaptive mechanism(s) to constrain this hypoxic response (non-CMS). In this study, we utilized an in vitro induced pluripotent stem cell model system to study both populations using genomic and molecular approaches. Our whole genome analysis of the two groups identified differential SNPs between the CMS and non-CMS subjects in the ARID1B region. Under hypoxia, the expression levels of ARID1B significantly increased in the non-CMS cells but decreased in the CMS cells. At the molecular level, ARID1B knockdown (KD) in non-CMS cells increased the levels of the transcriptional regulator GATA1 by 3-fold and RBC levels by 100-fold under hypoxia. ARID1B KD in non-CMS cells led to increased proliferation and EPO sensitivity by lowering p53 levels and decreasing apoptosis through GATA1 mediation. Interestingly, under hypoxia ARID1B showed an epigenetic role, altering the chromatin states of erythroid genes. Indeed, combined Real-time PCR and ATAC-Seq results showed that ARID1B modulates the expression of GATA1 and p53 and chromatin accessibility at GATA1/p53 target genes. We conclude that ARID1B is a novel erythroid regulator under hypoxia that controls various aspects of erythropoiesis in high-altitude dwellers.
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Affiliation(s)
- Priti Azad
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Andrew B Caldwell
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ali Akbari
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Francisco C Villafuerte
- Laboratorio de Fisiología del Transporte de Oxigeno/Fisiología Comparada, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Daniela Bermudez
- Laboratorio de Fisiología del Transporte de Oxigeno/Fisiología Comparada, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Helen Zhao
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Orit Poulsen
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Dan Zhou
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.,Department of Nanoengineering, University of California, San Diego, La Jolla, CA, USA
| | - Gabriel G Haddad
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA. .,Department of Neurosciences, University of California, San Diego, La Jolla, CA, 92093, USA. .,Rady Children's Hospital, San Diego, CA, 92123, USA.
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3
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Kedhari Sundaram M, Haque S, Somvanshi P, Bhardwaj T, Hussain A. Epigallocatechin gallate inhibits HeLa cells by modulation of epigenetics and signaling pathways. 3 Biotech 2020; 10:484. [PMID: 33117625 PMCID: PMC7584697 DOI: 10.1007/s13205-020-02473-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022] Open
Abstract
This study examines the effect of epigallocatechin gallate (EGCG) on signaling pathways, epigenetic modulators and tumour suppressor genes in cervical cancer cells, HeLa. qRT-PCR, ELISA-based enzymatic assays and in silico studies were used to catalogue the modulation of these genes by EGCG treatment. qRT-PCR showed transcriptional modulation of several epigenetic modifiers including DNA methyltransferases and histone modifiers (DNMT1, DNMT3B, DNMT3A, AURKA, AURKC, AURKB, KDM4A, KDM5C, PRMT7, PRMT6, UBE2B, HDAC5, HDAC6, HDAC7 and HDAC11. Furthermore, ELISA-based assays showed that EGCG lowered the activity of DNA methyltransferases, histone deacetylases and histone methyltransferases (H3K9). Molecular docking results suggests that EGCG may competitively inhibit some epigenetic enzymes (DNMT1, DNMT3A, HDAC2, HDAC3, HDAC4, HDAC7 and EZH2). A functional outcome of these epigenetic alterations could be inferred from the reversal of promoter hypermethylation of tumour suppressor genes by quantitative methylation array and transcriptional re-expression of tumour suppressor genes including TP73, PTEN, SOCS1, CDH1, RARβ, and DAPK1 by qRT-PCR. Downregulation of key signaling moieties of PI3K, Wnt and MAPK pathways, cell cycle regulators, metastasis regulators and pro-inflammatory moieties including TERT, CCNB1, CCNB2, MMP2, MMP7. PIK3C2B, PIK3CA, MAPK8 and IL6 was also observed. In silico protein-protein interaction network analysis followed by KEGG analysis discerned the active participation of gene sets towards cancer pathways. This study comprehensively explains EGCG's anti-cancer mechanism via the synchronized transcriptional alteration of several molecular targets across different signaling pathways and reversal of tumour suppressor gene silencing through modulation of epigenetic enzymes.
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Affiliation(s)
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, 45142 Saudi Arabia
| | - Pallavi Somvanshi
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070 India
| | - Tulika Bhardwaj
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070 India
| | - Arif Hussain
- School of Life Sciences, Manipal Academy of Higher Education, PO Box 345050, Dubai, United Arab Emirates
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4
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Xu J, Wu G, Zhao Y, Han Y, Zhang S, Li C, Zhang J. Long Noncoding RNA DSCAM-AS1 Facilitates Colorectal Cancer Cell Proliferation and Migration via miR-137/Notch1 Axis. J Cancer 2020; 11:6623-6632. [PMID: 33046983 PMCID: PMC7545673 DOI: 10.7150/jca.46562] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/17/2020] [Indexed: 12/11/2022] Open
Abstract
Growing evidences demonstrate that long noncoding RNAs (lncRNAs) participate in various cancers including colorectal cancer (CRC). In the current study, we found that the expression of DSCAM-AS1 in CRC tissues and cell lines was significantly upregulated, and was positively correlated with metastasis status and advanced stage of CRC. In addition, Kaplan-Meier assays also indicated that the expression of DSCAM-AS1 was correlated with poor prognosis in patients with CRC. Silence of DSCAM-AS1 inhibited proliferation and migration of CRC cells. Subcellular fractionation and FISH analyses suggested that DSCAM-AS1 was majorly distributed in cytoplasm of HT29 and LOVO cells. Thus, DSCAM-AS1 might act as a competing endogenous RNA (ceRNA). Subsequently, RT-qPCR results displayed that the expression of miR-137 in CRC tissues was relatively lower than that in the neighboring normal tissues. The interaction between miR-137 and DSCAM-AS1 was demonstrated by luciferase reporter assay. Functionally, miR-137 reversed the pro-proliferation and -metastasis effect of DSCAM-AS1 on CRC cells. Collectively, DSCAM-AS1 promotes CRC progression via sponging miR-137. MiR-137 can suppress the expression of Notch-1, a novel signaling regulating cell proliferation and EMT, by working on the 3'UTR of Notch-1. At last, Notch-1 overexpression or miR-137 inhibition could restore the DSCAM-AS1 silencing-mediated repressive function on cell proliferation and migration. The above data suggested that, DSCAM-AS1 may contribute to CRC cell proliferation and migration by targeting miR-137/Notch-1 axis.
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Affiliation(s)
- Jing Xu
- Department of General Surgery, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, PR China
| | - Guanghai Wu
- Department of General Surgery, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, PR China
| | - Yongjie Zhao
- Department of General Surgery, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, PR China
| | - Youkui Han
- Department of General Surgery, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, PR China
| | - Shuai Zhang
- Department of General Surgery, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, PR China
| | - Chao Li
- Department of General Surgery, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, PR China
| | - Judong Zhang
- Department of General Surgery, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, PR China
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5
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Epigenetic Silencing of LMX1A Contributes to Cancer Progression in Lung Cancer Cells. Int J Mol Sci 2020; 21:ijms21155425. [PMID: 32751497 PMCID: PMC7432919 DOI: 10.3390/ijms21155425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/16/2020] [Accepted: 07/27/2020] [Indexed: 12/15/2022] Open
Abstract
Epigenetic modification is considered a major mechanism of the inactivation of tumor suppressor genes that finally contributes to carcinogenesis. LIM homeobox transcription factor 1α (LMX1A) is one of the LIM-homeobox-containing genes that is a critical regulator of growth and differentiation. Recently, LMX1A was shown to be hypermethylated and functioned as a tumor suppressor in cervical cancer, ovarian cancer, and gastric cancer. However, its role in lung cancer has not yet been clarified. In this study, we used public databases, methylation-specific PCR (MSP), reverse transcription PCR (RT-PCR), and bisulfite genomic sequencing to show that LMX1A was downregulated or silenced due to promoter hypermethylation in lung cancers. Treatment of lung cancer cells with the demethylating agent 5-aza-2'-deoxycytidine restored LMX1A expression. In the lung cancer cell lines H23 and H1299, overexpression of LMX1A did not affect cell proliferation but suppressed colony formation and invasion. These suppressive effects were reversed after inhibition of LMX1A expression in an inducible expression system in H23 cells. The quantitative RT-PCR (qRT-PCR) data showed that LMX1A could modulate epithelial mesenchymal transition (EMT) through E-cadherin (CDH1) and fibronectin (FN1). NanoString gene expression analysis revealed that all aberrantly expressed genes were associated with processes related to cancer progression, including angiogenesis, extracellular matrix (ECM) remodeling, EMT, cancer metastasis, and hypoxia-related gene expression. Taken together, these data demonstrated that LMX1A is inactivated through promoter hypermethylation and functions as a tumor suppressor. Furthermore, LMX1A inhibits non-small cell lung cancer (NSCLC) cell invasion partly through modulation of EMT, angiogenesis, and ECM remodeling.
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6
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Zhu H, Zhu H, Tian M, Wang D, He J, Xu T. DNA Methylation and Hydroxymethylation in Cervical Cancer: Diagnosis, Prognosis and Treatment. Front Genet 2020; 11:347. [PMID: 32328088 PMCID: PMC7160865 DOI: 10.3389/fgene.2020.00347] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/23/2020] [Indexed: 12/16/2022] Open
Abstract
Recent discoveries have led to the development of novel ideas and techniques that have helped elucidate the correlation between epigenetics and tumor biology. Nowadays, the field of tumor genetics has evolved to include a new type of regulation by epigenetics. An increasing number of studies have demonstrated the importance of DNA methylation and hydroxymethylation in specific genes in the progression of cervical cancer. Determining the methylation and hydroxymethylation profiles of these genes will help in the early prevention and diagnosis, monitoring recurrence, prognosis, and treatment of patients with cervical cancer. In this review, we focus on the significance of aberrant DNA methylation and hydroxymethylation in cervical cancer and the use of these epigenetic signatures in clinical settings.
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Affiliation(s)
- Hongming Zhu
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, China
| | - He Zhu
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, China
| | - Miao Tian
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, China
| | - Dongying Wang
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, China
| | - Jiaxing He
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, China
| | - Tianmin Xu
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, China
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7
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Wu G, Xue M, Zhao Y, Han Y, Li C, Zhang S, Zhang J, Xu J. Long noncoding RNA ZEB1-AS1 acts as a Sponge of miR-141-3p to Inhibit Cell Proliferation in Colorectal Cancer. Int J Med Sci 2020; 17:1589-1597. [PMID: 32669962 PMCID: PMC7359398 DOI: 10.7150/ijms.46698] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/12/2020] [Indexed: 12/21/2022] Open
Abstract
Evidence shows that long noncoding RNAs (lncRNAs) play key roles in various cancers, including colorectal cancer. In this current study, we found that the expression of ZEB1-AS1 in colorectal cancer tissues and cell lines was significantly upregulated, and positively correlated with advanced stage of colorectal cancer. Kaplan-Meier assays also indicated that the expression of ZEB1-AS1 was correlated with poor prognosis in patients with colorectal cancer. Knocking down of ZEB1-AS1 inhibited the proliferation of colorectal cancer cells. Subcellular fractionation analyses suggested that ZEB1-AS1 was majorly distributed in cytoplasm of SW480 and LOVO cells. Thus, ZEB1-AS1 might act as a competing endogenous RNA. MicroRNA array analysis suggested that miR-141-3p was significantly downregulated in CRC tissues, which was further verified by RT-qPCR. The results of luciferase reporter assay proved that miR-141-3p was a target of ZEB1-AS1. Functionally, miR-141-3p inhibitor reversed the anti-proliferation effect of sh-ZEB1-AS1 on colorectal cancer cells. Collectively, ZEB1-AS1 may contribute to colorectal cancer cell proliferation by sponging miR-141-3p.
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Affiliation(s)
- Guanghai Wu
- Department of General Surgery, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, China
| | - Mei Xue
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Yongjie Zhao
- Department of General Surgery, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, China
| | - Youkui Han
- Department of General Surgery, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, China
| | - Chao Li
- Department of General Surgery, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, China
| | - Shuai Zhang
- Department of General Surgery, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, China
| | - Judong Zhang
- Department of General Surgery, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, China
| | - Jing Xu
- Department of General Surgery, Tianjin Union Medical Center, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, China
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8
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Long noncoding RNA FLVCR1-AS1 aggravates biological behaviors of glioma cells via targeting miR-4731-5p/E2F2 axis. Biochem Biophys Res Commun 2019; 521:716-720. [PMID: 31699367 DOI: 10.1016/j.bbrc.2019.10.106] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/12/2019] [Indexed: 01/01/2023]
Abstract
Long noncoding RNAs (lncRNAs) display essential roles in cancer progression. FLVCR1-AS1 is a rarely investigated lncRNAs involved in various human cancers, such as hepatocellular carcinoma and lung cancer. However, its function in glioma has not been clarified. In our study, we found that FLVCR1-AS1 was highly expressed in glioma tissues and cell lines. And upregulation of FLVCR1-AS1 predicted poor prognosis in patients with glioma. Moreover, FLVCR1-AS1 knockdown inhibited proliferation, migration and invasion of glioma cells. Through bioinformatics analysis, we identified that FLVCR1-AS1 was a sponge for miR-4731-5p to upregulate E2F2 expression. Moreover, rescue assays indicated that FLVCR1-AS1 modulated E2F2 expression to participate in glioma progression. Altogether, our research demonstrates that the FLVCR1-AS1/miR-4731-5p/E2F2 axis is a novel signaling in glioma and may be a potential target for tumor therapy.
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9
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Ye W, Chen R, Chen X, Huang B, Lin R, Xie X, Chen J, Jiang J, Deng Y, Wen J. AhR regulates the expression of human cytochrome P450 1A1 (CYP1A1) by recruiting Sp1. FEBS J 2019; 286:4215-4231. [PMID: 31199573 DOI: 10.1111/febs.14956] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/09/2019] [Accepted: 06/11/2019] [Indexed: 12/28/2022]
Abstract
Cytochrome P450 1A1 (CYP1A1) is abundant in the kidney, liver, and intestine and is involved in the phase I metabolism of numerous endogenous and exogenous compounds. Therefore, exploring the regulatory mechanism of its basal expression in humans is particularly important to understand the bioactivation of several procarcinogens to their carcinogenic derivatives. Site-specific mutagenesis and deletion of the transcription factor binding site determined the core cis-acting elements in the human CYP1A1 proximal and distal promoter regions. The proximal promoter region [overlapping xenobiotic-responsive element (XRE) and GC box sequences] determined the basal expression of CYP1A1. In human hepatocellular carcinoma cells (HepG2) with aryl hydrocarbon receptor (AhR) or specificity protein 1 (Sp1) knockdown, we confirmed that AhR and Sp1 are involved in basal CYP1A1 expression. In HepG2 cells overexpressing either AhR or Sp1, AhR determined the proximal transactivation of basal CYP1A1 expression. Via DNA affinity precipitation assays and ChIP, we found that AhR bound to the promoter and recruited Sp1 to transactivate CYP1A1 expression. The coordinated interaction between Sp1 and AhR was identified to be DNA mediated. Our work revealed a basal regulatory mechanism of an interesting human gene by which AhR interacts with Sp1 through DNA and recruits Sp1 to regulate basal CYP1A1 expression.
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Affiliation(s)
- Wenchu Ye
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University Guangzhou, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Ruohong Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University Guangzhou, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Xiaoxuan Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University Guangzhou, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Boyan Huang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University Guangzhou, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Ruqin Lin
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University Guangzhou, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Xuan Xie
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University Guangzhou, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jiongjie Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University Guangzhou, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jun Jiang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University Guangzhou, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University Guangzhou, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jikai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University Guangzhou, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, China
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10
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Zong Z, Song Y, Xue Y, Ruan X, Liu X, Yang C, Zheng J, Cao S, Li Z, Liu Y. Knockdown of LncRNA SCAMP1 suppressed malignant biological behaviours of glioma cells via modulating miR-499a-5p/LMX1A/NLRC5 pathway. J Cell Mol Med 2019; 23:5048-5062. [PMID: 31207033 PMCID: PMC6653555 DOI: 10.1111/jcmm.14362] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/24/2019] [Accepted: 04/15/2019] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of long non‐coding RNAs (lncRNAs) confirm that it plays a crucial role in tumourigenesis and malignant progression of glioma. The present study demonstrated that LncRNA secretory carrier membrane protein 1 (SCAMP1) was up‐regulated and functioned as an oncogene in glioma cells. In addition, miR‐499a‐5p was down‐regulated meanwhile exerted tumour‐suppressive function in glioma cells. Subsequently, inhibition of SCAMP1 significantly restrained the cell proliferation, migration and invasion, as well as promoted apoptosis by acting as a molecular sponge of miR‐499a‐5p. Transcription factor LIM homeobox transcription factor 1, alpha (LMX1A) was overexpressed in glioma tissues and cells. Moreover, miR‐499a‐5p targeted LMX1A 3′‐UTR in a sequence‐specific manner. Hence, down‐regulation of SCAMP1 remarkably reduced the expression level of LMX1A, indicating that LMX1A participated in miR‐499a‐5p‐induced tumour‐suppressive effects on glioma cells. Furthermore, knockdown of LMX1A decreased NLR family, CARD domain containing 5 (NLRC5) mRNA and protein expression levels through directly binding to the NLRC5 promoter region. Down‐regulation of NLRC5 obviously inhibited malignant biological behaviours of glioma cells through attenuating the activity of Wnt/β‐catenin signalling pathway. In conclusion, our study clarifies that SCAMP1/miR‐499a‐5p/LMX1A/NLRC5 axis plays a critical role in modulating malignant progression of glioma cells, which provide a novel therapeutic strategy for glioma treatment.
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Affiliation(s)
- Zheqi Zong
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Yichen Song
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Yixue Xue
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, China
| | - Xuelei Ruan
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Chunqing Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Jian Zheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Shuo Cao
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, China
| | - Zhen Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
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11
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Kedhari Sundaram M, Hussain A, Haque S, Raina R, Afroze N. Quercetin modifies 5'CpG promoter methylation and reactivates various tumor suppressor genes by modulating epigenetic marks in human cervical cancer cells. J Cell Biochem 2019; 120:18357-18369. [PMID: 31172592 DOI: 10.1002/jcb.29147] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/14/2019] [Accepted: 05/20/2019] [Indexed: 12/31/2022]
Abstract
The central role of epigenomic alterations in carcinogenesis has been widely acknowledged, particularly the impact of DNA methylation on gene expression across all stages of carcinogenesis is considered vital for both diagnostic and therapeutic strategies. Dietary phytochemicals hold great promise as safe anticancer agents and effective epigenetic modulators. This study was designed to investigate the potential of a phytochemical, quercetin as a modulator of the epigenetic pathways for anticancer strategies. Biochemical activity of DNA methyltransferases (DNMTs), histone deacetylases (HDACs), histone methyltransferases (HMTs), and global genomic DNA methylation was quantitated by an enzyme-linked immunosorbent assay based assay in quercetin-treated HeLa cells. Molecular docking studies were performed to predict the interaction of quercetin with DNMTs and HDACs. Quantitative methylation array was used to assess quercetin-mediated alterations in the promoter methylation of selected tumor suppressor genes (TSGs). Quercetin induced modulation of chromatin modifiers including DNMTs, HDACs, histone acetyltransferases (HAT) and HMTs, and TSGs were assessed by quantitative reverse transcription PCR (qRT-PCR). It was found that quercetin modulates the expression of various chromatin modifiers and decreases the activity of DNMTs, HDACs, and HMTs in a dose-dependent manner. Molecular docking results suggest that quercetin could function as a competitive inhibitor by interacting with residues in the catalytic cavity of several DNMTs and HDACs. Quercetin downregulated global DNA methylation levels in a dose- and time-dependent manner. The tested TSGs showed steep dose-dependent decline in promoter methylation with the restoration of their expression. Our study provides an understanding of the quercetin's mechanism of action and will aid in its development as a candidate for epigenetic-based anticancer therapy.
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Affiliation(s)
| | - Arif Hussain
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Ritu Raina
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
| | - Nazia Afroze
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
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12
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Chang SY, Kuo CC, Wu CC, Hsiao CW, Hu JM, Hsu CH, Chou YC, Shih YL, Lin YW. NKX6.1 hypermethylation predicts the outcome of stage II colorectal cancer patients undergoing chemotherapy. Genes Chromosomes Cancer 2018; 57:268-277. [PMID: 29363224 DOI: 10.1002/gcc.22529] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 12/16/2022] Open
Abstract
Colorectal cancer (CRC) is a common malignancy worldwide. CRC patients in the same stage often present with dramatically different clinical scenarios. Thus, robust prognostic biomarkers are urgently needed to guide therapies and improve treatment outcomes. The NKX6.1 gene has been identified as a hypermethylation marker in cervical cancer, functioning as a metastasis suppressor by regulating epithelial-mesenchymal transition. Here, we investigated whether hypermethylation of NKX6.1 might be a prognostic biomarker for CRC. By analyzing the methylation and expression of NKX6.1 in CRC tissues and CRC cell lines. We quantitatively examined the NKX6.1 methylation levels in 151 pairs of CRC tissues by using methylation-specific polymerase chain reaction analysis and found that NKX6.1 was hypermethylated in 35 of 151 CRC tissues (23%). NKX6.1 gene expression was inversely correlated with the DNA methylation level in CRC cell lines in vitro. Then, we analyzed the association of NKX6.1 methylation with clinical characteristics of these CRC patients. Our data demonstrated that patients with NKX6.1 methylation presented poorer 5-year overall survival (P = 0.0167) and disease-free survival (P = 0.0083) than patients without NKX6.1 methylation after receiving adjuvant chemotherapy. Most importantly, these data revealed that stage II CRC patients with NKX6.1 methylation had poorer 5-year disease-free survival (P = 0.0322) than patients without NKX6.1 methylation after adjuvant chemotherapy. Our results demonstrate that methylation of NKX6.1 is a novel prognostic biomarker in CRC and that it may be used as a predictor of the response to chemotherapy.
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Affiliation(s)
- Sou-Yi Chang
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Division of Hematology & Oncology, Department of Internal Medicine, Taipei Tzu Chi Hospital, Taipei, Taiwan, Republic of China
| | - Chih-Chi Kuo
- Teaching and Research Office, Tri-Service General Hospital Songshan Branch, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chang-Chieh Wu
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Cheng-Wen Hsiao
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Je-Ming Hu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chih-Hsiung Hsu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,School of Medicine, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Yu-Ching Chou
- School of Public Health, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Yu-Lueng Shih
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Ya-Wen Lin
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan, Republic of China
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13
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Wang P, Chen Y, Li C, Zhao R, Wang F, Lin X, Cao L, Li S, Hu L, Gao Y, Li Y, Wu S. Drosophila eye developmental defect caused by elevation of the activity of the LIM-homeodomain protein, Lmx1a, requires its association with the Co-activator Chip. Biochem Biophys Res Commun 2015; 470:29-34. [PMID: 26718403 DOI: 10.1016/j.bbrc.2015.12.089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 12/20/2015] [Indexed: 11/18/2022]
Abstract
The LIM-homeodomain (LIM-HD) family member Lmx1a has been successfully used to induce dopaminergic neurons from other cell types, thus showing significant implications in replacement therapies of Parkinson's disease, but the underlying mechanism remains elusive. In this study, we used Drosophila eye as a model system to investigate how forced expression of dLmx1a, the fly homolog of human Lmx1a, alters cell identify. We found that ectopic expression of dLmx1a suppresses the formation of Drosophila eye tissue and identified the LIM and HD as two essential domains. dLmx1a requires and physically binds to Chip, a well-known cofactor of LIM-HD proteins. Chip connects two dLmx1a proteins to form a functional tetrameric complex. In addition, we provide evidence showing that dLmx1a expression results in the suppression of two retina determination gene eyes absent (eya) and string (stg). Taken together, our findings identified Chip as a novel partner of dLmx1a to alter cell differentiation in Drosophila eye through repressing eya and stg expression, and provide an animal model for further understanding the molecular mechanism whereby Lmx1a determines cell fate.
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Affiliation(s)
- Ping Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Yan Chen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Chaojie Li
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Runan Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Feng Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Xiaohui Lin
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Lei Cao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Shanshan Li
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Liangchang Hu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Yang Gao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Yuanpei Li
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Shian Wu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300071, PR China.
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14
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NKX6.1 functions as a metastatic suppressor through epigenetic regulation of the epithelial-mesenchymal transition. Oncogene 2015; 35:2266-78. [PMID: 26257059 PMCID: PMC4855079 DOI: 10.1038/onc.2015.289] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/14/2015] [Accepted: 06/29/2015] [Indexed: 01/27/2023]
Abstract
The transcription factor NKX6.1 (NK6 homeobox 1) is important in the development of pancreatic β-cells and neurons. Although recent publications show that NKX6.1 is hypermethylated and downregulated during tumorigenesis, the function of NKX6.1 in carcinogenesis remains elusive. Here, we address the metastasis suppressor function of human NKX6.1 using cell, animal and clinical analyses. Our data show that NKX6.1 represses tumor formation and metastatic ability both in vitro and in vivo. Mechanistically, NKX6.1 suppresses cell invasion by inhibiting the epithelial-to-mesenchymal transition (EMT). NKX6.1 directly enhances the mRNA level of E-cadherin by recruiting BAF155 coactivator and represses that of vimentin and N-cadherin by recruiting RBBP7 (retinoblastoma binding protein 7) corepressor. Clinical cancer tumors with metastasis show low NKX6.1 protein expression coinciding with low E-cadherin and high vimentin expression. Our results demonstrate that NKX6.1 functions as an EMT suppressor by interacting with different epigenetic modifiers, making it a potential novel therapeutic option.
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15
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Chen T, Sun Y, Ji P, Kopetz S, Zhang W. Topoisomerase IIα in chromosome instability and personalized cancer therapy. Oncogene 2014; 34:4019-31. [PMID: 25328138 PMCID: PMC4404185 DOI: 10.1038/onc.2014.332] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/08/2014] [Accepted: 09/08/2014] [Indexed: 12/29/2022]
Abstract
Genome instability is a hallmark of cancer cells. Chromosome instability (CIN), which is often mutually exclusive from hypermutation genotypes, represents a distinct subtype of genome instability. Hypermutations in cancer cells are due to defects in DNA repair genes, but the cause of CIN is still elusive. However, because of the extensive chromosomal abnormalities associated with CIN, its cause is likely a defect in a network of genes that regulate mitotic checkpoints and chromosomal organization and segregation. Emerging evidence has shown that the chromosomal decatenation checkpoint, which is critical for chromatin untangling and packing during genetic material duplication, is defective in cancer cells with CIN. The decatenation checkpoint is known to be regulated by a family of enzymes called topoisomerases. Among them, the gene encoding topoisomerase IIα (TOP2A) is commonly altered at both gene copy number and gene expression level in cancer cells. Thus, abnormal alterations of TOP2A, its interacting proteins, and its modifications may play a critical role in CIN in human cancers. Clinically, a large arsenal of topoisomerase inhibitors have been used to suppress DNA replication in cancer. However, they often lead to the secondary development of leukemia because of their effect on the chromosomal decatenation checkpoint. Therefore, topoisomerase drugs must be used judiciously and administered on an individual basis. In this review, we highlight the biological function of TOP2A in chromosome segregation and the mechanisms that regulate this enzyme's expression and activity. We also review the roles of TOP2A and related proteins in human cancers, and raise a perspective for how to target TOP2A in personalized cancer therapy.
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Affiliation(s)
- T Chen
- 1] Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA [2] Department of Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Y Sun
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - P Ji
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - S Kopetz
- Department of Gastrointestinal Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - W Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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