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Loaiza-Moss J, Braun U, Leitges M. Transcriptome Profiling of Mouse Embryonic Fibroblast Spontaneous Immortalization: A Comparative Analysis. Int J Mol Sci 2024; 25:8116. [PMID: 39125691 PMCID: PMC11311763 DOI: 10.3390/ijms25158116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/17/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Cell immortalization, a hallmark of cancer development, is a process that cells can undergo on their path to carcinogenesis. Spontaneously immortalized mouse embryonic fibroblasts (MEFs) have been used for decades; however, changes in the global transcriptome during this process have been poorly described. In our research, we characterized the poly-A RNA transcriptome changes after spontaneous immortalization. To this end, differentially expressed genes (DEGs) were screened using DESeq2 and characterized by gene ontology enrichment analysis and protein-protein interaction (PPI) network analysis to identify the potential hub genes. In our study, we identified changes in the expression of genes involved in proliferation regulation, cell adhesion, immune response and transcriptional regulation in immortalized MEFs. In addition, we performed a comparative analysis with previously reported MEF immortalization data, where we propose a predicted gene regulatory network model in immortalized MEFs based on the altered expression of Mapk11, Cdh1, Chl1, Zic1, Hoxd10 and the novel hub genes Il6 and Itgb2.
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Affiliation(s)
| | | | - Michael Leitges
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, 300 Prince Philip Drive, St. Johns, NL A1B 3V6, Canada; (J.L.-M.); (U.B.)
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2
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Deb P, Chini A, Guha P, Rishi A, Bhan A, Brady B, Perrotti LI, Mandal SS. Dynamic regulation of BDNF gene expression by estradiol and lncRNA HOTAIR. Gene 2024; 897:148055. [PMID: 38043834 DOI: 10.1016/j.gene.2023.148055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Brain derived neurotrophic factor (BDNF) is a major neurotransmitter that controls growth and maintenance of neurons and its misregulation is linked to neurodegeneration and human diseases. Estradiol (E2) is well-known to regulate the process of differentiation and plasticity of hippocampal neurons. Here we examined the mechanisms of BDNF gene regulation under basal conditions and under stimuli such as E2. Our results demonstrated that BDNF expression is induced by E2 in vitro in HT22 cells (hippocampal neuronal cells) and in vivo (in ovariectomized mouse brain under E2-treatment). Using chromatin immunoprecipitation assay, we demonstrated that estrogen receptors (ERα, ERβ) were enriched at the BDNF promoter in presence of E2. Additionally, ER-coregulators (e.g., CBP/p300, MLL3), histone acetylation, H3K4-trimethylation, and RNA polymerase II levels were also elevated at the BDNF promoter in an E2-dependent manner. Additionally, under the basal conditions (in the absence of E2), the long noncoding RNA HOTAIR and its interacting partners PRC2 and LSD1 complexes binds to the promoter of BDNF and represses its expression. HOTAIR knockdown -relieves the repression resulting in elevation of BDNF expression. Further, levels of HOTAIR-interacting partners, EZH2 and LSD1 were reduced at the BDNF promoter upon HOTAIR-knockdown revealing that HOTAIR plays a regulatory role in BDNF gene expression by modulating promoter histone modifications. Additionally, we showed that E2 induced-BDNF expression is mediated by the displacement of silencing factors, EZH2 and LSD1 at BDNF promoter and subsequent recruitment of active transcription machinery. These results reveal the mechanisms of BDNF gene regulation under the basal condition and in presence of a positive regulator such as E2 in neuronal cells.
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Affiliation(s)
- Paromita Deb
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Avisankar Chini
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Prarthana Guha
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Ashcharya Rishi
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Arunoday Bhan
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Blake Brady
- Department of Psychology, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Linda I Perrotti
- Department of Psychology, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Subhrangsu S Mandal
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States.
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3
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Wang L, Wang X, Sun H, Wang W, Cao L. A pan-cancer analysis of the role of HOXD1, HOXD3, and HOXD4 and validation in renal cell carcinoma. Aging (Albany NY) 2023; 15:10746-10766. [PMID: 37827698 PMCID: PMC10599751 DOI: 10.18632/aging.205116] [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: 06/12/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
HOXD1, HOXD3, and HOXD4 are members of the HOXD genes family and are related to tumorigenesis of the tumor. However, whether HOXDs (1, 3, 4) have a crucial role across pan-cancer is still unknown. HOXD1, HOXD3, and HOXD4 expressions were analyzed using public databases in 33 types of tumors. The UCSC Xena website was carried out to investigate the relationship between the expression of genes and the progress of cancers. The biological functions of HOXD3 were tested by colony forming, transwell, wound healing, and xenograft assay in vitro and in vivo. GSEA was used to identify the associated cancer hallmarks with HOXDs expression. Immune cell infiltration analysis was applied to verify the immune cell infiltrations related to genes. The results showed HOXD1, HOXD3, and HOXD4 co-low expressed in BRCA, COAD, KICH, KIRC, KIRP, READ, and TGCT. In the KIRC, all of HOXDs expression was connected with tumor stage and histological grade. Upregulation of HOXDs was associated with improved OS, DSS, and PFI. Down-expression of HOXD3 induced cell proliferation, migration, and invasion in vivo and in vitro. In addition, HOXDs were connected with immune-activated hallmarks and cancer immune cell infiltrations. These findings demonstrated that HOXDs may be indicative biomarkers for the prognosis and immunotherapy in pan-cancer.
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Affiliation(s)
- Lumin Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi 710004, P.R. China
| | - Xiaofei Wang
- Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi 710061, P.R. China
| | - Haifeng Sun
- The Third Department of Medical Oncology, Shaanxi Provincial Cancer Hospital Affiliated to Medical College of Xi’an Jiaotong University, Xi’an, Shaanxi 710065, P.R. China
| | - Wenjing Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi 710061, P.R. China
| | - Li Cao
- Key Laboratory of Environment and Genes Related to Diseases, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi 710061, P.R. China
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4
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Bagci O, Tumer S, Altungoz O. Chromosome 1p status in neuroblastoma correlates with higher expression levels of miRNAs targeting neuronal differentiation pathway. In Vitro Cell Dev Biol Anim 2023; 59:100-108. [PMID: 36800078 DOI: 10.1007/s11626-023-00750-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023]
Abstract
Neuroblastoma (NB) is characterized by acquired segmental and numerical chromosome aberrations. Although deletions of distal 1p and 11q are frequent alterations, no candidate tumor suppressor gene residing in these chromosomal sites could be identified so far. In the present study, we detected the genomic imbalances of six neuroblastoma cell lines using the multiplex ligation-dependent probe amplification (MLPA) technique and the microRNA (miRNA) expression profiles of the cell lines by a microarray study. According to MLPA results, we aimed to assess the miRNA expression profiles of the cell lines harboring 11q and 1p deletions. The cell lines with 1p deletions revealed statistically significant higher levels of expression for 29 miRNAs in contrast to the cell lines without 1p deletion in microarray study. We also performed GO enrichment analysis for predicted targets of the differentially expressed miRNAs. According to GO enrichment analysis, miRNAs that showed the high change in expression was associated with neuronal differentiation. We showed that hsa-miR-494, hsa-miR-495, and hsa-miR-543 target most of mRNAs in neuronal differentiation pathway. Although limited to the cell lines, our results highly suggest that NBs with different segmental chromosome abnormalities may have different dysregulated miRNA expression signatures that target the genes involved in neuronal differentiation.
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Affiliation(s)
- Ozkan Bagci
- Department of Medical Biology and Genetics, School of Medicine, Dokuz Eylul University, 35340, Balcova, Izmir, Turkey.,Department of Medical Genetics, School of Medicine, Selcuk University, Konya, Turkey
| | - Sait Tumer
- Department of Medical Biology and Genetics, School of Medicine, Dokuz Eylul University, 35340, Balcova, Izmir, Turkey.,Acibadem Genetic Diagnosis Center, Istanbul, Turkey
| | - Oguz Altungoz
- Department of Medical Biology and Genetics, School of Medicine, Dokuz Eylul University, 35340, Balcova, Izmir, Turkey.
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5
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Wang L, Qiao C, Cao L, Cai S, Ma X, Song X, Jiang Q, Huang C, Wang J. Significance of HOXD transcription factors family in progression, migration and angiogenesis of cancer. Crit Rev Oncol Hematol 2022; 179:103809. [PMID: 36108961 DOI: 10.1016/j.critrevonc.2022.103809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 10/31/2022] Open
Abstract
The transcription factors (TFs) of the HOX family play significant roles during early embryonic development and cellular processes. They also play a key role in tumorigenesis as tumor oncogenes or suppressors. Furthermore, TFs of the HOXD geFIne cluster affect proliferation, migration, and invasion of tumors. Consequently, dysregulated activity of HOXD TFs has been linked to clinicopathological characteristics of cancer. HOXD TFs are regulated by non-coding RNAs and methylation of DNA on promoter and enhancer regions. In addition, HOXD genes modulate the biological function of cancer cells via the MEK and AKT signaling pathways, thus, making HOXD TFs, a suitable molecular marker for cancer prognosis and therapy. In this review, we summarized the roles of HOXD TFs in different cancers and highlighted its potential as a diagnostic and therapeutic target.
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Affiliation(s)
- Lumin Wang
- Gastroenterology department, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China; Institute of precision medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China
| | - Chenyang Qiao
- Gastroenterology department, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China
| | - Li Cao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China
| | - Shuang Cai
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China
| | - Xiaoping Ma
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China
| | - Xinqiu Song
- Department of Cell Biology and Genetics, Medical College of Yan'an University, Yan'an, Shaanxi, PR China
| | - Qiuyu Jiang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China; Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, PR China.
| | - Jinhai Wang
- Gastroenterology department, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China; Institute of precision medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China.
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6
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Khazeem MM, Casement JW, Schlossmacher G, Kenneth NS, Sumbung NK, Chan JYT, McGow JF, Cowell IG, Austin CA. TOP2B Is Required to Maintain the Adrenergic Neural Phenotype and for ATRA-Induced Differentiation of SH-SY5Y Neuroblastoma Cells. Mol Neurobiol 2022; 59:5987-6008. [PMID: 35831557 PMCID: PMC9463316 DOI: 10.1007/s12035-022-02949-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/23/2022] [Indexed: 12/13/2022]
Abstract
The neuroblastoma cell line SH-SY5Y is widely used to study retinoic acid (RA)-induced gene expression and differentiation and as a tool to study neurodegenerative disorders. SH-SY5Y cells predominantly exhibit adrenergic neuronal properties, but they can also exist in an epigenetically interconvertible alternative state with more mesenchymal characteristics; as a result, these cells can be used to study gene regulation circuitry controlling neuroblastoma phenotype. Using a combination of pharmacological inhibition and targeted gene inactivation, we have probed the requirement for DNA topoisomerase IIB (TOP2B) in RA-induced gene expression and differentiation and in the balance between adrenergic neuronal versus mesenchymal transcription programmes. We found that expression of many, but not all genes that are rapidly induced by ATRA in SH-SY5Y cells was significantly reduced in the TOP2B null cells; these genes include BCL2, CYP26A1, CRABP2, and NTRK2. Comparing gene expression profiles in wild-type versus TOP2B null cells, we found that long genes and genes expressed at a high level in WT SH-SY5Y cells were disproportionately dependent on TOP2B. Notably, TOP2B null SH-SY5Y cells upregulated mesenchymal markers vimentin (VIM) and fibronectin (FN1) and components of the NOTCH signalling pathway. Enrichment analysis and comparison with the transcription profiles of other neuroblastoma-derived cell lines supported the conclusion that TOP2B is required to fully maintain the adrenergic neural-like transcriptional signature of SH-SY5Y cells and to suppress the alternative mesenchymal epithelial-like epigenetic state.
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Affiliation(s)
- Mushtaq M Khazeem
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,National Center of Hematology, Mustansiriyah University, Baghdad, Iraq
| | - John W Casement
- Bioinformatics Support Unit, The Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - George Schlossmacher
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Niall S Kenneth
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Nielda K Sumbung
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Janice Yuen Tung Chan
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Jade F McGow
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Ian G Cowell
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - Caroline A Austin
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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7
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Yu B, Guo X. Prognostic significance of HOXD4 protein expression in human ovarian cancers. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2021; 24:1561-1567. [PMID: 35317110 PMCID: PMC8917843 DOI: 10.22038/ijbms.2021.58396.12969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/17/2021] [Indexed: 11/06/2022]
Abstract
Objectives Ovarian cancer is the most common gynecological malignancy, ranking as the fifth leading cause of cancer-related deaths among females in the United States. Homeobox D4 (HOXD4) is a transcription factor belonging to the homeobox protein family, which plays a critical role in morphogenesis during embryo development. Here we aimed to study the HOXD4 expression in ovarian serous carcinoma (OSC) and determine its clinical significance. Materials and Methods Real-time quantitative PCR and immunohistochemistry targeting human OSC tissues and adjacent ovarian tissues were performed to correlate the patterns of HOXD4 expression with clinical characteristics and survival outcomes. Cell lines and nude mice were used for verifying the role of HOXD4 in OSC. Results HOXD4 protein was predominantly expressed in OSC tissues compared with nontumorous tissues. The correlation test demonstrated a significant correlation between HOXD4 with tumor FIGO stage. Univariate and multivariate analyses found that HOXD4 expression was associated with poorer overall survival. Furthermore, high expression of HOXD4 protein was observed in OSC cell lines in vitro. Finally, the oncogenic effect of HOXD4 was confirmed by cellular and xenograft experiments. Conclusion HOXD4 protein expression may be associated with a poorer prognosis in OSC. The unfavorable prognostic value of HOXD4 in malignancies and its underlying mechanism are worthy of further investigation.
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Affiliation(s)
- Bo Yu
- Department of General Surgery, The Second People's Hospital of Lanzhou, Lanzhou 730000, China
| | - Xiaoqing Guo
- Department of Gynecology and Obstetrics, Affiliated Hospital of Gansu University of Traditional Chinese Medicine, Lanzhou, 730000, China
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8
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Bai Z, Li H, Li C, Sheng C, Zhao X. Integrated analysis identifies a long non-coding RNAs-messenger RNAs signature for prediction of prognosis in hepatitis B virus-hepatocellular carcinoma patients. Medicine (Baltimore) 2020; 99:e21503. [PMID: 33019382 PMCID: PMC7535691 DOI: 10.1097/md.0000000000021503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepatitis B virus (HBV) infection is a leading cause of hepatocellular carcinoma (HCC), but HBV-HCC related prognosis signature remains rarely investigated. This study was to identify an integrated long non-coding RNAs-messenger RNAs (lncRNA-mRNA) signature for prediction of overall survival (OS) and explore their underlying functions.One RNA-sequencing dataset (training set, n = 95) and one microarray dataset E-TABM-36 (validation set, n = 44) were collected. Least absolute shrinkage and selection operator analysis was performed to identify an lncRNA-mRNA prognosis signature. The OS difference of patients in the high-risk and low-risk risk groups was evaluated by Kaplan-Meier curve. Area under the receiver operating characteristic curve (AUC), Harrell concordance index (C-index) calculation, and multivariate analyses with clinical characteristics were used to determine the prognostic ability. Furthermore, a coexpression network was constructed to interpret the functions.Nine signature genes (3 lncRNAs and 6 mRNAs) were selected to generate the risk score model. Patients belonging to the high-risk group showed a significantly shorter survival than those of the low-risk group. The prediction accuracy of the risk score for 5-year OS was 0.936 and 0.905 for the training set and validation set, respectively. Also, this risk score was independent of various clinical variables for the prognosis prediction. Incorporation of the risk score remarkably increased the predictive power of the routine clinical prognostic factors (vascular invasion status, tumor recurrence status) (AUC = 0.942 vs 0.628; C-index = 0.7997 vs 0.6908). Furthermore, LncRNA insulin-like growth factor 2 antisense RNA (IGF2-AS) and long intergenic non-protein coding RNA 342 (LINC00342) were predicted to exert tumor suppression effects by regulating homeobox D1 (HOXD1) and secreted frizzled related protein 5 (SFRP5), respectively; while lncRNA rhophilin Rho GTPase binding protein 1 antisense RNA 1 (RHPN1-AS1) may possess carcinogenic potential by promoting the transcription of chromobox 2 (CBX2), cell division cycle 20 (CDC20), matrix metallopeptidase 12 (MMP12), stratifin (SFN), tripartite motif containing 16 (TRIM16), and uroplakin 3A (UPK3A). These mRNAs may be associated with cell proliferation or apoptosis related pathways.This study may provide a novel, effective prognostic biomarker, and some therapeutic targets for HBV-HCC patients.
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Rajagopal T, Talluri S, Akshaya R, Dunna NR. HOTAIR LncRNA: A novel oncogenic propellant in human cancer. Clin Chim Acta 2020; 503:1-18. [DOI: 10.1016/j.cca.2019.12.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 12/27/2019] [Accepted: 12/30/2019] [Indexed: 02/08/2023]
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10
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Safari M, Noroozi R, Taheri M, Ghafouri-Fard S. The rs12826786 in HOTAIR lncRNA Is Associated with Risk of Autism Spectrum Disorder. J Mol Neurosci 2019; 70:175-179. [PMID: 31654274 DOI: 10.1007/s12031-019-01421-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/10/2019] [Indexed: 11/30/2022]
Abstract
Autism spectrum disorder (ASD) encompasses a group of neurodevelopmental disorders with complex pattern of inheritance. Several single nucleotide polymorphisms (SNPs) within coding or non-coding regions of genome have been associated with risk of this disorder. In the current study, we genotyped rs12826786, rs1899663, and rs4759314 SNPs within HOX transcript antisense RNA (HOTAIR) in 427 ASD cases and 430 normally developed children. The rs12826786 was associated with ASD in allelic (T vs. C: OR (95% CI) = 1.29 (1.07-1.57), adjusted P value = 0.03) and recessive (TT vs. TC + CC: OR (95% CI) = 1.60 (1.10-2.32), adjusted P value = 0.04) models. However, the other SNPs were not associated with ASD in any inheritance model. No estimated haplotype within HOTAIR was associated with risk of ASD in the assessed population. Based on the results of the current investigation, the rs12826786 can be regarded as a risk locus for ASD in Iranian population.
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Affiliation(s)
- Mohammadreza Safari
- Department of Medical Laboratory Sciences, School of Para Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Rezvan Noroozi
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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11
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Yang L, Zha Y, Ding J, Ye B, Liu M, Yan C, Dong Z, Cui H, Ding HF. Histone demethylase KDM6B has an anti-tumorigenic function in neuroblastoma by promoting differentiation. Oncogenesis 2019; 8:3. [PMID: 30631055 PMCID: PMC6328563 DOI: 10.1038/s41389-018-0112-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/19/2018] [Accepted: 12/11/2018] [Indexed: 02/07/2023] Open
Abstract
Induction of differentiation is a therapeutic strategy in high-risk neuroblastoma, a childhood cancer of the sympathetic nervous system. Neuroblastoma differentiation requires transcriptional upregulation of neuronal genes. How this process is regulated at epigenetic levels is not well understood. Here we report that the histone H3 lysine 27 demethylase KDM6B is an epigenetic activator of neuroblastoma cell differentiation. KDM6B mRNA expression is downregulated in poorly differentiated high-risk neuroblastomas and upregulated in differentiated tumors, and high KDM6B expression is prognostic for better survival in neuroblastoma patients. In neuroblastoma cell lines, KDM6B depletion promotes cell proliferation, whereas KDM6B overexpression induces neuronal differentiation and inhibits cell proliferation and tumorgenicity. Mechanistically, KDM6B epigenetically activates the transcription of neuronal genes by removing the repressive chromatin marker histone H3 lysine 27 trimethylation. In addition, we show that KDM6B functions downstream of the retinoic acid-HOXC9 axis in inducing neuroblastoma cell differentiation: KDM6B expression is upregulated by retinoic acid via HOXC9, and KDM6B is required for HOXC9-induced neuroblastoma cell differentiation. Finally, we present evidence that KDM6B interacts with HOXC9 to target neuronal genes for epigenetic activation. These findings identify a KDM6B-dependent epigenetic mechanism in the control of neuroblastoma cell differentiation, providing a rationale for reducing histone H3 lysine 27 trimethylation as a strategy for enhancing differentiation-based therapy in high-risk neuroblastoma.
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Affiliation(s)
- Liqun Yang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Yunhong Zha
- Institute of Neural Regeneration and Repair and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang, 443000, China
| | - Jane Ding
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Bingwei Ye
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Mengling Liu
- Institute of Neural Regeneration and Repair and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang, 443000, China
| | - Chunhong Yan
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA.,Department of Biochemistry and Molecular, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Zheng Dong
- Department of Cell Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.,Charlie Norwood VA Medical Center, Augusta, GA, 30904, USA
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China.
| | - Han-Fei Ding
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA. .,Department of Biochemistry and Molecular, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA. .,Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
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12
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Liu H, Tian H, Zhao J, Jia Y. High HOXD4 protein expression in gastric adenocarcinoma tissues indicates unfavorable clinical outcomes. Saudi J Gastroenterol 2019; 25:46-54. [PMID: 30588951 PMCID: PMC6373212 DOI: 10.4103/sjg.sjg_105_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND/AIM Homeobox D4 (HOXD4) belongs to the homeobox (HOX) family, which plays a crucial role in the early embryo development and cell differentiation. The role of HOXD4 in human gastric adenocarcinoma has not been elucidated. In the present study, we aimed to examine the expression levels of HOXD4 and dissect whether the HOXD4 expression is associated with aggressive clinicopathological outcomes of patients with gastric adenocarcinoma. PATIENTS AND METHODS Clinicopathological analyses were performed in 127 patients with gastric adenocarcinoma. Expression of HOXD4 was tested by immunohistochemistry staining and quantitative RT-PCR. Clinical outcomes were evaluated by the Kaplan-Meier method and log-rank test. The prognostic role of HOXD4 in gastric adenocarcinoma patients was assessed by univariate and multivariate analyses. The effects and mechanisms of HOXD4 on cell proliferation, migration and invasion were explored through cellular experiments. RESULTS HOXD4 expression was elevated in gastric adenocarcinoma tissues compared to non-tumorous gastric tissues (P = 0.018). High expression of HOXD4 was significantly associated with larger tumor size (P = 0.008), advanced tumor invasion depth (P = 0.014), and positive lymph node metastasis (P < 0.001). Moreover, patients with high HOXD4 expression had poorer overall survival (P = 0.001), and HOXD4 was identified as an independent prognosis factor according to multivariate analysis [hazard ratio (HR) =2.253, 95% confident interval (CI) 1.028-4.979, P = 0.044]. Cellular results revealed that HOXD4 can promote tumor cell proliferation by upregulating c-Myc and cyclin D1. CONCLUSIONS Our study demonstrated that overexpression of HOXD4 was significantly correlated with poorer prognosis of gastric adenocarcinoma patients, indicating the potential of HOXD4 as a novel clinical predictive biomarker and drug target.
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Affiliation(s)
- Hui Liu
- Department of Traditional Chinese Medicine, Yidu Central Hospital of Weifang, Weifang, Shandong, China
| | - Hequn Tian
- Department of Traditional Chinese Medicine, Yidu Central Hospital of Weifang, Weifang, Shandong, China
| | - Jing Zhao
- Department of Traditional Chinese Medicine, Yidu Central Hospital of Weifang, Weifang, Shandong, China
| | - Yong Jia
- Department of Surgical Oncology, Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, Shaanxi Province, China,Address for correspondence: Dr. Yong Jia, Vice #2 Weiyangxi Road, Xianyang 712000, Shaanxi Province, China. E-mail:
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13
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Conway K, Edmiston SN, Parker JS, Kuan PF, Tsai YH, Groben PA, Zedek DC, Scott GA, Parrish EA, Hao H, Pearlstein MV, Frank JS, Carson CC, Wilkerson MD, Zhao X, Slater NA, Moschos SJ, Ollila DW, Thomas NE. Identification of a Robust Methylation Classifier for Cutaneous Melanoma Diagnosis. J Invest Dermatol 2018; 139:1349-1361. [PMID: 30529013 DOI: 10.1016/j.jid.2018.11.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022]
Abstract
Early diagnosis improves melanoma survival, yet the histopathological diagnosis of cutaneous primary melanoma can be challenging, even for expert dermatopathologists. Analysis of epigenetic alterations, such as DNA methylation, that occur in melanoma can aid in its early diagnosis. Using a genome-wide methylation screening, we assessed CpG methylation in a diverse set of 89 primary invasive melanomas, 73 nevi, and 41 melanocytic proliferations of uncertain malignant potential, classified based on interobserver review by dermatopathologists. Melanomas and nevi were split into training and validation sets. Predictive modeling in the training set using ElasticNet identified a 40-CpG classifier distinguishing 60 melanomas from 48 nevi. High diagnostic accuracy (area under the receiver operator characteristic curve = 0.996, sensitivity = 96.6%, and specificity = 100.0%) was independently confirmed in the validation set (29 melanomas, 25 nevi) and other published sample sets. The 40-CpG melanoma classifier included homeobox transcription factors and genes with roles in stem cell pluripotency or the nervous system. Application of the 40-CpG melanoma classifier to the diagnostically uncertain samples assigned melanoma or nevus status, potentially offering a diagnostic tool to assist dermatopathologists. In summary, the robust, accurate 40-CpG melanoma classifier offers a promising assay for improving primary melanoma diagnosis.
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Affiliation(s)
- Kathleen Conway
- Department of Epidemiology, School of Public Health, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Dermatology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center (LCCC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| | - Sharon N Edmiston
- Lineberger Comprehensive Cancer Center (LCCC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center (LCCC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Pei Fen Kuan
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center (LCCC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Pamela A Groben
- Department of Dermatology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Daniel C Zedek
- Department of Dermatology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Glynis A Scott
- Department of Dermatology, University of Rochester School of Medicine, Rochester, New York, USA; Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine, Rochester, New York, USA
| | - Eloise A Parrish
- Lineberger Comprehensive Cancer Center (LCCC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Honglin Hao
- Department of Dermatology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Michelle V Pearlstein
- Department of Dermatology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jill S Frank
- Lineberger Comprehensive Cancer Center (LCCC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Craig C Carson
- Department of Dermatology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Matthew D Wilkerson
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Xiaobei Zhao
- Lineberger Comprehensive Cancer Center (LCCC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nathaniel A Slater
- Department of Dermatology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Stergios J Moschos
- Lineberger Comprehensive Cancer Center (LCCC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - David W Ollila
- Lineberger Comprehensive Cancer Center (LCCC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Surgery, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Nancy E Thomas
- Department of Dermatology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center (LCCC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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14
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Role of HOX Genes in Stem Cell Differentiation and Cancer. Stem Cells Int 2018; 2018:3569493. [PMID: 30154863 PMCID: PMC6081605 DOI: 10.1155/2018/3569493] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/08/2018] [Accepted: 05/15/2018] [Indexed: 02/07/2023] Open
Abstract
HOX genes encode an evolutionarily conserved set of transcription factors that control how the phenotype of an organism becomes organized during development based on its genetic makeup. For example, in bilaterian-type animals, HOX genes are organized in gene clusters that encode anatomic segment identity, that is, whether the embryo will form with bilateral symmetry with a head (anterior), tail (posterior), back (dorsal), and belly (ventral). Although HOX genes are known to regulate stem cell (SC) differentiation and HOX genes are dysregulated in cancer, the mechanisms by which dysregulation of HOX genes in SCs causes cancer development is not fully understood. Therefore, the purpose of this manuscript was (i) to review the role of HOX genes in SC differentiation, particularly in embryonic, adult tissue-specific, and induced pluripotent SC, and (ii) to investigate how dysregulated HOX genes in SCs are responsible for the development of colorectal cancer (CRC) and acute myeloid leukemia (AML). We analyzed HOX gene expression in CRC and AML using information from The Cancer Genome Atlas study. Finally, we reviewed the literature on HOX genes and related therapeutics that might help us understand ways to develop SC-specific therapies that target aberrant HOX gene expression that contributes to cancer development.
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15
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Yang X, He J, Chang Y, Luo A, Luo A, Zhang J, Zhang R, Xia H, Xu L. HOTAIR gene polymorphisms contribute to increased neuroblastoma susceptibility in Chinese children. Cancer 2018; 124:2599-2606. [PMID: 29603181 DOI: 10.1002/cncr.31353] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/28/2018] [Accepted: 03/05/2018] [Indexed: 02/05/2023]
Abstract
BACKGROUND Neuroblastoma is the most frequently diagnosed extracranial solid tumor in children. Previous studies have shown that single-nucleotide polymorphisms in some genes are associated with the risk of multiple cancers, including neuroblastoma. Although Hox transcript antisense intergenic RNA (HOTAIR) gene polymorphisms have been investigated in a variety of cancers, to the authors' knowledge the relationships between HOTAIR gene polymorphisms and neuroblastoma susceptibility have not been reported to date. The objective of the current study was to evaluate the correlation between HOTAIR gene polymorphisms and neuroblastoma risk in Chinese children. METHODS The authors genotyped 6 polymorphisms (rs920778 A>G, rs12826786 C>T, rs4759314 A>G, rs7958904 G>C, rs874945 C>T, and rs1899663 C>A) of the HOTAIR gene in 2 Chinese populations including 393 neuroblastoma cases and 812 healthy controls. The strength of the associations was evaluated using odds ratios and 95% confidence intervals. Further stratification analyses were conducted to explore the association between the HOTAIR gene polymorphisms rs12826786 C>T, rs874945 C>T, and rs1899663 C>A with neuroblastoma susceptibility in terms of age, sex, clinical stage of disease, and sites of origin. RESULTS The authors found that the rs12826786 C>T (P =.013), rs874945 C>T (P =.020), and rs1899663 C>A (P =.029) polymorphisms were significantly associated with increased neuroblastoma risk. In stratification analyses, these associations were more predominant in females and among patients with tumor in the retroperitoneal region or mediastinum. The remaining 3 polymorphisms were not found to be related to neuroblastoma susceptibility. CONCLUSIONS The results of the current study verified that HOTAIR gene polymorphisms are associated with increased neuroblastoma risk and suggest that HOTAIR gene polymorphisms might be a potential biomarker for neuroblastoma susceptibility. Cancer 2018;124:2599-606. © 2018 American Cancer Society.
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Affiliation(s)
- Xu Yang
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Yitian Chang
- Department of Clinical Medicine, Jilin University, Changchun, Jilin, China
| | - Annie Luo
- Department of Science, Fraser Heights Secondary School, Surrey, British Columbia, Canada
| | - Ailing Luo
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiao Zhang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ruizhong Zhang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Ling Xu
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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16
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Zhao XW, Zhan YB, Bao JJ, Zhou JQ, Zhang FJ, Bin Y, Bai YH, Wang YM, Zhang ZY, Liu XZ. Clinicopathological analysis of HOXD4 expression in diffuse gliomas and its correlation with IDH mutations and 1p/19q co-deletion. Oncotarget 2017; 8:115657-115666. [PMID: 29383189 PMCID: PMC5777801 DOI: 10.18632/oncotarget.23371] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/05/2017] [Indexed: 12/11/2022] Open
Abstract
Backgrounds HOX (homologous box) is known as the dominant gene of vertebrate growth and cell differentiation. Abnormal expression of HOX gene in various tumors has attracted the attention of scholars. As a component of HOX clusters, HOXD4 plays a controversial role in the tumorigenesis of central nervous system. Results The data demonstrated that and the results demonstrated that HOXD4 was overexpressed in glioma tissues compared to that of normal brain tissues. patients with high HOXD4 expression had a significant shorter survival than those with low HOXD4 expression in total glioma cohort (p<0.001), WHO Grade II cohort (p=0.003) and Grade III cohort (p<0.001), but not in Grade IV cohort when OS (overall survival) was analyzed (p=0.216). The findings were confirmed by the large-scale omics data analysis including lower-grade glioma (LGG) and glioblastoma multiforme (GBM) in TCGA (the cancer genome atlas) and CGGA (Chinese glioma genome atlas). Moreover, it was revealed that the expression of HOXD4 have a significant impact on the OS of Grade IV glioma with IDH wild-type and 1p/19q intact according to TCGA data. Methods Clinicopathological analysis of HOXD4 expression in 453 glioma patients was performed in the current study. Expression of HOXD4 was evaluated by qPCR and immunohistochemical (IHC) staining. Univariate and multivariate analysis were conducted to investigate the prognostic role of HOXD4 in glioma patients. Conclusions Expression of HOXD4 was closely related to the clinical outcomes of patients with gliomas, and HOXD4 may be a potential prognostic biomarker of gliomas.
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Affiliation(s)
- Xin-Wei Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Yun-Bo Zhan
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Jian-Ji Bao
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Jin-Qiao Zhou
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Feng-Jiang Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Yu Bin
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Ya-Hui Bai
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Yan-Min Wang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Zhen-Yu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xian-Zhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China
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17
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Alternative SET/TAFI Promoters Regulate Embryonic Stem Cell Differentiation. Stem Cell Reports 2017; 9:1291-1303. [PMID: 28966118 PMCID: PMC5639460 DOI: 10.1016/j.stemcr.2017.08.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/27/2017] [Accepted: 08/28/2017] [Indexed: 01/21/2023] Open
Abstract
Embryonic stem cells (ESCs) are regulated by pluripotency-related transcription factors in concert with chromatin regulators. To identify additional stem cell regulators, we screened a library of endogenously labeled fluorescent fusion proteins in mouse ESCs for fluorescence loss during differentiation. We identified SET, which displayed a rapid isoform shift during early differentiation from the predominant isoform in ESCs, SETα, to the primary isoform in differentiated cells, SETβ, through alternative promoters. SETα is selectively bound and regulated by pluripotency factors. SET depletion causes proliferation slowdown and perturbed neuronal differentiation in vitro and developmental arrest in vivo, and photobleaching methods demonstrate SET's role in maintaining a dynamic chromatin state in ESCs. This work identifies an important regulator of pluripotency and early differentiation, which is controlled by alternative promoter usage. We identify SETα to be rapidly downregulated during ESC differentiation SETα is regulated by pluripotency factors and replaced by SETβ during differentiation SETα/SETβ switch is crucial for ESC differentiation SETα regulates chromatin plasticity in ESCs
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18
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Mansour MA, Senga T. HOXD8 exerts a tumor-suppressing role in colorectal cancer as an apoptotic inducer. Int J Biochem Cell Biol 2017; 88:1-13. [PMID: 28457970 DOI: 10.1016/j.biocel.2017.04.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/16/2017] [Accepted: 04/26/2017] [Indexed: 02/06/2023]
Abstract
Homeobox (HOX) genes are conserved transcription factors which determine the anterior-posterior body axis patterning. HOXD8 is a member of HOX genes deregulated in several tumors such as lung carcinoma, neuroblastoma, glioma and colorectal cancer (CRC) in a context-dependent manner. In CRC, HOXD8 is downregulated in cancer tissues and metastatic foci as compared to normal tissues. Whether HOXD8 acts as a tumor suppressor of malignant progression and metastasis is still unclear. Also, the underlying mechanism of its function including the downstream targets is totally unknown. Here, we clarified the lower expression of HOXD8 in clinical colorectal cancer vs. normal colon tissues. Also, we showed that stable expression of HOXD8 in colorectal cancer cells significantly reduced the cell proliferation, anchorage-independent growth and invasion. Further, using The Cancer Genome Atlas (TCGA), we identified the genes associated with HOXD8 in order to demonstrate its function as a suppressor or a promoter of colorectal carcinoma. Among inversely related genes, apoptotic inhibitors like STK38 kinase and MYC were shown to be negatively associated with HOXD8. We demonstrated the ability of HOXD8 to upregulate executioner caspases 6 & 7 and cleaved PARP, thus inducing the apoptotic events in colorectal cancer cells.
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Affiliation(s)
- Mohammed A Mansour
- Biochemistry Division, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt; Cancer Research UK Beatson Institute, Switchback Road, Glasgow, G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
| | - Takeshi Senga
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa, Nagoya, 466-8550 Japan
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19
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Klein S, Dieterich LC, Mathelier A, Chong C, Sliwa-Primorac A, Hong YK, Shin JW, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Hayashizaki Y, Forrest ARR, Wasserman WW, Detmar M. DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C. J Cell Sci 2016; 129:2573-85. [PMID: 27199372 DOI: 10.1242/jcs.186767] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/11/2016] [Indexed: 01/15/2023] Open
Abstract
Lymphangiogenesis plays a crucial role during development, in cancer metastasis and in inflammation. Activation of VEGFR-3 (also known as FLT4) by VEGF-C is one of the main drivers of lymphangiogenesis, but the transcriptional events downstream of VEGFR-3 activation are largely unknown. Recently, we identified a wave of immediate early transcription factors that are upregulated in human lymphatic endothelial cells (LECs) within the first 30 to 80 min after VEGFR-3 activation. Expression of these transcription factors must be regulated by additional pre-existing transcription factors that are rapidly activated by VEGFR-3 signaling. Using transcription factor activity analysis, we identified the homeobox transcription factor HOXD10 to be specifically activated at early time points after VEGFR-3 stimulation, and to regulate expression of immediate early transcription factors, including NR4A1. Gain- and loss-of-function studies revealed that HOXD10 is involved in LECs migration and formation of cord-like structures. Furthermore, HOXD10 regulates expression of VE-cadherin, claudin-5 and NOS3 (also known as e-NOS), and promotes lymphatic endothelial permeability. Taken together, these results reveal an important and unanticipated role of HOXD10 in the regulation of VEGFR-3 signaling in lymphatic endothelial cells, and in the control of lymphangiogenesis and permeability.
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Affiliation(s)
- Sarah Klein
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich 8093, Switzerland
| | - Lothar C Dieterich
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich 8093, Switzerland
| | - Anthony Mathelier
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University British Columbia, Vancouver, British Columbia, Canada V5Z 4H4
| | - Chloé Chong
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich 8093, Switzerland
| | - Adriana Sliwa-Primorac
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich 8093, Switzerland
| | - Young-Kwon Hong
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Jay W Shin
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Marina Lizio
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hideya Kawaji
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Timo Lassmann
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia 6008, Australia
| | - Carsten O Daub
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Erik Arner
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | | | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Alistair R R Forrest
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan Cancer and Cell Biology Division, Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia 6009, Australia
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University British Columbia, Vancouver, British Columbia, Canada V5Z 4H4
| | - Michael Detmar
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich 8093, Switzerland
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20
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Ren X, Yang GL, Peng WF, Zhao YX, Zhang M, Chen ZH, Wu FA, Kantanen J, Shen M, Li MH. A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries). Sci Rep 2016; 6:21111. [PMID: 26883901 PMCID: PMC4756668 DOI: 10.1038/srep21111] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/18/2016] [Indexed: 01/06/2023] Open
Abstract
Horns are a cranial appendage found exclusively in Bovidae, and play important roles in accessing resources and mates. In sheep (Ovies aries), horns vary from polled to six-horned, and human have been selecting polled animals in farming and breeding. Here, we conducted a genome-wide association study on 24 two-horned versus 22 four-horned phenotypes in a native Chinese breed of Sishui Fur sheep. Together with linkage disequilibrium (LD) analyses and haplotype-based association tests, we identified a genomic region comprising 132.0–133.1 Mb on chromosome 2 that contained the top 10 SNPs (including 4 significant SNPs) and 5 most significant haplotypes associated with the polycerate phenotype. In humans and mice, this genomic region contains the HOXD gene cluster and adjacent functional genes EVX2 and KIAA1715, which have a close association with the formation of limbs and genital buds. Our results provide new insights into the genetic basis underlying variable numbers of horns and represent a new resource for use in sheep genetics and breeding.
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Affiliation(s)
- Xue Ren
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Guang-Li Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,Department of Life Sciences, Shangqiu Normal University, Shangqiu 476000, China
| | - Wei-Feng Peng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Min Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Fu-An Wu
- Bureau of Animal Husbandry and Veterinary Medicine, Sishui County, Jining 273200, China
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen 31600, Finland.,Department of Biology, University of Eastern Finland, Kuopio 70211, Finland
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China.,Key Laboratory of Sheep Breeding and Development Technology of Xinjiang Production and Construction Crops (XPCC), Shihezi 832000, China
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
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21
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Ackermann S, Kocak H, Hero B, Ehemann V, Kahlert Y, Oberthuer A, Roels F, Theißen J, Odenthal M, Berthold F, Fischer M. FOXP1 inhibits cell growth and attenuates tumorigenicity of neuroblastoma. BMC Cancer 2014; 14:840. [PMID: 25406647 PMCID: PMC4251948 DOI: 10.1186/1471-2407-14-840] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 10/30/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Segmental genomic copy number alterations, such as loss of 11q or 3p and gain of 17q, are well established markers of poor outcome in neuroblastoma, and have been suggested to comprise tumor suppressor genes or oncogenes, respectively. The gene forkhead box P1 (FOXP1) maps to chromosome 3p14.1, a tumor suppressor locus deleted in many human cancers including neuroblastoma. FoxP1 belongs to a family of winged-helix transcription factors that are involved in processes of cellular proliferation, differentiation and neoplastic transformation. METHODS Microarray expression profiles of 476 neuroblastoma specimens were generated and genes differentially expressed between favorable and unfavorable neuroblastoma were identified. FOXP1 expression was correlated to clinical markers and patient outcome. To determine whether hypermethylation is involved in silencing of FOXP1, methylation analysis of the 5' region of FOXP1 in 47 neuroblastomas was performed. Furthermore, FOXP1 was re-expressed in three neuroblastoma cell lines to study the effect of FOXP1 on growth characteristics of neuroblastoma cells. RESULTS Low expression of FOXP1 is associated with markers of unfavorable prognosis like stage 4, age >18 months and MYCN amplification and unfavorable gene expression-based classification (P < 0.001 each). Moreover, FOXP1 expression predicts patient outcome accurately and independently from well-established prognostic markers. Array-based CGH analysis of 159 neuroblastomas revealed that heterozygous loss of the FOXP1 locus was a rare event (n = 4), but if present, was associated with low FOXP1 expression. By contrast, DNA methylation analysis in 47 neuroblastomas indicated that hypermethylation is not regularly involved in FOXP1 gene silencing. Re-expression of FoxP1 significantly impaired cell proliferation, viability and colony formation in soft agar. Furthermore, induction of FOXP1 expression led to cell cycle arrest and apoptotic cell death of neuroblastoma cells. CONCLUSIONS Our results suggest that down-regulation of FOXP1 expression is a common event in high-risk neuroblastoma pathogenesis and may contribute to tumor progression and unfavorable patient outcome.
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Affiliation(s)
- Sandra Ackermann
- Department of Pediatric Oncology and Hematology and Center for Molecular Medicine Cologne (CMMC), Children's Hospital, University of Cologne, Kerpener Straße 62, Cologne 50924, Germany.
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22
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Wolter JM, Kotagama K, Pierre-Bez AC, Firago M, Mangone M. 3'LIFE: a functional assay to detect miRNA targets in high-throughput. Nucleic Acids Res 2014; 42:e132. [PMID: 25074381 PMCID: PMC4176154 DOI: 10.1093/nar/gku626] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene output at the post-transcriptional level by targeting degenerate elements primarily in 3'untranslated regions (3'UTRs) of mRNAs. Individual miRNAs can regulate networks of hundreds of genes, yet for the majority of miRNAs few, if any, targets are known. Misexpression of miRNAs is also a major contributor to cancer progression, thus there is a critical need to validate miRNA targets in high-throughput to understand miRNAs' contribution to tumorigenesis. Here we introduce a novel high-throughput assay to detect miRNA targets in 3'UTRs, called Luminescent Identification of Functional Elements in 3'UTRs (3'LIFE). We demonstrate the feasibility of 3'LIFE using a data set of 275 human 3'UTRs and two cancer-relevant miRNAs, let-7c and miR-10b, and compare our results to alternative methods to detect miRNA targets throughout the genome. We identify a large number of novel gene targets for these miRNAs, with only 32% of hits being bioinformatically predicted and 27% directed by non-canonical interactions. Functional analysis of target genes reveals consistent roles for each miRNA as either a tumor suppressor (let-7c) or oncogenic miRNA (miR-10b), and preferentially target multiple genes within regulatory networks, suggesting 3'LIFE is a rapid and sensitive method to detect miRNA targets in high-throughput.
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Affiliation(s)
- Justin M Wolter
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 S. McAllister Dr., Tempe, AZ 85287, USA
| | - Kasuen Kotagama
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA Barrett, The Honors College, Arizona State University, 751 E Lemon Mall, Tempe, AZ 85287, USA
| | - Alexandra C Pierre-Bez
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 S. McAllister Dr., Tempe, AZ 85287, USA
| | - Mari Firago
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA
| | - Marco Mangone
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 S. McAllister Dr., Tempe, AZ 85287, USA Barrett, The Honors College, Arizona State University, 751 E Lemon Mall, Tempe, AZ 85287, USA
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Lubanska D, Porter LA. The atypical cell cycle regulator Spy1 suppresses differentiation of the neuroblastoma stem cell population. Oncoscience 2014; 1:336-48. [PMID: 25594028 PMCID: PMC4278303 DOI: 10.18632/oncoscience.36] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 05/04/2014] [Indexed: 12/28/2022] Open
Abstract
Neuroblastoma is an aggressive pediatric cancer originating embryonically from the neural crest. The heterogeneity of the disease, as most solid tumors, complicates diagnosis and treatment. In neuroblastoma this heterogeneity is well represented in both primary tumours and derived cell lines and has been shown to be driven by a population of stem-like tumour initiating cells. Resolving the molecular mediators driving the division of this population of cells may indicate effective therapeutic options for neuroblastoma patients. This study has determined that the atypical cyclin-like protein Spy1, recently indicated in driving symmetric division of glioma stem cells, is a critical factor in the stem-like properties of neuroblastoma tumor initiating cell populations. Spy1 activates Cyclin Dependent Kinases (CDK) in a manner that is unique from classical cyclins. Hence this discovery may represent an important opportunity to design CDK inhibitor drugs to uniquely target subpopulations of cells within these aggressive neural tumours.
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Affiliation(s)
- Dorota Lubanska
- Department of Biological Sciences University of Windsor OntarioWindsor, ON
| | - Lisa A. Porter
- Department of Biological Sciences University of Windsor OntarioWindsor, ON
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24
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Li Q, Ding C, Chen C, Zhang Z, Xiao H, Xie F, Lei L, Chen Y, Mao B, Jiang M, Li J, Wang D, Wang G. miR-224 promotion of cell migration and invasion by targeting Homeobox D 10 gene in human hepatocellular carcinoma. J Gastroenterol Hepatol 2014; 29:835-42. [PMID: 24219032 DOI: 10.1111/jgh.12429] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/24/2013] [Indexed: 01/23/2023]
Abstract
BACKGROUND AND AIM MicroRNAs (miRNAs) are small noncoding RNA molecules that control target gene expression and are implicated in the regulation of diverse cellular pathways. In our previous research, we have demonstrated that miR-224 was overexpressed in liver cancer cells and tissues, which was an important factor in the regulation of cell migration and invasion. This study aimed to further explore the regulatory mechanism of miR-224 in the migration and invasion in liver cancer cells. METHODS A luciferase reporter assay was used to confirm that the HOXD10 gene was a direct target of miR-224. Quantitative reverse transcriptase-polymerase chain reaction, Western blotting, Transwell migration, and Matrigel invasion assays were performed to clarify the molecular mechanism of miR-224 in the regulation of cell migration and invasion in human hepatocellular carcinoma (HCC). RESULTS (i) The expression of miR-224 was strongly upregulated in MHHC97H and MHCC97L cells, and its expression level was significantly associated with cell invasive potential. (ii) The HOXD10 gene was confirmed to be a direct target of miR-224. Compared with normal liver tissues and cells, HOXD10 had lower expression in HCC tissues and cells and inversely regulated HCC cell invasion. (iii) miR-224 promoted expression of the tumor invasion-associated proteins p-PAK4 and MMP-9 by directly targeting HOXD10. CONCLUSION Our findings suggest a previously undescribed regulatory pathway in which the miR-224/HOXD10/p-PAK4/MMP-9 signaling pathway contributes to the regulation of cell migration and invasion and provides a new biotarget for HCC treatment.
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Affiliation(s)
- Qiong Li
- Experimental Center of Basic Medicine, College of Basic Medical Science, Third Military Medical University, Chongqing, China
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25
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A 92-gene cancer classifier predicts the site of origin for neuroendocrine tumors. Mod Pathol 2014; 27:44-54. [PMID: 23846576 DOI: 10.1038/modpathol.2013.105] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/08/2013] [Accepted: 05/11/2013] [Indexed: 01/04/2023]
Abstract
A diagnosis of neuroendocrine carcinoma is often morphologically straight-forward; however, the tumor site of origin may remain elusive in a metastatic presentation. Neuroendocrine tumor subtyping has important implications for staging and patient management. In this study, the novel use and performance of a 92-gene molecular cancer classifier for determination of the site of tumor origin are described in a series of 75 neuroendocrine tumors (44 metastatic, 31 primary; gastrointestinal (n=12), pulmonary (n=22), Merkel cell (n=10), pancreatic (n=10), pheochromocytoma (n=10), and medullary thyroid carcinoma (n=11)). Formalin-fixed, paraffin-embedded samples passing multicenter pathologist adjudication were blinded and tested by a 92-gene molecular assay that predicts tumor type/subtype based upon relative quantitative PCR expression measurements for 87 tumor-related and 5 reference genes. The 92-gene assay demonstrated 99% (74/75; 95% confidence interval (CI) 0.93-0.99) accuracy for classification of neuroendocrine carcinomas and correctly subtyped the tumor site of origin in 95% (71/75; 95% CI 0.87-0.98) of cases. Analysis of gene expression subsignatures within the 92-gene assay panel showed 4 genes with promising discriminatory value for tumor typing and 15 genes for tumor subtyping. The 92-gene classifier demonstrated excellent accuracy for classifying and determining the site of origin in tumors with neuroendocrine differentiation. These results show promise for use of this test to aid in classifying neuroendocrine tumors of indeterminate primary site, particularly in the metastatic setting.
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Wang X, Choi JH, Ding J, Yang L, Ngoka LC, Lee EJ, Zha Y, Mao L, Jin B, Ren M, Cowell J, Huang S, Shi H, Cui H, Ding HF. HOXC9 directly regulates distinct sets of genes to coordinate diverse cellular processes during neuronal differentiation. BMC Genomics 2013; 14:830. [PMID: 24274069 PMCID: PMC3906982 DOI: 10.1186/1471-2164-14-830] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 11/20/2013] [Indexed: 01/06/2023] Open
Abstract
Background Cellular differentiation is characterized by the acquisition of specialized structures and functions, cell cycle exit, and global attenuation of the DNA damage response. It is largely unknown how these diverse cellular events are coordinated at the molecular level during differentiation. We addressed this question in a model system of neuroblastoma cell differentiation induced by HOXC9. Results We conducted a genome-wide analysis of the HOXC9-induced neuronal differentiation program. Microarray gene expression profiling revealed that HOXC9-induced differentiation was associated with transcriptional regulation of 2,370 genes, characterized by global upregulation of neuronal genes and downregulation of cell cycle and DNA repair genes. Remarkably, genome-wide mapping by ChIP-seq demonstrated that HOXC9 bound to 40% of these genes, including a large number of genes involved in neuronal differentiation, cell cycle progression and the DNA damage response. Moreover, we showed that HOXC9 interacted with the transcriptional repressor E2F6 and recruited it to the promoters of cell cycle genes for repressing their expression. Conclusions Our results demonstrate that HOXC9 coordinates diverse cellular processes associated with differentiation by directly activating and repressing the transcription of distinct sets of genes.
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Affiliation(s)
- Xiangwei Wang
- Cancer Center, Georgia Regents University, Augusta, GA 30912, USA.
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Batagov AO, Yarmishyn AA, Jenjaroenpun P, Tan JZ, Nishida Y, Kurochkin IV. Role of genomic architecture in the expression dynamics of long noncoding RNAs during differentiation of human neuroblastoma cells. BMC SYSTEMS BIOLOGY 2013; 7 Suppl 3:S11. [PMID: 24555823 PMCID: PMC3852107 DOI: 10.1186/1752-0509-7-s3-s11] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Mammalian genomes are extensively transcribed producing thousands of long non-protein-coding RNAs (lncRNAs). The biological significance and function of the vast majority of lncRNAs remain unclear. Recent studies have implicated several lncRNAs as playing important roles in embryonic development and cancer progression. LncRNAs are characterized with different genomic architectures in relationship with their associated protein-coding genes. Our study aimed at bridging lncRNA architecture with dynamical patterns of their expression using differentiating human neuroblastoma cells model. RESULTS LncRNA expression was studied in a 120-hours timecourse of differentiation of human neuroblastoma SH-SY5Y cells into neurons upon treatment with retinoic acid (RA), the compound used for the treatment of neuroblastoma. A custom microarray chip was utilized to interrogate expression levels of 9,267 lncRNAs in the course of differentiation. We categorized lncRNAs into 19 architecture classes according to their position relatively to protein-coding genes. For each architecture class, dynamics of expression of lncRNAs was studied in association with their protein-coding partners. It allowed us to demonstrate positive correlation of lncRNAs with their associated protein-coding genes at bidirectional promoters and for sense-antisense transcript pairs. In contrast, lncRNAs located in the introns and downstream of the protein-coding genes were characterized with negative correlation modes. We further classified the lncRNAs by the temporal patterns of their expression dynamics. We found that intronic and bidirectional promoter architectures are associated with rapid RA-dependent induction or repression of the corresponding lncRNAs, followed by their constant expression. At the same time, lncRNAs expressed downstream of protein-coding genes are characterized by rapid induction, followed by transcriptional repression. Quantitative RT-PCR analysis confirmed the discovered functional modes for several selected lncRNAs associated with proteins involved in cancer and embryonic development. CONCLUSIONS This is the first report detailing dynamical changes of multiple lncRNAs during RA-induced neuroblastoma differentiation. Integration of genomic and transcriptomic levels of information allowed us to demonstrate specific behavior of lncRNAs organized in different genomic architectures. This study also provides a list of lncRNAs with possible roles in neuroblastoma.
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Ashoor H, Hérault A, Kamoun A, Radvanyi F, Bajic VB, Barillot E, Boeva V. HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data. ACTA ACUST UNITED AC 2013; 29:2979-86. [PMID: 24021381 PMCID: PMC3834794 DOI: 10.1093/bioinformatics/btt524] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
MOTIVATION Cancer cells are often characterized by epigenetic changes, which include aberrant histone modifications. In particular, local or regional epigenetic silencing is a common mechanism in cancer for silencing expression of tumor suppressor genes. Though several tools have been created to enable detection of histone marks in ChIP-seq data from normal samples, it is unclear whether these tools can be efficiently applied to ChIP-seq data generated from cancer samples. Indeed, cancer genomes are often characterized by frequent copy number alterations: gains and losses of large regions of chromosomal material. Copy number alterations may create a substantial statistical bias in the evaluation of histone mark signal enrichment and result in underdetection of the signal in the regions of loss and overdetection of the signal in the regions of gain. RESULTS We present HMCan (Histone modifications in cancer), a tool specially designed to analyze histone modification ChIP-seq data produced from cancer genomes. HMCan corrects for the GC-content and copy number bias and then applies Hidden Markov Models to detect the signal from the corrected data. On simulated data, HMCan outperformed several commonly used tools developed to analyze histone modification data produced from genomes without copy number alterations. HMCan also showed superior results on a ChIP-seq dataset generated for the repressive histone mark H3K27me3 in a bladder cancer cell line. HMCan predictions matched well with experimental data (qPCR validated regions) and included, for example, the previously detected H3K27me3 mark in the promoter of the DLEC1 gene, missed by other tools we tested.
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Affiliation(s)
- Haitham Ashoor
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia, Institut Curie, 75248 Paris Cedex 05, France, INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Mines ParisTech, Fontainebleau 77300, France and UMR 144 CNRS, Subcellular Structure and Cellular Dynamics
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Avci CB, Dodurga Y, Gundogdu G, Caglar HO, Kucukatay V, Gunduz C, Satiroglu-Tufan NL. Regulation of URG4/URGCP and PPARα gene expressions after retinoic acid treatment in neuroblastoma cells. Tumour Biol 2013; 34:3853-7. [PMID: 23821302 DOI: 10.1007/s13277-013-0970-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 06/24/2013] [Indexed: 10/26/2022] Open
Abstract
Neuroblastoma (NB), originating from neural crest cells, is the most common extracranial tumor of childhood. Retinoic acid (RA) which is the biological active form of vitamin A regulates differentiation of NB cells, and RA derivatives have been used for NB treatment. PPARα (peroxisome proliferator-activated receptor) plays an important role in the oxidation of fatty acids, carcinogenesis, and differentiation. URG4/URGCP gene is a proto-oncogene and that overexpression of URG4/URGCP is associated with metastasis and tumor recurrence in osteosarcoma. It has been known that URG4/URGCP gene is an overexpressed gene in hepatocellular carcinoma and gastric cancers. This study aims to detect gene expression patterns of PPARα and URG4/URGCP genes in SH-SY5Y NB cell line after RA treatment. Expressions levels of PPARα and URG4/URGCP genes were analyzed after RA treatment for reducing differentiation in SH-SY5Y NB cell line. To induce differentiation, the cells were treated with 10 μM RA in the dark for 3-10 days. Gene expression of URG4/URGCP and PPARα genes were presented as the yield of polymerase chain reaction (PCR) products from target genes compared with the yield of PCR products from the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene. SH-SY5Y cells possess small processes in an undifferentiated state, and after treatment with RA, the cells developed long neurites, resembling a neuronal phenotype. PPARα gene expression increased in RA-treated groups; URG4/URGCP gene expression decreased in SH-SY5Y cells after RA treatment compared with that in the control cells. NB cell differentiation might associate with PPARα and URG4/URGCP gene expression profile after RA treatment.
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Affiliation(s)
- Cigir Biray Avci
- Department of Medical Biology, School of Medicine, Ege University, Bornova, Izmir, 35100, Turkey,
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