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Hu W, Wang M, Sun G, Zhang L, Lu H. Early B Cell Factor 3 (EBF3) attenuates Parkinson's disease through directly regulating contactin-associated protein-like 4 (CNTNAP4) transcription: An experimental study. Cell Signal 2024; 118:111139. [PMID: 38479556 DOI: 10.1016/j.cellsig.2024.111139] [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: 11/29/2023] [Revised: 03/05/2024] [Accepted: 03/09/2024] [Indexed: 03/19/2024]
Abstract
Parkinson's disease (PD) is a gradually debilitating neurodegenerative syndrome. Here, we analyzed GSE7621 chip data obtained from the Gene Expression Omnibus (GEO) database to explore the pathogenesis of PD. Early B Cell Factor 3 (EBF3), a member of the highly evolutionarily conserved EBF-transcription factor family, is involved in neuronal development. EBF3 expression is low in the substantia nigra of patients with PD. However, whether EBF3 is implicated in dopaminergic neuron death during PD has not yet been investigated. Therefore, we aimed to reveal the potential anti-apoptotic effect and molecular mechanism of EBF3 in PD. We established a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD mouse model in vivo and a 1-methyl-4-phenylpyridine (MPP+)-induced SH-SY5Y cell model in vitro. EBF3 was downregulated in the substantia nigra of PD mice and SH-SY5Y cells treated with MPP+, and the m6A methylation modification level was low. Fat mass and obesity-associated protein (FTO) siRNA upregulated m6A methylation modification of EBF3 and extended the EBF3 mRNA half-life. Functionally, as demonstrated by the results of the open-field test, pole test and gait analysis, EBF3 overexpression ameliorated MPTP-induced behavioral disorder. Further, EBF3 overexpression suppressed neuronal apoptosis in vivo, as evidenced by decreased TUNEL+ cells, and the increased activation of caspase-3 and caspase-9. Similar results were obtained in vitro, as reflected by increased cell viability, decreased LDH activity and restored mitochondrial function, collectively protecting SH-SY5Y cells from MPP+-induced apoptosis. Mechanistically, the results of luciferase reporter, ch-IP and DNA pull-down assays confirmed that, as a transcription factor, EBF3 bound to the promoter of CNTNAP4 (a protein associated with neuronal differentiation) and directly regulated CNTNAP4 transcription. Strikingly, CNTNAP4 knockdown markedly abolished the effect of EBF3 on cell apoptosis, thus aggravating PD. In conclusion, the low level of m6A methylation modification may contribute to the low expression of EBF3 during PD. Additionally, EBF3 attenuates PD by activating CNTNAP4 transcription, suggesting that EBF3 may be a novel therapeutic target in PD.
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Affiliation(s)
- Wentao Hu
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China.
| | - Menghan Wang
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Guifang Sun
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Limin Zhang
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Hong Lu
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China.
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2
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Chen H, Li J, Cao D, Tang H. Construction of a Prognostic Model for Hepatocellular Carcinoma Based on Macrophage Polarization-Related Genes. J Hepatocell Carcinoma 2024; 11:857-878. [PMID: 38751862 PMCID: PMC11095518 DOI: 10.2147/jhc.s453080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Background The progression of hepatocellular carcinoma (HCC) is related to macrophage polarization (MP). Our aim was to identify genes associated with MP in HCC patients and develop a prognostic model based on these genes. Results We successfully developed a prognostic model consisting of six MP-related genes (SCN4A, EBF3, ADGRB2, HOXD9, CLEC1B, and MSC) to calculate the risk score for each patient. Patients were then classified into high- and low-risk groups based on their median risk score. The performance of the MP-related prognostic model was evaluated using Kaplan-Meier and ROC curves, which yielded favorable results. Additionally, the nomogram demonstrated good clinical effectiveness and displayed consistent survival predictions with actual observations. Gene Set Enrichment Analysis (GSEA) revealed enrichment of pathways related to KRAS signaling downregulation, the G2M checkpoint, and E2F targets in the high-risk group. Conversely, pathways associated with fatty acid metabolism, xenobiotic metabolism, bile acid metabolism, and adipogenesis were enriched in the low-risk group. The risk score positively correlated with the number of invasion-related genes. Immune checkpoint expression differed significantly between the two groups. Patients in the high-risk group exhibited increased sensitivity to mitomycin C, cisplatin, gemcitabine, rapamycin, and paclitaxel, while those in the low-risk group showed heightened sensitivity to doxorubicin. These findings suggest that the high-risk group may have more invasive HCC with greater susceptibility to specific drugs. IHC staining revealed higher expression levels of SCN4A in HCC tissues. Furthermore, experiments conducted on HepG2 cells demonstrated that supernatants from cells with reduced SCN4A expression promoted M2 macrophage polarization marker, CD163 in THP-1 cells. Reduced SCN4A expression induced HCC-related genes, while increased SCN4A expression reduced their expression in HepG2 cells. Conclusion The MP-related prognostic model comprising six MPRGs can effectively predict HCC prognosis, infer invasiveness, and guide drug therapy. SCN4A is identified as a suppressor gene in HCC.
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Affiliation(s)
- Han Chen
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
| | - Jianhao Li
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
| | - Dan Cao
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
| | - Hong Tang
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, 610041, People’s Republic of China
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Zhang Y, Liu F, Zheng J, Jiang K, Ai H, Liu L, Mao D. MAPRE3 as an epigenetic target of EZH2 restricts ovarian cancer proliferation in vitro and in vivo. Exp Cell Res 2024; 435:113913. [PMID: 38199479 DOI: 10.1016/j.yexcr.2024.113913] [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: 10/02/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/12/2024]
Abstract
Ovarian cancer (OC) is a lethal gynecologic cancer and the common cause of death within women worldwide. The polycomb group protein enhancer of zeste homolog 2 (EZH2) is a histone methyltransferase highly expressed in various tumors, including OC. However, the mechanistic basis of EZH2 oncogenic activity in OC remain incompletely understood. Bioinformatics analysis showed that the expression of MAPRE3 was lower in OC tissues than in normal tissues, and was positively correlated with the overall survival. MAPRE3 overexpression decreased cell growth, inducing cell cycle arrest and apoptosis in OC cells, whereas MAPRE3 silencing promoted proliferation and accelerated cell cycle progression of OC cells. The in vivo study validated that overexpression of MAPRE3 impeded tumor formation and growth of OC xenografts in nude mice. In addition, knockdown of EZH2 in OC cells downregulated H3K27me3 expression and increased MAPRE3 expression. Inhibiting EZH2 in OC cells reduced the enrichment of H3K27me3 on the promoter of MAPRE3. Furthermore, MAPRE3 silencing significantly reversed changes in the expression of cell cycle and apoptosis-related markers and cell growth mediated by EZH2 knockdown in OC cells. MAPRE3 functions as a suppressor of OC and is epigenetic repressed by EZH2, suggesting a potential therapeutic strategy for OC by targeting EZH2/MAPRE3 axis.
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Affiliation(s)
- Yun Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China; Liaoning Key Laboratory of Follicular Development and Reproductive Health, Jinzhou, Liaoning, China.
| | - Fanglin Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
| | - Jindan Zheng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
| | - Keping Jiang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
| | - Hao Ai
- Liaoning Key Laboratory of Follicular Development and Reproductive Health, Jinzhou, Liaoning, China; Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
| | - Lili Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
| | - Dong Mao
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
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4
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Saleh O, Albakri K, Altiti A, Abutair I, Shalan S, Mohd OB, Negida A, Mushtaq G, Kamal MA. The Role of Non-coding RNAs in Alzheimer's Disease: Pathogenesis, Novel Biomarkers, and Potential Therapeutic Targets. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2024; 23:731-745. [PMID: 37211844 DOI: 10.2174/1871527322666230519113201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 05/23/2023]
Abstract
Long non-coding RNAs (IncRNAs) are regulatory RNA transcripts that have recently been associated with the onset of many neurodegenerative illnesses, including Alzheimer's disease (AD). Several IncRNAs have been found to be associated with AD pathophysiology, each with a distinct mechanism. In this review, we focused on the role of IncRNAs in the pathogenesis of AD and their potential as novel biomarkers and therapeutic targets. Searching for relevant articles was done using the PubMed and Cochrane library databases. Studies had to be published in full text in English in order to be considered. Some IncRNAs were found to be upregulated, while others were downregulated. Dysregulation of IncRNAs expression may contribute to AD pathogenesis. Their effects manifest as the synthesis of beta-amyloid (Aβ) plaques increases, thereby altering neuronal plasticity, inducing inflammation, and promoting apoptosis. Despite the need for more investigations, IncRNAs could potentially increase the sensitivity of early detection of AD. Until now, there has been no effective treatment for AD. Hence, InRNAs are promising molecules and may serve as potential therapeutic targets. Although several dysregulated AD-associated lncRNAs have been discovered, the functional characterization of most lncRNAs is still lacking.
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Affiliation(s)
- Othman Saleh
- Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Khaled Albakri
- Faculty of Medicine, The Hashemite University, Zarqa, Jordan
- Medical Research Group of Egypt, Cairo, Egypt
| | | | - Iser Abutair
- Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Suhaib Shalan
- Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | | | - Ahmed Negida
- Medical Research Group of Egypt, Cairo, Egypt
- Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Ave, Boston, MA, 02115, USA
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
- Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Gohar Mushtaq
- Center for Scientific Research, Faculty of Medicine, Idlib University, Idlib, Syria
| | - Mohammad A Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Sichuan, China
- King Fahd Medical Research Center, King Abdulaziz University, Saudi Arabia
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Daffodil Smart City, Birulia 1216, Bangladesh
- Enzymoics, 7 Peterlee place, Hebersham, NSW 2770, Novel Global Community Educational Foundation, Hebersham, Australia
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Zhu J, Li W, Yu S, Lu W, Xu Q, Wang S, Qian Y, Guo Q, Xu S, Wang Y, Zhang P, Zhao X, Ni Q, Liu R, Li X, Wu B, Zhou S, Wang H. Further delineation of EBF3-related syndromic neurodevelopmental disorder in twelve Chinese patients. Front Pediatr 2023; 11:1091532. [PMID: 36937983 PMCID: PMC10020332 DOI: 10.3389/fped.2023.1091532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) have heterogeneity in both clinical characteristics and genetic factors. EBF3 is a recently discovered gene associated with a syndromic form of NDDs characterized by hypotonia, ataxia and facial features. In this study, we report twelve unrelated individuals with EBF3 variants using next-generation sequencing. Five missense variants (four novel variants and one known variant) and seven copy number variations (CNVs) of EBF3 gene were identified. All of these patients exhibited developmental delay/intellectual disability. Ataxia was observed in 33% (6/9) of the patients, and abnormal muscle tone was observed in 55% (6/11) of the patients. Aberrant MRI reports were noted in 64% (7/11) of the patients. Four novel missense variants were all located in the DNA-binding domain. The pathogenicity of these variants was validated by in vitro experiments. We found that the subcellular protein localization of the R152C and F211L mutants was changed, and the distribution pattern of the R163G mutant was changed from even to granular. Luciferase assay results showed that the four EBF3 mutants' transcriptional activities were all significantly decreased (p < 0.01). Our study further expanded the gene mutation spectrum of EBF3-related NDD.
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Affiliation(s)
- Jitao Zhu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Wenhui Li
- Neurology Department, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Sha Yu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Wei Lu
- Department of Endocrinology and Inherited Metabolic Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Qiong Xu
- Department of Child Health Care, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Sujuan Wang
- Department of Rehabilitation, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Yanyan Qian
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Qiufang Guo
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Suzhen Xu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Yao Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Xuemei Zhao
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Qi Ni
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Renchao Liu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Xu Li
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Correspondence: Bingbing Wu Shuizhen Zhou Huijun Wang
| | - Shuizhen Zhou
- Neurology Department, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Correspondence: Bingbing Wu Shuizhen Zhou Huijun Wang
| | - Huijun Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Correspondence: Bingbing Wu Shuizhen Zhou Huijun Wang
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6
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Jiang Y, Meyers TJ, Emeka AA, Cooley LF, Cooper PR, Lancki N, Helenowski I, Kachuri L, Lin DW, Stanford JL, Newcomb LF, Kolb S, Finelli A, Fleshner NE, Komisarenko M, Eastham JA, Ehdaie B, Benfante N, Logothetis CJ, Gregg JR, Perez CA, Garza S, Kim J, Marks LS, Delfin M, Barsa D, Vesprini D, Klotz LH, Loblaw A, Mamedov A, Goldenberg SL, Higano CS, Spillane M, Wu E, Carter HB, Pavlovich CP, Mamawala M, Landis T, Carroll PR, Chan JM, Cooperberg MR, Cowan JE, Morgan TM, Siddiqui J, Martin R, Klein EA, Brittain K, Gotwald P, Barocas DA, Dallmer JR, Gordetsky JB, Steele P, Kundu SD, Stockdale J, Roobol MJ, Venderbos LD, Sanda MG, Arnold R, Patil D, Evans CP, Dall’Era MA, Vij A, Costello AJ, Chow K, Corcoran NM, Rais-Bahrami S, Phares C, Scherr DS, Flynn T, Karnes RJ, Koch M, Dhondt CR, Nelson JB, McBride D, Cookson MS, Stratton KL, Farriester S, Hemken E, Stadler WM, Pera T, Banionyte D, Bianco FJ, Lopez IH, Loeb S, Taneja SS, Byrne N, Amling CL, Martinez A, Boileau L, Gaylis FD, Petkewicz J, Kirwen N, Helfand BT, Xu J, Scholtens DM, Catalona WJ, Witte JS. Genetic Factors Associated with Prostate Cancer Conversion from Active Surveillance to Treatment. HGG ADVANCES 2022; 3:100070. [PMID: 34993496 PMCID: PMC8725988 DOI: 10.1016/j.xhgg.2021.100070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/12/2021] [Indexed: 12/18/2022] Open
Abstract
Men diagnosed with low-risk prostate cancer (PC) are increasingly electing active surveillance (AS) as their initial management strategy. While this may reduce the side effects of treatment for prostate cancer, many men on AS eventually convert to active treatment. PC is one of the most heritable cancers, and genetic factors that predispose to aggressive tumors may help distinguish men who are more likely to discontinue AS. To investigate this, we undertook a multi-institutional genome-wide association study (GWAS) of 5,222 PC patients and 1,139 other patients from replication cohorts, all of whom initially elected AS and were followed over time for the potential outcome of conversion from AS to active treatment. In the GWAS we detected 18 variants associated with conversion, 15 of which were not previously associated with PC risk. With a transcriptome-wide association study (TWAS), we found two genes associated with conversion (MAST3, p = 6.9×10-7 and GAB2, p = 2.0×10-6). Moreover, increasing values of a previously validated 269-variant genetic risk score (GRS) for PC was positively associated with conversion (e.g., comparing the highest to the two middle deciles gave a hazard ratio [HR] = 1.13; 95% Confidence Interval [CI]= 0.94-1.36); whereas, decreasing values of a 36-variant GRS for prostate-specific antigen (PSA) levels were positively associated with conversion (e.g., comparing the lowest to the two middle deciles gave a HR = 1.25; 95% CI, 1.04-1.50). These results suggest that germline genetics may help inform and individualize the decision of AS-or the intensity of monitoring on AS-versus treatment for the initial management of patients with low-risk PC.
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Affiliation(s)
- Yu Jiang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Travis J. Meyers
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adaeze A. Emeka
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lauren Folgosa Cooley
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Phillip R. Cooper
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nicola Lancki
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Irene Helenowski
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel W. Lin
- Fred Hutchinson Cancer Research Center, Cancer Prevention Program, Public Health Sciences, Seattle, WA 98109, USA
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Janet L. Stanford
- Fred Hutchinson Cancer Research Center, Cancer Epidemiology Program, Public Health Sciences, Seattle, WA 98109, USA
- Department of Epidemiology, University of Washington, School of Public Health, Seattle, WA 98195, USA
| | - Lisa F. Newcomb
- Fred Hutchinson Cancer Research Center, Cancer Prevention Program, Public Health Sciences, Seattle, WA 98109, USA
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Suzanne Kolb
- Fred Hutchinson Cancer Research Center, Cancer Epidemiology Program, Public Health Sciences, Seattle, WA 98109, USA
- Department of Epidemiology, University of Washington, School of Public Health, Seattle, WA 98195, USA
| | - Antonio Finelli
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Neil E. Fleshner
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Maria Komisarenko
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - James A. Eastham
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Behfar Ehdaie
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicole Benfante
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher J. Logothetis
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Justin R. Gregg
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cherie A. Perez
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sergio Garza
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeri Kim
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Leonard S. Marks
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Merdie Delfin
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Danielle Barsa
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Danny Vesprini
- Odette Cancer Centre, Sunnybrook Health and Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Laurence H. Klotz
- Odette Cancer Centre, Sunnybrook Health and Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Andrew Loblaw
- Odette Cancer Centre, Sunnybrook Health and Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Alexandre Mamedov
- Odette Cancer Centre, Sunnybrook Health and Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - S. Larry Goldenberg
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Celestia S. Higano
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Maria Spillane
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Eugenia Wu
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - H. Ballentine Carter
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christian P. Pavlovich
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mufaddal Mamawala
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tricia Landis
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter R. Carroll
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - June M. Chan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew R. Cooperberg
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Janet E. Cowan
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Todd M. Morgan
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Javed Siddiqui
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rabia Martin
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Eric A. Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Karen Brittain
- Glickman Urological and Kidney Institute, Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Paige Gotwald
- Glickman Urological and Kidney Institute, Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Daniel A. Barocas
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeremiah R. Dallmer
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jennifer B. Gordetsky
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pam Steele
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shilajit D. Kundu
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jazmine Stockdale
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Monique J. Roobol
- Department of Urology, Erasmus Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Lionne D.F. Venderbos
- Department of Urology, Erasmus Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Martin G. Sanda
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Rebecca Arnold
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Dattatraya Patil
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Christopher P. Evans
- Department of Urologic Surgery, University of California, Davis Medical Center, Sacramento, CA, USA
| | - Marc A. Dall’Era
- Department of Urologic Surgery, University of California, Davis Medical Center, Sacramento, CA, USA
| | - Anjali Vij
- Department of Urologic Surgery, University of California, Davis Medical Center, Sacramento, CA, USA
| | - Anthony J. Costello
- Department of Urology, Royal Melbourne Hospital and University of Melbourne, Melbourne, VIC, Australia
| | - Ken Chow
- Department of Urology, Royal Melbourne Hospital and University of Melbourne, Melbourne, VIC, Australia
| | - Niall M. Corcoran
- Department of Urology, Royal Melbourne Hospital and University of Melbourne, Melbourne, VIC, Australia
| | - Soroush Rais-Bahrami
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Courtney Phares
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Douglas S. Scherr
- Department of Urology, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | - Thomas Flynn
- Department of Urology, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | | | - Michael Koch
- Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Courtney Rose Dhondt
- Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Joel B. Nelson
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Dawn McBride
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael S. Cookson
- Department of Urology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kelly L. Stratton
- Department of Urology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Stephen Farriester
- Department of Urology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Erin Hemken
- Department of Urology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | | | - Tuula Pera
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | | | | | | | - Stacy Loeb
- Departments of Urology and Population Health, New York University Langone Health and Manhattan Veterans Affairs Medical Center, New York, NY, USA
| | - Samir S. Taneja
- Departments of Urology and Population Health, New York University Langone Health and Manhattan Veterans Affairs Medical Center, New York, NY, USA
| | - Nataliya Byrne
- Departments of Urology and Population Health, New York University Langone Health and Manhattan Veterans Affairs Medical Center, New York, NY, USA
| | | | - Ann Martinez
- Department of Urology, Oregon Health and Science University, Portland, OR, USA
| | - Luc Boileau
- Department of Urology, Oregon Health and Science University, Portland, OR, USA
| | - Franklin D. Gaylis
- Genesis Healthcare Partners, Department of Urology, University of California, San Diego, CA, USA
| | | | - Nicholas Kirwen
- Division of Urology, NorthShore University Health System, Evanston, IL, USA
| | - Brian T. Helfand
- Division of Urology, NorthShore University Health System, Evanston, IL, USA
| | - Jianfeng Xu
- Division of Urology, NorthShore University Health System, Evanston, IL, USA
| | - Denise M. Scholtens
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - William J. Catalona
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - John S. Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Departments of Epidemiology and Population Health, Biomedical Data Science, and Genetics, Stanford University, Stanford, CA, USA
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7
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Ding S, Wang X, Lv D, Tao Y, Liu S, Chen C, Huang Z, Zheng S, Wei Y, Kang T, Xia Y. EBF3 reactivation by inhibiting the EGR1/EZH2/HDAC9 complex promotes metastasis via transcriptionally enhancing vimentin in nasopharyngeal carcinoma. Cancer Lett 2021; 527:49-65. [PMID: 34906623 DOI: 10.1016/j.canlet.2021.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/18/2021] [Accepted: 12/08/2021] [Indexed: 01/31/2023]
Abstract
Metastasis is the major reason for treatment failure and accounts for cancer-related death in patients with nasopharyngeal carcinoma. However, the genetic alterations and molecular mechanisms that cause nasopharyngeal carcinoma metastasis are elusive. Herein, we performed RNA sequencing in patients with or without metastasis, and found that the early B-cell factor 3 (EBF3) was significantly elevated in the samples with metastasis. Mechanistically, EBF3 promoted metastasis by directly combining with the promoter of Vimentin and transcriptionally upregulating it. In addition, EBF3 was epigenetically silenced by EGR1/EZH2/HDAC9 complexes via sustaining the high level of H3K27-Me3 at its promoter. Clinically, there was a positive correlation between EBF3 and Vimentin in nasopharyngeal carcinoma tissues. Moreover, high expression of EBF3 or Vimentin was correlated with poor overall survival, while the combination of high EBF3 and Vimentin expression was associated with more significant poor prognosis. Therefore, specific agents targeting EBF3 or stabilizing the EGR1/EZH2/HDAC9 complex could be novel therapeutic strategies for cancer metastasis.
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Affiliation(s)
- Shirong Ding
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Xin Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; The Department of Liver Surgery, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Dongming Lv
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yalan Tao
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Songran Liu
- Department of Pathology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Chen Chen
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Zilu Huang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Shuohan Zheng
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Yinghong Wei
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Yunfei Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China.
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8
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Bhattacharyya N, Pandey V, Bhattacharyya M, Dey A. Regulatory role of long non coding RNAs (lncRNAs) in neurological disorders: From novel biomarkers to promising therapeutic strategies. Asian J Pharm Sci 2021; 16:533-550. [PMID: 34849161 PMCID: PMC8609388 DOI: 10.1016/j.ajps.2021.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/28/2021] [Accepted: 02/18/2021] [Indexed: 01/12/2023] Open
Abstract
Long non coding RNAs (lncRNAs) are non-protein or low-protein coding transcripts that contain more than 200 nucleotides. They representing a large share of the cell's transcriptional output, demonstrate functional attributes viz. tissue-specific expression, determination of cell fate, controlled expression, RNA processing and editing, dosage compensation, genomic imprinting, conserved evolutionary traits etc. These long non coding variants are well associated with pathogenicity of various diseases including the neurological disorders like Alzheimer's disease, schizophrenia, Huntington's disease, Parkinson's disease etc. Neurological disorders are widespread and there knowing the underlying mechanisms become crucial. The lncRNAs take part in the pathogenesis by a plethora of mechanisms like decoy, scaffold, mi-RNA sequestrator, histone modifiers and in transcriptional interference. Detailed knowledge of the role of lncRNAs can help to use them further as novel biomarkers for therapeutic aspects. Here, in this review we discuss regulation and functional roles of lncRNAs in eight neurological diseases and psychiatric disorders, and the mechanisms by which they act. With these, we try to establish their roles as potential markers and viable diagnostic tools in these disorders.
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Affiliation(s)
| | - Vedansh Pandey
- Department of Life Sciences, Presidency University, Kolkata, India
| | | | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, India
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9
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García-Fonseca Á, Martin-Jimenez C, Barreto GE, Pachón AFA, González J. The Emerging Role of Long Non-Coding RNAs and MicroRNAs in Neurodegenerative Diseases: A Perspective of Machine Learning. Biomolecules 2021; 11:1132. [PMID: 34439798 PMCID: PMC8391852 DOI: 10.3390/biom11081132] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 12/20/2022] Open
Abstract
Neurodegenerative diseases (NDs) are characterized by progressive neuronal dysfunction and death of brain cells population. As the early manifestations of NDs are similar, their symptoms are difficult to distinguish, making the timely detection and discrimination of each neurodegenerative disorder a priority. Several investigations have revealed the importance of microRNAs and long non-coding RNAs in neurodevelopment, brain function, maturation, and neuronal activity, as well as its dysregulation involved in many types of neurological diseases. Therefore, the expression pattern of these molecules in the different NDs have gained significant attention to improve the diagnostic and treatment at earlier stages. In this sense, we gather the different microRNAs and long non-coding RNAs that have been reported as dysregulated in each disorder. Since there are a vast number of non-coding RNAs altered in NDs, some sort of synthesis, filtering and organization method should be applied to extract the most relevant information. Hence, machine learning is considered as an important tool for this purpose since it can classify expression profiles of non-coding RNAs between healthy and sick people. Therefore, we deepen in this branch of computer science, its different methods, and its meaningful application in the diagnosis of NDs from the dysregulated non-coding RNAs. In addition, we demonstrate the relevance of machine learning in NDs from the description of different investigations that showed an accuracy between 85% to 95% in the detection of the disease with this tool. All of these denote that artificial intelligence could be an excellent alternative to help the clinical diagnosis and facilitate the identification diseases in early stages based on non-coding RNAs.
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Affiliation(s)
- Ángela García-Fonseca
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (Á.G.-F.); (C.M.-J.); (A.F.A.P.)
| | - Cynthia Martin-Jimenez
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (Á.G.-F.); (C.M.-J.); (A.F.A.P.)
| | - George E. Barreto
- Department of Biological Sciences, University of Limerick, V94 T9PX Limerick, Ireland;
| | - Andres Felipe Aristizábal Pachón
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (Á.G.-F.); (C.M.-J.); (A.F.A.P.)
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (Á.G.-F.); (C.M.-J.); (A.F.A.P.)
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10
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Li D, Zhang J, Li X, Chen Y, Yu F, Liu Q. Insights into lncRNAs in Alzheimer's disease mechanisms. RNA Biol 2021; 18:1037-1047. [PMID: 32605500 PMCID: PMC8216181 DOI: 10.1080/15476286.2020.1788848] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the most common dementia among the elderly. The pathophysiology of AD is characterized by two hallmarks: amyloid plaques, produced by amyloid β (Aβ) aggregation, and neurofibrillary tangle (NFT), produced by accumulation of phosphorylated tau. The regulatory roles of non-coding RNAs (ncRNAs), particularly long noncoding RNAs (lncRNAs), have been widely recognized in gene expression at the transcriptional and posttranscriptional levels. Mounting evidence shows that lncRNAs are aberrantly expressed in AD progression. Here, we review the lncRNAs that implicated in the regulation of Aβ peptide, tau, inflammation, cell death, and other aspects which are the main mechanisms of AD pathology. We also discuss the possible clinical or therapeutic utility of lncRNA detection or targeting to help diagnose or possibly combat AD.
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Affiliation(s)
- Dingfeng Li
- Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
- Neurodegenerative Disease Research Center, University of Science and Technology of China, Hefei, China
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, China
| | - Juan Zhang
- Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
- Neurodegenerative Disease Research Center, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, China
| | - Xiaohui Li
- Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
- Neurodegenerative Disease Research Center, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, China
| | - Yuhua Chen
- Department of Neurology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Feng Yu
- Department of Neurology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Qiang Liu
- Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
- Neurodegenerative Disease Research Center, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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11
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Tian R, Abarientos A, Hong J, Hashemi SH, Yan R, Dräger N, Leng K, Nalls MA, Singleton AB, Xu K, Faghri F, Kampmann M. Genome-wide CRISPRi/a screens in human neurons link lysosomal failure to ferroptosis. Nat Neurosci 2021; 24:1020-1034. [PMID: 34031600 PMCID: PMC8254803 DOI: 10.1038/s41593-021-00862-0] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 04/23/2021] [Indexed: 02/08/2023]
Abstract
Single-cell transcriptomics provide a systematic map of gene expression in different human cell types. The next challenge is to systematically understand cell-type-specific gene function. The integration of CRISPR-based functional genomics and stem cell technology enables the scalable interrogation of gene function in differentiated human cells. Here we present the first genome-wide CRISPR interference and CRISPR activation screens in human neurons. We uncover pathways controlling neuronal response to chronic oxidative stress, which is implicated in neurodegenerative diseases. Unexpectedly, knockdown of the lysosomal protein prosaposin strongly sensitizes neurons, but not other cell types, to oxidative stress by triggering the formation of lipofuscin, a hallmark of aging, which traps iron, generating reactive oxygen species and triggering ferroptosis. We also determine transcriptomic changes in neurons after perturbation of genes linked to neurodegenerative diseases. To enable the systematic comparison of gene function across different human cell types, we establish a data commons named CRISPRbrain.
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Affiliation(s)
- Ruilin Tian
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
- School of Medicine, Southern University of Science and Technology, Shenzhen, China.
| | - Anthony Abarientos
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Jason Hong
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Sayed Hadi Hashemi
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rui Yan
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Nina Dräger
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Kun Leng
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, LLC, Glen Echo, MD, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Faraz Faghri
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, LLC, Glen Echo, MD, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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12
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Bertho S, Kaufman O, Lee K, Santos-Ledo A, Dellal D, Marlow FL. A transgenic system for targeted ablation of reproductive and maternal-effect genes. Development 2021; 148:269197. [PMID: 34143203 DOI: 10.1242/dev.198010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 05/21/2021] [Indexed: 10/21/2022]
Abstract
Maternally provided gene products regulate the earliest events of embryonic life, including formation of the oocyte that will develop into an egg, and eventually into an embryo. Forward genetic screens have provided invaluable insights into the molecular regulation of embryonic development, including the essential contributions of some genes whose products must be provided to the transcriptionally silent early embryo for normal embryogenesis, called maternal-effect genes. However, other maternal-effect genes are not accessible due to their essential zygotic functions during embryonic development. Identifying these regulators is essential to fill the large gaps in our understanding of the mechanisms and molecular pathways contributing to fertility and to maternally regulated developmental processes. To identify these maternal factors, it is necessary to bypass the earlier requirement for these genes so that their potential later functions can be investigated. Here, we report reverse genetic systems to identify genes with essential roles in zebrafish reproductive and maternal-effect processes. As proof of principle and to assess the efficiency and robustness of mutagenesis, we used these transgenic systems to disrupt two genes with known maternal-effect functions: kif5ba and bucky ball.
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Affiliation(s)
- Sylvain Bertho
- Department of Cell, Developmental and Regenerative Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1020 New York, NY 10029-6574, USA
| | - Odelya Kaufman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx NY 10461, USA
| | - KathyAnn Lee
- Department of Cell, Developmental and Regenerative Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1020 New York, NY 10029-6574, USA
| | - Adrian Santos-Ledo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx NY 10461, USA
| | - Daniel Dellal
- Department of Cell, Developmental and Regenerative Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1020 New York, NY 10029-6574, USA
| | - Florence L Marlow
- Department of Cell, Developmental and Regenerative Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1020 New York, NY 10029-6574, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx NY 10461, USA
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13
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Genomics for conservation: a case study of behavioral genes in the Tasmanian devil. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01354-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Mahmud I, Liao D. DAXX in cancer: phenomena, processes, mechanisms and regulation. Nucleic Acids Res 2019; 47:7734-7752. [PMID: 31350900 PMCID: PMC6735914 DOI: 10.1093/nar/gkz634] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022] Open
Abstract
DAXX displays complex biological functions. Remarkably, DAXX overexpression is a common feature in diverse cancers, which correlates with tumorigenesis, disease progression and treatment resistance. Structurally, DAXX is modular with an N-terminal helical bundle, a docking site for many DAXX interactors (e.g. p53 and ATRX). DAXX's central region folds with the H3.3/H4 dimer, providing a H3.3-specific chaperoning function. DAXX has two functionally critical SUMO-interacting motifs. These modules are connected by disordered regions. DAXX's structural features provide a framework for deciphering how DAXX mechanistically imparts its functions and how its activity is regulated. DAXX modulates transcription through binding to transcription factors, epigenetic modifiers, and chromatin remodelers. DAXX's localization in the PML nuclear bodies also plays roles in transcriptional regulation. DAXX-regulated genes are likely important effectors of its biological functions. Deposition of H3.3 and its interactions with epigenetic modifiers are likely key events for DAXX to regulate transcription, DNA repair, and viral infection. Interactions between DAXX and its partners directly impact apoptosis and cell signaling. DAXX's activity is regulated by posttranslational modifications and ubiquitin-dependent degradation. Notably, the tumor suppressor SPOP promotes DAXX degradation in phase-separated droplets. We summarize here our current understanding of DAXX's complex functions with a focus on how it promotes oncogenesis.
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Affiliation(s)
- Iqbal Mahmud
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, 1333 Center Drive, Gainesville, FL 32610-0235, USA
| | - Daiqing Liao
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, 1333 Center Drive, Gainesville, FL 32610-0235, USA
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15
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Mortezaei Z, Tavallaei M, Hosseini SM. Considering smoking status, coexpression network analysis of non-small cell lung cancer at different cancer stages, exhibits important genes and pathways. J Cell Biochem 2019; 120:19172-19185. [PMID: 31271232 DOI: 10.1002/jcb.29246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/23/2019] [Indexed: 02/01/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the most common subtype of lung cancer among smokers, nonsmokers, women, and young individuals. Tobacco smoking and different stages of the NSCLC have important roles in cancer evolution and require different treatments. Existence of poorly effective therapeutic options for the NSCLC brings special attention to targeted therapies by considering genetic alterations. In this study, we used RNA-Seq data to compare expression levels of RefSeq genes and to find some genes with similar expression levels. We utilized the "Weighted Gene Co-expression Network Analysis" method for three different datasets to create coexpressed genetic modules having relations with the smoking status and different stages of the NSCLC. Our results indicate seven important genetic modules having important associations with the smoking status and cancer stages. Based on investigated genetic modules and their biological explanation, we then identified 13 newly candidate genes and 7 novel transcription factors in association with the NSCLC, the smoking status, and cancer stages. We then examined those results using other datasets and explained our results biologically to illustrate some important genes in relation with the smoking status and metastatic stage of the NSCLC that can bring some crucial information about cancer evolution. Our genetic findings also can be used as some therapeutic targets for different clinical conditions of the NSCLC.
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Affiliation(s)
- Zahra Mortezaei
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahmood Tavallaei
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Sayed Mostafa Hosseini
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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16
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Zhang J, Zhang Y, Tan X, Zhang Q, Liu C, Zhang Y. MiR-23b-3p induces the proliferation and metastasis of esophageal squamous cell carcinomas cells through the inhibition of EBF3. Acta Biochim Biophys Sin (Shanghai) 2018; 50:605-614. [PMID: 29750239 DOI: 10.1093/abbs/gmy049] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs (miRNAs), some small non-coding RNAs that regulate gene expression at the posttranscriptional level, are always aberrantly expressed in carcinomas. In this study, we found that miR-23b-3p was remarkably up-regulated in human esophageal squamous cell carcinoma cells and tissues. Moreover, miR-23b-3p could induce the proliferation, invasion, and metastasis in vitro. EBF3 was identified as the direct downstream target gene of miR-23b-3p and ectogenic EBF3 could strongly inhibit the proliferation, invasion, and metastasis in vitro. Furthermore, it was found that miR-23b-3p could regulate epithelial-to-mesenchymal transition progress by blocking EBF3. Therefore, it was concluded that miR-23b-3p targeted EBF3 to accelerate the proliferation, invasion, and metastasis in ESCC.
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Affiliation(s)
- Jing Zhang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Medical School of Yangtze University, Jingzhou 434023, China
| | - Yan Zhang
- Department of Gastroenterology, No. 1 Hospital Affiliated to Yangtze University, Jingzhou 434000, China
| | - Xiaoping Tan
- Department of Gastroenterology, No. 1 Hospital Affiliated to Yangtze University, Jingzhou 434000, China
| | - Qing Zhang
- Department of Gastroenterology, No. 1 Hospital Affiliated to Yangtze University, Jingzhou 434000, China
| | - Chaoyong Liu
- Department of Gastroenterology, No. 1 Hospital Affiliated to Yangtze University, Jingzhou 434000, China
| | - Yali Zhang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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17
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Gu C, Chen C, Wu R, Dong T, Hu X, Yao Y, Zhang Y. Long Noncoding RNA EBF3-AS Promotes Neuron Apoptosis in Alzheimer's Disease. DNA Cell Biol 2018; 37:220-226. [PMID: 29298096 DOI: 10.1089/dna.2017.4012] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia; its pathophysiological mechanism remains unclear. Long noncoding RNAs (lncRNAs) play key roles in AD. lncRNA EBF3-AS has been found dysregulated in AD, which is abundantly expressed in the brain. The aim of this study was to investigate the role of EBF3-AS in AD. Results showed that the expressions of lncRNA EBF3-AS and EBF3 (early B cell factor 3) were upregulated in hippocampus of APP/PS1 mice (AD model mice). EBF3-AS knockdown by siRNA inhibited the apoptosis induced by Aβ25-35 and okadaic acid (OA) in SH-SY5Y. The expression of EBF3 was downregulated in Aβ25-35- and OA-treated SH-SY5Y, which was reversed by EBF3-AS knockdown. EBF3 knockdown can reverse the Aβ25-35-induced apoptosis in SH-SY5Y. These results revealed that lncRNA EBF3-AS promoted neuron apoptosis in AD, and involved in regulating EBF3 expression. EBF3-AS may be a new therapeutic target for treatment of AD.
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Affiliation(s)
- Cheng Gu
- 1 Department of Neurology, Gansu Provincial Hospital , Lanzhou, China
| | - Cheng Chen
- 2 Department of Galactophore, The First Hospital of Lanzhou University , Lanzhou, China
| | - Ruipeng Wu
- 1 Department of Neurology, Gansu Provincial Hospital , Lanzhou, China
| | - Tong Dong
- 1 Department of Neurology, Gansu Provincial Hospital , Lanzhou, China
| | - Xiaojuan Hu
- 1 Department of Neurology, Gansu Provincial Hospital , Lanzhou, China
| | - Yuping Yao
- 1 Department of Neurology, Gansu Provincial Hospital , Lanzhou, China
| | - Yi Zhang
- 1 Department of Neurology, Gansu Provincial Hospital , Lanzhou, China
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18
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Tanaka AJ, Cho MT, Willaert R, Retterer K, Zarate YA, Bosanko K, Stefans V, Oishi K, Williamson A, Wilson GN, Basinger A, Barbaro-Dieber T, Ortega L, Sorrentino S, Gabriel MK, Anderson IJ, Sacoto MJG, Schnur RE, Chung WK. De novo variants in EBF3 are associated with hypotonia, developmental delay, intellectual disability, and autism. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a002097. [PMID: 29162653 PMCID: PMC5701309 DOI: 10.1101/mcs.a002097] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/05/2017] [Indexed: 01/07/2023] Open
Abstract
Using whole-exome sequencing, we identified seven unrelated individuals with global developmental delay, hypotonia, dysmorphic facial features, and an increased frequency of short stature, ataxia, and autism with de novo heterozygous frameshift, nonsense, splice, and missense variants in the Early B-cell Transcription Factor Family Member 3 (EBF3) gene. EBF3 is a member of the collier/olfactory-1/early B-cell factor (COE) family of proteins, which are required for central nervous system (CNS) development. COE proteins are highly evolutionarily conserved and regulate neuronal specification, migration, axon guidance, and dendritogenesis during development and are essential for maintaining neuronal identity in adult neurons. Haploinsufficiency of EBF3 may affect brain development and function, resulting in developmental delay, intellectual disability, and behavioral differences observed in individuals with a deleterious variant in EBF3.
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Affiliation(s)
- Akemi J Tanaka
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
| | | | | | | | - Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Katie Bosanko
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Vikki Stefans
- Departments of Pediatrics and Physical Medicine and Rehabilitation, Arkansas Children's Hospital, Little Rock, Arkansas 72202, USA
| | - Kimihiko Oishi
- Department of Genetics and Genomic Sciences, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Amy Williamson
- Department of Genetics and Genomic Sciences, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Golder N Wilson
- KinderGenome Genetics, Medical City Hospital Dallas, Dallas, Texas 75230, USA, and Department of Pediatrics, Texas Tech University Health Science Center, Lubbock, Texas 79430, USA
| | | | | | - Lucia Ortega
- Cook Children's Genetics, Fort Worth, Texas 76102, USA
| | - Susanna Sorrentino
- Department of Genetics and Metabolism, Valley Children's Hospital, Madera, California 93636, USA
| | - Melissa K Gabriel
- Children's Hospital of Los Angeles, Los Angeles, California 90027, USA
| | - Ilse J Anderson
- Department of Genetics, University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA.,Department of Medicine, Columbia University Medical Center, New York, New York 10032, USA
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19
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Wittig-Blaich S, Wittig R, Schmidt S, Lyer S, Bewerunge-Hudler M, Gronert-Sum S, Strobel-Freidekind O, Müller C, List M, Jaskot A, Christiansen H, Hafner M, Schadendorf D, Block I, Mollenhauer J. Systematic screening of isogenic cancer cells identifies DUSP6 as context-specific synthetic lethal target in melanoma. Oncotarget 2017; 8:23760-23774. [PMID: 28423600 PMCID: PMC5410342 DOI: 10.18632/oncotarget.15863] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/06/2017] [Indexed: 12/19/2022] Open
Abstract
Next-generation sequencing has dramatically increased genome-wide profiling options and conceptually initiates the possibility for personalized cancer therapy. State-of-the-art sequencing studies yield large candidate gene sets comprising dozens or hundreds of mutated genes. However, few technologies are available for the systematic downstream evaluation of these results to identify novel starting points of future cancer therapies. We improved and extended a site-specific recombination-based system for systematic analysis of the individual functions of a large number of candidate genes. This was facilitated by a novel system for the construction of isogenic constitutive and inducible gain- and loss-of-function cell lines. Additionally, we demonstrate the construction of isogenic cell lines with combinations of the traits for advanced functional in vitro analyses. In a proof-of-concept experiment, a library of 108 isogenic melanoma cell lines was constructed and 8 genes were identified that significantly reduced viability in a discovery screen and in an independent validation screen. Here, we demonstrate the broad applicability of this recombination-based method and we proved its potential to identify new drug targets via the identification of the tumor suppressor DUSP6 as potential synthetic lethal target in melanoma cell lines with BRAF V600E mutations and high DUSP6 expression.
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Affiliation(s)
- Stephanie Wittig-Blaich
- Former Affiliation: Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69118 Heidelberg, Germany.,Institute for Comparative Molecular Endocrinology, Ulm University, 89081 Ulm, Germany
| | - Rainer Wittig
- Former Affiliation: Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69118 Heidelberg, Germany.,Institute for Laser Technologies in Medicine and Metrology, Ulm University, 89081 Ulm, Germany
| | - Steffen Schmidt
- Former Affiliation: Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.,Former Affiliation: Molecular Oncology, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Stefan Lyer
- Former Affiliation: Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69118 Heidelberg, Germany.,Department of Otorhinolaryngology, Section for Experimental Oncology and Nanomedicine (SEON), University Hospital Erlangen, 91054 Erlangen, Germany
| | - Melanie Bewerunge-Hudler
- Former Affiliation: Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69118 Heidelberg, Germany.,Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), 69118 Heidelberg, Germany
| | - Sabine Gronert-Sum
- Former Affiliation: Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69118 Heidelberg, Germany
| | - Olga Strobel-Freidekind
- Former Affiliation: Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69118 Heidelberg, Germany
| | - Carolin Müller
- Former Affiliation: Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.,Former Affiliation: Molecular Oncology, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Markus List
- Former Affiliation: Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.,Former Affiliation: Molecular Oncology, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Aleksandra Jaskot
- Former Affiliation: Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.,Former Affiliation: Molecular Oncology, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Helle Christiansen
- Former Affiliation: Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.,Former Affiliation: Molecular Oncology, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Mathias Hafner
- Department of Biotechnology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Duisburg-Essen, 45147 Essen, Germany and German Cancer Consortium, 69118 Heidelberg, Germany
| | - Ines Block
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark.,Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Jan Mollenhauer
- Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.,Molecular Oncology, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
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20
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De Santis R, Santini L, Colantoni A, Peruzzi G, de Turris V, Alfano V, Bozzoni I, Rosa A. FUS Mutant Human Motoneurons Display Altered Transcriptome and microRNA Pathways with Implications for ALS Pathogenesis. Stem Cell Reports 2017; 9:1450-1462. [PMID: 28988989 PMCID: PMC5830977 DOI: 10.1016/j.stemcr.2017.09.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 12/13/2022] Open
Abstract
The FUS gene has been linked to amyotrophic lateral sclerosis (ALS). FUS is a ubiquitous RNA-binding protein, and the mechanisms leading to selective motoneuron loss downstream of ALS-linked mutations are largely unknown. We report the transcriptome analysis of human purified motoneurons, obtained from FUS wild-type or mutant isogenic induced pluripotent stem cells (iPSCs). Gene ontology analysis of differentially expressed genes identified significant enrichment of pathways previously associated to sporadic ALS and other neurological diseases. Several microRNAs (miRNAs) were also deregulated in FUS mutant motoneurons, including miR-375, involved in motoneuron survival. We report that relevant targets of miR-375, including the neural RNA-binding protein ELAVL4 and apoptotic factors, are aberrantly increased in FUS mutant motoneurons. Characterization of transcriptome changes in the cell type primarily affected by the disease contributes to the definition of the pathogenic mechanisms of FUS-linked ALS.
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Affiliation(s)
- Riccardo De Santis
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Laura Santini
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessio Colantoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Valeria de Turris
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Vincenzo Alfano
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Irene Bozzoni
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Institute Pasteur Fondazione Cenci-Bolognetti, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessandro Rosa
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
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21
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Dubois-Camacho K, Ottum PA, Franco-Muñoz D, De la Fuente M, Torres-Riquelme A, Díaz-Jiménez D, Olivares-Morales M, Astudillo G, Quera R, Hermoso MA. Glucocorticosteroid therapy in inflammatory bowel diseases: From clinical practice to molecular biology. World J Gastroenterol 2017; 23:6628-6638. [PMID: 29085208 PMCID: PMC5643284 DOI: 10.3748/wjg.v23.i36.6628] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 05/25/2017] [Accepted: 07/04/2017] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel diseases (IBDs), such as ulcerative colitis and Crohn’s disease, are chronic pathologies associated with a deregulated immune response in the intestinal mucosa, and they are triggered by environmental factors in genetically susceptible individuals. Exogenous glucocorticoids (GCs) are widely used as anti-inflammatory therapy in IBDs. In the past, patients with moderate or severe states of inflammation received GCs as a first line therapy with an important effectiveness in terms of reduction of the disease activity and the induction of remission. However, this treatment often results in detrimental side effects. This downside drove the development of second generation GCs and more precise (non-systemic) drug-delivery methods. Recent clinical trials show that most of these new treatments have similar effectiveness to first generation GCs with fewer adverse effects. The remaining challenge in successful treatment of IBDs concerns the refractoriness and dependency that some patients encounter during GCs treatment. A deeper understanding of the molecular mechanisms underlying GC response is key to personalizing drug choice for IBDs patients to optimize their response to treatment. In this review, we examine the clinical characteristics of treatment with GCs, followed by an in depth analysis of the proposed molecular mechanisms involved in its resistance and dependence associated with IBDs. This thorough analysis of current clinical and biomedical literature may help guide physicians in determining a course of treatment for IBDs patients and identifies important areas needing further study.
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Affiliation(s)
- Karen Dubois-Camacho
- Innate Immunity Laboratory, Immunology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
| | - Payton A Ottum
- Neuroimmunology Laboratory, Immunology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
| | - Daniel Franco-Muñoz
- Innate Immunity Laboratory, Immunology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
| | - Marjorie De la Fuente
- Innate Immunity Laboratory, Immunology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Division of Research, Clínica Las Condes, Santiago 7591046, Chile
| | - Alejandro Torres-Riquelme
- Innate Immunity Laboratory, Immunology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
| | - David Díaz-Jiménez
- Innate Immunity Laboratory, Immunology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
| | - Mauricio Olivares-Morales
- Innate Immunity Laboratory, Immunology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
| | - Gonzalo Astudillo
- Innate Immunity Laboratory, Immunology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
| | - Rodrigo Quera
- Gastroenterology Department, Inflammatory Bowel Disease Program, Clínica Las Condes, Santiago 7591046, Chile
| | - Marcela A Hermoso
- Innate Immunity Laboratory, Immunology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
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22
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Thamsermsang O, Akarasereenont P, Laohapand T, Panich U. IL-1β-induced modulation of gene expression profile in human dermal fibroblasts: the effects of Thai herbal Sahatsatara formula, piperine and gallic acid possessing antioxidant properties. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 17:32. [PMID: 28068976 PMCID: PMC5223377 DOI: 10.1186/s12906-016-1515-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 12/14/2016] [Indexed: 01/04/2023]
Abstract
Background Pain is the main symptom of most musculoskeletal disorders and can be caused by inflammation in association with oxidative stress. Thai herbal Sahatsatara formula (STF), a polyherbal formula, has been traditionally used for relieving muscle pain and limb numbness. This study aimed to investigate biologically active compounds of STF and its pharmacological effects related to antioxidant and anti-inflammatory activities. Methods The identification of possibly active compounds of STF was performed by high performance liquid chromatography (HPLC). Moreover, this study also assessed the free radical scavenging activities of STF and its components using DPPH radical scavenging assay and their inhibitory effects on IL-1β-induced intracellular reactive oxygen species (ROS) formation in primary human dermal fibroblasts (NHDFs) using DCFDA-flow cytometry analysis. Modulation of human gene expression by STF and its active compounds was investigated by microarray analyzed through Gene Ontology (GO) classification and pathway enrichment analysis. Results HPLC analysis has revealed the presence of gallic acid (GA) and piperine (PP) as the major compounds in STF extracts. Our finding discovered that STF and its active compounds (GA and PP) yielded free radical scavenging activities and abilities to inhibit IL-1β-induced cellular ROS formation in NHDFs. Furthermore, microarray analysis demonstrated that a total of 84 genes (54 upregulated and 30 downregulated) were significantly affected by IL-1β involved in inflammatory cytokines, chemokines, transcription factors, cell adhesion molecules and other immunomodulators participating in NF-κB signaling. The significantly upregulated genes in IL-1β-treated in NHDFs participate in interleukin and cholecystokinin (CCRK) signaling pathways. The GO analysis of the target genes showed that all test compounds including indomethacin, STF and its active compounds, can downregulate the genes involved in NF-кB signaling pathway in IL-1β-treated NHDFs compared to the cells treated with IL-1β alone. Conclusions STF and its active compounds possessing antioxidant actions can modulate the effects of IL-1β-mediated alteration of gene expression profiles associated with inflammatory signaling in NHDFs. Electronic supplementary material The online version of this article (doi:10.1186/s12906-016-1515-0) contains supplementary material, which is available to authorized users.
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23
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Harms FL, Girisha KM, Hardigan AA, Kortüm F, Shukla A, Alawi M, Dalal A, Brady L, Tarnopolsky M, Bird LM, Ceulemans S, Bebin M, Bowling KM, Hiatt SM, Lose EJ, Primiano M, Chung WK, Juusola J, Akdemir ZC, Bainbridge M, Charng WL, Drummond-Borg M, Eldomery MK, El-Hattab AW, Saleh MAM, Bézieau S, Cogné B, Isidor B, Küry S, Lupski JR, Myers RM, Cooper GM, Kutsche K. Mutations in EBF3 Disturb Transcriptional Profiles and Cause Intellectual Disability, Ataxia, and Facial Dysmorphism. Am J Hum Genet 2017; 100:117-127. [PMID: 28017373 PMCID: PMC5223027 DOI: 10.1016/j.ajhg.2016.11.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/11/2016] [Indexed: 10/20/2022] Open
Abstract
From a GeneMatcher-enabled international collaboration, we identified ten individuals affected by intellectual disability, speech delay, ataxia, and facial dysmorphism and carrying a deleterious EBF3 variant detected by whole-exome sequencing. One 9-bp duplication and one splice-site, five missense, and two nonsense variants in EBF3 were found; the mutations occurred de novo in eight individuals, and the missense variant c.625C>T (p.Arg209Trp) was inherited by two affected siblings from their healthy mother, who is mosaic. EBF3 belongs to the early B cell factor family (also known as Olf, COE, or O/E) and is a transcription factor involved in neuronal differentiation and maturation. Structural assessment predicted that the five amino acid substitutions have damaging effects on DNA binding of EBF3. Transient expression of EBF3 mutant proteins in HEK293T cells revealed mislocalization of all but one mutant in the cytoplasm, as well as nuclear localization. By transactivation assays, all EBF3 mutants showed significantly reduced or no ability to activate transcription of the reporter gene CDKN1A, and in situ subcellular fractionation experiments demonstrated that EBF3 mutant proteins were less tightly associated with chromatin. Finally, in RNA-seq and ChIP-seq experiments, EBF3 acted as a transcriptional regulator, and mutant EBF3 had reduced genome-wide DNA binding and gene-regulatory activity. Our findings demonstrate that variants disrupting EBF3-mediated transcriptional regulation cause intellectual disability and developmental delay and are present in ∼0.1% of individuals with unexplained neurodevelopmental disorders.
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Affiliation(s)
- Frederike Leonie Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, 576104 Manipal, India
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, 576104 Manipal, India
| | - Malik Alawi
- Bioinformatics Service Facility, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Center for Bioinformatics, University of Hamburg, 20246 Hamburg, Germany; Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20246 Hamburg, Germany
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, 500001 Hyderabad, Telangana, India
| | - Lauren Brady
- Department of Pediatrics, McMaster University Medical Center, Hamilton, ON L8N 3Z5, Canada
| | - Mark Tarnopolsky
- Department of Pediatrics, McMaster University Medical Center, Hamilton, ON L8N 3Z5, Canada
| | - Lynne M Bird
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92123, USA; Division of Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA
| | - Sophia Ceulemans
- Division of Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA
| | - Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL35294, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Edward J Lose
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michelle Primiano
- Department of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | | | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew Bainbridge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Department of Pediatrics, Tawam Hospital, 15258 Al-Ain, United Arab Emirates
| | - Mohammed A M Saleh
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, 11564 Riyadh, Saudi Arabia
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, 44093 Nantes Cedex 1, France
| | - Benjamin Cogné
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, 44093 Nantes Cedex 1, France
| | - Bertrand Isidor
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, 44093 Nantes Cedex 1, France; INSERM UMR-S 957, 44035 Nantes, France
| | - Sébastien Küry
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, 44093 Nantes Cedex 1, France
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
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24
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Wlochowitz D, Haubrock M, Arackal J, Bleckmann A, Wolff A, Beißbarth T, Wingender E, Gültas M. Computational Identification of Key Regulators in Two Different Colorectal Cancer Cell Lines. Front Genet 2016; 7:42. [PMID: 27092172 PMCID: PMC4820448 DOI: 10.3389/fgene.2016.00042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 03/14/2016] [Indexed: 12/12/2022] Open
Abstract
Transcription factors (TFs) are gene regulatory proteins that are essential for an effective regulation of the transcriptional machinery. Today, it is known that their expression plays an important role in several types of cancer. Computational identification of key players in specific cancer cell lines is still an open challenge in cancer research. In this study, we present a systematic approach which combines colorectal cancer (CRC) cell lines, namely 1638N-T1 and CMT-93, and well-established computational methods in order to compare these cell lines on the level of transcriptional regulation as well as on a pathway level, i.e., the cancer cell-intrinsic pathway repertoire. For this purpose, we firstly applied the Trinity platform to detect signature genes, and then applied analyses of the geneXplain platform to these for detection of upstream transcriptional regulators and their regulatory networks. We created a CRC-specific position weight matrix (PWM) library based on the TRANSFAC database (release 2014.1) to minimize the rate of false predictions in the promoter analyses. Using our proposed workflow, we specifically focused on revealing the similarities and differences in transcriptional regulation between the two CRC cell lines, and report a number of well-known, cancer-associated TFs with significantly enriched binding sites in the promoter regions of the signature genes. We show that, although the signature genes of both cell lines show no overlap, they may still be regulated by common TFs in CRC. Based on our findings, we suggest that canonical Wnt signaling is activated in 1638N-T1, but inhibited in CMT-93 through cross-talks of Wnt signaling with the VDR signaling pathway and/or LXR-related pathways. Furthermore, our findings provide indication of several master regulators being present such as MLK3 and Mapk1 (ERK2) which might be important in cell proliferation, migration, and invasion of 1638N-T1 and CMT-93, respectively. Taken together, we provide new insights into the invasive potential of these cell lines, which can be used for development of effective cancer therapy.
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Affiliation(s)
- Darius Wlochowitz
- Institute of Bioinformatics, University Medical Center Göttingen Göttingen, Germany
| | - Martin Haubrock
- Institute of Bioinformatics, University Medical Center Göttingen Göttingen, Germany
| | - Jetcy Arackal
- Department of Hematology/Medical Oncology, University Medical Center Göttingen Göttingen, Germany
| | - Annalen Bleckmann
- Department of Hematology/Medical Oncology, University Medical Center Göttingen Göttingen, Germany
| | - Alexander Wolff
- Department of Medical Statistics, University Medical Center Göttingen Göttingen, Germany
| | - Tim Beißbarth
- Department of Medical Statistics, University Medical Center Göttingen Göttingen, Germany
| | - Edgar Wingender
- Institute of Bioinformatics, University Medical Center Göttingen Göttingen, Germany
| | - Mehmet Gültas
- Institute of Bioinformatics, University Medical Center Göttingen Göttingen, Germany
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Chen L, Yang J, Huang T, Kong X, Lu L, Cai YD. Mining for novel tumor suppressor genes using a shortest path approach. J Biomol Struct Dyn 2015. [PMID: 26209080 DOI: 10.1080/07391102.2015.1042915] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cancer, being among the most serious diseases, causes many deaths every year. Many investigators have devoted themselves to designing effective treatments for this disease. Cancer always involves abnormal cell growth with the potential to invade or spread to other parts of the body. In contrast, tumor suppressor genes (TSGs) act as guardians to prevent a disordered cell cycle and genomic instability in normal cells. Studies on TSGs can assist in the design of effective treatments against cancer. In this study, we propose a computational method to discover potential TSGs. Based on the known TSGs, a number of candidate genes were selected by applying the shortest path approach in a weighted graph that was constructed using protein-protein interaction network. The analysis of selected genes shows that some of them are new TSGs recently reported in the literature, while others may be novel TSGs.
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Affiliation(s)
- Lei Chen
- a College of Life Science , Shanghai University , Shanghai 200444 , P.R. China.,b College of Information Engineering , Shanghai Maritime University , Shanghai 201306 , P.R. China
| | - Jing Yang
- c The Key Laboratory of Stem Cell Biology , Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) , Shanghai 200025 , P.R. China
| | - Tao Huang
- c The Key Laboratory of Stem Cell Biology , Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) , Shanghai 200025 , P.R. China
| | - Xiangyin Kong
- c The Key Laboratory of Stem Cell Biology , Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) , Shanghai 200025 , P.R. China
| | - Lin Lu
- d Department of Radiology , Columbia University Medical Center , New York , NY 10032 , USA
| | - Yu-Dong Cai
- a College of Life Science , Shanghai University , Shanghai 200444 , P.R. China
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26
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Jin S, Choi H, Kwon JT, Kim J, Jeong J, Kim J, Ham S, Cho BN, Yoo YJ, Cho C. Identification and characterization of reproductive KRAB-ZF genes in mice. Gene 2015; 565:45-55. [DOI: 10.1016/j.gene.2015.03.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/03/2015] [Accepted: 03/27/2015] [Indexed: 11/30/2022]
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Wang J, Chitturi J, Ge Q, Laskova V, Wang W, Li X, Ding M, Zhen M, Huang X. The C. elegans COE transcription factor UNC-3 activates lineage-specific apoptosis and affects neurite growth in the RID lineage. Development 2015; 142:1447-57. [PMID: 25790851 DOI: 10.1242/dev.119479] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 02/17/2015] [Indexed: 12/23/2022]
Abstract
Mechanisms that regulate apoptosis in a temporal and lineage-specific manner remain poorly understood. The COE (Collier/Olf/EBF) transcription factors have been implicated in the development of many cell types, including neurons. Here, we show that the sole Caenorhabditis elegans COE protein, UNC-3, together with a histone acetyltransferase, CBP-1/P300, specifies lineage-specific apoptosis and certain aspects of neurite trajectory. During embryogenesis, the RID progenitor cell gives rise to the RID neuron and RID sister cell; the latter undergoes apoptosis shortly after cell division upon expression of the pro-apoptotic gene egl-1. We observe UNC-3 expression in the RID progenitor, and the absence of UNC-3 results in the failure of the RID lineage to express a Pegl-1::GFP reporter and in the survival of the RID sister cell. Lastly, UNC-3 interacts with CBP-1, and cbp-1 mutants exhibit a similar RID phenotype to unc-3. Thus, in addition to playing a role in neuronal terminal differentiation, UNC-3 is a cell lineage-specific regulator of apoptosis.
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Affiliation(s)
- Jinbo Wang
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jyothsna Chitturi
- Lunenfeld and Tanebaum Research Institute, University of Toronto, Toronto, Ontario, Canada M5G 1X5
| | - Qinglan Ge
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Valeriya Laskova
- Lunenfeld and Tanebaum Research Institute, University of Toronto, Toronto, Ontario, Canada M5G 1X5
| | - Wei Wang
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xia Li
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mei Ding
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mei Zhen
- Lunenfeld and Tanebaum Research Institute, University of Toronto, Toronto, Ontario, Canada M5G 1X5
| | - Xun Huang
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Tao YF, Xu LX, Lu J, Hu SY, Fang F, Cao L, Xiao PF, Du XJ, Sun LC, Li ZH, Wang NN, Su GH, Li YH, Li G, Zhao H, Li YP, Xu YY, Zhou HT, Wu Y, Jin MF, Liu L, Zhu XM, Ni J, Wang J, Xing F, Zhao WL, Pan J. Early B-cell factor 3 (EBF3) is a novel tumor suppressor gene with promoter hypermethylation in pediatric acute myeloid leukemia. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:4. [PMID: 25609158 PMCID: PMC4311429 DOI: 10.1186/s13046-014-0118-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/27/2014] [Indexed: 12/21/2022]
Abstract
Background Pediatric acute myeloid leukemia (AML) comprises up to 20% of all childhood leukemia. Recent research shows that aberrant DNA methylation patterning may play a role in leukemogenesis. The epigenetic silencing of the EBF3 locus is very frequent in glioblastoma. However, the expression profiles and molecular function of EBF3 in pediatric AML is still unclear. Methods Twelve human acute leukemia cell lines, 105 pediatric AML samples and 30 normal bone marrow/idiopathic thrombocytopenic purpura (NBM/ITP) control samples were analyzed. Transcriptional level of EBF3 was evaluated by semi-quantitative and real-time PCR. EBF3 methylation status was determined by methylation specific PCR (MSP) and bisulfite genomic sequencing (BGS). The molecular mechanism of EBF3 was investigated by apoptosis assays and PCR array analysis. Results EBF3 promoter was hypermethylated in 10/12 leukemia cell lines. Aberrant EBF3 methylation was observed in 42.9% (45/105) of the pediatric AML samples using MSP analysis, and the BGS results confirmed promoter methylation. EBF3 expression was decreased in the AML samples compared with control. Methylated samples revealed similar survival outcomes by Kaplan-Meier survival analysis. EBF3 overexpression significantly inhibited cell proliferation and increased apoptosis. Real-time PCR array analysis revealed 93 dysregulated genes possibly implicated in the apoptosis of EBF3-induced AML cells. Conclusion In this study, we firstly identified epigenetic inactivation of EBF3 in both AML cell lines and pediatric AML samples for the first time. Our findings also showed for the first time that transcriptional overexpression of EBF3 could inhibit proliferation and induce apoptosis in AML cells. We identified 93 dysregulated apoptosis-related genes in EBF3-overexpressing, including DCC, AIFM2 and DAPK1. Most of these genes have never been related with EBF3 over expression. These results may provide new insights into the molecular mechanism of EBF3-induced apoptosis; however, further research will be required to determine the underlying details. Our findings suggest that EBF3 may act as a putative tumor suppressor gene in pediatric AML.
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Affiliation(s)
- Yan-Fang Tao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Li-Xiao Xu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Jun Lu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Shao-Yan Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Fang Fang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Lan Cao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Pei-Fang Xiao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Xiao-Juan Du
- Department of Gastroenterology, the 5th Hospital of Chinese PLA, Yin chuan, China.
| | - Li-Chao Sun
- Department of Cell and Molecular Biology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
| | - Zhi-Heng Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Na-Na Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Guang-Hao Su
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Yan-Hong Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Gang Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - He Zhao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Yi-Ping Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Yun-Yun Xu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Hui-Ting Zhou
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Yi Wu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Mei-Fang Jin
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Lin Liu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Xue-Ming Zhu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Jian Ni
- Translational Research Center, Second Hospital, The Second Clinical School, Nanjing Medical University, Nanjing, China.
| | - Jian Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Feng Xing
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Wen-Li Zhao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Jian Pan
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
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29
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Cowles MW, Omuro KC, Stanley BN, Quintanilla CG, Zayas RM. COE loss-of-function analysis reveals a genetic program underlying maintenance and regeneration of the nervous system in planarians. PLoS Genet 2014; 10:e1004746. [PMID: 25356635 PMCID: PMC4214590 DOI: 10.1371/journal.pgen.1004746] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 09/10/2014] [Indexed: 12/17/2022] Open
Abstract
Members of the COE family of transcription factors are required for central nervous system (CNS) development. However, the function of COE in the post-embryonic CNS remains largely unknown. An excellent model for investigating gene function in the adult CNS is the freshwater planarian. This animal is capable of regenerating neurons from an adult pluripotent stem cell population and regaining normal function. We previously showed that planarian coe is expressed in differentiating and mature neurons and that its function is required for proper CNS regeneration. Here, we show that coe is essential to maintain nervous system architecture and patterning in intact (uninjured) planarians. We took advantage of the robust phenotype in intact animals to investigate the genetic programs coe regulates in the CNS. We compared the transcriptional profiles of control and coe RNAi planarians using RNA sequencing and identified approximately 900 differentially expressed genes in coe knockdown animals, including 397 downregulated genes that were enriched for nervous system functional annotations. Next, we validated a subset of the downregulated transcripts by analyzing their expression in coe-deficient planarians and testing if the mRNAs could be detected in coe+ cells. These experiments revealed novel candidate targets of coe in the CNS such as ion channel, neuropeptide, and neurotransmitter genes. Finally, to determine if loss of any of the validated transcripts underscores the coe knockdown phenotype, we knocked down their expression by RNAi and uncovered a set of coe-regulated genes implicated in CNS regeneration and patterning, including orthologs of sodium channel alpha-subunit and pou4. Our study broadens the knowledge of gene expression programs regulated by COE that are required for maintenance of neural subtypes and nervous system architecture in adult animals. COE transcription factors are conserved across widely divergent animals and are crucial for organismal development. COE genes also play roles in adult animals and have been implicated in central nervous system (CNS) diseases; however, the function of COE in the post-embryonic CNS remains poorly understood. Planarian regeneration provides an excellent model to study the function of transcription factors in cell differentiation and in terminally differentiated cells. In planarians, coe is expressed in differentiating and mature neurons, and its function is required for CNS regeneration. In this study, we show that coe is required to maintain structure and function of the CNS in uninjured planarians. We took advantage of this phenotype to identify genes regulated by coe by comparing global gene expression changes between control and coe mRNA-deficient planarians. This approach revealed downregulated genes downstream of coe with biological roles in CNS function. Expression analysis of downregulated genes uncovered previously unknown candidate targets of coe in the CNS. Furthermore, functional analysis of downstream targets identified coe-regulated genes required for CNS regeneration. These results demonstrate that the roles of COE in stem cell specification and neuronal function are active and indispensable during CNS renewal in adult animals.
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Affiliation(s)
- Martis W. Cowles
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Kerilyn C. Omuro
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Brianna N. Stanley
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Carlo G. Quintanilla
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Ricardo M. Zayas
- Department of Biology, San Diego State University, San Diego, California, United States of America
- * E-mail:
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30
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Jin S, Kim J, Willert T, Klein-Rodewald T, Garcia-Dominguez M, Mosqueira M, Fink R, Esposito I, Hofbauer LC, Charnay P, Kieslinger M. Ebf factors and MyoD cooperate to regulate muscle relaxation via Atp2a1. Nat Commun 2014; 5:3793. [PMID: 24786561 DOI: 10.1038/ncomms4793] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/02/2014] [Indexed: 01/08/2023] Open
Abstract
Myogenic regulatory factors such as MyoD and Myf5 lie at the core of vertebrate muscle differentiation. However, E-boxes, the cognate binding sites for these transcription factors, are not restricted to the promoters/enhancers of muscle cell-specific genes. Thus, the specificity in myogenic transcription is poorly defined. Here we describe the transcription factor Ebf3 as a new determinant of muscle cell-specific transcription. In the absence of Ebf3 the lung does not unfold at birth, resulting in respiratory failure and perinatal death. This is due to a hypercontractile diaphragm with impaired Ca(2+) efflux-related muscle functions. Expression of the Ca(2+) pump Serca1 (Atp2a1) is downregulated in the absence of Ebf3, and its transgenic expression rescues this phenotype. Ebf3 binds directly to the promoter of Atp2a1 and synergises with MyoD in the induction of Atp2a1. In skeletal muscle, the homologous family member Ebf1 is strongly expressed and together with MyoD induces Atp2a1. Thus, Ebf3 is a new regulator of terminal muscle differentiation in the diaphragm, and Ebf factors cooperate with MyoD in the induction of muscle-specific genes.
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Affiliation(s)
- Saihong Jin
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Zentrum München, National Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Jeehee Kim
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Zentrum München, National Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Torsten Willert
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Zentrum München, National Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Tanja Klein-Rodewald
- Institute of Pathology, Helmholtz Zentrum München, National Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, 81377 Munich, Germany
| | - Mario Garcia-Dominguez
- 1] Developmental Biology Section, Ecole Normale Supérieure, Rue d'Ulm 46, 75230 Paris, France [2] Stem Cells Department, CABIMER (CISC), Av Américo Vespucio, 41092 Sevilla, Spain
| | - Matias Mosqueira
- Medical Biophysics Unit, Institute of Physiology and Pathophysiology, University of Heidelberg, Im Neuenheimer Feld 326, 69120 Heidelberg, Germany
| | - Rainer Fink
- Medical Biophysics Unit, Institute of Physiology and Pathophysiology, University of Heidelberg, Im Neuenheimer Feld 326, 69120 Heidelberg, Germany
| | - Irene Esposito
- 1] Institute of Pathology, Helmholtz Zentrum München, National Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, 81377 Munich, Germany [2] Institute of Pathology, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - Lorenz C Hofbauer
- Division of Endocrinology, Diabetes and Metabolic Bone Diseases, Department of Medicine III, TU Dresden Medical Center, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Patrick Charnay
- Developmental Biology Section, Ecole Normale Supérieure, Rue d'Ulm 46, 75230 Paris, France
| | - Matthias Kieslinger
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Zentrum München, National Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
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Demokan S, Chuang AY, Pattani KM, Sidransky D, Koch W, Califano JA. Validation of nucleolar protein 4 as a novel methylated tumor suppressor gene in head and neck cancer. Oncol Rep 2013; 31:1014-20. [PMID: 24337411 PMCID: PMC3896520 DOI: 10.3892/or.2013.2927] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 11/27/2013] [Indexed: 11/10/2022] Open
Abstract
Methylation of CpG islands in the promoter region of genes acts as a significant mechanism of epigenetic gene silencing in head and neck cancer. In the present study, we assessed the association of epigenetic alterations of a panel of 12 genes [nucleolar protein 4 (NOL4), iroquois homeobox 1 (IRX1), SLC5A8, LRRC3B, FUSSEL18, EBF3, GBX2, HMX2, SEPT9, ALX3, SOCS3 and LHX6] with head and neck squamous cell carcinoma (HNSCC) via a candidate gene approach. After the initial screening of methylated CpG islands on the promoter regions by bisulfite sequencing using salivary rinse samples, only two genes had methylated CpG dinucleotides on their promoter regions in tumor samples and absence of methylated CpGs were found in normal salivary rinse samples after bisulfite modification and bisulfite sequencing. We then performed real-time quantitative methylation-specific PCR (QMSP) on 16 salivary rinse and 14 normal mucosal samples from healthy subjects and 33 HNSCC tumor samples for the two genes selected. After validation with QMSP, one gene, NOL4, was highly methylated (91%) in tumor samples and unmethylated in normal salivary rinses and minimally methylated in normal mucosal samples demonstrating cancer-specific methylation in HNSCC tissues. Although the IRX1 gene was observed as methylated in normal mucosal and salivary rinse samples, the methylation values of these normal samples were very low (<10%). In conclusion, we identified NOL4 as a highly specific promoter methylated gene associated with HNSCC. IRX1 may have potential as a biomarker for HNSCC and should be assessed in a larger cohort.
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Affiliation(s)
- Semra Demokan
- Department of Basic Oncology, Oncology Institute, Istanbul University, Capa, Istanbul 34093, Turkey
| | - Alice Y Chuang
- Department of Dermatology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Kavita M Pattani
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Wayne Koch
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Joseph A Califano
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
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32
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Chung GT, Lung RW, Hui AB, Yip KY, Woo JK, Chow C, Tong CY, Lee SD, Yuen JW, Lun SW, Tso KK, Wong N, Tsao SW, Yip TT, Busson P, Kim H, Seo JS, O'Sullivan B, Liu FF, To KF, Lo KW. Identification of a recurrent transforming UBR5-ZNF423 fusion gene in EBV-associated nasopharyngeal carcinoma. J Pathol 2013; 231:158-67. [PMID: 23878065 PMCID: PMC4166696 DOI: 10.1002/path.4240] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/23/2013] [Accepted: 07/15/2013] [Indexed: 11/30/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a distinct type of head and neck cancer which is prevalent in southern China, south-east Asia and northern Africa. The development and stepwise progression of NPC involves accumulation of multiple gross genetic changes during the clonal expansion of Epstein–Barr virus (EBV)-infected nasopharyngeal epithelial cell population. Here, using paired-end whole-transcriptome sequencing, we discovered a number of chimeric fusion transcripts in a panel of EBV-positive tumour lines. Among these transcripts, a novel fusion of ubiquitin protein ligase E3 component n-recognin 5 (UBR5) on 8q22.3 and zinc finger protein 423 (ZNF423) on 16q12.1, identified from the NPC cell line C666-1, was recurrently detected in 12/144 (8.3%) of primary tumours. The fusion gene contains exon 1 of UBR5 and exons 7–9 of ZNF423 and produces a 94 amino acid chimeric protein including the original C-terminal EBF binding domain (ZF29-30) of ZNF423. Notably, the growth of NPC cells with UBR5–ZNF423 rearrangement is dependent on expression of this fusion protein. Knock-down of UBR5–ZNF423 by fusion-specific siRNA significantly inhibited the cell proliferation and colony-forming ability of C666-1 cells. The transforming ability of UBR5–ZNF423 fusion was also confirmed in NIH3T3 fibroblasts. Constitutive expression of UBR5–ZNF423 in NIH3T3 fibroblasts significantly enhanced its anchorage-independent growth in soft agar and induced tumour formation in a nude mouse model. These findings suggest that expression of UBR5–ZNF423 protein might contribute to the transformation of a subset of NPCs, possibly by altering the activity of EBFs (early B cell factors). Identification of the oncogenic UBR5–ZNF423 provides new potential opportunities for therapeutic intervention in NPC. © 2013 The Authors. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Grace Ty Chung
- Department of Anatomical and Cellular Pathology, State Key Laboratory in Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, SAR; Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, SAR
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33
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Le TP, Sun M, Luo X, Kraus WL, Greene GL. Mapping ERβ genomic binding sites reveals unique genomic features and identifies EBF1 as an ERβ interactor. PLoS One 2013; 8:e71355. [PMID: 23951143 PMCID: PMC3738513 DOI: 10.1371/journal.pone.0071355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 06/29/2013] [Indexed: 12/31/2022] Open
Abstract
Considerable effort by numerous laboratories has resulted in an improved understanding of estrogen and SERM action mediated by the two estrogen receptors, ERα and ERβ. However, many of the targets for ERβ in cell physiology remain elusive. Here, the C4-12/Flag.ERβ cell line which stably expressed Flag.ERβ is used to study ERβ genomic functions without ERα interference. Mapping ERβ binding sites in these cells reveals ERβ unique distribution and motif enrichment patterns. Accompanying our mapping results, nascent RNA profiling is performed on cells at the same treatment time. The combined results allow the identification of ERβ target genes. Gene ontology analysis reveals that ERβ targets are enriched in differentiation, development and apoptosis. Concurrently, E2 treatment suppresses proliferation in these cells. Within ERβ binding sites, while the most prevalent binding motif is the canonical ERE, motifs of known ER interactors are also enriched in ERβ binding sites. Moreover, among enriched binding motifs are those of GFI, REST and EBF1, which are unique to ERβ binding sites in these cells. Further characterization confirms the association between EBF1 and the estrogen receptors, which favors the N-terminal region of the receptor. Furthermore, EBF1 negatively regulates ERs at the protein level. In summary, by studying ERβ genomic functions in our cell model, we confirm the anti-proliferative role of ERβ and discover the novel cross talk of ERβ with EBF1 which has various implications in normal physiology.
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Affiliation(s)
- Thien P. Le
- Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois, United States of America
| | - Miao Sun
- Green Center for Reproductive Biology Sciences, University of Texas Southwestern, Dallas, Texas, United States of America
| | - Xin Luo
- Green Center for Reproductive Biology Sciences, University of Texas Southwestern, Dallas, Texas, United States of America
| | - W. Lee Kraus
- Green Center for Reproductive Biology Sciences, University of Texas Southwestern, Dallas, Texas, United States of America
| | - Geoffrey L. Greene
- Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois, United States of America
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34
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Byrne EM, Gehrman PR, Medland SE, Nyholt DR, Heath AC, Madden PAF, Hickie IB, Van Duijn CM, Henders AK, Montgomery GW, Martin NG, Wray NR. A genome-wide association study of sleep habits and insomnia. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:439-51. [PMID: 23728906 PMCID: PMC4083458 DOI: 10.1002/ajmg.b.32168] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 04/11/2013] [Indexed: 01/15/2023]
Abstract
Several aspects of sleep behavior such as timing, duration and quality have been demonstrated to be heritable. To identify common variants that influence sleep traits in the population, we conducted a genome-wide association study of six sleep phenotypes assessed by questionnaire in a sample of 2,323 individuals from the Australian Twin Registry. Genotyping was performed on the Illumina 317, 370, and 610K arrays and the SNPs in common between platforms were used to impute non-genotyped SNPs. We tested for association with more than 2,000,000 common polymorphisms across the genome. While no SNPs reached the genome-wide significance threshold, we identified a number of associations in plausible candidate genes. Most notably, a group of SNPs in the third intron of the CACNA1C gene ranked as most significant in the analysis of sleep latency (P = 1.3 × 10⁻⁶). We attempted to replicate this association in an independent sample from the Chronogen Consortium (n = 2,034), but found no evidence of association (P = 0.73). We have identified several other suggestive associations that await replication in an independent sample. We did not replicate the results from previous genome-wide analyses of self-reported sleep phenotypes after correction for multiple testing.
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Affiliation(s)
- Enda M Byrne
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia.
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35
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Minhas HM, Pescosolido MF, Schwede M, Piasecka J, Gaitanis J, Tantravahi U, Morrow EM. An unbalanced translocation involving loss of 10q26.2 and gain of 11q25 in a pedigree with autism spectrum disorder and cerebellar juvenile pilocytic astrocytoma. Am J Med Genet A 2013; 161A:787-91. [PMID: 23495067 DOI: 10.1002/ajmg.a.35841] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 12/12/2012] [Indexed: 01/20/2023]
Abstract
We report on a pedigree with a pair of brothers each with minor anomalies, developmental delay, and autistic-symptoms who share an unbalanced translocation (not detectable by karyotype). The unbalanced translocation involves a 7.1 Mb loss of the terminal portion of 10q, and a 4.2 Mb gain of 11q. One of the brothers also developed a cerebellar juvenile pilocytic astrocytoma. The father was found to be a balanced carrier and the couple had a previous miscarriage. We demonstrate that the breakpoint for the triplicated region from chromosome 11 is adjacent to two IgLON genes, namely Neurotrimin (NTM) and Opioid Binding Protein/Cell Adhesion Molecule-like (OPCML). These genes are highly similar neural cell adhesion molecules that have been implicated in synaptogenesis and oncogenesis, respectively. The children also have a 10q deletion and are compared to other children with the 10q deletion syndrome which generally does not involve autism spectrum disorders (ASDs) or cancer. Together these data support a role for NTM and OPCML in developmental delay and potentially in cancer susceptibility.
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Affiliation(s)
- Hassan M Minhas
- Developmental Disorders Genetics Research Program, Emma Pendleton Bradley Hospital, The Warren Alpert Medical School of Brown University, Providence, RI 02912, USA
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Hu XT, He C. Recent progress in the study of methylated tumor suppressor genes in gastric cancer. CHINESE JOURNAL OF CANCER 2013; 32:31-41. [PMID: 22059906 PMCID: PMC3845584 DOI: 10.5732/cjc.011.10175] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 07/27/2011] [Accepted: 08/17/2011] [Indexed: 12/14/2022]
Abstract
Gastric cancer is one of the most common malignancies and a leading cause of cancer mortality worldwide. The pathogenesis mechanisms of gastric cancer are still not fully clear. Inactivation of tumor suppressor genes and activation of oncogenes caused by genetic and epigenetic alterations are known to play significant roles in carcinogenesis. Accumulating evidence has shown that epigenetic silencing of the tumor suppressor genes, particularly caused by hypermethylation of CpG islands in promoters, is critical to carcinogenesis and metastasis. Here, we review the recent progress in the study of methylations of tumor suppressor genes involved in the pathogenesis of gastric cancer. We also briefly describe the mechanisms that induce tumor suppressor gene methylation and the status of translating these molecular mechanisms into clinical applications.
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Affiliation(s)
- Xiao-Tong Hu
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province,
| | - Chao He
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province,
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, Hangzhou, Zhejiang 310016, P. R. China.
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37
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Lautz TB, Jie C, Clark S, Naiditch JA, Jafari N, Qiu YY, Zheng X, Chu F, Madonna MB. The effect of vorinostat on the development of resistance to doxorubicin in neuroblastoma. PLoS One 2012; 7:e40816. [PMID: 22829886 PMCID: PMC3400660 DOI: 10.1371/journal.pone.0040816] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 06/18/2012] [Indexed: 11/25/2022] Open
Abstract
Histone deacetylase (HDAC) inhibitors, especially vorinostat, are currently under investigation as potential adjuncts in the treatment of neuroblastoma. The effect of vorinostat co-treatment on the development of resistance to other chemotherapeutic agents is unknown. In the present study, we treated two human neuroblastoma cell lines [SK-N-SH and SK-N-Be(2)C] with progressively increasing doses of doxorubicin under two conditions: with and without vorinsotat co-therapy. The resultant doxorubicin-resistant (DoxR) and vorinostat-treated doxorubicin resistant (DoxR-v) cells were equally resistant to doxorubicin despite significantly lower P-glycoprotein expression in the DoxR-v cells. Whole genome analysis was performed using the Ilumina Human HT-12 v4 Expression Beadchip to identify genes with differential expression unique to the DoxR-v cells. We uncovered a number of genes whose differential expression in the DoxR-v cells might contribute to their resistant phenotype, including hypoxia inducible factor-2. Finally, we used Gene Ontology to categorize the biological functions of the differentially expressed genes unique to the DoxR-v cells and found that genes involved in cellular metabolism were especially affected.
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Affiliation(s)
- Timothy B. Lautz
- Department of Surgery, Lurie Children’s Hospital, Northwestern University, Chicago, Illinois, United States of America
- Cancer Biology Program, Children’s Memorial Research Center, Northwestern University, Chicago, Illinois, United States of America
| | - Chunfa Jie
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Sandra Clark
- Cancer Biology Program, Children’s Memorial Research Center, Northwestern University, Chicago, Illinois, United States of America
| | - Jessica A. Naiditch
- Department of Surgery, Lurie Children’s Hospital, Northwestern University, Chicago, Illinois, United States of America
- Cancer Biology Program, Children’s Memorial Research Center, Northwestern University, Chicago, Illinois, United States of America
| | - Nadereh Jafari
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Yi-Yong Qiu
- Cancer Biology Program, Children’s Memorial Research Center, Northwestern University, Chicago, Illinois, United States of America
| | - Xin Zheng
- Cancer Biology Program, Children’s Memorial Research Center, Northwestern University, Chicago, Illinois, United States of America
| | - Fei Chu
- Cancer Biology Program, Children’s Memorial Research Center, Northwestern University, Chicago, Illinois, United States of America
- * E-mail: (MBM); (FC)
| | - Mary Beth Madonna
- Department of Surgery, Lurie Children’s Hospital, Northwestern University, Chicago, Illinois, United States of America
- Cancer Biology Program, Children’s Memorial Research Center, Northwestern University, Chicago, Illinois, United States of America
- * E-mail: (MBM); (FC)
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Corno D, Pala M, Cominelli M, Cipelletti B, Leto K, Croci L, Barili V, Brandalise F, Melzi R, Di Gregorio A, Sergi LS, Politi LS, Piemonti L, Bulfone A, Rossi P, Rossi F, Consalez GG, Poliani PL, Galli R. Gene Signatures Associated with Mouse Postnatal Hindbrain Neural Stem Cells and Medulloblastoma Cancer Stem Cells Identify Novel Molecular Mediators and Predict Human Medulloblastoma Molecular Classification. Cancer Discov 2012; 2:554-68. [DOI: 10.1158/2159-8290.cd-11-0199] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Hong SM, Omura N, Vincent A, Li A, Knight S, Yu J, Hruban RH, Goggins M. Genome-wide CpG island profiling of intraductal papillary mucinous neoplasms of the pancreas. Clin Cancer Res 2011; 18:700-12. [PMID: 22173550 DOI: 10.1158/1078-0432.ccr-11-1718] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE Intraductal papillary mucinous neoplasms (IPMN) are precursors to infiltrating pancreatic ductal adenocarcinomas. Widespread epigenetic alterations are characteristic of many cancers, yet few studies have systematically analyzed epigenetic alterations of neoplastic precursors. Our goal was to conduct genome-wide CpG island methylation profiling to identify aberrantly methylated loci in IPMNs. EXPERIMENTAL DESIGN We compared the CpG island methylation profiles of six IPMNs to normal primary pancreatic duct samples using methylation CpG island amplification (MCA) and Agilent CpG island microarray (MCAM) analysis. When selected 13 genes identified as differentially methylated by MCAM for methylation-specific PCR (MSP) analysis in an independent set of IPMNs and normal pancreas samples and conducted expression analysis of selected genes. RESULTS We identified 2,259 loci as differentially methylated in at least one of six IPMNs including 245 genes hypermethylated in IPMNs with high-grade dysplasia compared with normal pancreatic duct samples. Eleven of 13 genes evaluated by MSP were more commonly methylated in 61 IPMNs than in 43 normal pancreas samples. Several genes (BNIP3, PTCHD2, SOX17, NXPH1, EBF3) were significantly more likely to be methylated in IPMNs with high-grade than with low-grade dysplasia. One gene, SOX17, showed loss of protein expression by immunohistochemistry in 22% (19 of 88) of IPMNs. The most specific marker, BNIP3, was not methylated in any IPMNs with low-grade dysplasia or in normal pancreas samples. CONCLUSIONS IPMNs undergo extensive aberrant CpG island hypermethylation. The detection of genes selectively methylated in high-grade IPMNs such as BNIP3 may have use in the clinical evaluation of IPMNs.
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Affiliation(s)
- Seung-Mo Hong
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, USA
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Enroth S, Rada-Iglesisas A, Andersson R, Wallerman O, Wanders A, Påhlman L, Komorowski J, Wadelius C. Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa. BMC Cancer 2011; 11:450. [PMID: 22011431 PMCID: PMC3216894 DOI: 10.1186/1471-2407-11-450] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 10/19/2011] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Despite their well-established functional roles, histone modifications have received less attention than DNA methylation in the cancer field. In order to evaluate their importance in colorectal cancer (CRC), we generated the first genome-wide histone modification profiles in paired normal colon mucosa and tumor samples. METHODS Chromatin immunoprecipitation and microarray hybridization (ChIP-chip) was used to identify promoters enriched for histone H3 trimethylated on lysine 4 (H3K4me3) and lysine 27 (H3K27me3) in paired normal colon mucosa and tumor samples from two CRC patients and for the CRC cell line HT29. RESULTS By comparing histone modification patterns in normal mucosa and tumors, we found that alterations predicted to have major functional consequences were quite rare. Furthermore, when normal or tumor tissue samples were compared to HT29, high similarities were observed for H3K4me3. However, the differences found for H3K27me3, which is important in determining cellular identity, indicates that cell lines do not represent optimal tissue models. Finally, using public expression data, we uncovered previously unknown changes in CRC expression patterns. Genes positive for H3K4me3 in normal and/or tumor samples, which are typically already active in normal mucosa, became hyperactivated in tumors, while genes with H3K27me3 in normal and/or tumor samples and which are expressed at low levels in normal mucosa, became hypersilenced in tumors. CONCLUSIONS Genome wide histone modification profiles can be used to find epigenetic aberrations in genes associated with cancer. This strategy gives further insights into the epigenetic contribution to the oncogenic process and may identify new biomarkers.
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Affiliation(s)
- Stefan Enroth
- The Linnaeus Centre for Bioinformatics, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden
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41
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Castro DS, Martynoga B, Parras C, Ramesh V, Pacary E, Johnston C, Drechsel D, Lebel-Potter M, Garcia LG, Hunt C, Dolle D, Bithell A, Ettwiller L, Buckley N, Guillemot F. A novel function of the proneural factor Ascl1 in progenitor proliferation identified by genome-wide characterization of its targets. Genes Dev 2011; 25:930-45. [PMID: 21536733 DOI: 10.1101/gad.627811] [Citation(s) in RCA: 307] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proneural genes such as Ascl1 are known to promote cell cycle exit and neuronal differentiation when expressed in neural progenitor cells. The mechanisms by which proneural genes activate neurogenesis--and, in particular, the genes that they regulate--however, are mostly unknown. We performed a genome-wide characterization of the transcriptional targets of Ascl1 in the embryonic brain and in neural stem cell cultures by location analysis and expression profiling of embryos overexpressing or mutant for Ascl1. The wide range of molecular and cellular functions represented among these targets suggests that Ascl1 directly controls the specification of neural progenitors as well as the later steps of neuronal differentiation and neurite outgrowth. Surprisingly, Ascl1 also regulates the expression of a large number of genes involved in cell cycle progression, including canonical cell cycle regulators and oncogenic transcription factors. Mutational analysis in the embryonic brain and manipulation of Ascl1 activity in neural stem cell cultures revealed that Ascl1 is indeed required for normal proliferation of neural progenitors. This study identified a novel and unexpected activity of the proneural gene Ascl1, and revealed a direct molecular link between the phase of expansion of neural progenitors and the subsequent phases of cell cycle exit and neuronal differentiation.
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Affiliation(s)
- Diogo S Castro
- Medical Research Council National Institute for Medical Research, Division of Molecular Neurobiology, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom.
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Kim J, Min SY, Lee HE, Kim WH. Aberrant DNA methylation and tumor suppressive activity of the EBF3 gene in gastric carcinoma. Int J Cancer 2011; 130:817-26. [PMID: 21387304 DOI: 10.1002/ijc.26038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 02/17/2011] [Indexed: 11/11/2022]
Abstract
The early B-cell factors (EBFs) are a group of four highly conserved DNA-binding transcription factors with an atypical zinc-finger and a helix-loop-helix domain. The EBF3 locus on chromosome 10q26.3 is epigenetically silenced or deleted in several types of cancers. In addition, EBF3 activates genes involved in cell cycle arrest and inhibits cell survival. However, inactivation of EBF3 gene expression was not fully studied in gastric carcinoma and the functions of EBF3 that underlie EBF3-regulated tumor suppression have not been identified. In our study, we found that inactivation of the EBF3 gene is frequently accompanied by promoter region hypermethylation in several gastric cancer cell lines and that the gene is reactivated by 5-aza-2'-deoxycytidine (5-aza-dc) and/or trichostatin A (TSA) in all ten gastric cancer cell lines. We performed functional analysis using small interfering RNA or expressional cDNA transfection in gastric cancer cell lines and demonstrate that EBF3 represses gastric cancer cell growth and migration, but activates cell cycle arrest and apoptosis. Promoter methylation of EBF3 was detected in 42/104 (40.4%) gastric cancer tissues but not in normal gastric tissues. Furthermore, promoter methylation of EBF3 was found to be significantly correlated with lymphatic invasion (p = 0.013) and poor survival (p = 0.038) in gastric carcinoma. These results suggest that EBF3 tumor suppressor is epigenetically silenced and that it serves as an independent prognostic marker in gastric carcinoma.
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Affiliation(s)
- Jin Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
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43
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Dioxin exposure of human CD34+ hemopoietic cells induces gene expression modulation that recapitulates its in vivo clinical and biological effects. Toxicology 2011; 283:18-23. [DOI: 10.1016/j.tox.2011.01.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 01/25/2011] [Accepted: 01/28/2011] [Indexed: 11/22/2022]
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44
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Bennett KL, Lee W, Lamarre E, Zhang X, Seth R, Scharpf J, Hunt J, Eng C. HPV status-independent association of alcohol and tobacco exposure or prior radiation therapy with promoter methylation of FUSSEL18, EBF3, IRX1, and SEPT9, but not SLC5A8, in head and neck squamous cell carcinomas. Genes Chromosomes Cancer 2010; 49:319-26. [PMID: 20029986 DOI: 10.1002/gcc.20742] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy with more than half a million people being diagnosed with the disease annually. Within the last 2 decades, the human papillomavirus (HPV) has been found to be associated with this malignancy. More recently, HPV-infected HNSCC has been found to exhibit higher levels of global DNA methylation. In a recent study, we identified five tumor suppressive genes (IRX1, EBF3, SLC5A8, SEPT9, and FUSSEL18) as frequently methylated in HNSCC biopsies using a global methylation analysis via restriction landmark genomic scanning. In this study, we verify these genes as valid methylation markers in two separate sets of HNSCC specimens. By using the available clinical information linked to the patient specimens, we found a strong association between promoter methylation of FUSSEL18, IRX1, and EBF3 and prior radiation therapy (P < 0.0001) irrespective of HPV status. Also, promoter methylation of FUSSEL18 and SEPTIN9 was found to correlate significantly with exposure to alcohol and tobacco (P = 0.021). Importantly, in this study, we preliminarily show a trend between HPV16 positivity and specific target gene hypermethylation of IRX1, EBF3, SLC5A8, and SEPT9. If replicated in a larger study, the HPV status may be a patient selection biomarker when determining the most efficacious treatment modality for these different subsets of patients (e.g., inclusion or exclusion of epigenetic therapies). Equally notable and independent of HPV status, hypermethylation of the promoters of a subset of these genes in recurrences especially in the setting of prior radiation or in the setting of alcohol and tobacco use might help guide adjunctive inclusion or exclusion or epigenetic therapy.
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Affiliation(s)
- Kristi L Bennett
- Genomic Medicine Institute Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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45
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Salgado R, Servitje O, Gallardo F, Vermeer MH, Ortiz-Romero PL, Karpova MB, Zipser MC, Muniesa C, García-Muret MP, Estrach T, Salido M, Sánchez-Schmidt J, Herrera M, Romagosa V, Suela J, Ferreira BI, Cigudosa JC, Barranco C, Serrano S, Dummer R, Tensen CP, Solé F, Pujol RM, Espinet B. Oligonucleotide Array-CGH Identifies Genomic Subgroups and Prognostic Markers for Tumor Stage Mycosis Fungoides. J Invest Dermatol 2010; 130:1126-35. [DOI: 10.1038/jid.2009.306] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Bennett KL, Romigh T, Eng C. Disruption of transforming growth factor-beta signaling by five frequently methylated genes leads to head and neck squamous cell carcinoma pathogenesis. Cancer Res 2010; 69:9301-5. [PMID: 19934318 DOI: 10.1158/0008-5472.can-09-3073] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is an aggressive cancer with low survival rates in advanced stages. To facilitate timely diagnosis and improve outcome, early detection markers (e.g., DNA methylation) are crucial for timely cancer diagnosis. In a recent publication, an epigenome-wide screen revealed a set of genes that are commonly methylated and downregulated in head and neck cancers (SEPT9, SLC5A8, FUSSEL18, EBF3, and IRX1). Interestingly, these candidates are potentially involved in the transforming growth factor-beta (TGF-beta) signaling pathway, which is often disrupted in HNSCC. Therefore, we sought to determine coordinated epigenetic silencing of these candidate genes in HNSCC as potential key disruptors of TGF-beta signaling, which could ultimately result in HNSCC progression. Through immunoprecipitation studies, all five of the investigated candidate genes were found to interact with components of the TGF-beta pathway. Overexpression of SLC5A8, EBF3, and IRX1 resulted in decreased mitotic activity and increased apoptosis. In addition, EBF3 was found to increase p21 promoter activity, and SMAD2 significantly increased IRX1 promoter activity. These findings are significant because they reveal a set of genes that interact with components of the TGF-beta pathway, and their silencing via methylation in HNSCC results in coordinated decrease in apoptosis, increased proliferation, and decreased differentiation.
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Affiliation(s)
- Kristi L Bennett
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
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McEwen GK, Goode DK, Parker HJ, Woolfe A, Callaway H, Elgar G. Early evolution of conserved regulatory sequences associated with development in vertebrates. PLoS Genet 2009; 5:e1000762. [PMID: 20011110 PMCID: PMC2781166 DOI: 10.1371/journal.pgen.1000762] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 11/10/2009] [Indexed: 01/22/2023] Open
Abstract
Comparisons between diverse vertebrate genomes have uncovered thousands of highly conserved non-coding sequences, an increasing number of which have been shown to function as enhancers during early development. Despite their extreme conservation over 500 million years from humans to cartilaginous fish, these elements appear to be largely absent in invertebrates, and, to date, there has been little understanding of their mode of action or the evolutionary processes that have modelled them. We have now exploited emerging genomic sequence data for the sea lamprey, Petromyzon marinus, to explore the depth of conservation of this type of element in the earliest diverging extant vertebrate lineage, the jawless fish (agnathans). We searched for conserved non-coding elements (CNEs) at 13 human gene loci and identified lamprey elements associated with all but two of these gene regions. Although markedly shorter and less well conserved than within jawed vertebrates, identified lamprey CNEs are able to drive specific patterns of expression in zebrafish embryos, which are almost identical to those driven by the equivalent human elements. These CNEs are therefore a unique and defining characteristic of all vertebrates. Furthermore, alignment of lamprey and other vertebrate CNEs should permit the identification of persistent sequence signatures that are responsible for common patterns of expression and contribute to the elucidation of the regulatory language in CNEs. Identifying the core regulatory code for development, common to all vertebrates, provides a foundation upon which regulatory networks can be constructed and might also illuminate how large conserved regulatory sequence blocks evolve and become fixed in genomic DNA. Recent comparative analyses of vertebrate genomes has resulted in the identification of highly conserved non-coding sequences near genes that coordinate early development. Many of these sequences can activate gene expression and are thought to be important regulatory elements. Surprisingly, a large set of these long, near-identical sequences is found in every jawed vertebrate, including sharks, yet almost completely absent in non-vertebrates. This study looks for this set of sequences in the lamprey, a representative of our most distant vertebrate relatives, in order to determine when and how such a large set of important non-coding regulatory sequences became established in the genome. Although the lamprey divergence is only a little older than the divergence of cartilaginous fish (including sharks), relatively few, and considerably shorter, conserved non-coding sequences are identifiable. Nevertheless, these shorter lamprey sequences are capable of driving gene expression in a precise spatial pattern in zebrafish embryos in the same way as the equivalent human elements. This analysis has shed light on the emergence of these regulatory sequences during early vertebrate evolution, at a time of whole-genome duplications and considerable morphological variation, consistent with a role for these sequences in directing gene regulatory networks for vertebrate development.
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Affiliation(s)
- Gayle K. McEwen
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Debbie K. Goode
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Hugo J. Parker
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Adam Woolfe
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Heather Callaway
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Greg Elgar
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
- * E-mail:
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48
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Abstract
Alterations in various developmental pathways are common themes in cancer. The early B-cell factors (EBF) are a family of four highly conserved DNA-binding transcription factors with an atypical zinc-finger and helix-loop-helix motif. They are involved in the differentiation and maturation of several cell lineages including B-progenitor lymphoblasts, neuronal precursors, and osteoblast progenitors. During B-cell development, EBF1 is required for the expression of Pax5, an essential factor for the production of antibody-secreting cells. Accumulating evidence indicates that genomic deletion of the EBF1 gene contributes to the pathogenesis, drug resistance, and relapse of B-progenitor acute lymphoblastic leukemia (ALL). Epigenetic silencing and genomic deletion of the EBF3 locus in chromosome 10q are very frequent in glioblastoma (GBM). Strikingly, the frequency of EBF3 loss in GBM is similar to that of the loss of Pten, a key suppressor of gliomagenesis. Cancer-specific somatic mutations were detected in EBF3 in GBM and in both EBF1 and EBF3 in pancreatic ductal adenocarcinoma. These missense mutations occur in the DNA-binding domain or the conserved IPT/TIG domain, suggesting that they might disrupt the functions of these two proteins. Functional studies revealed that EBF3 represses the expression of genes required for cell proliferation [e.g., cyclins and cyclin-dependent kinases (CDK)] and survival (e.g., Mcl-1 and Daxx) but activates those involved in cell cycle arrest (e.g., p21 and p27), leading to growth suppression and apoptosis. Therefore, EBFs represent new tumor suppressors whose inactivation blocks normal development and contributes to tumorigenesis of diverse types of human cancer.
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Affiliation(s)
- Daiqing Liao
- Department of Anatomy and Cell Biology, UF Shands Cancer Center, University of Florida, Gainesville, FL 32611-3633, USA.
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49
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Eilon T, Barash I. Distinct gene-expression profiles characterize mammary tumors developed in transgenic mice expressing constitutively active and C-terminally truncated variants of STAT5. BMC Genomics 2009; 10:231. [PMID: 19450255 PMCID: PMC2689279 DOI: 10.1186/1471-2164-10-231] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 05/18/2009] [Indexed: 01/06/2023] Open
Abstract
Background Stat5 is a latent transcription factor that regulates essential growth and survival functions in normal cells. Constitutive activity of Stat5 and the involvement of its C-terminally truncated variant have been implicated in blood cell malignancies and mammary or breast cancer. To distinguish the individual contributions of the Stat5 variants to mammary tumorigenesis, global gene-expression profiling was performed on transgenic STAT5-induced tumors. Results We identified 364 genes exhibiting differential expression in mammary tumors developed in transgenic mice expressing constitutively active STAT5 (STAT5ca) vs. its C-terminally truncated variant (STAT5Δ750). These genes mediate established Stat5 effects on cellular processes such as proliferation and cell death, as well as yet-unrelated homeostatic features, e.g. carbohydrate metabolism. A set of 14 genes linked STAT5Δ750 expression to the poorly differentiated carcinoma phenotype and STAT5ca to the highly differentiated papillary adenocarcinoma. Specifically affected genes exhibited differential expression in an individual tumor set vs. its counterpart and the intact mammary gland: 50 genes were specifically affected by STAT5ca, and 94% of these were downregulated, the latter involved in suppression of tumor suppressors and proliferation antagonistics. This substantial downregulation distinguishes the STAT5ca-induced tumorigenic consequences from the relatively equal effect of the STAT5Δ750 on gene expression, which included significant elevation in the expression of oncogenes and growth mediators. STAT5Δ750 mRNA expression was below detection levels in the tumors and the amount of STAT5ca transcript was not correlated with the expression of its specifically affected genes. Interestingly, we identified several groups of three to eight genes affected by a particular STAT5 variant with significant correlated expression at distinct locations in the clustergram. Conclusion The different gene-expression profiles in mammary tumors caused by the STAT5Δ750 and STAT5ca variants, corroborated by the absence of a direct link to transgenic STAT5 expression, imply distinct metabolic consequences for their oncogenic role which probably initiate early in tumor development. Tumorigenesis may involve induction of growth factor and oncogenes by STAT5Δ750 or suppression of tumor suppressors and growth antagonists by STAT5ca. The list of genes specifically affected by the STAT5 variants may provide a basis for the development of a marker set for their distinct oncogenic role.
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Affiliation(s)
- Tali Eilon
- Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, Israel.
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Mao L, Wang H, Wang Y, Ju S, Wu Y, Jin X. Increased Expression of Early B-cell Factor 3 in Human Hepatocellular Carcinoma and the Effect of EBF3 Overexpression on HepG2 Cell Cycling. Lab Med 2009. [DOI: 10.1309/lm3db8xpeud4htui] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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