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Zhang D, Wu D, Zhang S, Zhang M, Zhou Y, An X, Li Q, Li Z. Transcription factor AP-2 gamma affects porcine early embryo development by regulating epigenetic modification. Reprod Biomed Online 2024; 49:103772. [PMID: 38749801 DOI: 10.1016/j.rbmo.2023.103772] [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: 09/08/2023] [Revised: 11/09/2023] [Accepted: 12/12/2023] [Indexed: 09/15/2024]
Abstract
RESEARCH QUESTION What is the role and mechanism of action of transcription factor AP-2 gamma (TFAP2C) in porcine early embryo development? DESIGN TFAP2C siRNA were injected into porcine oocytes, which subsequently underwent IVF. Different stages of embryos were collected for RNA sequencing, quantitative polymerase chain reaction, immunofluorescence staining to explore the affects in gene expression and epigenetic modification. Porcine fetal fibroblasts were transfected with siRNA, and cells were collected for chromatin immunoprecipitation and dual luciferase reporter assays. RESULTS The deficiency of TFAP2C led to disorders in early embryonic development; 1208 genes were downregulated and 792 genes were upregulated in TFAP2C knockdown (TFAP2C-KD) embryos. The expression of epigenetic modification enzymes KDM5B, SETD2 were significantly elevated in the TFAP2C-KD group (P < 0.001). Meanwhile, the modification levels of H3K4me3 and H3K4me2 were significantly decreased (P = 0.0021, P = 0.0029), and H3K36me3 and DNA methylation were significantly increased in TFAP2C-KD group (P = 0.0045, P = 0.0025). DNMT1 was mainly expressed in nuclei in the TFAP2C-KD group (P = 0.0103). In addition, TFAP2C could bind to the promoter region of SETD2, and the mutation of the TFAP2C binding site resulted in increased activity of SETD2 promoter (P < 0.001). CONCLUSIONS The knockdown of TFAP2C affects early embryonic development by regulating histone modification and DNA methylation.
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Affiliation(s)
- Daoyu Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun 130021, China
| | - Di Wu
- First Hospital, Jilin University, Changchun 130021, China
| | - Sheng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun 130021, China
| | - Meng Zhang
- The Jackson Laboratory for Genome Technology, 10 Discovery Drive Farmington, Connecticut, 06932, USA
| | - Yongfeng Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun 130021, China
| | - Xinglan An
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun 130021, China
| | - Qi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun 130021, China
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun 130021, China..
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Abou Kors T, Meier M, Mühlenbruch L, Betzler AC, Oliveri F, Bens M, Thomas J, Kraus JM, Doescher J, von Witzleben A, Hofmann L, Ezic J, Huber D, Benckendorff J, Barth TFE, Greve J, Schuler PJ, Brunner C, Blackburn JM, Hoffmann TK, Ottensmeier C, Kestler HA, Rammensee HG, Walz JS, Laban S. Multi-omics analysis of overexpressed tumor-associated proteins: gene expression, immunopeptide presentation, and antibody response in oropharyngeal squamous cell carcinoma, with a focus on cancer-testis antigens. Front Immunol 2024; 15:1408173. [PMID: 39136024 PMCID: PMC11317303 DOI: 10.3389/fimmu.2024.1408173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024] Open
Abstract
Introduction The human leukocyte antigen complex (HLA) is essential for inducing specific immune responses to cancer by presenting tumor-associated peptides (TAP) to T cells. Overexpressed tumor associated antigens, mainly cancer-testis antigens (CTA), are outlined as essential targets for immunotherapy in oropharyngeal squamous cell carcinoma (OPSCC). This study assessed the degree to which presentation, gene expression, and antibody response (AR) of TAP, mainly CTA, are correlated in OPSCC patients to evaluate their potential as immunotherapy targets. Materials and methods Snap-frozen tumor (NLigand/RNA=40), healthy mucosa (NRNA=6), and healthy tonsils (NLigand=5) samples were obtained. RNA-Seq was performed using Illumina HiSeq 2500/NovaSeq 6000 and whole exome sequencing (WES) utilizing NextSeq500. HLA ligands were isolated from tumor tissue using immunoaffinity purification, UHPLC, and analyzed by tandem MS. Antibodies were measured in serum (NAb=27) utilizing the KREX™ CT262 protein array. Data analysis focused on 312 proteins (KREX™ CT262 panel + overexpressed self-proteins). Results 183 and 94 of HLA class I and II TAP were identified by comparative profiling with healthy tonsils. Genes from 26 TAP were overexpressed in tumors compared to healthy mucosa (LFC>1; FDR<0.05). Low concordance (r=0.25; p<0.0001) was found between upregulated mRNA and class I TAP. The specific mode of correlation of TAP was found to be dependent on clinical parameters. A lack of correlation was observed both between mRNA and class II TAP, as well as between class II tumor-unique TAP (TAP-U) presentation and antibody response (AR) levels. Discussion This study demonstrates that focusing exclusively on gene transcript levels fails to capture the full extent of TAP presentation in OPSCC. Furthermore, our findings reveal that although CTA are presented at relatively low levels, a few CTA TAP-U show potential as targets for immunotherapy.
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Affiliation(s)
- Tsima Abou Kors
- Department of Otorhinolaryngology and Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Matthias Meier
- Department of Otorhinolaryngology and Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Lena Mühlenbruch
- Department of Immunology, Institute for Cell Biology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, Eberhard Karls University and University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen, Germany
| | - Annika C. Betzler
- Department of Otorhinolaryngology and Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
- Core Facility Immune Monitoring, Ulm University Medical Center, Ulm, Germany
| | - Franziska Oliveri
- Department of Otorhinolaryngology and Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Martin Bens
- Core Facility Next Generation Sequencing, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Jaya Thomas
- Cancer Sciences Unit, University of Southampton, Faculty of Medicine, Southampton, United Kingdom
| | - Johann M. Kraus
- Institute of Medical Systems Biology, Faculty of Medicine, Ulm University, Ulm, Germany
| | - Johannes Doescher
- Department of Otorhinolaryngology and Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
- Department of Otolaryngology, Augsburg University Hospital, Augsburg, Germany
| | - Adrian von Witzleben
- Department of Otorhinolaryngology and Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Linda Hofmann
- Department of Otorhinolaryngology and Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Jasmin Ezic
- Department of Otorhinolaryngology and Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Diana Huber
- Department of Otorhinolaryngology and Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | | | | | - Jens Greve
- Department of Otorhinolaryngology and Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Patrick J. Schuler
- Department of Otorhinolaryngology and Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
- Surgical Oncology Ulm, i2SOUL Consortium, Ulm, Germany
| | - Cornelia Brunner
- Department of Otorhinolaryngology and Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
- Core Facility Immune Monitoring, Ulm University Medical Center, Ulm, Germany
| | - Jonathan M. Blackburn
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Thomas K. Hoffmann
- Department of Otorhinolaryngology and Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
- Surgical Oncology Ulm, i2SOUL Consortium, Ulm, Germany
| | - Christian Ottensmeier
- Institute of Systems, Molecular and Integrative Biology, Liverpool Head and Neck Center, University of Liverpool, Faculty of Medicine, Liverpool, United Kingdom
| | - Hans A. Kestler
- Institute of Medical Systems Biology, Faculty of Medicine, Ulm University, Ulm, Germany
- Surgical Oncology Ulm, i2SOUL Consortium, Ulm, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen, Germany
| | - Juliane S. Walz
- Department of Peptide-based Immunotherapy, Eberhard Karls University and University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Simon Laban
- Department of Otorhinolaryngology and Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
- Surgical Oncology Ulm, i2SOUL Consortium, Ulm, Germany
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Simonenko SY, Bogdanova DA, Kuldyushev NA. Emerging Roles of Vitamin B 12 in Aging and Inflammation. Int J Mol Sci 2024; 25:5044. [PMID: 38732262 PMCID: PMC11084641 DOI: 10.3390/ijms25095044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Vitamin B12 (cobalamin) is an essential nutrient for humans and animals. Metabolically active forms of B12-methylcobalamin and 5-deoxyadenosylcobalamin are cofactors for the enzymes methionine synthase and mitochondrial methylmalonyl-CoA mutase. Malfunction of these enzymes due to a scarcity of vitamin B12 leads to disturbance of one-carbon metabolism and impaired mitochondrial function. A significant fraction of the population (up to 20%) is deficient in vitamin B12, with a higher rate of deficiency among elderly people. B12 deficiency is associated with numerous hallmarks of aging at the cellular and organismal levels. Cellular senescence is characterized by high levels of DNA damage by metabolic abnormalities, increased mitochondrial dysfunction, and disturbance of epigenetic regulation. B12 deficiency could be responsible for or play a crucial part in these disorders. In this review, we focus on a comprehensive analysis of molecular mechanisms through which vitamin B12 influences aging. We review new data about how deficiency in vitamin B12 may accelerate cellular aging. Despite indications that vitamin B12 has an important role in health and healthy aging, knowledge of the influence of vitamin B12 on aging is still limited and requires further research.
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Affiliation(s)
- Sergey Yu. Simonenko
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia;
| | - Daria A. Bogdanova
- Division of Immunobiology and Biomedicine, Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Nikita A. Kuldyushev
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia;
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Duan Y, Du Y, Gu Z, Zheng X, Wang C. Expression, Prognostic Value, and Functional Mechanism of the KDM5 Family in Pancreatic Cancer. Front Cell Dev Biol 2022; 10:887385. [PMID: 35493099 PMCID: PMC9043291 DOI: 10.3389/fcell.2022.887385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/24/2022] [Indexed: 12/12/2022] Open
Abstract
Background: The histone lysine demethylase KDM5 family is an important epigenetic state-modifying enzyme family. Increasing evidence supports that epigenetic abnormalities in the KDM5 family are related to multiple cancers in humans. However, the role of the KDM5 family in pancreatic cancer is not clear, and related research is very scarce. Methods: R software, Kaplan–Meier Plotter, cBioPortal, TIMER, LinkedOmics, STRING, Metascape, TISIDB, and the GSCA Lite online tool were utilized for bioinformatics analysis. Results: KDM5A/B/C was significantly overexpressed in many kinds of tumor tissues, including pancreatic adenocarcinoma (PAAD), while the expression of KDM5D was significantly downregulated. The high expression of KDM5A/B/C was related to poor clinical features, such as worse treatment efficacy, higher tumor grade, and more advanced clinical stage. Patients with a family history of breast cancer and melanoma, history of drinking or history chronic pancreatitis were more likely to have KDM5A/B/C gene abnormalities, which were related to a variety of adverse clinical features. The results of gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway analyses of the KDM5 family and its 800 co-expressed genes showed that many gene terms related to cell proliferation, migration and many carcinogenic pathways. Notably, we found that the expression level of KDM5A/B/C was positively correlated with the expression of multiple key driver genes such as KRAS, BRCA1, and BRCA2 etc. In addition, PPI network analysis showed KDM5 family proteins have strong interactions with histone deacetylase family 1 (HDAC1), which could modify the lysines of histone H3, and co-act on many pathways, including the “longevity-regulating pathway” and “Notch signaling pathway”. Moreover, the upregulation of KDM5A/B/C expression was associated with an increase in the infiltration of B cells, CD8+ T cells and other infiltrating immune lymphocytes and the expression levels of immune molecules such as NT5E and CD274. Interestingly, the overexpression of KDM5A/C was also corelated with reduced sensitivity of pancreatic cancer cells to many kinds of pancreatic cancer-targeting or chemotherapeutic drugs, including axitinib and gemcitabine. Conclusion: KDM5 family members may be prognostic markers and new therapeutic targets for patients with pancreatic cancer.
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Wang Y, Ye W, Tian G, Zhang Y. Identification of a new RNA-binding proteins-based signature for prognostic prediction in gastric cancer. Medicine (Baltimore) 2022; 101:e28901. [PMID: 35212295 PMCID: PMC8878810 DOI: 10.1097/md.0000000000028901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/01/2022] [Indexed: 01/04/2023] Open
Abstract
Gastric cancer (GC) is one of the most common cancers with high incidence and mortality worldwide. Recently, RNA-binding proteins (RBPs) have drawn more and more attention for its role in cancer pathophysiology. However, the function and clinical implication of RBPs in GC have not been fully elucidated. RNA sequencing data along with the corresponding clinical information of GC patients were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed RNA-binding proteins (DERBPs) between tumor and normal tissues were identified by "limma" package. Functional enrichment analysis and the protein-protein interaction (PPI) network were harnessed to explore the function and interaction of DERBPs. Next, univariate and multiple Cox regression were applied to screen prognosis-related hub RBPs and to construct a signature for GC. Meanwhile, a nomogram was built on the basis of the independent factors. A total of 296 DERBPs were found, and most of them mainly related to post-transcriptional regulation of RNA and ribonucleoprotein. A PPI network of DERBPs was constructed, consisting of 262 nodes and 2567 edges. A prognostic signature was built depending on 7 prognosis-related hub RBPs that could divide GC patients into high-risk and low-risk groups. Survival analysis showed that high-risk group had a worse prognosis compared with the low-risk group and the time-dependent receiver operating characteristic (ROC) curves suggested that signature existed moderate predictive capacities of survival for GC patients. Similar results were obtained from another independent set GSE62254, confirming the robustness of signature. Besides, the genetic variation and immune heterogeneity differences were identified between the high-risk and low-risk groups by bioinformatics methods. These findings would provide evidence of the effect of RBPs and offer a novel potential biomarker in prognostic prediction and clinical decision for GC.
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Affiliation(s)
- Yuzhi Wang
- Department of Laboratory Medicine, People's Hospital of Deyang City, Deyang, Sichuan, China
| | - Weixia Ye
- Department of Gastroenterology, Luzhou People's Hospital, Luzhou, Sichuan, China
| | - Gang Tian
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yi Zhang
- Department of Blood Transfusion, People's Hospital of Deyang City, Deyang, Sichuan, China
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Cai Q, Gan C, Tang C, Wu H, Gao J. Mechanism and Therapeutic Opportunities of Histone Modifications in Chronic Liver Disease. Front Pharmacol 2021; 12:784591. [PMID: 34887768 PMCID: PMC8650224 DOI: 10.3389/fphar.2021.784591] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/08/2021] [Indexed: 02/05/2023] Open
Abstract
Chronic liver disease (CLD) represents a global health problem, accounting for the heavy burden of disability and increased health care utilization. Epigenome alterations play an important role in the occurrence and progression of CLD. Histone modifications, which include acetylation, methylation, and phosphorylation, represent an essential part of epigenetic modifications that affect the transcriptional activity of genes. Different from genetic mutations, histone modifications are plastic and reversible. They can be modulated pharmacologically without changing the DNA sequence. Thus, there might be chances to establish interventional solutions by targeting histone modifications to reverse CLD. Here we summarized the roles of histone modifications in the context of alcoholic liver disease (ALD), metabolic associated fatty liver disease (MAFLD), viral hepatitis, autoimmune liver disease, drug-induced liver injury (DILI), and liver fibrosis or cirrhosis. The potential targets of histone modifications for translation into therapeutics were also investigated. In prospect, high efficacy and low toxicity drugs that are selectively targeting histone modifications are required to completely reverse CLD and prevent the development of liver cirrhosis and malignancy.
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Affiliation(s)
- Qiuyu Cai
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Can Gan
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Chengwei Tang
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Wu
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Jinhang Gao
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
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Basinski BW, Balikov DA, Aksu M, Li Q, Rao RC. Ubiquitous Chromatin Modifiers in Congenital Retinal Diseases: Implications for Disease Modeling and Regenerative Medicine. Trends Mol Med 2021; 27:365-378. [PMID: 33573910 DOI: 10.1016/j.molmed.2021.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/11/2022]
Abstract
Retinal congenital malformations known as microphthalmia, anophthalmia, and coloboma (MAC) are associated with alterations in genes encoding epigenetic proteins that modify chromatin. We review newly discovered functions of such chromatin modifiers in retinal development and discuss the role of epigenetics in MAC in humans and animal models. Further, we highlight how advances in epigenomic technologies provide foundational and regenerative medicine-related insights into blinding disorders. Combining knowledge of epigenetics and pluripotent stem cells (PSCs) is a promising avenue because epigenetic factors cooperate with eye field transcription factors (EFTFs) to direct PSC fate - a foundation for congenital retinal disease modeling and cell therapy.
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Affiliation(s)
- Brian W Basinski
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel A Balikov
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA
| | - Michael Aksu
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA
| | - Qiang Li
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA
| | - Rajesh C Rao
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; A. Alfred Taubman Medical Research Institute, University of Michigan, Ann Arbor, MI, USA; Section of Ophthalmology, Surgery Service, Veterans Administration Ann Arbor Healthsystem, Ann Arbor, MI, USA.
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Zhang Y, Guo D. Epigenetic Variation Analysis Leads to Biomarker Discovery in Gastric Adenocarcinoma. Front Genet 2020; 11:551787. [PMID: 33363566 PMCID: PMC7753064 DOI: 10.3389/fgene.2020.551787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 11/13/2020] [Indexed: 12/24/2022] Open
Abstract
As one of the most common malignant tumors worldwide, gastric adenocarcinoma (GC) and its prognosis are still poorly understood. Various genetic and epigenetic factors have been indicated in GC carcinogenesis. However, a comprehensive and in-depth investigation of epigenetic alteration in gastric cancer is still missing. In this study, we systematically investigated some key epigenetic features in GC, including DNA methylation and five core histone modifications. Data from The Cancer Genome Atlas Program and other studies (Gene Expression Omnibus) were collected, analyzed, and validated with multivariate statistical analysis methods. The landscape of epi-modifications in gastric cancer was described. Chromatin state transition analysis showed a histone marker shift in gastric cancer genome by employing a Hidden-Markov-Model based approach, indicated that histone marks tend to label different sets of genes in GC compared to control. An additive effect of these epigenetic marks was observed by integrated analysis with gene expression data, suggesting epigenetic modifications may cooperatively regulate gene expression. However, the effect of DNA methylation was found more significant without the presence of the five histone modifications in our study. By constructing a PPI network, key genes to distinguish GC from normal samples were identified, and distinct patterns of oncogenic pathways in GC were revealed. Some of these genes can also serve as potential biomarkers to classify various GC molecular subtypes. Our results provide important insights into the epigenetic regulation in gastric cancer and other cancers in general. This study describes the aberrant epigenetic variation pattern in GC and provides potential direction for epigenetic biomarker discovery.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
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Histone Demethylase KDM5B as a Therapeutic Target for Cancer Therapy. Cancers (Basel) 2020; 12:cancers12082121. [PMID: 32751840 PMCID: PMC7465382 DOI: 10.3390/cancers12082121] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 12/14/2022] Open
Abstract
Lysine-specific demethylase 5B (KDM5B/PLU1/JARID1B) is found to be overexpressed in numerous malignancies, including breast, lung, skin, liver, and prostate cancer. Identification of molecules targeting the KDM5B enzyme could be a potential lead in cancer research. Although many KDM5B inhibitors with promising outcomes have been developed so far, its further application in clinical practice is limited due to toxicity and lack of target specificity. Here, we summarize the significance of targeting KDM5B in anticancer therapy and report the molecular docking studies of some known anti-viral agents, decitabine, entecavir, abacavir, penciclovir, and 3-deazaneplanocin A in the catalytic domain JmjC of KDM5B. These studies show the repurposing potential of identified anti-viral agents in cancer therapy.
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Kozako T, Itoh Y, Honda SI, Suzuki T. Epigenetic Control Using Small Molecules in Cancer. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/978-3-030-32857-3_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Zhao M, Wang K, Shang J, Liang Z, Zheng W, Gu J. MiR-345-5p inhibits tumorigenesis of papillary thyroid carcinoma by targeting SETD7. Arch Med Sci 2020; 16:888-897. [PMID: 32542092 PMCID: PMC7286325 DOI: 10.5114/aoms.2019.83823] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/08/2019] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION This study aimed to explore the effects of miR-345-5p on papillary thyroid carcinoma (PTC) and uncover the possible mechanisms. MATERIAL AND METHODS MiR-345-5p and SETD7 mRNA levels were analyzed by quantitative real-time PCR and SETD7 protein level was measured by Western blot. The viability, colony formation ability and apoptosis of PTC cells were measured with CCK-8, soft agar colony formation and flow cytometry assay, respectively. Luciferase reporter assay was used to identify miR-345-5p's target. RESULTS Compared to neighboring normal tissues, there was lower miR-345-5p expression and higher SETD7 expression in PTC tissues. Moreover, Spearman's correlation analysis indicated that there was a negative correlation between miR-345-5p and SETD7 expression in PTC tissues. MiR-345-5p mimics inhibited the viability and colony formation of TPC1 and B-CPAP cells and promoted apoptosis, whereas anti-miR-345-5p promoted PTC cell proliferation and inhibited apoptosis. SETD7 was confirmed to be a direct target of miR-345-5p through target scan analysis and luciferase reporter assay. Additionally, overexpression of SETD7 promoted the viability and colony formation of TPC1 and B-CPAP cells and inhibited apoptosis, whereas downregulation of SETD7 by shRNAs had opposite effects on PTC cells. Furthermore, overexpression of SETD7 attenuated the miR-345-5p induced anti-tumor effects on PTC cells. CONCLUSIONS MiR-345-5p exhibited suppressive effects on PTC via targeting SETD7.
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Affiliation(s)
| | - Kejing Wang
- Corresponding author: Kejing Wang, Department of Head and Neck Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang Province, China, Phone: +86 571 88122233, Fax: +86 571 88122233, E-mail:
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Li W, Wong WH, Jiang R. DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning. Nucleic Acids Res 2019; 47:e60. [PMID: 30869141 PMCID: PMC6547469 DOI: 10.1093/nar/gkz167] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 02/08/2019] [Accepted: 02/28/2019] [Indexed: 12/20/2022] Open
Abstract
Interactions between regulatory elements are of crucial importance for the understanding of transcriptional regulation and the interpretation of disease mechanisms. Hi-C technique has been developed for genome-wide detection of chromatin contacts. However, unless extremely deep sequencing is performed on a very large number of input cells, which is technically limited and expensive, current Hi-C experiments do not have high enough resolution to resolve contacts between regulatory elements. Here, we develop DeepTACT, a bootstrapping deep learning model, to integrate genome sequences and chromatin accessibility data for the prediction of chromatin contacts between regulatory elements. DeepTACT can infer not only promoter-enhancer interactions, but also promoter-promoter interactions. In tests based on promoter capture Hi-C data, DeepTACT shows better performance over existing methods. DeepTACT analysis also identifies a class of hub promoters, which are correlated with transcriptional activation across cell lines, enriched in housekeeping genes, functionally related to fundamental biological processes, and capable of reflecting cell similarity. Finally, the utility of chromatin contacts in the study of human diseases is illustrated by the association of IFNA2 to coronary artery disease via an integrative analysis of GWAS data and interactions predicted by DeepTACT.
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Affiliation(s)
- Wenran Li
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Department of Automation, Tsinghua University, Beijing 100084, China
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Rui Jiang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Department of Automation, Tsinghua University, Beijing 100084, China
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13
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Singh PK. Histone methyl transferases: A class of epigenetic opportunities to counter uncontrolled cell proliferation. Eur J Med Chem 2019; 166:351-368. [PMID: 30735901 DOI: 10.1016/j.ejmech.2019.01.069] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/03/2019] [Accepted: 01/28/2019] [Indexed: 02/06/2023]
Abstract
With each newly disclosed resistance mechanism, management of cancer with previously established targets have become a "failure" oriented approach. Molecular targets such as kinases did initially provide a ray of hope against cancer but with decades of struggle between novel therapeutic agents and more sophisticated resistance mechanisms, they seem to have saturated as anti-cancer targets. Now, with more exhaustive molecular recognition techniques and approaches, epigenetic targets have accessed the centre stage as anti-cancer targets. Accordingly, several classes of epigenetic enzymes are being studied for this role and histone methyltransferases form one such class. They include a class of epigenetic enzymes which transfer methyl group from histone proteins and maintain genetic homeostasis. In cancer, several reports have deduced upregulation of different members of this family according to the tumor environment, establishing them as one of the novel anti-cancer targets. This compilation provides an updated information on several members of histone methyltransferases family as epigenetic targets for developing novel anti-cancer agents.
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Affiliation(s)
- Pankaj Kumar Singh
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India.
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14
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Lee H, Lee HJ, Jung JH, Shin EA, Kim SH. Melatonin disturbs SUMOylation-mediated crosstalk between c-Myc and nestin via MT1 activation and promotes the sensitivity of paclitaxel in brain cancer stem cells. J Pineal Res 2018; 65:e12496. [PMID: 29654697 DOI: 10.1111/jpi.12496] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 04/03/2018] [Indexed: 02/06/2023]
Abstract
Here the underlying antitumor mechanism of melatonin and its potency as a sensitizer of paclitaxel was investigated in X02 cancer stem cells. Melatonin suppressed sphere formation and induced G2/M arrest in X02 cells expressing nestin, CD133, CXCR4, and SOX-2 as biomarkers of stemness. Furthermore, melatonin reduced the expression of CDK2, CDK4, cyclin D1, cyclin E, and c-Myc and upregulated cyclin B1 in X02 cells. Notably, genes of c-Myc related mRNAs were differentially expressed in melatonin-treated X02 cells by microarray analysis. Consistently, melatonin reduced the expression of c-Myc at mRNA and protein levels, which was blocked by MG132. Of note, overexpression of c-Myc increased the expression of nestin, while overexpression of nestin enhanced c-Myc through crosstalk despite different locations, nucleus, and cytoplasm. Interestingly, melatonin attenuated small ubiquitin-related modifier-1 (SUMO-1) more than SUMO-2 or SUMO-3 and disturbed nuclear translocation of nestin for direct binding to c-Myc by SUMOylation of SUMO-1 protein by immunofluorescence and immunoprecipitation. Also, melatonin reduced trimethylated histone H3K4me3 and H3K36me3 more than dimethylation in X02 cells by Western blotting and chromatin immunoprecipitation assay. Notably, melatonin upregulated MT1, not MT2, in X02 cells and melatonin receptor inhibitor luzindole blocked the ability of melatonin to decrease the expression of nestin, p-c-Myc(S62), and c-Myc. Furthermore, melatonin promoted cytotoxicity, sub-G1 accumulation, and apoptotic body formation by Paclitaxcel in X02 cells. Taken together, these findings suggest that melatonin inhibits stemness via suppression of c-Myc, nestin, and histone methylation via MT1 activation and promotes anticancer effect of Paclitaxcel in brain cancer stem cells.
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Affiliation(s)
- Hyemin Lee
- College of Korean Medicine, Kyung Hee University, Seoul, Korea
| | - Hyo-Jung Lee
- College of Korean Medicine, Kyung Hee University, Seoul, Korea
| | - Ji Hoon Jung
- College of Korean Medicine, Kyung Hee University, Seoul, Korea
| | - Eun Ah Shin
- College of Korean Medicine, Kyung Hee University, Seoul, Korea
| | - Sung-Hoon Kim
- College of Korean Medicine, Kyung Hee University, Seoul, Korea
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15
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Little imaginal discs, a Trithorax group member, is a constituent of nuclear matrix of Drosophila melanogaster embryos. J Biosci 2018. [DOI: 10.1007/s12038-018-9773-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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16
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Shen X, Cheng G, Xu L, Wu W, Chen Z, Du P. Jumonji AT-rich interactive domain 1B promotes the growth of pancreatic tumors via the phosphatase and tensin homolog/protein kinase B signaling pathway. Oncol Lett 2018; 16:267-275. [PMID: 29928411 PMCID: PMC6006380 DOI: 10.3892/ol.2018.8618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 01/10/2018] [Indexed: 02/06/2023] Open
Abstract
Jumonji AT-rich interactive domain 1B (JARID1B) has been revealed to remove methyl residues from methylated lysine 4 on histone H3 (H3K4) and has also been reported to be associated with the progression of numerous types of tumor. However, its roles and mechanisms in pancreatic cancer (PC) remain unknown. The present study demonstrated that JARID1B is elevated in PC and is associated with the growth of pancreatic tumors. Overexpression of JARID1B significantly promoted the proliferation in vitro and tumor formation in vivo of PC cells. Furthermore, silencing the expression of JARID1B in other PC cells revealed opposite effects. Further research revealed that JARID1B exerted its function through modulation of H3K4me3 at the phosphatase and tensin homolog (PTEN) gene promoter which was associated with inactive PTEN transcription. To the best of our knowledge, the present study was the first to demonstrate that JARID1B promotes the growth of PC and that targeting JARID1B may be a useful strategy to suppress the progression of PC.
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Affiliation(s)
- Xudong Shen
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Guilian Cheng
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Liming Xu
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Wei Wu
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Zhengrong Chen
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Peng Du
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China,Correspondence to: Mr. Peng Du, Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, Jiangsu 215004, P.R. China, E-mail:
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17
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Dai B, Huang H, Guan F, Zhu G, Xiao Z, Mao B, Su H, Hu Z. Histone demethylase KDM5A inhibits glioma cells migration and invasion by down regulating ZEB1. Biomed Pharmacother 2018; 99:72-80. [PMID: 29324315 DOI: 10.1016/j.biopha.2018.01.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 01/01/2018] [Accepted: 01/03/2018] [Indexed: 01/16/2023] Open
Abstract
Malignant gliomas are highly lethal cancers worldwide as tumor cells infiltrate to healthy brain tissue invariably. Histone demethylase KDM5A as an oncogene or tumor suppressor in cancer still has been controversial. KDM5A may have a different function in different type cancer cells. However, the specific roles of KDM5A in the progression of glioma remain undiscovered. In this study, we found that compared with primary glioma, metastasis glioma had low KDM5A levels. Besides, lower KDM5A levels were linked to poor survival in glioma cancer patients, indicating that KDM5A is a new prognostic marker for glioma cancer. KDM5A knockdown increases the invasive abilities of glioma cancer cells and changes the EMT markers. A mechanism, KDM5A suppressing the expression of ZEB1, and its catalytic activity is indispensable for anti-invasive function. Our study revealed that histone demethylase KDM5A exerts anti-invasiveness function partly through repressing oncogenic ZEB1 expression by mediating H3K4 demethylation. We also demonstrate that ZEB1 play a crucial role in KDM5A induced function. In summary, in this study, we showed that KDM5A has a crucial role in glioma and therefore may serve as a novel therapeutic target and prognostic marker in glioma.
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Affiliation(s)
- Bin Dai
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China
| | - Hui Huang
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China
| | - Feng Guan
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China
| | - Guangtong Zhu
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China
| | - Zhiyong Xiao
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China
| | - Beibei Mao
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China
| | - Haiyang Su
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China
| | - Zhiqiang Hu
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China.
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18
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SETD7 is a prognosis predicting factor of breast cancer and regulates redox homeostasis. Oncotarget 2017; 8:94080-94090. [PMID: 29212211 PMCID: PMC5706857 DOI: 10.18632/oncotarget.21583] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/21/2017] [Indexed: 01/23/2023] Open
Abstract
SETD7 is a methyltransferase that specifically catalyzes the monomethylation of lysine 4 on histone H3. A variety of studies has revealed the role of SETD7 in posttranslational modifications of non-histone proteins. However, the prognostic value of SETD7 on breast cancer and the ability of SETD7 of regulating intrinsic redox homeostasis has never been investigated. In this study, using The Cancer Genome Atlas (TCGA) database, we revealed that SETD7 was a potential prognostic marker of breast cancer. Median survival time of patients with low SETD7 expression (18.1 years) was twice than that of SETD7 low-expressed patients (9.5 years). We demonstrated that SETD7 promoted tumor cell proliferation and prevented cell apoptosis and that SETD7 delicately maintained the redox homeostasis through regulating the levels of GSH/GSSG and ROS. Further studies indicated that SETD7 was a positive activator of KEAP1-NRF2 pathway. Using dual luciferase assay, we revealed the role of SETD7 as a transcriptional activator of antioxidant enzymes. Downregulation of SETD7 in MCF7 and MDA-MB-231 cells impaired the expression of antioxidant enzymes and induces imbalance of redox status. Together, we proposed SETD7 as a prognostic marker of breast cancer and a novel antioxidant promoter under oxidative stress in breast cancer.
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19
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Maggi EC, Crabtree JS. Novel targets in the treatment of neuroendocrine tumors: RBP2. INTERNATIONAL JOURNAL OF ENDOCRINE ONCOLOGY 2017. [DOI: 10.2217/ije-2016-0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Retinoblastoma binding protein 2, also known as RBP2, JARID1A or KDM5A, is an H3K4 demethylase implicated in a variety of non-neuroendocrine, and more recently, neuroendocrine tumors (NETs). NETs are tumors that form from neuroendocrine cells in tissues of the GI tract, endocrine pancreas, lung, skin and other tissues. RBP2 is expressed at abnormally high levels in NETs and recent work demonstrates that modulation of RBP2 in vitro and in vivo impacts end points of tumorigenesis. Interestingly, the demethylase activity of RBP2 is not exclusively responsible for these changes, as RBP2's binding partners may mediate its activity in a tissue- or context-dependent manner. Here, we discuss the features of RBP2 and its role in cell cycle regulation, angiogenesis and drug resistance in cancer.
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Affiliation(s)
- Elaine C Maggi
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Judy S Crabtree
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, USA
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20
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Neault M, Couteau F, Bonneau É, De Guire V, Mallette FA. Molecular Regulation of Cellular Senescence by MicroRNAs: Implications in Cancer and Age-Related Diseases. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 334:27-98. [DOI: 10.1016/bs.ircmb.2017.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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21
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Gehling VS, Bellon SF, Harmange JC, LeBlanc Y, Poy F, Odate S, Buker S, Lan F, Arora S, Williamson KE, Sandy P, Cummings RT, Bailey CM, Bergeron L, Mao W, Gustafson A, Liu Y, VanderPorten E, Audia JE, Trojer P, Albrecht BK. Identification of potent, selective KDM5 inhibitors. Bioorg Med Chem Lett 2016; 26:4350-4. [DOI: 10.1016/j.bmcl.2016.07.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/08/2016] [Accepted: 07/09/2016] [Indexed: 12/26/2022]
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22
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Tang B, Qi G, Tang F, Yuan S, Wang Z, Liang X, Li B, Yu S, Liu J, Huang Q, Wei Y, Zhai R, Lei B, Yu H, Jiao X, He S. JARID1B promotes metastasis and epithelial-mesenchymal transition via PTEN/AKT signaling in hepatocellular carcinoma cells. Oncotarget 2016; 6:12723-39. [PMID: 25909289 PMCID: PMC4494969 DOI: 10.18632/oncotarget.3713] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 03/10/2015] [Indexed: 01/02/2023] Open
Abstract
JARID1B is a member of the family of JmjC domain-containing proteins that removes methyl residues from methylated lysine 4 on histone H3 lysine 4 (H3K4). JARID1B has been proposed as an oncogene in many types of tumors; however, its role and underlying mechanisms in hepatocellular carcinoma (HCC) remain unknown. Here we show that JARID1B is elevated in HCC and its expression level is positively correlated with metastasis. In addition Kaplan-Meier survival analysis showed that high expression of JARID1B was associated with decreased overall survival of HCC patients. Overexpression of JARID1B in HCC cells increased proliferation, epithelial-mesenchymal transition, migration and invasion in vitro, and enhanced tumorigenic and metastatic capacities in vivo. In contrast, silencing JARID1B in aggressive and invasive HCC cells inhibited these processes. Mechanistically, we found JARID1B exerts its function through modulation of H3K4me3 at the PTEN gene promoter, which was associated with inactive PTEN transcription. PTEN overexpression blocked JARID1B-driven proliferation, EMT, and metastasis. Our results, for the first time, portray a pivotal role of JARID1B in stimulating metastatic behaviors of HCC cells. Targeting JARID1B may thus be a useful strategy to impede HCC cell invasion and metastasis.
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Affiliation(s)
- Bo Tang
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Guangying Qi
- Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China.,Department of Pathology and Physiopathology, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Fang Tang
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Shengguang Yuan
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Zhenran Wang
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Xingsi Liang
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Bo Li
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Shuiping Yu
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Jie Liu
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Qi Huang
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Yangchao Wei
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Run Zhai
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Biao Lei
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Hongping Yu
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical College, Guilin, Guangxi, People's Republic of China
| | - Xingyuan Jiao
- Department of General Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Songqing He
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
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23
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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24
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Gajan A, Barnes VL, Liu M, Saha N, Pile LA. The histone demethylase dKDM5/LID interacts with the SIN3 histone deacetylase complex and shares functional similarities with SIN3. Epigenetics Chromatin 2016; 9:4. [PMID: 26848313 PMCID: PMC4740996 DOI: 10.1186/s13072-016-0053-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/14/2016] [Indexed: 01/01/2023] Open
Abstract
Background Regulation of gene expression by histone-modifying enzymes is essential to control cell fate decisions and developmental processes. Two histone-modifying enzymes, RPD3, a deacetylase, and dKDM5/LID, a demethylase, are present in a single complex, coordinated through the SIN3 scaffold protein. While the SIN3 complex has been demonstrated to have functional histone deacetylase activity, the role of the demethylase dKDM5/LID as part of the complex has not been investigated. Results Here, we analyzed the developmental and transcriptional activities of dKDM5/LID in relation to SIN3. Knockdown of either Sin3A or lid resulted in decreased cell proliferation in S2 cells and wing imaginal discs. Conditional knockdown of either Sin3A or lid resulted in flies that displayed wing developmental defects. Interestingly, overexpression of dKDM5/LID rescued the wing developmental defect due to reduced levels of SIN3 in female flies, indicating a major role for dKDM5/LID in cooperation with SIN3 during development. Together, these observed phenotypes strongly suggest that dKDM5/LID as part of the SIN3 complex can impact previously uncharacterized transcriptional networks. Transcriptome analysis revealed that SIN3 and dKDM5/LID regulate many common genes. While several genes implicated in cell cycle and wing developmental pathways were affected upon altering the level of these chromatin factors, a significant affect was also observed on genes required to mount an effective stress response. Further, under conditions of induced oxidative stress, reduction of SIN3 and/or dKDM5/LID altered the expression of a greater number of genes involved in cell cycle-related processes relative to normal conditions. This highlights an important role for SIN3 and dKDM5/LID proteins to maintain proper progression through the cell cycle in environments of cellular stress. Further, we find that target genes are bound by both SIN3 and dKDM5/LID, however, histone acetylation, not methylation, plays a predominant role in gene regulation by the SIN3 complex. Conclusions We have provided genetic evidence to demonstrate functional cooperation between the histone demethylase dKDM5/LID and SIN3. Biochemical and transcriptome data further support functional links between these proteins. Together, the data provide a solid framework for analyzing the gene regulatory pathways through which SIN3 and dKDM5/LID control diverse biological processes in the organism. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0053-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ambikai Gajan
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Valerie L Barnes
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Mengying Liu
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Nirmalya Saha
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
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Mariani L, Lussi YC, Vandamme J, Riveiro A, Salcini AE. The H3K4me3/2 histone demethylase RBR-2 controls axon guidance by repressing the actin-remodeling gene wsp-1. Development 2016; 143:851-63. [PMID: 26811384 DOI: 10.1242/dev.132985] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/16/2016] [Indexed: 12/25/2022]
Abstract
The dynamic regulation of histone modifications is important for modulating transcriptional programs during development. Aberrant H3K4 methylation is associated with neurological disorders, but how the levels and the recognition of this modification affect specific neuronal processes is unclear. Here, we show that RBR-2, the sole homolog of the KDM5 family of H3K4me3/2 demethylases in Caenorhabditis elegans, ensures correct axon guidance by controlling the expression of the actin regulator wsp-1. Loss of rbr-2 results in increased levels of H3K4me3 at the transcriptional start site of wsp-1, with concomitant higher wsp-1 expression responsible for defective axon guidance. In agreement, overexpression of WSP-1 mimics rbr-2 loss, and its depletion restores normal axon guidance in rbr-2 mutants. NURF-1, an H3K4me3-binding protein and member of the chromatin-remodeling complex NURF, is required for promoting aberrant wsp-1 transcription in rbr-2 mutants and its ablation restores wild-type expression of wsp-1 and axon guidance. Thus, our results establish a precise role for epigenetic regulation in neuronal development by demonstrating a functional link between RBR-2 activity, H3K4me3 levels, the NURF complex and the expression of WSP-1.
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Affiliation(s)
- Luca Mariani
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Yvonne C Lussi
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Julien Vandamme
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alba Riveiro
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anna Elisabetta Salcini
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
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Liu X, Secombe J. The Histone Demethylase KDM5 Activates Gene Expression by Recognizing Chromatin Context through Its PHD Reader Motif. Cell Rep 2015; 13:2219-31. [PMID: 26673323 DOI: 10.1016/j.celrep.2015.11.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/05/2015] [Accepted: 10/31/2015] [Indexed: 12/22/2022] Open
Abstract
KDM5 family proteins are critically important transcriptional regulators whose physiological functions in the context of a whole animal remain largely unknown. Using genome-wide gene expression and binding analyses in Drosophila adults, we demonstrate that KDM5 (Lid) is a direct regulator of genes required for mitochondrial structure and function. Significantly, this occurs independently of KDM5's well-described JmjC domain-encoded histone demethylase activity. Instead, it requires the PHD motif of KDM5 that binds to histone H3 that is di- or trimethylated on lysine 4 (H3K4me2/3). Genome-wide, KDM5 binding overlaps with the active chromatin mark H3K4me3, and a fly strain specifically lacking H3K4me2/3 binding shows defective KDM5 promoter recruitment and gene activation. KDM5 therefore plays a central role in regulating mitochondrial function by utilizing its ability to recognize specific chromatin contexts. Importantly, KDM5-mediated regulation of mitochondrial activity is likely to be key in human diseases caused by dysfunction of this family of proteins.
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Affiliation(s)
- Xingyin Liu
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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27
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Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease. Int J Mol Sci 2015; 16:27270-87. [PMID: 26580603 PMCID: PMC4661880 DOI: 10.3390/ijms161126022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/01/2015] [Accepted: 11/04/2015] [Indexed: 11/30/2022] Open
Abstract
Mutations in KDM5C gene are linked to X-linked mental retardation, the syndromic Claes-Jensen-type disease. This study focuses on non-synonymous mutations in the KDM5C ARID domain and evaluates the effects of two disease-associated missense mutations (A77T and D87G) and three not-yet-classified missense mutations (R108W, N142S, and R179H). We predict the ARID domain’s folding and binding free energy changes due to mutations, and also study the effects of mutations on protein dynamics. Our computational results indicate that A77T and D87G mutants have minimal effect on the KDM5C ARID domain stability and DNA binding. In parallel, the change in the free energy unfolding caused by the mutants A77T and D87G were experimentally measured by urea-induced unfolding experiments and were shown to be similar to the in silico predictions. The evolutionary conservation analysis shows that the disease-associated mutations are located in a highly-conserved part of the ARID structure (N-terminal domain), indicating their importance for the KDM5C function. N-terminal residues’ high conservation suggests that either the ARID domain utilizes the N-terminal to interact with other KDM5C domains or the N-terminal is involved in some yet unknown function. The analysis indicates that, among the non-classified mutations, R108W is possibly a disease-associated mutation, while N142S and R179H are probably harmless.
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28
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Huang Y, Chen D, Liu C, Shen W, Ruan Y. Evolution and conservation of JmjC domain proteins in the green lineage. Mol Genet Genomics 2015; 291:33-49. [PMID: 26152513 DOI: 10.1007/s00438-015-1089-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/29/2015] [Indexed: 10/25/2022]
Abstract
Histone modification regulates plant development events by epigenetically silencing or activating gene expression, and histone methylation is regulated by histone lysine methyltransferases (KMTs) and histone lysine demethylases (KDMs). The JmjC domain proteins, an important KDM family, erase methyl marks (CH3-) from histones and play key roles in maintaining homeostasis of histone methylation in vivo. Here, we analyzed 169 JmjC domain proteins from whole genomes of plants ranging from green alga to higher plants together with 36 from two animals (fruit fly and human). The plant JmjC domain proteins were divided into seven groups. Group-I KDM4/JHDM3 and Group-V JMJD6 were found in all the plant species and the other groups were detected mainly in vascular or seed plants. Group-I KDM4/JHDM3 was potentially associated with demethylation of H3K9me2/3, H3K27me2/3, and H3K36me1/2/3, Group-II KDM5A with H3K4me1/2/3, Group-III KDM5B with H3K4me1/2/3 and H3K9me1/2/3, Group-V JMJD6 with H3R2, H4R3, and hydroxylation of H4, and Group-VII KDM3/JHDM2 with H3K9me1/2/3. Group-IV/Group-VI JmjC domain-only A/B proteins were involved in hydroxylation and demethylation of unknown substrate sites. The binding sites for the cofactors Fe(II) and α-ketoglutarate in the JmjC domains also were analyzed. In the α-ketoglutarate binding sites, Thr/Phe/Ser and Lys were conserved and in the Fe(II) binding sites, two His and Glu/Asp were conserved. The results show that JmjC domain proteins are a conserved family in which domain organization and cofactor binding sites have been modified in some species. Our results provide insights into KDM evolution and lay a foundation for functional characterization of KDMs.
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Affiliation(s)
- Yong Huang
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China. .,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, 410128, Changsha, China.
| | - Donghong Chen
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China.,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, 410128, Changsha, China
| | - Chunlin Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, 410128, Changsha, China
| | - Wenhui Shen
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China.,Institut de Biologie Moléculaire Des Plantes Du CNRS, Université de Strasbourg, 12 Rue Du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Ying Ruan
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China. .,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, 410128, Changsha, China. .,Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, 410128, Changsha, China.
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29
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IUGR prevents IGF-1 upregulation in juvenile male mice by perturbing postnatal IGF-1 chromatin remodeling. Pediatr Res 2015; 78:14-23. [PMID: 25826117 DOI: 10.1038/pr.2015.70] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/09/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Intrauterine growth restriction (IUGR) offspring with rapid catch-up growth are at increased risk for early obesity especially in males. Persistent insulin-like growth factor-1 (IGF-1) reduction is an important risk factor. Using a mouse model of maternal hypertension-induced IUGR, we examined IGF-1 levels, promoter DNA methylation, and histone H3 covalent modifications at birth (D1). We additionally investigated whether prenatal perturbations could reset at preadolescence (D21). METHODS IUGR was induced via maternal thromboxane A2-analog infusion in mice. RESULTS IUGR uniformly decreased D1 IGF-1 mRNA and protein levels with reduced promoter 1 (P1) transcription and increased P1 DNA methylation. IUGR males also had increased H3K4ac at exon 5 and 3' distal UTR. At D21, IUGR males continued to have decreased IGF-1 levels, originating from both P1 and P2 with reduced 1A variant. IUGR males also had decreased activation mark of H3K4me3 at P1 compared with sham males. In contrast, D21 IUGR females normalized their IGF-1 levels, in association with an increased activation mark of H3K4me3 at P1 compared with sham females. CONCLUSION IUGR uniformly affected D1 hepatic IGF-1 epigenetic modifications in both sexes. However, at preadolescence, IUGR males are unable to correct for the prenatal reduction possibly due to a more perturbed IGF-1 chromatin structure.
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30
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Huang J, Zhang H, Wang X, Dobbs KB, Yao J, Qin G, Whitworth K, Walters EM, Prather RS, Zhao J. Impairment of preimplantation porcine embryo development by histone demethylase KDM5B knockdown through disturbance of bivalent H3K4me3-H3K27me3 modifications. Biol Reprod 2015; 92:72. [PMID: 25609834 DOI: 10.1095/biolreprod.114.122762] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
KDM5B (JARID1B/PLU1) is a H3K4me2/3 histone demethylase that is implicated in cancer development and proliferation and is also indispensable for embryonic stem cell self-renewal, cell fate, and murine embryonic development. However, little is known about the role of KDM5B during preimplantation embryo development. Here we show that KDM5B is critical to porcine preimplantation development. KDM5B was found to be expressed in a stage-specific manner, consistent with demethylation of H3K4me3, with the highest expression being observed from the 4-cell to the blastocyst stages. Knockdown of KDM5B by morpholino antisense oligonucleotides injection impaired porcine embryo development to the blastocyst stage. The impairment of embryo development might be caused by increased expression of H3K4me3 at the 4-cell and blastocyst stages, which disturbs the balance of bivalent H3K4me3-H3K27me3 modifications at the blastocyst stage. Decreased abundance of H3K27me3 at blastocyst stage activates multiple members of homeobox genes (HOX), which need to be silenced for faithful embryo development. Additionally, the histone demethylase KDM6A was found to be upregulated by knockdown of KDM5B, which indicated it was responsible for the decreased abundance of H3K27me3 at the blastocyst stage. The transcriptional levels of Ten-Eleven Translocation gene family members (TET1, TET2, and TET3) are found to be increased by knockdown of KDM5B, which indicates cross talk between histone modifications and DNA methylation. The studies above indicate that KDM5B is required for porcine embryo development through regulating the balance of bivalent H3K4me3-H3K27me3 modifications.
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Affiliation(s)
- Jiaojiao Huang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Hongyong Zhang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Xianlong Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Kyle B Dobbs
- National Swine Resource and Research Center & Division of Animal Science, University of Missouri, Columbia, Missouri Department of Biology, Northeastern University, Boston, Massachusetts
| | - Jing Yao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Guosong Qin
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Kristin Whitworth
- National Swine Resource and Research Center & Division of Animal Science, University of Missouri, Columbia, Missouri
| | - Eric M Walters
- National Swine Resource and Research Center & Division of Animal Science, University of Missouri, Columbia, Missouri
| | - Randall S Prather
- National Swine Resource and Research Center & Division of Animal Science, University of Missouri, Columbia, Missouri
| | - Jianguo Zhao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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31
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Accari SL, Fisher PR. Emerging Roles of JmjC Domain-Containing Proteins. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 319:165-220. [DOI: 10.1016/bs.ircmb.2015.07.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Vázquez-Martínez ER, Mendoza-Garcés L, Vergara-Castañeda E, Cerbón M. Epigenetic regulation of Progesterone Receptor isoforms: from classical models to the sexual brain. Mol Cell Endocrinol 2014; 392:115-24. [PMID: 24859604 DOI: 10.1016/j.mce.2014.05.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 05/12/2014] [Indexed: 01/29/2023]
Abstract
Progesterone Receptor is a member of the nuclear receptor superfamily, which regulates several functions in both reproductive and non-reproductive tissues. Progesterone Receptor gene encodes for two main isoforms, A and B, and contains two specific promoters with their respective transcription start sites. The mRNA expression of both isoforms is mainly regulated by estrogens and specifically via the Estrogen Receptor Alpha, in a context specific manner. Furthermore, it has been reported in extensive physiological and pathological models that Progesterone Receptor isoforms regulation is related to the epigenetic state of their respective promoters. Epigenetic regulation of Progesterone Receptor isoforms in the brain is a recent and scarcely explored field in neurosciences. This review focuses on the epigenetic mechanisms involved in Progesterone Receptor regulation, emphasizing the implications for the sexual brain. Future directions for research about this important field are also discussed.
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Affiliation(s)
- Edgar Ricardo Vázquez-Martínez
- Departamento de Biología, Facultad de Química, Av Universidad 3000, Universidad Nacional Autónoma de México (UNAM), Coyoacán, 04510, Distrito Federal, México, Mexico
| | - Luciano Mendoza-Garcés
- Instituto Nacional de Geriatría, Periférico Sur 2767, San Jerónimo Lídice, Magdalena Contreras, 10200, Distrito Federal, México, Mexico
| | - Edgar Vergara-Castañeda
- Departamento de Biología, Facultad de Química, Av Universidad 3000, Universidad Nacional Autónoma de México (UNAM), Coyoacán, 04510, Distrito Federal, México, Mexico
| | - Marco Cerbón
- Departamento de Biología, Facultad de Química, Av Universidad 3000, Universidad Nacional Autónoma de México (UNAM), Coyoacán, 04510, Distrito Federal, México, Mexico.
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Wang H, Ji B, Ren H, Meng C. The relationship between lysine 4 on histone H3 methylation levels of alcohol tolerance genes and changes of ethanol tolerance in Saccharomyces cerevisiae. Microb Biotechnol 2014; 7:307-14. [PMID: 24779776 PMCID: PMC4241724 DOI: 10.1111/1751-7915.12121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/31/2013] [Accepted: 01/22/2013] [Indexed: 01/09/2023] Open
Abstract
We evaluated whether epigenetic changes contributed to improve ethanol tolerance in mutant
populations of Saccharomyces cerevisiae (S. cerevisiae). Two
ethanol-tolerant variants of S. cerevisiae were used to evaluate the genetic
stability in the process of stress-free passage cultures. We found that acquired ethanol tolerance
was lost and transcription level of some genes (HSP104, PRO1,
TPS1, and SOD1) closely related to ethanol tolerance decreased
significantly after the 10th passage in ethanol-free medium. Tri-methylation of lysine 4 on histone
H3 (H3K4) enhanced at the promoter of HSP104, PRO1,
TPS1 and SOD1 in ethanol-tolerant variants of S.
cerevisiae was also diminished after tenth passage in stress-free cultures. The ethanol
tolerance was reacquired when exogenous SOD1 transferred in some tolerance-lost
strains. This showed that H3K4 methylation is involved in phenotypic variation with regard to
ethanol tolerance with respect to classic breeding methods used in yeast.
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Affiliation(s)
- Hang Wang
- Department of Bioengineering, College of Biological Science and Biotechnology, Fuzhou University, Fuzhou, Fujian, China
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Ramakrishnan SK, Varshney A, Sharma A, Das BC, Yadava PK. Expression of targeted ribozyme against telomerase RNA causes altered expression of several other genes in tumor cells. Tumour Biol 2014; 35:5539-50. [PMID: 24664581 DOI: 10.1007/s13277-014-1729-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 02/04/2014] [Indexed: 01/11/2023] Open
Abstract
Telomeres are tandem repeat sequences present at chromosome end that are synthesized by RNA-protein enzyme called telomerase. The RNA component (TR) serves as template for telomerase reverse transcriptase (TERT) for generating telomere repeats. TERT is overexpressed in actively dividing cells including cancerous cells, absent in differentiated somatic cells whereas human telomerase RNA (hTR) is present in normal as well as in cancer cells. Telomerase overexpression in cancer cells ensures telomere length maintenance that actually provides proliferative advantage to cells. Stable expression of ribozyme against hTR in HeLa cells results in reduction of hTR levels, telomerase activity, and telomere length which is accompanied by altered cell morphology and expression of several specific cellular genes. The altered genes deduced from differentially display PCR and 2D gel electrophoresis upon hTR knockdown have function in ribosome biogenesis, chromatin modulation, cell cycle control, and p63-dependant pathways. Our observations shows hTR participates in diverse cellular functions other than telomere maintenance, validates as a possible drug targets in p53- and pRB-negative status, and indicated possible cross-talks between telomerase and other cellular pathways.
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Affiliation(s)
- Suresh Kumar Ramakrishnan
- Applied Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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Jeong HM, Kwon MJ, Shin YK. Overexpression of Cancer-Associated Genes via Epigenetic Derepression Mechanisms in Gynecologic Cancer. Front Oncol 2014; 4:12. [PMID: 24551595 PMCID: PMC3912470 DOI: 10.3389/fonc.2014.00012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Accepted: 01/20/2014] [Indexed: 12/15/2022] Open
Abstract
Like other cancers, most gynecologic cancers are caused by aberrant expression of cancer-related genes. Epigenetics is one of the most important gene expression mechanisms, which contribute to cancer development and progression by regulating cancer-related genes. Since the discovery of differential gene expression patterns in cancer cells when compared with normal cells, extensive efforts have been made to explore the origins of abnormal gene expression in cancer. Epigenetics, the study of inheritable changes in gene expression that do not alter DNA sequence is a key area of this research. DNA methylation and histone modification are well-known epigenetic mechanisms, while microRNAs and alternative splicing have recently been identified as important regulators of epigenetic mechanisms. These mechanisms not only affect specific target gene expression but also regulate the functioning of other epigenetic mechanisms. Moreover, these diverse epigenetic regulations occur simultaneously. Epigenetic regulation of gene expression is extraordinarily complicated and all epigenetic mechanisms to be studied at once to determine the exact gene regulation mechanisms. Traditionally, the contribution of epigenetics to cancer is thought to be mediated through the inactivation of tumor suppressor genes expression. But recently, it is arising that some oncogenes or cancer-promoting genes (CPGs) are overexpressed in diverse type of cancers through epigenetic derepression mechanism, such as DNA and histone demethylation. Epigenetic derepression arises from diverse epigenetic changes, and all of these mechanisms actively interact with each other to increase oncogenes or CPGs expression in cancer cell. Oncogenes or CPGs overexpressed through epigenetic derepression can initiate cancer development, and accumulation of these abnormal epigenetic changes makes cancer more aggressive and treatment resistance. This review discusses epigenetic mechanisms involved in the overexpression of oncogenes or CPGs via epigenetic derepression in gynecologic cancers. Therefore, improved understanding of these epigenetic mechanisms will provide new targets for gynecologic cancer treatment.
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Affiliation(s)
- Hae Min Jeong
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University , Seoul , South Korea
| | - Mi Jeong Kwon
- College of Pharmacy, Kyungpook National University , Daegu , South Korea ; Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University , Daegu , South Korea
| | - Young Kee Shin
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University , Seoul , South Korea ; Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul , South Korea ; Advanced Institutes of Convergence Technology , Suwon , South Korea ; Bio-MAX Institute, Seoul National University , Seoul , South Korea
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Alemu EY, Carl JW, Corrada Bravo H, Hannenhalli S. Determinants of expression variability. Nucleic Acids Res 2014; 42:3503-14. [PMID: 24435799 PMCID: PMC3973347 DOI: 10.1093/nar/gkt1364] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The amount of tissue-specific expression variability (EV) across individuals is an essential characteristic of a gene and believed to have evolved, in part, under functional constraints. However, the determinants and functional implications of EV are only beginning to be investigated. Our analyses based on multiple expression profiles in 41 primary human tissues show that a gene’s EV is significantly correlated with a number of features pertaining to the genomic, epigenomic, regulatory, polymorphic, functional, structural and network characteristics of the gene. We found that (i) EV of a gene is encoded, in part, by its genomic context and is further influenced by the epigenome; (ii) strong promoters induce less variable expression; (iii) less variable gene loci evolve under purifying selection against copy number polymorphisms; (iv) genes that encode inherently disordered or highly interacting proteins exhibit lower variability; and (v) genes with less variable expression are enriched for house-keeping functions, while genes with highly variable expression tend to function in development and extra-cellular response and are associated with human diseases. Thus, our analysis reveals a number of potential mediators as well as functional and evolutionary correlates of EV, and provides new insights into the inherent variability in eukaryotic gene expression.
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Affiliation(s)
- Elfalem Y Alemu
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
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37
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Zheng W, Huang Y. The chemistry and biology of the α-ketoglutarate-dependent histone Nε-methyl-lysine demethylases. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00325f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
This review describes the current knowledge of the chemistry and biology of the physiologically and therapeutically important histone/protein Nε-methyl-lysine demethylation reactions catalyzed by the JMJD2 and JARID1 families of the α-ketoglutarate-dependent demethylases.
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Affiliation(s)
- Weiping Zheng
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Yajun Huang
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
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38
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Sinha KM, Zhou X. Genetic and molecular control of osterix in skeletal formation. J Cell Biochem 2013; 114:975-84. [PMID: 23225263 DOI: 10.1002/jcb.24439] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 10/23/2012] [Indexed: 12/16/2022]
Abstract
Osteoblast differentiation is a multi-step process where mesenchymal cells differentiate into osteoblast lineage cells including osteocytes. Osterix (Osx) is an osteoblast-specific transcription factor which activates a repertoire of genes during differentiation of preosteoblasts into mature osteoblasts and osteocytes. The essential role of Osx in the genetic program of bone formation and in bone homeostasis is well established. Osx mutant embryos do not form bone and fail to express osteoblast-specific marker genes. Inactivation of Osx in mice after birth causes multiple skeletal phenotypes including lack of new bone formation, absence of resorption of mineralized cartilage, and defects in osteocyte maturation and function. Since Osx is a major effector in skeletal formation, studies on Osx gained momentum over the last 5-7 years and implicated its important function in tooth formation as well as in healing of bone fractures. This review outlines mouse genetic studies that establish the essential role of Osx in bone and tooth formation as well as in healing of bone fractures. We also discuss the recent advances in regulation of Osx expression, which is under control of a transcriptional network, signaling pathways, and epigenetic regulation. Finally, we summarize important findings on the positive and negative regulation of Osx's transcriptional activity through protein-protein interactions in expression of its target genes during osteoblast differentiation. In particular, the identification of the histone demethylase NO66 as an Osx-interacting protein, which negatively regulates Osx activity opens further avenues in studying epigenetic control of Osx target genes during differentiation and maturation of osteoblasts.
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Affiliation(s)
- Krishna M Sinha
- Department of Endocrine Neoplasia and Hormonal Disorders, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
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39
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Sanfilippo PG, Hewitt AW. Translating the ENCyclopedia Of DNA Elements Project findings to the clinic: ENCODE's implications for eye disease. Clin Exp Ophthalmol 2013; 42:78-83. [PMID: 24433357 DOI: 10.1111/ceo.12150] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 05/05/2013] [Indexed: 12/17/2022]
Abstract
Approximately 10 years after the Human Genome Project unravelled the sequence of our DNA, the ENCyclopedia Of DNA Elements (ENCODE) Project sought to interpret it. Data from the recently completed project have shed new light on the proportion of biologically active human DNA, assigning a biochemical role to much of the sequence previously considered to be 'junk'. Many of these newly catalogued functional elements represent epigenetic mechanisms involved in regulation of gene expression. Analogous to an Ishihara plate, a gene-coding region of DNA (target dots) only comes into context when the non-coding DNA (surrounding dots) is appreciated. In this review we provide an overview of the ENCODE project, discussing the significance of these data for ophthalmic research and eye disease. The novel insights afforded by the ENCODE project will in time allow for the development of new therapeutic strategies in the management of common blinding disorders.
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Affiliation(s)
- Paul G Sanfilippo
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, Melbourne, Australia; Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
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40
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Teng YC, Lee CF, Li YS, Chen YR, Hsiao PW, Chan MY, Lin FM, Huang HD, Chen YT, Jeng YM, Hsu CH, Yan Q, Tsai MD, Juan LJ. Histone demethylase RBP2 promotes lung tumorigenesis and cancer metastasis. Cancer Res 2013; 73:4711-21. [PMID: 23722541 DOI: 10.1158/0008-5472.can-12-3165] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The retinoblastoma binding protein RBP2 (KDM5A) is a histone demethylase that promotes gastric cancer cell growth and is enriched in drug-resistant lung cancer cells. In tumor-prone mice lacking the tumor suppressor gene RB or MEN1, genetic ablation of RBP2 can suppress tumor initiation, but the pathogenic breadth and mechanistic aspects of this effect relative to human tumors have not been defined. Here, we approached this question in the context of lung cancer. RBP2 was overexpressed in human lung cancer tissues where its depletion impaired cell proliferation, motility, migration, invasion, and metastasis. RBP2 oncogenicity relied on its demethylase and DNA-binding activities. RBP2 upregulated expression of cyclins D1 and E1 while suppressing the expression of cyclin-dependent kinase inhibitor p27 (CDKN1B), each contributing to RBP2-mediated cell proliferation. Expression microarray analyses revealed that RBP2 promoted expression of integrin-β1 (ITGB1), which is implicated in lung cancer metastasis. Mechanistic investigations established that RBP2 bound directly to the p27, cyclin D1, and ITGB1 promoters and that exogenous expression of cyclin D1, cyclin E1, or ITGB1 was sufficient to rescue proliferation or migration/invasion, respectively. Taken together, our results establish an oncogenic role for RBP2 in lung tumorigenesis and progression and uncover novel RBP2 targets mediating this role.
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Affiliation(s)
- Yu-Ching Teng
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang, Taipei, 115, Taiwan
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41
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Abstract
Since its discovery more than a decade ago, H3K4 methylation has become synonymous with transcription. We only now have begun to realize that the distinct states of H3K4 methylation have unique distributions and specialized roles in other chromatin-related processes. Here, I discuss recent findings addressing their regulation and functions.
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Affiliation(s)
- Thomas Kusch
- Department of Molecular Biology and Biochemistry; Rutgers, The State University of New Jersey, Nelson Laboratories A233, Piscataway, NJ, USA.
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42
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Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z. Modeling gene expression using chromatin features in various cellular contexts. Genome Biol 2012; 13:R53. [PMID: 22950368 PMCID: PMC3491397 DOI: 10.1186/gb-2012-13-9-r53] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 06/13/2012] [Accepted: 06/19/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Previous work has demonstrated that chromatin feature levels correlate with gene expression. The ENCODE project enables us to further explore this relationship using an unprecedented volume of data. Expression levels from more than 100,000 promoters were measured using a variety of high-throughput techniques applied to RNA extracted by different protocols from different cellular compartments of several human cell lines. ENCODE also generated the genome-wide mapping of eleven histone marks, one histone variant, and DNase I hypersensitivity sites in seven cell lines. RESULTS We built a novel quantitative model to study the relationship between chromatin features and expression levels. Our study not only confirms that the general relationships found in previous studies hold across various cell lines, but also makes new suggestions about the relationship between chromatin features and gene expression levels. We found that expression status and expression levels can be predicted by different groups of chromatin features, both with high accuracy. We also found that expression levels measured by CAGE are better predicted than by RNA-PET or RNA-Seq, and different categories of chromatin features are the most predictive of expression for different RNA measurement methods. Additionally, PolyA+ RNA is overall more predictable than PolyA- RNA among different cell compartments, and PolyA+ cytosolic RNA measured with RNA-Seq is more predictable than PolyA+ nuclear RNA, while the opposite is true for PolyA- RNA. CONCLUSIONS Our study provides new insights into transcriptional regulation by analyzing chromatin features in different cellular contexts.
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Affiliation(s)
- Xianjun Dong
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Melissa C Greven
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, 318 Campus Drive, Stanford, CA 94304, USA
| | - Sarah Djebali
- Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - James B Brown
- Department of Statistics, University of California, Berkeley, 367 Evans Hall, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chao Cheng
- Computational Biology and Bioinformatics Program, Yale University, 266 Whitney Ave, New Haven, CT 06511, USA
| | - Thomas R Gingeras
- Cold Spring Harbor Laboratory, Genome Center, Woodbury, New York 11797, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics Program, Yale University, 266 Whitney Ave, New Haven, CT 06511, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - Ewan Birney
- Vertebrate Genomics Group, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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43
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Stem cells in ectodermal development. J Mol Med (Berl) 2012; 90:783-90. [PMID: 22570240 PMCID: PMC3383946 DOI: 10.1007/s00109-012-0908-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/24/2012] [Accepted: 04/29/2012] [Indexed: 11/06/2022]
Abstract
Tissue-specific stem cells sustain organs for a lifetime through self-renewal and generating differentiated progeny. Although tissue stem cells are established during organogenesis, the precise origin of most adult stem cells in the developing embryo is unclear. Mammalian skin is one of the best-studied epithelial systems containing stem cells to date, however the origin of most of the stem cell populations found in the adult epidermis is unknown. Here, we try to recapitulate the emergence and genesis of an ectodermal stem cell during development until the formation of an adult skin. We ask whether skin stem cells share key transcriptional regulators with their embryonic counterparts and discuss whether embryonic-like stem cells may persist through to adulthood in vivo.
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44
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Li Y, Zhong XB. Epigenetic regulation of developmental expression of Cyp2d genes in mouse liver. Acta Pharm Sin B 2012. [DOI: 10.1016/j.apsb.2012.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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45
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Abstract
The histone demethylases are a relatively novel family of histone-modifying enzymes. Their gene expression suggests that each of the subfamily members may have a discrete role in cell function. The KDM5 family of H3K4 histone demethylases has four members. Each family member has a distinct cellular role, including KDM5a, which is a tumor suppressor (Christensen et al. Cell 128: 1063-1076, 2007); KDM5b, which is an oncogene (Dey et al. Mol Cell Biol 17: 5312-5327, 2008); and KDM5c (Iwase et al. Cell 128: 1077-1088, 2007), which is expressed in terminally differentiated populations. To properly analyze how these enzymes are regulated, we interrogate their bioactivity in ES cells (ESCs) and during neural differentiation of ESCs. We evaluate the bioactivity from both affinity-purified complexes and reconstituted complexes and directly in the cell. These assays have allowed us to define a set of factors that regulate the KDM5 family of histone demethylases.
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46
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Islam ABMMK, Richter WF, Jacobs LA, Lopez-Bigas N, Benevolenskaya EV. Co-regulation of histone-modifying enzymes in cancer. PLoS One 2011; 6:e24023. [PMID: 21886846 PMCID: PMC3160334 DOI: 10.1371/journal.pone.0024023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 07/28/2011] [Indexed: 01/25/2023] Open
Abstract
Cancer is characterized by aberrant patterns of expression of multiple genes. These major shifts in gene expression are believed to be due to not only genetic but also epigenetic changes. The epigenetic changes are communicated through chemical modifications, including histone modifications. However, it is unclear whether the binding of histone-modifying proteins to genomic regions and the placing of histone modifications efficiently discriminates corresponding genes from the rest of the genes in the human genome. We performed gene expression analysis of histone demethylases (HDMs) and histone methyltransferases (HMTs), their target genes and genes with relevant histone modifications in normal and tumor tissues. Surprisingly, this analysis revealed the existence of correlations in the expression levels of different HDMs and HMTs. The observed HDM/HMT gene expression signature was specific to particular normal and cancer cell types and highly correlated with target gene expression and the expression of genes with histone modifications. Notably, we observed that trimethylation at lysine 4 and lysine 27 separated preferentially expressed and underexpressed genes, which was strikingly different in cancer cells compared to normal cells. We conclude that changes in coordinated regulation of enzymes executing histone modifications may underlie global epigenetic changes occurring in cancer.
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Affiliation(s)
- Abul B. M. M. K. Islam
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Research Unit on Biomedical Informatics, Department of Experimental Health and Sciences, PRBB, Universitat Pompeu Fabra, Barcelona, Spain
| | - William F. Richter
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Laura A. Jacobs
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Nuria Lopez-Bigas
- Research Unit on Biomedical Informatics, Department of Experimental Health and Sciences, PRBB, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elizaveta V. Benevolenskaya
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
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47
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Svotelis A, Bianco S, Madore J, Huppé G, Nordell-Markovits A, Mes-Masson AM, Gévry N. H3K27 demethylation by JMJD3 at a poised enhancer of anti-apoptotic gene BCL2 determines ERα ligand dependency. EMBO J 2011; 30:3947-61. [PMID: 21841772 DOI: 10.1038/emboj.2011.284] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 07/18/2011] [Indexed: 12/16/2022] Open
Abstract
Chromatin represents a repressive barrier to the process of ligand-dependent transcriptional activity of nuclear receptors. Here, we show that H3K27 methylation imposes ligand-dependent regulation of the oestrogen receptor α (ERα)-dependent apoptotic response via Bcl-2 in breast cancer cells. The activation of BCL2 transcription is dependent on the simultaneous inactivation of the H3K27 methyltransferase, EZH2, and the demethylation of H3K27 at a poised enhancer by the ERα-dependent recruitment of JMJD3 in hormone-dependent breast cancer cells. We also provide evidence that this pathway is modified in cells resistant to anti-oestrogen (AE), which constitutively express BCL2. We show that the lack of H3K27 methylation at BCL2 regulatory elements due to the inactivation of EZH2 by the HER2 pathway leads to this constitutive activation of BCL2 in these AE-resistant cells. Our results describe a mechanism in which the epigenetic state of chromatin affects ligand dependency during ERα-regulated gene expression.
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Affiliation(s)
- Amy Svotelis
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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48
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Stratmann A, Haendler B. The histone demethylase JARID1A regulates progesterone receptor expression. FEBS J 2011; 278:1458-69. [DOI: 10.1111/j.1742-4658.2011.08058.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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49
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Islam ABMMK, Richter WF, Lopez-Bigas N, Benevolenskaya EV. Selective targeting of histone methylation. Cell Cycle 2011; 10:413-24. [PMID: 21270517 DOI: 10.4161/cc.10.3.14705] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Histones are post-translationally modified by multiple histone-modifying enzymes, which in turn influences gene expression. Much of the work in the field to date has focused on genetic, biochemical and structural characterization of these enzymes. The most recent genome-wide methods provide insights into specific recruitment of histone-modifying enzymes in vivo and, therefore, onto mechanisms of establishing a differential expression pattern. Here we focus on the recruitment mechanisms of the enzymes involved in the placement of two contrasting histone marks, histone H3 lysine 4 (H3K4) methylation and histone H3 lysine 27 (H3K27) methylation. We describe distribution of their binding sites and show that recruitment of different histone-modifying proteins can be coordinated, opposed, or alternating. Specifically, genomic sites of the H3K4 histone demethylase KDM5A become accessible to its homolog KDM5B in cells with a lowered KDM5A level. The currently available data on recruitment of H3K4/H3K27 modifying enzymes suggests that the formed protein complexes are targeted in a sequential and temporal manner, but that additional, still unknown, interactions contribute to targeting specificity.
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Affiliation(s)
- Abul B M M K Islam
- Research Unit on Biomedical Informatics, Department of Experimental Health and Sciences, PRBB, Universitat Pompeu Fabra, Barcelona, Spain
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50
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Beshiri ML, Islam A, DeWaal DC, Richter WF, Love J, Lopez-Bigas N, Benevolenskaya EV. Genome-wide analysis using ChIP to identify isoform-specific gene targets. J Vis Exp 2010:2101. [PMID: 20644511 PMCID: PMC3156076 DOI: 10.3791/2101] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Recruitment of transcriptional and epigenetic factors to their targets is a key step in their regulation. Prominently featured in recruitment are the protein domains that bind to specific histone modifications. One such domain is the plant homeodomain (PHD), found in several chromatin-binding proteins. The epigenetic factor RBP2 has multiple PHD domains, however, they have different functions (Figure 4). In particular, the C-terminal PHD domain, found in a RBP2 oncogenic fusion in human leukemia, binds to trimethylated lysine 4 in histone H3 (H3K4me3)1. The transcript corresponding to the RBP2 isoform containing the C-terminal PHD accumulates during differentiation of promonocytic, lymphoma-derived, U937 cells into monocytes2. Consistent with both sets of data, genome-wide analysis showed that in differentiated U937 cells, the RBP2 protein gets localized to genomic regions highly enriched for H3K4me33. Localization of RBP2 to its targets correlates with a decrease in H3K4me3 due to RBP2 histone demethylase activity and a decrease in transcriptional activity. In contrast, two other PHDs of RBP2 are unable to bind H3K4me3. Notably, the C-terminal domain PHD of RBP2 is absent in the smaller RBP2 isoform4. It is conceivable that the small isoform of RBP2, which lacks interaction with H3K4me3, differs from the larger isoform in genomic location. The difference in genomic location of RBP2 isoforms may account for the observed diversity in RBP2 function. Specifically, RBP2 is a critical player in cellular differentiation mediated by the retinoblastoma protein (pRB). Consistent with these data, previous genome-wide analysis, without distinction between isoforms, identified two distinct groups of RBP2 target genes: 1) genes bound by RBP2 in a manner that is independent of differentiation; 2) genes bound by RBP2 in a differentiation-dependent manner. To identify differences in localization between the isoforms we performed genome-wide location analysis by ChIP-Seq. Using antibodies that detect both RBP2 isoforms we have located all RBP2 targets. Additionally we have antibodies that only bind large, and not small RBP2 isoform (Figure 4). After identifying the large isoform targets, one can then subtract them from all RBP2 targets to reveal the targets of small isoform. These data show the contribution of chromatin-interacting domain in protein recruitment to its binding sites in the genome.
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Affiliation(s)
- Michael L Beshiri
- Department of Biochemistry and Molecular Genetics, University of Illinois Chicago - UIC, USA
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