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Moccia A, Martin DM. Nervous system development and disease: A focus on trithorax related proteins and chromatin remodelers. Mol Cell Neurosci 2018; 87:46-54. [PMID: 29196188 PMCID: PMC5828982 DOI: 10.1016/j.mcn.2017.11.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 11/08/2017] [Accepted: 11/27/2017] [Indexed: 01/12/2023] Open
Abstract
The nervous system comprises many different cell types including neurons, glia, macrophages, and immune cells, each of which is defined by specific patterns of gene expression, morphology, function, and anatomical location. Establishment of these complex and highly regulated cell fates requires spatial and temporal coordination of gene transcription. Open chromatin (euchromatin) allows transcription factors to interact with gene promoters and activate lineage specific genes, whereas closed chromatin (heterochromatin) remains inaccessible to transcriptional activation. Changes in the genome-wide distribution of euchromatin accompany transcriptional plasticity that allows the diversity of mature cell fates to be generated during development. In the past 20years, many new genes and gene families have been identified to participate in regulation of chromatin accessibility. These genes include chromatin remodelers that interact with Trithorax group (TrxG) and Polycomb group (PcG) proteins to activate or repress transcription, respectively. Here we review the role of TrxG proteins in neurodevelopment and disease.
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Affiliation(s)
- Amanda Moccia
- Department of Human Genetics, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Donna M Martin
- Department of Human Genetics, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Pediatrics and Communicable Diseases, The University of Michigan Medical School, Ann Arbor, MI 48109, United States.
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52
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Nasser MM, Mehdipour P. Exploration of Involved Key Genes and Signaling Diversity in Brain Tumors. Cell Mol Neurobiol 2018; 38:393-419. [PMID: 28493234 DOI: 10.1007/s10571-017-0498-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 05/02/2017] [Indexed: 02/05/2023]
Abstract
Brain tumors are becoming a major cause of death. The classification of brain tumors has gone through restructuring with regard to some criteria such as the presence or absence of a specific genetic alteration in the 2016 central nervous system World Health Organization update. Two categories of genes with a leading role in tumorigenesis and cancer induction include tumor suppressor genes and oncogenes; tumor suppressor genes are inactivated through a variety of mechanisms that result in their loss of function. As for the oncogenes, overexpression and amplification are the most common mechanisms of alteration. Important cell cycle genes such as p53, ATM, cyclin D2, and Rb have shown altered expression patterns in different brain tumors such as meningioma and astrocytoma. Some genes in signaling pathways have a role in brain tumorigenesis. These pathways include hedgehog, EGFR, Notch, hippo, MAPK, PI3K/Akt, and WNT signaling. It has been shown that telomere length in some brain tumor samples is shortened compared to that in normal cells. As the shortening of telomere length triggers chromosome instability early in brain tumors, it could lead to initiation of cancer. On the other hand, telomerase activity was positive in some brain tumors. It is suggestive that telomere length and telomerase activity are important diagnostic markers in brain tumors. This review focuses on brain tumors with regard to the status of oncogenes, tumor suppressors, cell cycle genes, and genes in signaling pathways as well as the role of telomere length and telomerase in brain tumors.
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Affiliation(s)
- Mojdeh Mahdian Nasser
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Parvin Mehdipour
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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53
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Johnsen JI, Dyberg C, Fransson S, Wickström M. Molecular mechanisms and therapeutic targets in neuroblastoma. Pharmacol Res 2018; 131:164-176. [PMID: 29466695 DOI: 10.1016/j.phrs.2018.02.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/13/2018] [Accepted: 02/14/2018] [Indexed: 12/20/2022]
Abstract
Neuroblastoma is the most common extracranical tumor of childhood and the most deadly tumor of infancy. It is characterized by early age onset and high frequencies of metastatic disease but also the capacity to spontaneously regress. Despite intensive therapy, the survival for patients with high-risk neuroblastoma and those with recurrent or relapsed disease is low. Hence, there is an urgent need to develop new therapies for these patient groups. The molecular pathogenesis based on high-throughput omics technologies of neuroblastoma is beginning to be resolved which have given the opportunity to develop personalized therapies for high-risk patients. Here we discuss the potential of developing targeted therapies against aberrantly expressed molecules detected in sub-populations of neuroblastoma patients and how these selected targets can be drugged in order to overcome treatment resistance, improve survival and quality of life for these patients and also the possibilities to transfer preclinical research into clinical testing.
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Affiliation(s)
- John Inge Johnsen
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital Solna, 171 77 Stockholm, Sweden.
| | - Cecilia Dyberg
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital Solna, 171 77 Stockholm, Sweden
| | - Susanne Fransson
- Department of Pathology and Genetics, Sahlgrenska Academy at the University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Malin Wickström
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital Solna, 171 77 Stockholm, Sweden
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54
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Durinck K, Speleman F. Epigenetic regulation of neuroblastoma development. Cell Tissue Res 2018; 372:309-324. [PMID: 29350283 DOI: 10.1007/s00441-017-2773-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/16/2017] [Indexed: 02/07/2023]
Abstract
In recent years, technological advances have enabled a detailed landscaping of the epigenome and the mechanisms of epigenetic regulation that drive normal cell function, development and cancer. Rather than merely a structural entity to support genome compaction, we now look at chromatin as a very dynamic and essential constellation that is actively participating in the tight orchestration of transcriptional regulation as well as DNA replication and repair. The unique feature of chromatin flexibility enabling fast switches towards more or less restricted epigenetic cellular states is, not surprisingly, intimately connected to cancer development and treatment resistance, and the central role of epigenetic alterations in cancer is illustrated by the finding that up to 50% of all mutations across cancer entities affect proteins controlling the chromatin status. We summarize recent insights into epigenetic rewiring underlying neuroblastoma (NB) tumor formation ranging from changes in DNA methylation patterns and mutations in epigenetic regulators to global effects on transcriptional regulatory circuits that involve key players in NB oncogenesis. Insights into the disruption of the homeostatic epigenetic balance contributing to developmental arrest of sympathetic progenitor cells and subsequent NB oncogenesis are rapidly growing and will be exploited towards the development of novel therapeutic strategies to increase current survival rates of patients with high-risk NB.
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Affiliation(s)
- Kaat Durinck
- Center for Medical Genetics, Ghent University, Ghent, Belgium.
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium
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55
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Bokhari Y, Arodz T. QuaDMutEx: quadratic driver mutation explorer. BMC Bioinformatics 2017; 18:458. [PMID: 29065872 PMCID: PMC5655866 DOI: 10.1186/s12859-017-1869-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/16/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Somatic mutations accumulate in human cells throughout life. Some may have no adverse consequences, but some of them may lead to cancer. A cancer genome is typically unstable, and thus more mutations can accumulate in the DNA of cancer cells. An ongoing problem is to figure out which mutations are drivers - play a role in oncogenesis, and which are passengers - do not play a role. One way of addressing this question is through inspection of somatic mutations in DNA of cancer samples from a cohort of patients and detection of patterns that differentiate driver from passenger mutations. RESULTS We propose QuaDMutEx, a method that incorporates three novel elements: a new gene set penalty that includes non-linear penalization of multiple mutations in putative sets of driver genes, an ability to adjust the method to handle slow- and fast-evolving tumors, and a computationally efficient method for finding gene sets that minimize the penalty, through a combination of heuristic Monte Carlo optimization and exact binary quadratic programming. Compared to existing methods, the proposed algorithm finds sets of putative driver genes that show higher coverage and lower excess coverage in eight sets of cancer samples coming from brain, ovarian, lung, and breast tumors. CONCLUSIONS Superior ability to improve on both coverage and excess coverage on different types of cancer shows that QuaDMutEx is a tool that should be part of a state-of-the-art toolbox in the driver gene discovery pipeline. It can detect genes harboring rare driver mutations that may be missed by existing methods. QuaDMutEx is available for download from https://github.com/bokhariy/QuaDMutEx under the GNU GPLv3 license.
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Affiliation(s)
- Yahya Bokhari
- Department of Computer Science, School of Engineering, Virginia Commonwealth University, 401 W. Main St., Richmond, 23284, VA, USA
| | - Tomasz Arodz
- Department of Computer Science, School of Engineering, Virginia Commonwealth University, 401 W. Main St., Richmond, 23284, VA, USA. .,Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, 23284, VA, USA.
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56
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A systems medicine approach for finding target proteins affecting treatment outcomes in patients with non-Hodgkin lymphoma. PLoS One 2017; 12:e0183969. [PMID: 28892521 PMCID: PMC5593188 DOI: 10.1371/journal.pone.0183969] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 08/15/2017] [Indexed: 02/07/2023] Open
Abstract
Autoantibody profiling with a systems medicine approach can help identify critical dysregulated signaling pathways (SPs) in cancers. In this way, immunoglobulins G (IgG) purified from the serum samples of 92 healthy controls, 10 pre-treated (PR) non-Hodgkin lymphoma (NHL) patients, and 20 NHL patients who underwent chemotherapy (PS) were screened with a phage-displayed random peptide library. Protein-protein interaction networks of the PR and PS groups were analyzed and visualized by Gephi. The results indicated AXIN2, SENP2, TOP2A, FZD6, NLK, HDAC2, HDAC1, and EHMT2, in addition to CAMK2A, PLCG1, PLCG2, GRM5, GRIN2B, GRIN2D, CACNA2D3, and SPTAN1 as hubs in 11 and 7 modules of PR and PS networks, respectively. PR- and PS-specific hubs were evaluated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome databases. The PR-specific hubs were involved in Wnt SP, signaling by Notch1 in cancer, telomere maintenance, and transcriptional misregulation. In contrast, glutamate receptor SP, Fc receptor-related pathways, growth factors-related SPs, and Wnt SP were statistically significant enriched pathways, based on the pathway analysis of PS hubs. The results revealed that the most PR-specific proteins were associated with events involved in tumor development, while chemotherapy in the PS group was associated with side effects of drugs and/or cancer recurrence. As the findings demonstrated, PR- and PS-specific proteins in this study can be promising therapeutic targets in future studies.
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57
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Pisansky MT, Young AE, O'Connor MB, Gottesman II, Bagchi A, Gewirtz JC. Mice lacking the chromodomain helicase DNA-binding 5 chromatin remodeler display autism-like characteristics. Transl Psychiatry 2017; 7:e1152. [PMID: 28608855 PMCID: PMC5537637 DOI: 10.1038/tp.2017.111] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 04/20/2017] [Indexed: 12/12/2022] Open
Abstract
Although autism spectrum disorders (ASDs) share a core set of nosological features, they exhibit substantial genetic heterogeneity. A parsimonious hypothesis posits that dysregulated epigenetic mechanisms represent common pathways in the etiology of ASDs. To investigate this hypothesis, we generated a novel mouse model resulting from brain-specific deletion of chromodomain helicase DNA-binding 5 (Chd5), a chromatin remodeling protein known to regulate neuronal differentiation and a member of a gene family strongly implicated in ASDs. RNA sequencing of Chd5-/- mouse forebrain tissue revealed a preponderance of changes in expression of genes important in cellular development and signaling, sociocommunicative behavior and ASDs. Pyramidal neurons cultured from Chd5-/- cortex displayed alterations in dendritic morphology. Paralleling ASD nosology, Chd5-/- mice exhibited abnormal sociocommunicative behavior and a strong preference for familiarity. Chd5-/- mice further showed deficits in responding to the distress of a conspecific, a mouse homolog of empathy. Thus, dysregulated chromatin remodeling produces a pattern of transcriptional, neuronal and behavioral effects consistent with the presentation of ASDs.
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Affiliation(s)
- M T Pisansky
- Graduate Program in Neuroscience University of Minnesota —Twin Cities, Minneapolis, MN, USA
| | - A E Young
- Department of Psychology, University of Minnesota —Twin Cities, Minneapolis, MN, USA
| | - M B O'Connor
- Department of Genetics, Cell Biology, and Development, University of Minnesota —Twin Cities, Minneapolis, MN, USA
| | - I I Gottesman
- Department of Psychology, University of Minnesota —Twin Cities, Minneapolis, MN, USA
| | - A Bagchi
- Department of Genetics, Cell Biology, and Development, University of Minnesota —Twin Cities, Minneapolis, MN, USA
| | - J C Gewirtz
- Department of Psychology, University of Minnesota —Twin Cities, Minneapolis, MN, USA
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58
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Heidari N, Abroun S, Bertacchini J, Vosoughi T, Rahim F, Saki N. Significance of Inactivated Genes in Leukemia: Pathogenesis and Prognosis. CELL JOURNAL 2017; 19:9-26. [PMID: 28580304 PMCID: PMC5448318 DOI: 10.22074/cellj.2017.4908] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/14/2017] [Indexed: 11/04/2022]
Abstract
Epigenetic and genetic alterations are two mechanisms participating in leukemia, which can inactivate genes involved in leukemia pathogenesis or progression. The purpose of this review was to introduce various inactivated genes and evaluate their possible role in leukemia pathogenesis and prognosis. By searching the mesh words "Gene, Silencing AND Leukemia" in PubMed website, relevant English articles dealt with human subjects as of 2000 were included in this study. Gene inactivation in leukemia is largely mediated by promoter's hypermethylation of gene involving in cellular functions such as cell cycle, apoptosis, and gene transcription. Inactivated genes, such as ASPP1, TP53, IKZF1 and P15, may correlate with poor prognosis in acute lymphoid leukemia (ALL), chronic lymphoid leukemia (CLL), chronic myelogenous leukemia (CML) and acute myeloid leukemia (AML), respectively. Gene inactivation may play a considerable role in leukemia pathogenesis and prognosis, which can be considered as complementary diagnostic tests to differentiate different leukemia types, determine leukemia prognosis, and also detect response to therapy. In general, this review showed some genes inactivated only in leukemia (with differences between B-ALL, T-ALL, CLL, AML and CML). These differences could be of interest as an additional tool to better categorize leukemia types. Furthermore; based on inactivated genes, a diverse classification of Leukemias could represent a powerful method to address a targeted therapy of the patients, in order to minimize side effects of conventional therapies and to enhance new drug strategies.
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Affiliation(s)
- Nazanin Heidari
- Health Research Institute, Thalassemia and Hemoglobinopathy Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Saeid Abroun
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Jessika Bertacchini
- Signal Transduction Unit, Department of Surgery, Medicine, Dentistry and Morphology, University of Modena and Reggio Emilia, Modena, Italy
| | - Tina Vosoughi
- Health Research Institute, Thalassemia and Hemoglobinopathy Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Fakher Rahim
- Health Research Institute, Thalassemia and Hemoglobinopathy Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Najmaldin Saki
- Health Research Institute, Thalassemia and Hemoglobinopathy Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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59
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Su M, Guo J, Huang J. Meta-analysis of the correlation between the rs17401966 polymorphism in kinesin family member 1B and susceptibility to hepatitis B virus related hepatocellular carcinoma. Clin Mol Hepatol 2017; 23:138-146. [PMID: 28427253 PMCID: PMC5497661 DOI: 10.3350/cmh.2016.0083] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 02/09/2017] [Accepted: 02/14/2017] [Indexed: 01/02/2023] Open
Abstract
Background/Aims The association between the kinesin family member 1B (KIF1B) gene polymorphism and the risk of hepatitis B virus-related hepatocellular carcinoma (HCC) has been investigated in many peer-reviewed studies. However, scholars have failed to replicate these results in validation tests. The purpose of the present study was to explore whether the KIF1B rs17401966 polymorphism was associated with susceptibility to HCC. Methods The results of case-controlled studies on the correlation between the KIF1B rs17401966 polymorphism and HCC susceptibility were collected using Google Scholar and the EMBASE, PubMed and CNKI databases. Based on inclusion and exclusion criteria, 5 papers with a total of 12 cohorts were included in this study. Results The 12 cohorts were integrated, and the results showed that the rs17401966 polymorphism reduced the risk for HCC under the allele, heterozygous, homozygous, and dominant models but not under the additive or recessive models. Moreover, the merged results showed strong heterogeneity, and the cumulative meta-analysis results were unreliable. A genetic differentiation analysis of the 12 cohorts found different degrees of genetic differentiation between the 5 cohorts in Zhang et al.’s study and the cohorts in the other studies. We further divided the 12 study cohorts into 2 subgroups based on fixation index value; however, the results of that analysis were inconsistent. Conclusions The results of this meta-analysis were not able to verify the association between the KIF1B rs1740199 polymorphism and HCC risk. Therefore, a well-designed, large-scale, multicenter validation study is needed to confirm the relationship.
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Affiliation(s)
- Mingkuan Su
- Department of Laboratory Medicine, Mindong Hospital Affiliated to Fujian Medical University, Fuan, Fujian, China
| | - Jianfeng Guo
- Department of Laboratory Medicine, Mindong Hospital Affiliated to Fujian Medical University, Fuan, Fujian, China
| | - Jiancheng Huang
- Department of Laboratory Medicine, Mindong Hospital Affiliated to Fujian Medical University, Fuan, Fujian, China
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Baykara O, Tansarikaya M, Bulut P, Demirkaya A, Buyru N. CHD5 is a potential tumor suppressor in non small cell lung cancer (NSCLC). Gene 2017; 618:65-68. [PMID: 28400267 DOI: 10.1016/j.gene.2017.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/17/2017] [Accepted: 04/07/2017] [Indexed: 01/17/2023]
Abstract
Lung cancer is one of the deadliest types of cancers and genetic and epigenetic alterations play major roles in its development. Chromodomain (CHD) protein family acts in chromatin organization, regulation of transcription and also genomic stability and cancer prevention. Although CHD5, a member of this family was shown to contribute to major cellular events and functions as a tumor suppressor gene in various types of cancer, it is not clear whether CHD5 plays a role in lung carcinogenesis. The aim of this study was to investigate the possible role of CHD5 in progression of non-small cell lung cancer (NSCLC). Expression levels of CHD5 gene in 59 tumor and corresponding non-cancerous lung tissue samples were analyzed by qRT-PCR and the methylation status of the promoter region was investigated by methylation specific PCR (MS-PCR). The Akt phosphorylation levels were investigated by Western Blot (WB). CHD5 was down-regulated in 17 (39.5%) and up-regulated in 24 (55.8%) of tumor specimens. Even though the promoter of CHD5 was hypermethylated in 8 patients, it was not found associated with CHD5 gene expression (p=0.08). Akt phosphorylation was increased in 14 (53.8%) and decreased in 12 (46.2%) of the samples but no significant association was found between p-Akt phosphorylation and CHD5 expression (p=0.67). We suggest that CHD5 may act as a tumor suppressor gene in NSCLC.
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Affiliation(s)
- Onur Baykara
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Medical Biology and Genetics, Istanbul 34098, Turkey
| | - Merve Tansarikaya
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Medical Biology and Genetics, Istanbul 34098, Turkey
| | - Pelin Bulut
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Medical Biology and Genetics, Istanbul 34098, Turkey
| | - Ahmet Demirkaya
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Thoracic Surgery, Istanbul 34098, Turkey
| | - Nur Buyru
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Medical Biology and Genetics, Istanbul 34098, Turkey.
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Mills AA. The Chromodomain Helicase DNA-Binding Chromatin Remodelers: Family Traits that Protect from and Promote Cancer. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026450. [PMID: 28096241 DOI: 10.1101/cshperspect.a026450] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A plethora of mutations in chromatin regulators in diverse human cancers is emerging, attesting to the pivotal role of chromatin dynamics in tumorigenesis. A recurrent theme is inactivation of the chromodomain helicase DNA-binding (CHD) family of proteins-ATP-dependent chromatin remodelers that govern the cellular machinery's access to DNA, thereby controlling fundamental processes, including transcription, proliferation, and DNA damage repair. This review highlights what is currently known about how genetic and epigenetic perturbation of CHD proteins and the pathways that they regulate set the stage for cancer, providing new insight for designing more effective anti-cancer therapies.
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Affiliation(s)
- Alea A Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724
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62
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Molecular mechanisms involved in gliomagenesis. Brain Tumor Pathol 2017; 34:1-7. [DOI: 10.1007/s10014-017-0278-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 01/12/2017] [Indexed: 10/20/2022]
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63
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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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64
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Runx3 and Cell Fate Decisions in Pancreas Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 962:333-352. [PMID: 28299667 DOI: 10.1007/978-981-10-3233-2_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The RUNX family transcription factors are critical regulators of development and frequently dysregulated in cancer. RUNX3, the least well characterized of the three family members, has been variously described as a tumor promoter or suppressor, sometimes with conflicting results and opinions in the same cancer and likely reflecting a complex role in oncogenesis. We recently identified RUNX3 expression as a crucial determinant of the predilection for pancreatic ductal adenocarcinoma (PDA) cells to proliferate locally or promulgate throughout the body. High RUNX3 expression induces the production and secretion of soluble factors that support metastatic niche construction and stimulates PDA cells to migrate and invade, while simultaneously suppressing proliferation through increased expression of cell cycle regulators such as CDKN1A/p21 WAF1/CIP1 . RUNX3 expression and function are coordinated by numerous transcriptional and post-translational inputs, and interactions with diverse cofactors influence whether the resulting RUNX3 complexes enact tumor suppressive or tumor promoting programs. Understanding these exquisitely context-dependent tumor cell behaviors has the potential to inform clinical decision-making including the most appropriate timing and sequencing of local vs. systemic therapies.
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Abstract
In this chapter we summarize the pros and cons of the notion that Runx3 is a major tumor suppressor gene (TSG). Inactivation of TSGs in normal cells provides a viability/growth advantage that contributes cell-autonomously to cancer. More than a decade ago it was suggested that RUNX3 is involved in gastric cancer development, a postulate extended later to other epithelial cancers portraying RUNX3 as a major TSG. However, evidence that Runx3 is not expressed in normal gastric and other epithelia has challenged the RUNX3-TSG paradigm. In contrast, RUNX3 is overexpressed in a significant fraction of tumor cells in various human epithelial cancers and its overexpression in pancreatic cancer cells promotes their migration, anchorage-independent growth and metastatic potential. Moreover, recent high-throughput quantitative genome-wide studies on thousands of human samples of various tumors and new investigations of the role of Runx3 in mouse cancer models have unequivocally demonstrated that RUNX3 is not a bona fide cell-autonomous TSG. Importantly, accumulating data demonstrated that RUNX3 functions in control of immunity and inflammation, thereby indirectly influencing epithelial tumor development.
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Sun X, Xiao D, Xu T, Yuan Y. miRNA-24-3p promotes cell proliferation and regulates chemosensitivity in head and neck squamous cell carcinoma by targeting CHD5. Future Oncol 2016; 12:2701-2712. [PMID: 27513190 DOI: 10.2217/fon-2016-0179] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Aim: To investigate the role of miR-24-3p in tumorigenesis and chemosensitivity in head and neck squamous cell carcinoma (HNSCC). Methods: Growth rate and colony formation assays were performed after transfection with miR-24-3p mimic and inhibitor in cultured SCC-15 cells, followed by a CellTiter-Glo® assay. Western blot and luciferase assays were performed to investigate the direct target of miR-24-3p. Xenograft mouse model was used to evaluate combinatorial effects of miR-24-3p inhibitor and 5-fluorouracil. Results & conclusion: Inhibition of miR-24-3p reduced cell proliferation, colony formation efficiency and reversed chemoresistance in HNSCC cells. CHD5 is the direct target of miR-24-3p which is required for the regulatory role of miR-24-3p in chemoresistance. miR-24-3p may represent a new therapeutic target for the improvement of clinical outcome in HNSCC.
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Affiliation(s)
- Xiaofeng Sun
- Department of Stomatology, The Second People’s Hospital of Wuxi, 68 Zhong Shan Road, Wuxi 214002, Jiangsu, PR China
| | - Dajiang Xiao
- Department of Otolaryngology, The Second People’s Hospital of Wuxi, 68 Zhong Shan Road, Wuxi 214002, Jiangsu, PR China
| | - Ting Xu
- Department of Otolaryngology, The Second People’s Hospital of Wuxi, 68 Zhong Shan Road, Wuxi 214002, Jiangsu, PR China
| | - Yuan Yuan
- Department of Otolaryngology, The Second People’s Hospital of Wuxi, 68 Zhong Shan Road, Wuxi 214002, Jiangsu, PR China
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Ma Z, Song J, Liu S, Han L, Chen Y, Wang Y, Yu C, Hou L. Decreased expression of the CHD5 gene and its clinicopathological significance in breast cancer: Correlation with aberrant DNA methylation. Oncol Lett 2016; 12:4021-4026. [PMID: 27895765 DOI: 10.3892/ol.2016.5147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 08/09/2016] [Indexed: 12/23/2022] Open
Abstract
Chromodomain helicase DNA binding protein 5 (CHD5) has been identified as a tumor suppressor in mouse models. Downregulation of CHD5 gene expression is frequently observed in breast cancer cells and tissues. This may be explained by deletions or other mutations; however, alternative mechanisms require investigation. Therefore, the present study evaluated whether CHD5 aberrant methylation has a role in primary breast tumors. A total of 389 patients with primary breast cancer (including 252 paraffin-embedded specimens and 137 fresh-frozen samples) were enrolled in the present study. In the current study, reverse transcription-polymerase chain reaction (RT-PCR) and nested-methylation-specific PCR were used to analyze the mRNA expression and promoter methylation of CHD5 genes in a large cohort of breast cancer patients, and to investigate their associations with the clinicopathological features of tumors. CHD5 expression was significantly suppressed in breast cancer tissues compared with normal breast tissues when analyzed by RT-PCR. Furthermore, DNA methylation of CHD5 was more prevalent in breast tumors than in normal tissues. CHD5 mRNA levels correlated with the degree of CHD5 methylation in breast cancer tissues. Clinicopathological correlation analysis revealed that CHD5 promoter methylation was associated with estrogen receptor and progesterone receptor status. Thus, downregulation of CHD5, mediated by abnormal methylation, may contribute to the development and progression of breast cancer.
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Affiliation(s)
- Zhongliang Ma
- Department of Breast Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Jinlian Song
- Department of Laboratory Medicine, The Affiliated Qingdao Women and Children's Hospital of Qingdao, Qingdao, Shandong 266034, P.R. China
| | - Simin Liu
- Department of PET Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Linlin Han
- Department of Pediatrics, Jinan Children's Hospital, Jinan, Shandong 250022, P.R. China
| | - Yangping Chen
- Department of Laboratory Medicine, The Affiliated Qingdao Women and Children's Hospital of Qingdao, Qingdao, Shandong 266034, P.R. China
| | - Yaqiu Wang
- Department of Laboratory Medicine, The Affiliated Qingdao Women and Children's Hospital of Qingdao, Qingdao, Shandong 266034, P.R. China
| | - Chundong Yu
- Department of Laboratory Medicine, The Affiliated Qingdao Women and Children's Hospital of Qingdao, Qingdao, Shandong 266034, P.R. China
| | - Lin Hou
- Department of Biochemistry, Medical College, Qingdao University, Qingdao, Shandong 266021, P.R. China
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Abstract
SUMMARYEpigenetic changes are present in all human cancers and are now known to cooperate with genetic alterations to drive the cancer phenotype. These changes involve DNA methylation, histone modifiers and readers, chromatin remodelers, microRNAs, and other components of chromatin. Cancer genetics and epigenetics are inextricably linked in generating the malignant phenotype; epigenetic changes can cause mutations in genes, and, conversely, mutations are frequently observed in genes that modify the epigenome. Epigenetic therapies, in which the goal is to reverse these changes, are now one standard of care for a preleukemic disorder and form of lymphoma. The application of epigenetic therapies in the treatment of solid tumors is also emerging as a viable therapeutic route.
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Affiliation(s)
- Stephen B Baylin
- Cancer Biology Program, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21287
| | - Peter A Jones
- Van Andel Research Institute, Grand Rapids, Michigan 49503
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69
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Och W, Kulbacki K, Szostak B, Sikorska B, Zakrzewska M, Szmuda T, Liberski PP, Budzisz T. The molecular pattern of histopathological progression to anaplastic meningioma – A case report. Neurol Neurochir Pol 2016; 50:288-93. [DOI: 10.1016/j.pjnns.2016.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 02/28/2016] [Accepted: 03/23/2016] [Indexed: 11/16/2022]
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70
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Du Z, Li L, Huang X, Jin J, Huang S, Zhang Q, Tao Q. The epigenetic modifier CHD5 functions as a novel tumor suppressor for renal cell carcinoma and is predominantly inactivated by promoter CpG methylation. Oncotarget 2016; 7:21618-30. [PMID: 26943038 PMCID: PMC5008310 DOI: 10.18632/oncotarget.7822] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/29/2016] [Indexed: 12/31/2022] Open
Abstract
Renal cell carcinoma (RCC) is the most common urological cancer with steadily increasing incidence. A series of tumor suppressor genes (TSGs) have been identified methylated in RCC as potential epigenetic biomarkers. We identified a 1p36.3 TSG candidate CHD5 as a methylated target in RCC through epigenome study. As the role of CHD5 in RCC pathogenesis remains elusive, we further studied its expression and molecular functions in RCC cells. We found that CHD5 was broadly expressed in most normal genitourinary tissues including kidney, but frequently silenced or downregulated by promoter CpG methylation in 78% of RCC cell lines and 44% (24/55) of primary tumors. In addition, CHD5 mutations appear to be rare in RCC tumors through genome database mining. In methylated/silenced RCC cell lines, CHD5 expression could be restored with azacytidine demethylation treatment. Ectopic expression of CHD5 in RCC cells significantly inhibited their clonogenicity, migration and invasion. Moreover, we found that CHD5, as a chromatin remodeling factor, suppressed the expression of multiple targets including oncogenes (MYC, MDM2, STAT3, CCND1, YAP1), epigenetic master genes (Bmi-1, EZH2, JMJD2C), as well as epithelial-mesenchymal transition and stem cell markers (SNAI1, FN1, OCT4). Further chromatin immunoprecipitation (ChIP) assays confirmed the binding of CHD5 to target gene promoters. Thus, we demonstrate that CHD5 functions as a novel TSG for RCC, but is predominantly inactivated by promoter methylation in primary tumors.
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Affiliation(s)
- Zhenfang Du
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong and CUHK-Shenzhen Research Institute, Shatin, Hong Kong
| | - Lili Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong and CUHK-Shenzhen Research Institute, Shatin, Hong Kong
| | - Xin Huang
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong and CUHK-Shenzhen Research Institute, Shatin, Hong Kong
| | - Jie Jin
- Department of Urology, Peking University First Hospital and Institute of Urology, National Research Center for Genitourinary Oncology, Beijing, China
| | - Suming Huang
- Departments of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Qian Zhang
- Department of Urology, Peking University First Hospital and Institute of Urology, National Research Center for Genitourinary Oncology, Beijing, China
| | - Qian Tao
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong and CUHK-Shenzhen Research Institute, Shatin, Hong Kong
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71
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Seldon CS, Colbert LE, Hall WA, Fisher SB, Yu DS, Landry JC. Chromodomain-helicase-DNA binding protein 5, 7 and pronecrotic mixed lineage kinase domain-like protein serve as potential prognostic biomarkers in patients with resected pancreatic adenocarcinomas. World J Gastrointest Oncol 2016; 8:358-365. [PMID: 27096031 PMCID: PMC4824714 DOI: 10.4251/wjgo.v8.i4.358] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 12/05/2015] [Accepted: 01/11/2016] [Indexed: 02/05/2023] Open
Abstract
Pancreatic cancer is one of the deadliest cancers with a very poor prognosis. Recently, there has been a significant increase in research directed towards identifying potential biomarkers that can be used to diagnose and provide prognostic information for pancreatic cancer. These markers can be used clinically to optimize and personalize therapy for individual patients. In this review, we focused on 3 biomarkers involved in the DNA damage response pathway and the necroptosis pathway: Chromodomain-helicase-DNA binding protein 5, chromodomain-helicase-DNA binding protein 7, and mixed lineage kinase domain-like protein. The aim of this article is to review present literature provided for these biomarkers and current studies in which their effectiveness as prognostic biomarkers are analyzed in order to determine their future use as biomarkers in clinical medicine. Based on the data presented, these biomarkers warrant further investigation, and should be validated in future studies.
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72
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Neault M, Mallette F, Richard S. miR-137 Modulates a Tumor Suppressor Network-Inducing Senescence in Pancreatic Cancer Cells. Cell Rep 2016; 14:1966-78. [DOI: 10.1016/j.celrep.2016.01.068] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 12/10/2015] [Accepted: 01/22/2016] [Indexed: 12/18/2022] Open
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73
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Xie CR, Li Z, Sun HG, Wang FQ, Sun Y, Zhao WX, Zhang S, Zhao WX, Wang XM, Yin ZY. Mutual regulation between CHD5 and EZH2 in hepatocellular carcinoma. Oncotarget 2015; 6:40940-52. [PMID: 26517514 PMCID: PMC4747380 DOI: 10.18632/oncotarget.5724] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/20/2015] [Indexed: 11/25/2022] Open
Abstract
Chromodomain helicase DNA binding protein 5 (CHD5) acts as a tumor suppressor in many cancers. In the present study, we demonstrated that reduced levels of CHD5 in hepatocellular carcinoma (HCC) tissues were significantly associated with metastasis and poor prognosis. Gain-of-function assays revealed that CHD5 suppressed motility and invasion of HCC cells. Subsequent investigations showed that CHD5 was epigenetically silenced by polycomb repressive complex 2 (PRC2)-mediated the trimethylation of histone H3 at lysine 27 (H3K27me3) in HCC cells. Furthermore, overexpression of CHD5 repressed enhancer of zeste homolog 2 (EZH2) and activated PRC2 target genes, such as p16 and p21. Chromatin immunoprecipitation and luciferase reporter assays also showed that CHD5 and EZH2 bind to each other's promoters and inhibit transcription. These findings uncovered, for the first time, a mutual suppression regulation between CHD5 and EZH2, which may provide new insights into their potential therapeutic significance for HCC.
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Affiliation(s)
- Cheng-Rong Xie
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Zhao Li
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Hong-Guang Sun
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Fu-Qiang Wang
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Yu Sun
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Wen-Xiu Zhao
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Sheng Zhang
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Wen-Xing Zhao
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Xiao-Min Wang
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Zhen-Yu Yin
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
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74
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Zepeda-Mendoza CJ, Mukhopadhyay S, Wong ES, Harder N, Splinter E, de Wit E, Eckersley-Maslin MA, Ried T, Eils R, Rohr K, Mills A, de Laat W, Flicek P, Sengupta AM, Spector DL. Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2. BMC Genomics 2015; 16:982. [PMID: 26589460 PMCID: PMC4654810 DOI: 10.1186/s12864-015-2137-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/23/2015] [Indexed: 11/26/2022] Open
Abstract
Background Circular chromosome conformation capture (4C) has provided important insights into three dimensional (3D) genome organization and its critical impact on the regulation of gene expression. We developed a new quantitative framework based on polymer physics for the analysis of paired-end sequencing 4C (PE-4Cseq) data. We applied this strategy to the study of chromatin interaction changes upon a 4.3 Mb DNA deletion in mouse region 4E2. Results A significant number of differentially interacting regions (DIRs) and chromatin compaction changes were detected in the deletion chromosome compared to a wild-type (WT) control. Selected DIRs were validated by 3D DNA FISH experiments, demonstrating the robustness of our pipeline. Interestingly, significant overlaps of DIRs with CTCF/Smc1 binding sites and differentially expressed genes were observed. Conclusions Altogether, our PE-4Cseq analysis pipeline provides a comprehensive characterization of DNA deletion effects on chromatin structure and function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2137-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cinthya J Zepeda-Mendoza
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
| | | | - Emily S Wong
- The European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Nathalie Harder
- Department Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, University of Heidelberg, BioQuant, IPMB, and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.
| | - Erik Splinter
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT Utrecht, The Netherlands.
| | - Elzo de Wit
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT Utrecht, The Netherlands.
| | - Melanie A Eckersley-Maslin
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA. .,Epigenetics Programme, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - Thomas Ried
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, 50 South Drive, Bldg. 50, Rm. 1408, Bethesda, MD, 20892, USA.
| | - Roland Eils
- Department Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, University of Heidelberg, BioQuant, IPMB, and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.
| | - Karl Rohr
- Department Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, University of Heidelberg, BioQuant, IPMB, and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.
| | - Alea Mills
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA. .,Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
| | - Wouter de Laat
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT Utrecht, The Netherlands.
| | - Paul Flicek
- The European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Anirvan M Sengupta
- Department of Physics and Astronomy, Rutgers, The State University of New Jersey, 136 Frelinghuysen Road, Piscataway, NJ, 08854-8019, USA.
| | - David L Spector
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA. .,Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
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75
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Lee B, Duz MB, Sagong B, Koparir A, Lee KY, Choi JY, Seven M, Yuksel A, Kim UK, Ozen M. Revealing the function of a novel splice-site mutation of CHD7 in CHARGE syndrome. Gene 2015; 576:776-81. [PMID: 26551301 DOI: 10.1016/j.gene.2015.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/24/2015] [Accepted: 11/04/2015] [Indexed: 11/27/2022]
Abstract
Most cases of CHARGE syndrome are sporadic and autosomal dominant. CHD7 is a major causative gene of CHARGE syndrome. In this study, we screened CHD7 in two Turkish patients demonstrating symptoms of CHARGE syndrome such as coloboma, heart defect, choanal atresia, retarded growth, genital abnomalities and ear anomalies. Two mutations of CHD7 were identified including a novel splice-site mutation (c.2443-2A>G) and a previously known frameshift mutation (c.2504_2508delATCTT). We performed exon trapping analysis to determine the effect of the c.2443-2A>G mutation at the transcriptional level, and found that it caused a complete skip of exon 7 and splicing at a cryptic splice acceptor site. Our current study is the second study demonstrating an exon 7 deficit in CHD7. Results of previous studies suggest that the c.2443-2A>G mutation affects the formation of nasal tissues and the neural retina during early development, resulting in choanal atresia and coloboma, respectively. The findings of the present study will improve our understanding of the genetic causes of CHARGE syndrome.
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Affiliation(s)
- Byeonghyeon Lee
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
| | - Mehmet Bugrahan Duz
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey
| | - Borum Sagong
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
| | - Asuman Koparir
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey
| | - Kyu-Yup Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Jae Young Choi
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, South Korea
| | - Mehmet Seven
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey
| | - Adnan Yuksel
- Department of Medical Genetics, Biruni University Medical School, Istanbul, Turkey
| | - Un-Kyung Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea.
| | - Mustafa Ozen
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey; Department of Medical Genetics, Biruni University Medical School, Istanbul, Turkey; Department of Pathology & Immunology, Baylor College of Medicine, Michael E. DeBakey VAMC, Houston, TX, United States.
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76
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Hayashi M, Maehara K, Harada A, Semba Y, Kudo K, Takahashi H, Oki S, Meno C, Ichiyanagi K, Akashi K, Ohkawa Y. Chd5 Regulates MuERV-L/MERVL Expression in Mouse Embryonic Stem Cells Via H3K27me3 Modification and Histone H3.1/H3.2. J Cell Biochem 2015; 117:780-92. [PMID: 26359639 DOI: 10.1002/jcb.25368] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 09/09/2015] [Indexed: 12/12/2022]
Abstract
Chd5 is an essential factor for neuronal differentiation and spermatogenesis and is a known tumor suppressor. H3K27me3 and H3K4un are modifications recognized by Chd5; however, it remains unclear how Chd5 remodels chromatin structure. We completely disrupted the Chd5 locus using the CRISPR-Cas9 system to generate a 52 kbp long deletion and analyzed Chd5 function in mouse embryonic stem cells. Our findings show that Chd5 represses murine endogenous retrovirus-L (MuERV-L/MERVL), an endogenous retrovirus-derived retrotransposon, by regulating H3K27me3 and H3.1/H3.2 function.
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Affiliation(s)
- Masayasu Hayashi
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.,Department of Medicine and Biosystemic Science, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Kazumitsu Maehara
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Akihito Harada
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuichiro Semba
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.,Department of Medicine and Biosystemic Science, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Kensuke Kudo
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.,Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hidehisa Takahashi
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Hokkaido 060-8638, Japan
| | - Shinya Oki
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Chikara Meno
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Kenji Ichiyanagi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
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77
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Abstract
Unrestrained p53 activity during development, as occurs upon loss of the p53 negative regulators Mdm2 or Mdmx, causes early embryonic lethality. Surprisingly, co-expression of wild-type p53 and a transcriptionally-dead variant of p53, with mutations in both transactivation domains (p53(L25Q,W26S,F53Q,F54S)), also causes lethality, but later in gestation and in association with a host of very specific phenotypes reminiscent of a syndrome known as CHARGE. Molecular analyses revealed that wild-type p53 is inappropriately activated in p53(5,26,53,54/)(+) embryos, triggering cell-cycle arrest or apoptosis during development to cause CHARGE phenotypes. In addition, CHARGE syndrome is typically caused by mutations in the CHD7 chromatin remodeler, and we have shown that activated p53 contributes to phenotypes caused by CHD7-deficiency. Together, these studies provide new insight into CHARGE syndrome and expand our understanding of the role of p53 in diseases other than cancer.
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Affiliation(s)
- Jeanine L Van Nostrand
- a Division of Radiation and Cancer Biology; Department of Radiation Oncology ; Stanford School of Medicine ; Stanford , CA USA
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78
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Deubiquitylase OTUD3 regulates PTEN stability and suppresses tumorigenesis. Nat Cell Biol 2015; 17:1169-81. [PMID: 26280536 DOI: 10.1038/ncb3218] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 07/03/2015] [Indexed: 12/17/2022]
Abstract
PTEN is one of the most frequently mutated tumour suppressors and reduction in PTEN protein stability also plays a role in tumorigenesis. Although several ubiquitin ligases for PTEN have been identified, the deubiquitylase for de-polyubiquitylation and stabilization of PTEN is less defined. Here, we report OTUD3 as a deubiquitylase of PTEN. OTUD3 interacts with, de-polyubiquitylates and stabilizes PTEN. Depletion of OTUD3 leads to the activation of Akt signalling, induction of cellular transformation and cancer metastasis. OTUD3 transgenic mice exhibit higher levels of the PTEN protein and are less prone to tumorigenesis. Reduction of OTUD3 expression, concomitant with decreased PTEN abundance, correlates with human breast cancer progression. Furthermore, we identified loss-of-function OTUD3 mutations in human cancers, which either abolish OTUD3 catalytic activity or attenuate the interaction with PTEN. These findings demonstrate that OTUD3 is an essential regulator of PTEN and that the OTUD3-PTEN signalling axis plays a critical role in tumour suppression.
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79
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Higashi M, Kolla V, Iyer R, Naraparaju K, Zhuang T, Kolla S, Brodeur GM. Retinoic acid-induced CHD5 upregulation and neuronal differentiation of neuroblastoma. Mol Cancer 2015; 14:150. [PMID: 26245651 PMCID: PMC4527355 DOI: 10.1186/s12943-015-0425-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/30/2015] [Indexed: 01/09/2023] Open
Abstract
Background Chromodomain-helicase DNA binding protein 5 (CHD5) is an important tumor suppressor gene deleted from 1p36.31 in neuroblastomas (NBs). High CHD5 expression is associated with a favorable prognosis, but deletion or low expression is frequent in high-risk tumors. We explored the role of CHD5 expression in the neuronal differentiation of NB cell lines. Methods NB cell lines SH-SY5Y (SY5Y), NGP, SK-N-DZ, IMR5, LAN5, SK-N-FI, NB69 and SH-EP were treated with 1–10 μM 13-cis-retinoic acid (13cRA) for 3–12 days. qRT-PCR and Western blot analyses were performed to measure mRNA and protein expression levels, respectively. Morphological differences were examined by both phase contrast and immunofluorescence studies. Results Treatment of SY5Y cells with 13cRA caused upregulation of CHD5 expression in a time- and dose-dependent manner (1, 5, or 10 μM for 7 or 12 days) and also induced neuronal differentiation. Furthermore, both NGP and SK-N-DZ cells showed CHD5 upregulation and neuronal differentiation after 13cRA treatment. In contrast, 13cRA treatment of IMR5, LAN5, or SK-N-FI induced neither CHD5 expression nor neuronal differentiation. NB69 cells showed two different morphologies (neuronal and substrate adherent) after 12 days treatment with 10 μM of 13cRA. CHD5 expression was high in the neuronal cells, but low/absent in the flat, substrate adherent cells. Finally, NGF treatment caused upregulation of CHD5 expression and neuronal differentiation in SY5Y cells transfected to express TrkA (SY5Y-TrkA) but not in TrkA-null parental SY5Y cells, and both changes were blocked by a pan-TRK inhibitor. Conclusions Treatment with 13cRA induces neuronal differentiation only in NB cells that upregulate CHD5. In addition, NGF induced CHD5 upregulation and neuronal differentiation only in TrkA expressing cells. Together, these results suggest that CHD5 is downstream of TrkA, and CHD5 expression may be crucial for neuronal differentiation induced by either 13cRA or TrkA/NGF signaling. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0425-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mayumi Higashi
- Division of Oncology, Children's Hospital of Philadelphia, and the Department of Pediatrics, University of Pennsylvania School of Medicine, CTRB Rm. 3018, 3501 Civic Center Blvd, Philadelphia, PA, 19104 - 4302, USA. .,Department of Pediatric Surgery, Kyoto Prefectural University of Medicine, Kyoto, 602 - 8566, Japan.
| | - Venkatadri Kolla
- Division of Oncology, Children's Hospital of Philadelphia, and the Department of Pediatrics, University of Pennsylvania School of Medicine, CTRB Rm. 3018, 3501 Civic Center Blvd, Philadelphia, PA, 19104 - 4302, USA.
| | - Radhika Iyer
- Division of Oncology, Children's Hospital of Philadelphia, and the Department of Pediatrics, University of Pennsylvania School of Medicine, CTRB Rm. 3018, 3501 Civic Center Blvd, Philadelphia, PA, 19104 - 4302, USA.
| | - Koumudi Naraparaju
- Division of Oncology, Children's Hospital of Philadelphia, and the Department of Pediatrics, University of Pennsylvania School of Medicine, CTRB Rm. 3018, 3501 Civic Center Blvd, Philadelphia, PA, 19104 - 4302, USA.
| | - Tiangang Zhuang
- Division of Oncology, Children's Hospital of Philadelphia, and the Department of Pediatrics, University of Pennsylvania School of Medicine, CTRB Rm. 3018, 3501 Civic Center Blvd, Philadelphia, PA, 19104 - 4302, USA.
| | - Sriharsha Kolla
- Division of Oncology, Children's Hospital of Philadelphia, and the Department of Pediatrics, University of Pennsylvania School of Medicine, CTRB Rm. 3018, 3501 Civic Center Blvd, Philadelphia, PA, 19104 - 4302, USA.
| | - Garrett M Brodeur
- Division of Oncology, Children's Hospital of Philadelphia, and the Department of Pediatrics, University of Pennsylvania School of Medicine, CTRB Rm. 3018, 3501 Civic Center Blvd, Philadelphia, PA, 19104 - 4302, USA.
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Abstract
Eukaryotic gene expression is developmentally regulated, in part by chromatin remodelling, and its dysregulation has been linked to cancer. CHD5 (chromodomain helicase DNA-binding protein 5) is a tumour suppressor gene (TSG) that maps to a region of consistent deletion on 1p36.31 in neuroblastomas (NBs) and other tumour types. CHD5 encodes a protein with chromatin remodelling, helicase and DNA-binding motifs that is preferentially expressed in neural and testicular tissues. CHD5 is highly homologous to CHD3 and CHD4, which are the core subunits of nucleosome remodelling and deacetylation (NuRD) complexes. To determine if CHD5 forms a similar complex, we performed studies on nuclear extracts from NBLS, SY5Y (both with endogenous CHD5 expression), NLF (CHD5 null) and NLF cells stably transfected with CHD5 cDNA (wild-type and V5-histidine-tagged). Immunoprecipitation (IP) was performed with either CHD5 antibody or antibody to V5/histidine-tagged protein. We identified NuRD components both by GST-FOG1 (Friend Of GATA1) pull-down and by IP. We also performed MS/MS analysis to confirm the presence of CHD5 or other protein components of the NuRD complex, as well as to identify other novel proteins. CHD5 was clearly associated with all canonical NuRD components, including metastasis-associated protein (MTA)1/2, GATA zinc finger domain containing 2A (GATAD2A), histone deacetylase (HDAC)1/2, retinoblastoma-binding protein (RBBP)4/7 and methyl DNA-binding domain protein (MBD)2/3, as determined by Western blotting and MS/MS. Our data suggest CHD5 forms a NuRD complex similar to CHD4. However, CHD5-NuRD may also have unique protein associations that confer functional specificity and may contribute to normal development and to tumour suppression in NB and other cancers.
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81
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Lehman HL, Stairs DB. Single and Multiple Gene Manipulations in Mouse Models of Human Cancer. CANCER GROWTH AND METASTASIS 2015; 8:1-15. [PMID: 26380553 PMCID: PMC4558888 DOI: 10.4137/cgm.s21217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 06/17/2015] [Accepted: 06/20/2015] [Indexed: 12/14/2022]
Abstract
Mouse models of human cancer play a critical role in understanding the molecular and cellular mechanisms of tumorigenesis. Advances continue to be made in modeling human disease in a mouse, though the relevance of a mouse model often relies on how closely it is able to mimic the histologic, molecular, and physiologic characteristics of the respective human cancer. A classic use of a genetically engineered mouse in studying cancer is through the overexpression or deletion of a gene. However, the manipulation of a single gene often falls short of mimicking all the characteristics of the carcinoma in humans; thus a multiple gene approach is needed. Here we review genetic mouse models of cancers and their abilities to recapitulate human carcinoma with single versus combinatorial approaches with genes commonly involved in cancer.
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Affiliation(s)
- Heather L Lehman
- Department of Pathology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Douglas B Stairs
- Department of Pathology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
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82
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Li W, Mills AA. Architects of the genome: CHD dysfunction in cancer, developmental disorders and neurological syndromes. Epigenomics 2015; 6:381-95. [PMID: 25333848 DOI: 10.2217/epi.14.31] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Chromatin is vital to normal cells, and its deregulation contributes to a spectrum of human ailments. An emerging concept is that aberrant chromatin regulation culminates in gene expression programs that set the stage for the seemingly diverse pathologies of cancer, developmental disorders and neurological syndromes. However, the mechanisms responsible for such common etiology have been elusive. Recent evidence has implicated lesions affecting chromatin-remodeling proteins in cancer, developmental disorders and neurological syndromes, suggesting a common source for these different pathologies. Here, we focus on the chromodomain helicase DNA binding chromatin-remodeling family and the recent evidence for its deregulation in diverse pathological conditions, providing a new perspective on the underlying mechanisms and their implications for these prevalent human diseases.
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Affiliation(s)
- Wangzhi Li
- Cold Spring Harbor Laboratory Cold Spring Harbor, NY 11724, USA
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83
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Bishop B, Ho KK, Tyler K, Smith A, Bonilla S, Leung YF, Ogas J. The chromatin remodeler chd5 is necessary for proper head development during embryogenesis of Danio rerio. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1040-50. [PMID: 26092436 DOI: 10.1016/j.bbagrm.2015.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/05/2015] [Accepted: 06/12/2015] [Indexed: 12/12/2022]
Abstract
The chromatin remodeler CHD5 plays a critical role in tumor suppression and neurogenesis in mammals. CHD5 contributes to gene expression during neurogenesis, but there is still much to learn regarding how this class of remodelers contributes to differentiation and development. CHD5 remodelers are vertebrate-specific, raising the prospect that CHD5 plays one or more conserved roles in this phylum. Expression of chd5 in adult fish closely mirrors expression of CHD5 in adult mammals. Knockdown of Chd5 during embryogenesis suggests new roles for CHD5 remodelers based on resulting defects in craniofacial development including reduced head and eye size as well as reduced cartilage formation in the head. In addition, knockdown of Chd5 results in altered expression of neural markers in the developing brain and eye as well as a profound defect in differentiation of dopaminergic amacrine cells. Recombinant zebrafish Chd5 protein exhibits nucleosome remodeling activity in vitro, suggesting that it is the loss of this activity that contributes to the observed phenotypes. Our studies indicate that zebrafish is an appropriate model for functional characterization of CHD5 remodelers in vertebrates and highlight the potential of this model for generating novel insights into the role of this vital class of remodelers.
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Affiliation(s)
- Brett Bishop
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
| | - Kwok Ki Ho
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
| | - Kim Tyler
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
| | - Amanda Smith
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
| | - Sylvia Bonilla
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Yuk Fai Leung
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Joe Ogas
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States.
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84
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Mayes K, Qiu Z, Alhazmi A, Landry JW. ATP-dependent chromatin remodeling complexes as novel targets for cancer therapy. Adv Cancer Res 2015; 121:183-233. [PMID: 24889532 DOI: 10.1016/b978-0-12-800249-0.00005-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The progression to advanced stage cancer requires changes in many characteristics of a cell. These changes are usually initiated through spontaneous mutation. As a result of these mutations, gene expression is almost invariably altered allowing the cell to acquire tumor-promoting characteristics. These abnormal gene expression patterns are in part enabled by the posttranslational modification and remodeling of nucleosomes in chromatin. These chromatin modifications are established by a functionally diverse family of enzymes including histone and DNA-modifying complexes, histone deposition pathways, and chromatin remodeling complexes. Because the modifications these enzymes deposit are essential for maintaining tumor-promoting gene expression, they have recently attracted much interest as novel therapeutic targets. One class of enzyme that has not generated much interest is the chromatin remodeling complexes. In this review, we will present evidence from the literature that these enzymes have both causal and enabling roles in the transition to advanced stage cancers; as such, they should be seriously considered as high-value therapeutic targets. Previously published strategies for discovering small molecule regulators to these complexes are described. We close with thoughts on future research, the field should perform to further develop this potentially novel class of therapeutic target.
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Affiliation(s)
- Kimberly Mayes
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Zhijun Qiu
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Aiman Alhazmi
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Joseph W Landry
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.
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85
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Micucci JA, Sperry ED, Martin DM. Chromodomain helicase DNA-binding proteins in stem cells and human developmental diseases. Stem Cells Dev 2015; 24:917-26. [PMID: 25567374 DOI: 10.1089/scd.2014.0544] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Dynamic regulation of gene expression is vital for proper cellular development and maintenance of differentiated states. Over the past 20 years, chromatin remodeling and epigenetic modifications of histones have emerged as key controllers of rapid reversible changes in gene expression. Mutations in genes encoding enzymes that modify chromatin have also been identified in a variety of human neurodevelopmental disorders, ranging from isolated intellectual disability and autism spectrum disorder to multiple congenital anomaly conditions that affect major organ systems and cause severe morbidity and mortality. In this study, we review recent evidence that chromodomain helicase DNA-binding (CHD) proteins regulate stem cell proliferation, fate, and differentiation in a wide variety of tissues and organs. We also highlight known roles of CHD proteins in human developmental diseases and present current unanswered questions about the pleiotropic effects of CHD protein complexes, their genetic targets, nucleosome sliding functions, and enzymatic effects in cells and tissues.
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Affiliation(s)
- Joseph A Micucci
- 1 Division of Hematology, Children's Hospital of Philadelphia , Philadelphia, Pennsylvania
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86
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Quan J, Yusufzai T. The tumor suppressor chromodomain helicase DNA-binding protein 5 (CHD5) remodels nucleosomes by unwrapping. J Biol Chem 2015; 289:20717-26. [PMID: 24923445 DOI: 10.1074/jbc.m114.568568] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although mutations or deletions of chromodomain helicase DNA-binding protein 5 (CHD5) have been linked to cancer and implicate CHD5 in tumor suppression, the ATP-dependent activity of CHD5 is currently unknown. In this study, we discovered that CHD5 is a chromatin remodeling factor with a unique enzymatic activity. CHD5 can expose nucleosomal DNA at one or two discrete positions in the nucleosome. The exposure of the nucleosomal DNA by CHD5 is dependent on ATP hydrolysis, but continued ATP hydrolysis is not required to maintain the nucleosomes in their remodeled state. The activity of CHD5 is distinct from other related chromatin remodeling ATPases, such as ACF and BRG1, and does not lead to complete disruption or destabilization of the nucleosome. Rather, CHD5 likely initiates remodeling in a manner similar to that of other remodeling factors but does not significantly reposition the nucleosome. While the related factor CHD4 shows strong ATPase activity, it does not unwrap nucleosomes as efficiently as CHD5. Our findings add to the growing evidence that chromatin remodeling ATPases have diverse roles in modulating chromatin structure.
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87
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Lotem J, Levanon D, Negreanu V, Bauer O, Hantisteanu S, Dicken J, Groner Y. Runx3 at the interface of immunity, inflammation and cancer. Biochim Biophys Acta Rev Cancer 2015; 1855:131-43. [PMID: 25641675 DOI: 10.1016/j.bbcan.2015.01.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 02/06/2023]
Abstract
Inactivation of tumor suppressor genes (TSG) in normal cells provides a viability/growth advantage that contributes cell-autonomously to cancer. More than a decade ago claims arose that the RUNX3 member of the RUNX transcription factor family is a major TSG inactivated in gastric cancer, a postulate extended later to other cancers. However, evidence that Runx3 is not expressed in normal gastric and other epithelia has challenged the RUNX3-TSG paradigm. Here we critically re-appraise this paradigm in light of recent high-throughput, quantitative genome-wide studies on thousands of human samples of various tumors and new investigations of the role of Runx3 in mouse cancer models. Collectively, these studies unequivocally demonstrate that RUNX3 is not a bona fide cell-autonomous TSG. Accordingly, RUNX3 is not recognized as a TSG and is not included among the 2000 cancer genes listed in the "Cancer Gene Census" or "Network for Cancer Genes" repositories. In contrast, RUNX3 does play important functions in immunity and inflammation and may thereby indirectly influence epithelial tumor development.
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Affiliation(s)
- Joseph Lotem
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Ditsa Levanon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Varda Negreanu
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Omri Bauer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shay Hantisteanu
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joseph Dicken
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoram Groner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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88
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Guerra-Calderas L, González-Barrios R, Herrera LA, Cantú de León D, Soto-Reyes E. The role of the histone demethylase KDM4A in cancer. Cancer Genet 2014; 208:215-24. [PMID: 25633974 DOI: 10.1016/j.cancergen.2014.11.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 10/20/2014] [Accepted: 11/05/2014] [Indexed: 12/31/2022]
Abstract
Histone posttranslational modifications are important components of epigenetic regulation. One extensively studied modification is the methylation of lysine residues. These modifications were thought to be irreversible. However, several proteins with histone lysine demethylase functions have been discovered and characterized. Among these proteins, KDM4A is the first histone lysine demethylase shown to demethylate trimethylated residues. This enzyme plays an important role in gene expression, cellular differentiation, and animal development. Recently, it has also been shown to be involved in cancer. In this review, we focus on describing the structure, mechanisms, and function of KDM4A. We primarily discuss the role of KDM4A in cancer development and the importance of KDM4A as a potential therapeutic target.
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Affiliation(s)
- Lissania Guerra-Calderas
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - David Cantú de León
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Ernesto Soto-Reyes
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.
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89
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The chromatin remodeling factor CHD5 is a transcriptional repressor of WEE1. PLoS One 2014; 9:e108066. [PMID: 25247294 PMCID: PMC4172601 DOI: 10.1371/journal.pone.0108066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/26/2014] [Indexed: 11/19/2022] Open
Abstract
Loss of the chromatin remodeling ATPase CHD5 has been linked to the progression of neuroblastoma tumors, yet the underlying mechanisms behind the tumor suppressor role of CHD5 are unknown. In this study, we purified the human CHD5 complex and found that CHD5 is a component of the full NuRD transcriptional repressor complex, which also contains methyl-CpG binding proteins and histone deacetylases. The CHD5/NuRD complex appears mutually exclusive with the related CHD4/NuRD complex as overexpression of CHD5 results in loss of the CHD4 protein in cells. Following a search for genes that are regulated by CHD5 in neuroblastoma cells, we found that CHD5 binds to and represses the G2/M checkpoint gene WEE1. Reintroduction of CHD5 into neuroblastoma cells represses WEE1 expression, demonstrating that CHD5 can function as a repressor in cells. A catalytically inactive mutant version of CHD5 is able to associate with a NuRD cofactor but fails to repress transcription. Our study shows that CHD5 is a NuRD-associated transcriptional repressor and identifies WEE1 as one of the CHD5-regulated genes that may link CHD5 to tumor suppression.
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90
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Chi Y, Huang S, Wang L, Zhou R, Wang L, Xiao X, Li D, Cai Y, Zhou X, Wu J. CDK11p58 inhibits ERα-positive breast cancer invasion by targeting integrin β3 via the repression of ERα signaling. BMC Cancer 2014; 14:577. [PMID: 25106495 PMCID: PMC4138392 DOI: 10.1186/1471-2407-14-577] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 08/05/2014] [Indexed: 12/21/2022] Open
Abstract
Background CDK11p58, a Ser/Thr kinase that belongs to the cell division cycle 2-like 1 (CDC2L1) subfamily, is associated with cell cycle progression, tumorigenesis and apoptotic signaling. CDK11p58 is also involved in the regulation of steroid receptors, such as androgen and estrogen receptors. We previously found that CDK11p58 was abnormally expressed in prostate cancer. However, its role in breast cancer remains unclear. Methods CDK11p58 expression was evaluated by immunohistochemical staining in a tissue array. A Transwell assay was used to detect invasion and metastasis in breast cancer cells. The TaqMan® Metastasis Gene Expression Assay was used to search for potential downstream factors in the CDK11p58 signaling pathway. qRT-PCR was used to evaluate mRNA levels, and the dual luciferase array was used to analyze promoter activity. Western blotting was used to detect the protein level. Results CDK11p58 expression was negatively correlated with node status (P = 0.012), relapse status (P = 0.002) and metastasis status (P = 0.023). Kaplan-Meier survival curves indicated that the disease-free survival (DFS) was significantly poor in breast cancer patients with low CDK11 expression. Interestingly, using the breast cancer cell lines ZR-75-30 and MDA-MB-231, we found that CDK11p58 was capable of repressing the migration and invasion of ERα-positive breast cancer cells, but not ERα-negative breast cancer cells, in a kinase-dependent manner. Gene expression assays demonstrated that integrin β3 mRNA was dramatically repressed by CDK11p58, and luciferase results confirmed that the integrin β3 promoter was inhibited by CDK11p58 through ERα repression. The expression of integrin β3 was highly related to ERα signaling; ERα overexpression stimulated integrin β3 expression, whereas siRNA-mediated knockdown of ERα attenuated integrin β3 expression. Conclusions These data indicate that CDK11p58 is an anti-metastatic gene in ERα-positive breast cancer and that the regulation of integrin β3 by CDK11p58 via the repression of ERα signaling may constitute part of a signaling pathway underlying breast cancer invasion.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jiong Wu
- Breast Cancer Institute; Department of Breast Surgery, Fudan University Shanghai Cancer Center, Building 7, No, 270 Dong An Road, Shanghai 200032, China.
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91
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Zhao R, Wang N, Huang H, Ma W, Yan Q. CHD5 a tumour suppressor is epigenetically silenced in hepatocellular carcinoma. Liver Int 2014; 34:e151-60. [PMID: 24529164 DOI: 10.1111/liv.12503] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 02/08/2014] [Indexed: 12/24/2022]
Abstract
BACKGROUND Chromodomain helicase DNA binding protein 5 (CHD5) has recently been identified as a potent tumour suppressor by acting as a master regulator of a tumour-suppressive network. Its inactivation resulted from aberrant methylation in the promoter occurs in several types of human malignancy and is associated with malignant tumour behaviour. In human hepatocellular carcinoma (HCC), CHD5 gene expression, methylation status and tumour-suppressive function have not been elucidated. AIMS In this study, we focused on the epigenetic modification and tumour-suppressive mechanism of CHD5 gene in HCC. METHODS CHD5 expression in nine HCC cell lines and 30 pairs of HCC specimens and adjacent non-cancerous tissues were analysed by quantitative reverse transcription PCR and Western blotting. Methylation-specific sequencing and methylation-specific PCR were performed to examine DNA methylation status of the CHD5 promoter in HCC cell lines and samples. The effect of CHD5 restoration on proliferation, colony formation, senescence, apoptosis and tumourigenicity were examined. RESULTS CHD5 expression was sinificantly down-regulated in HCC cell lines and tissues examined, and the -841 to -470 region of CHD5 promoter was hypermethylated in these samples. Treatment with DNA methyltransferase inhibitor 5-aza-2-deoxycytidine resulted in a striking regional demethylation of the -841 to -470 region of CHD5 promoter and an increase in CHD5 expression. The restoration of CHD5 expression inhibited tumour cell proliferation, colony formation and tumourigenicity and caused cellular senescence. CONCLUSIONS Our findings demonstrate that CHD5 is a potential tumour suppressor gene epigenetically silenced in HCC.
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Affiliation(s)
- Rui Zhao
- Institute of Molecular Biology, Southern Medical University, Guangzhou, China
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92
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PVT1 dependence in cancer with MYC copy-number increase. Nature 2014; 512:82-6. [PMID: 25043044 DOI: 10.1038/nature13311] [Citation(s) in RCA: 557] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 04/08/2014] [Indexed: 12/22/2022]
Abstract
'Gain' of supernumerary copies of the 8q24.21 chromosomal region has been shown to be common in many human cancers and is associated with poor prognosis. The well-characterized myelocytomatosis (MYC) oncogene resides in the 8q24.21 region and is consistently co-gained with an adjacent 'gene desert' of approximately 2 megabases that contains the long non-coding RNA gene PVT1, the CCDC26 gene candidate and the GSDMC gene. Whether low copy-number gain of one or more of these genes drives neoplasia is not known. Here we use chromosome engineering in mice to show that a single extra copy of either the Myc gene or the region encompassing Pvt1, Ccdc26 and Gsdmc fails to advance cancer measurably, whereas a single supernumerary segment encompassing all four genes successfully promotes cancer. Gain of PVT1 long non-coding RNA expression was required for high MYC protein levels in 8q24-amplified human cancer cells. PVT1 RNA and MYC protein expression correlated in primary human tumours, and copy number of PVT1 was co-increased in more than 98% of MYC-copy-increase cancers. Ablation of PVT1 from MYC-driven colon cancer line HCT116 diminished its tumorigenic potency. As MYC protein has been refractory to small-molecule inhibition, the dependence of high MYC protein levels on PVT1 long non-coding RNA provides a much needed therapeutic target.
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93
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Bergs JW, Neuendorff N, van der Heijden G, Wassenaar E, Rexin P, Elsässer HP, Moll R, Baarends WM, Brehm A. Differential expression and sex chromosome association of CHD3/4 and CHD5 during spermatogenesis. PLoS One 2014; 9:e98203. [PMID: 24849318 PMCID: PMC4029951 DOI: 10.1371/journal.pone.0098203] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 04/30/2014] [Indexed: 01/20/2023] Open
Abstract
ATP-dependent nucleosome remodelers of the CHD family play important roles in chromatin regulation during development and differentiation. The ubiquitously expressed CHD3 and CHD4 proteins are essential for stem cell function and serve to orchestrate gene expression in different developmental settings. By contrast, the closely related CHD5 is predominantly expressed in neural tissue and its role is believed to be restricted to neural differentiation. Indeed, loss of CHD5 contributes to neuroblastoma. In this study, we first demonstrate that CHD5 is a nucleosome-stimulated ATPase. We then compare CHD3/4 and CHD5 expression in mouse brain and show that CHD5 expression is restricted to a subset of cortical and hippocampal neurons whereas CHD3/4 expression is more widespread. We also uncover high levels of CHD5 expression in testis. CHD5 is transiently expressed in differentiating germ cells. Expression is first detected in nuclei of post-meiotic round spermatids, reaches a maximum in stage VIII spermatids and then falls to undetectable levels in stage IX spermatids. Surprisingly, CHD3/4 and CHD5 show complementary expression patterns during spermatogenesis with CHD3/4 levels progressively decreasing as CHD5 expression increases. In spermatocytes, CHD3/4 localizes to the pseudoautosomal region, the X centromeric region and then spreads into the XY body chromatin. In postmeiotic cells, CHD5 colocalises with macroH2A1.2 in association with centromeres and part of the Y chromosome. The subnuclear localisations of CHD4 and CHD5 suggest specific roles in regulation of sex chromosome chromatin and pericentromeric chromatin structure prior to the histone-protamine switch.
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Affiliation(s)
- Judith W. Bergs
- Institute for Molecular Biology and Tumor Research (IMT), Philipps Universität Marburg, Marburg, Germany
| | - Nina Neuendorff
- Institute for Molecular Biology and Tumor Research (IMT), Philipps Universität Marburg, Marburg, Germany
| | - Godfried van der Heijden
- Department of Reproduction and Development, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Evelyne Wassenaar
- Department of Reproduction and Development, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Peter Rexin
- Institut für Pathologie, Philipps Universität Marburg, Marburg, Germany
| | - Hans-Peter Elsässer
- Institut für Zytobiologie und Zytopathologie, Philipps Universität Marburg, Marburg, Germany
| | - Roland Moll
- Institut für Pathologie, Philipps Universität Marburg, Marburg, Germany
| | - Willy M. Baarends
- Department of Reproduction and Development, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Alexander Brehm
- Institute for Molecular Biology and Tumor Research (IMT), Philipps Universität Marburg, Marburg, Germany
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94
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Li W, Wu J, Kim SY, Zhao M, Hearn SA, Zhang MQ, Meistrich ML, Mills AA. Chd5 orchestrates chromatin remodelling during sperm development. Nat Commun 2014; 5:3812. [PMID: 24818823 DOI: 10.1038/ncomms4812] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 04/04/2014] [Indexed: 12/12/2022] Open
Abstract
One of the most remarkable chromatin remodelling processes occurs during spermiogenesis, the post-meiotic phase of sperm development during which histones are replaced with sperm-specific protamines to repackage the genome into the highly compact chromatin structure of mature sperm. Here we identify Chromodomain helicase DNA binding protein 5 (Chd5) as a master regulator of the histone-to-protamine chromatin remodelling process. Chd5 deficiency leads to defective sperm chromatin compaction and male infertility in mice, mirroring the observation of low CHD5 expression in testes of infertile men. Chd5 orchestrates a cascade of molecular events required for histone removal and replacement, including histone 4 (H4) hyperacetylation, histone variant expression, nucleosome eviction and DNA damage repair. Chd5 deficiency also perturbs expression of transition proteins (Tnp1/Tnp2) and protamines (Prm1/2). These findings define Chd5 as a multi-faceted mediator of histone-to-protamine replacement and depict the cascade of molecular events underlying this process of extensive chromatin remodelling.
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Affiliation(s)
- Wangzhi Li
- 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, New York 11794, USA
| | - Jie Wu
- 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Sang-Yong Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ming Zhao
- Department of Experimental Radiation Oncology, MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Stephen A Hearn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Michael Q Zhang
- 1] Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas 75080, USA [2] MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Marvin L Meistrich
- Department of Experimental Radiation Oncology, MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Alea A Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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95
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ZENG LIANG, FEE BRIANE, RIVAS MIRIAMV, LIN JAMES, ADAMSON DAVIDCORY. Adherens junctional associated protein-1: A novel 1p36 tumor suppressor candidate in gliomas. Int J Oncol 2014; 45:13-7. [DOI: 10.3892/ijo.2014.2425] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 04/14/2014] [Indexed: 11/06/2022] Open
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96
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Shaltouki A, Peng J, Liu Q, Rao MS, Zeng X. Efficient generation of astrocytes from human pluripotent stem cells in defined conditions. Stem Cells 2014; 31:941-52. [PMID: 23341249 DOI: 10.1002/stem.1334] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 12/24/2012] [Indexed: 01/07/2023]
Abstract
Astrocytes can be generated from various tissue sources including human pluripotent stem cells (PSC). In this manuscript, we describe a chemically defined xeno-free medium culture system for rapidly generating astrocytes from neural stem cells derived from PSC. We show that astrocyte development in vitro, mimics normal development in vivo, and also passes through a CD44(+) astrocyte precursor stage. Astrocytes generated by our method display similar gene expression patterns, morphological characteristics and functional properties to primary astrocytes, and they survive and integrate after xenotransplantation. Whole genome expression profiling of astrocyte differentiation was performed at several time points of differentiation, and the results indicate the importance of known regulators and identify potential novel regulators and stage-specific lineage markers.
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97
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Lacrimal Gland Pleomorphic Adenoma and Carcinoma ex Pleomorphic Adenoma. Ophthalmology 2014; 121:1125-33. [DOI: 10.1016/j.ophtha.2013.11.037] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 11/20/2013] [Accepted: 11/21/2013] [Indexed: 12/28/2022] Open
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98
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Tahara T, Yamamoto E, Madireddi P, Suzuki H, Maruyama R, Chung W, Garriga J, Jelinek J, Yamano HO, Sugai T, Kondo Y, Toyota M, Issa JPJ, Estécio MRH. Colorectal carcinomas with CpG island methylator phenotype 1 frequently contain mutations in chromatin regulators. Gastroenterology 2014; 146:530-38.e5. [PMID: 24211491 PMCID: PMC3918446 DOI: 10.1053/j.gastro.2013.10.060] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 10/03/2013] [Accepted: 10/30/2013] [Indexed: 01/04/2023]
Abstract
BACKGROUND & AIMS Subgroups of colorectal carcinomas (CRCs) characterized by DNA methylation anomalies are termed CpG island methylator phenotype (CIMP)1, CIMP2, or CIMP-negative. The pathogenesis of CIMP1 colorectal carcinomas, and their effects on patients' prognoses and responses to treatment, differ from those of other CRCs. We sought to identify genetic somatic alterations associated with CIMP1 CRCs. METHODS We examined genomic DNA samples from 100 primary CRCs, 10 adenomas, and adjacent normal-appearing mucosae from patients undergoing surgery or colonoscopy at 3 tertiary medical centers. We performed exome sequencing of 16 colorectal tumors and their adjacent normal tissues. Extensive comparison with known somatic alterations in CRCs allowed segregation of CIMP1-exclusive alterations. The prevalence of mutations in selected genes was determined from an independent cohort. RESULTS We found that genes that regulate chromatin were mutated in CIMP1 CRCs; the highest rates of mutation were observed in CHD7 and CHD8, which encode members of the chromodomain helicase/adenosine triphosphate-dependent chromatin remodeling family. Somatic mutations in these 2 genes were detected in 5 of 9 CIMP1 CRCs. A prevalence screen showed that nonsilencing mutations in CHD7 and CHD8 occurred significantly more frequently in CIMP1 tumors (18 of 42 [43%]) than in CIMP2 (3 of 34 [9%]; P < .01) or CIMP-negative tumors (2 of 34 [6%]; P < .001). CIMP1 markers had increased binding by CHD7, compared with all genes. Genes altered in patients with CHARGE syndrome (congenital malformations involving the central nervous system, eye, ear, nose, and mediastinal organs) who had CHD7 mutations were also altered in CRCs with mutations in CHD7. CONCLUSIONS Aberrations in chromatin remodeling could contribute to the development of CIMP1 CRCs. A better understanding of the biological determinants of CRCs can be achieved when these tumors are categorized according to their epigenetic status.
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Affiliation(s)
- Tomomitsu Tahara
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Eiichiro Yamamoto
- First Department of Internal Medicine, Sapporo Medical University, Sapporo, Japan,Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Priyanka Madireddi
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Hiromu Suzuki
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Reo Maruyama
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Woonbok Chung
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Judith Garriga
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Hiro-o Yamano
- Department of Gastroenterology, Akita Red Cross Hospital, Akita, Japan
| | - Tamotsu Sugai
- Department of Pathology, Iwate Medical University, Morioka, Japan
| | - Yutaka Kondo
- Division of Molecular Oncology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Minoru Toyota
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Jean-Pierre J. Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Marcos R. H. Estécio
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
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99
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Wagner T, Robaa D, Sippl W, Jung M. Mind the Methyl: Methyllysine Binding Proteins in Epigenetic Regulation. ChemMedChem 2014; 9:466-83. [DOI: 10.1002/cmdc.201300422] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Indexed: 11/07/2022]
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100
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Kolla V, Zhuang T, Higashi M, Naraparaju K, Brodeur GM. Role of CHD5 in human cancers: 10 years later. Cancer Res 2014; 74:652-8. [PMID: 24419087 DOI: 10.1158/0008-5472.can-13-3056] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
CHD5 was first identified because of its location on 1p36 in a region of frequent deletion in neuroblastomas. CHD5 (chromodomain-helicase-DNA-binding-5) is the fifth member of a family of chromatin remodeling proteins, and it probably functions by forming a nucleosome remodeling and deacetylation (NuRD) complex that regulates transcription of particular genes. CHD5 is preferentially expressed in the nervous system and testis. On the basis of its position, pattern of expression, and function in neuroblastoma cells and xenografts, CHD5 was identified as a tumor suppressor gene (TSG). Evidence soon emerged that CHD5 also functioned as a TSG in gliomas and a variety of other tumor types, including breast, colon, lung, ovary, and prostate cancers. Although one copy of CHD5 is deleted frequently, inactivating mutations of the remaining allele are rare. However, DNA methylation of the CHD5 promoter is found frequently, and this epigenetic mechanism leads to biallelic inactivation. Furthermore, low CHD5 expression is strongly associated with unfavorable clinical and biologic features as well as outcome in neuroblastomas and many other tumor types. Thus, based on its likely involvement as a TSG in neuroblastomas, gliomas, and many common adult tumors, CHD5 may play an important developmental role in many other tissues besides the nervous system and testis.
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Affiliation(s)
- Venkatadri Kolla
- Authors' Affiliations: Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia; and The University of Pennsylvania, Philadelphia, Pennsylvania
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