1
|
Mason NR, Cahill H, Diamond Y, McCleary K, Kotecha RS, Marshall GM, Mateos MK. Down syndrome-associated leukaemias: current evidence and challenges. Ther Adv Hematol 2024; 15:20406207241257901. [PMID: 39050114 PMCID: PMC11268035 DOI: 10.1177/20406207241257901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 05/13/2024] [Indexed: 07/27/2024] Open
Abstract
Children with Down syndrome (DS) are at increased risk of developing haematological malignancies, in particular acute megakaryoblastic leukaemia and acute lymphoblastic leukaemia. The microenvironment established by abnormal haematopoiesis driven by trisomy 21 is compounded by additional genetic and epigenetic changes that can drive leukaemogenesis in patients with DS. GATA-binding protein 1 (GATA1) somatic mutations are implicated in the development of transient abnormal myelopoiesis and the progression to myeloid leukaemia of DS (ML-DS) and provide a model of the multi-step process of leukaemogenesis in DS. This review summarises key genetic drivers for the development of leukaemia in patients with DS, the biology and treatment of ML-DS and DS-associated acute lymphoblastic leukaemia, late effects of treatments for DS-leukaemias and the focus for future targeted therapy.
Collapse
Affiliation(s)
- Nicola R. Mason
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW, Australia
| | - Hilary Cahill
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW, Australia
| | - Yonatan Diamond
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW, Australia
| | - Karen McCleary
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, NSW, Australia
| | - Rishi S. Kotecha
- Department of Clinical Haematology, Oncology, Blood and Bone Marrow Transplantation, Perth Children’s Hospital, Perth, WA, Australia
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Glenn M. Marshall
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, Randwick, NSW, Australia School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, NSW, Australia Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Marion K. Mateos
- Kids Cancer Centre, Sydney Children’s Hospital, Level 1 South Wing, High Street, Randwick, NSW 2031, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, NSW, Australia
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| |
Collapse
|
2
|
Camerino M, Chang W, Cvekl A. Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers. Epigenetics Chromatin 2024; 17:10. [PMID: 38643244 PMCID: PMC11031936 DOI: 10.1186/s13072-024-00533-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/08/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Nuclear organization of interphase chromosomes involves individual chromosome territories, "open" and "closed" chromatin compartments, topologically associated domains (TADs) and chromatin loops. The DNA- and RNA-binding transcription factor CTCF together with the cohesin complex serve as major organizers of chromatin architecture. Cellular differentiation is driven by temporally and spatially coordinated gene expression that requires chromatin changes of individual loci of various complexities. Lens differentiation represents an advantageous system to probe transcriptional mechanisms underlying tissue-specific gene expression including high transcriptional outputs of individual crystallin genes until the mature lens fiber cells degrade their nuclei. RESULTS Chromatin organization between mouse embryonic stem (ES) cells, newborn (P0.5) lens epithelium and fiber cells were analyzed using Hi-C. Localization of CTCF in both lens chromatins was determined by ChIP-seq and compared with ES cells. Quantitative analyses show major differences between number and size of TADs and chromatin loop size between these three cell types. In depth analyses show similarities between lens samples exemplified by overlaps between compartments A and B. Lens epithelium-specific CTCF peaks are found in mostly methylated genomic regions while lens fiber-specific and shared peaks occur mostly within unmethylated DNA regions. Major differences in TADs and loops are illustrated at the ~ 500 kb Pax6 locus, encoding the critical lens regulatory transcription factor and within a larger ~ 15 Mb WAGR locus, containing Pax6 and other loci linked to human congenital diseases. Lens and ES cell Hi-C data (TADs and loops) together with ATAC-seq, CTCF, H3K27ac, H3K27me3 and ENCODE cis-regulatory sites are shown in detail for the Pax6, Sox1 and Hif1a loci, multiple crystallin genes and other important loci required for lens morphogenesis. The majority of crystallin loci are marked by unexpectedly high CTCF-binding across their transcribed regions. CONCLUSIONS Our study has generated the first data on 3-dimensional (3D) nuclear organization in lens epithelium and lens fibers and directly compared these data with ES cells. These findings generate novel insights into lens-specific transcriptional gene control, open new research avenues to study transcriptional condensates in lens fiber cells, and enable studies of non-coding genetic variants linked to cataract and other lens and ocular abnormalities.
Collapse
Affiliation(s)
- Michael Camerino
- The Departments Genetics, Albert Einstein College of Medicine, NY10461, Bronx, USA
| | - William Chang
- Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, NY10461, Bronx, USA
| | - Ales Cvekl
- The Departments Genetics, Albert Einstein College of Medicine, NY10461, Bronx, USA.
- Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, NY10461, Bronx, USA.
| |
Collapse
|
3
|
Sen D, Maniyadath B, Chowdhury S, Kaur A, Khatri S, Chakraborty A, Mehendale N, Nadagouda S, Sandra U, Kamat SS, Kolthur-Seetharam U. Metabolic regulation of CTCF expression and chromatin association dictates starvation response in mice and flies. iScience 2023; 26:107128. [PMID: 37416476 PMCID: PMC10320512 DOI: 10.1016/j.isci.2023.107128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 05/16/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023] Open
Abstract
Coordinated temporal control of gene expression is essential for physiological homeostasis, especially during metabolic transitions. However, the interplay between chromatin architectural proteins and metabolism in regulating transcription is less understood. Here, we demonstrate a conserved bidirectional interplay between CTCF (CCCTC-binding factor) expression/function and metabolic inputs during feed-fast cycles. Our results indicate that its loci-specific functional diversity is associated with physiological plasticity in mouse hepatocytes. CTCF differential expression and long non-coding RNA-Jpx mediated changes in chromatin occupancy, unraveled its paradoxical yet tuneable functions, which are governed by metabolic inputs. We illustrate the key role of CTCF in controlling temporal cascade of transcriptional response, with effects on hepatic mitochondrial energetics and lipidome. Underscoring the evolutionary conservation of CTCF-dependent metabolic homeostasis, CTCF knockdown in flies abrogated starvation resistance. In summary, we demonstrate the interplay between CTCF and metabolic inputs that highlights the coupled plasticity of physiological responses and chromatin function.
Collapse
Affiliation(s)
- Devashish Sen
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Babukrishna Maniyadath
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Shreyam Chowdhury
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Arshdeep Kaur
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Subhash Khatri
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Arnab Chakraborty
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Neelay Mehendale
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Snigdha Nadagouda
- Tata Institute of Fundamental Research- Hyderabad (TIFR-H), Hyderabad, Telangana 500046, India
| | - U.S. Sandra
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Siddhesh S. Kamat
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Ullas Kolthur-Seetharam
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
- Tata Institute of Fundamental Research- Hyderabad (TIFR-H), Hyderabad, Telangana 500046, India
| |
Collapse
|
4
|
Li J, Kalev-Zylinska ML. Advances in molecular characterization of myeloid proliferations associated with Down syndrome. Front Genet 2022; 13:891214. [PMID: 36035173 PMCID: PMC9399805 DOI: 10.3389/fgene.2022.891214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Myeloid leukemia associated with Down syndrome (ML-DS) has a unique molecular landscape that differs from other subtypes of acute myeloid leukemia. ML-DS is often preceded by a myeloproliferative neoplastic condition called transient abnormal myelopoiesis (TAM) that disrupts megakaryocytic and erythroid differentiation. Over the last two decades, many genetic and epigenetic changes in TAM and ML-DS have been elucidated. These include overexpression of molecules and micro-RNAs located on chromosome 21, GATA1 mutations, and a range of other somatic mutations and chromosomal alterations. In this review, we summarize molecular changes reported in TAM and ML-DS and provide a comprehensive discussion of these findings. Recent advances in the development of CRISPR/Cas9-modified induced pluripotent stem cell-based disease models are also highlighted. However, despite significant progress in this area, we still do not fully understand the pathogenesis of ML-DS, and there are no targeted therapies. Initial diagnosis of ML-DS has a favorable prognosis, but refractory and relapsed disease can be difficult to treat; therapeutic options are limited in Down syndrome children by their stronger sensitivity to the toxic effects of chemotherapy. Because of the rarity of TAM and ML-DS, large-scale multi-center studies would be helpful to advance molecular characterization of these diseases at different stages of development and progression.
Collapse
Affiliation(s)
- Jixia Li
- Blood and Cancer Biology Laboratory, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Department of Laboratory Medicine, School of Medicine, Foshan University, Foshan, China
- *Correspondence: Jixia Li, ; Maggie L. Kalev-Zylinska,
| | - Maggie L. Kalev-Zylinska
- Blood and Cancer Biology Laboratory, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Haematology Laboratory, Department of Pathology and Laboratory Medicine, Auckland City Hospital, Auckland, New Zealand
- *Correspondence: Jixia Li, ; Maggie L. Kalev-Zylinska,
| |
Collapse
|
5
|
Whole Genome DNA Methylation Profiling of D2 Medium Spiny Neurons in Mouse Nucleus Accumbens Using Two Independent Library Preparation Methods. Genes (Basel) 2022; 13:genes13020306. [PMID: 35205351 PMCID: PMC8872013 DOI: 10.3390/genes13020306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
DNA methylation plays essential roles in various cellular processes. Next-generation sequencing has enabled us to study the functional implication of DNA methylation across the whole genome. However, this approach usually requires a substantial amount of genomic DNA, which limits its application to defined cell types within a discrete brain region. Here, we applied two separate protocols, Accel-NGS Methyl-Seq (AM-seq) and Enzymatic Methyl-seq (EM-seq), to profile the methylome of D2 dopamine receptor-expressing medium spiny neurons (D2-MSNs) in mouse nucleus accumbens (NAc). Using 40 ng DNA extracted from FACS-isolated D2-MSNs, we found that both methods yielded comparably high-quality methylome data. Additionally, we identified numerous unmethylated regions (UMRs) as cell type-specific regulatory regions. By comparing the NAc D2-MSN methylome with the published methylomes of mouse prefrontal cortex excitatory neurons and neural progenitor cells (NPCs), we identified numerous differentially methylated CpG and non-CpG regions. Our study not only presents a comparison of these two low-input DNA whole genome methylation profiling protocols, but also provides a resource of DNA methylome of mouse accumbal D2-MSNs, a neuron type that has critical roles in addiction and other neuropsychiatric disorders.
Collapse
|
6
|
Li J, Shen Z, Wang Z, Chao H, Xu Y, Zeng Z, Bian X, Zhang J, Pan J, Miao W, Wu W, Yao L, Chen S, Wen L. CTCF: A novel fusion partner of ETO2 in a multiple relapsed acute myeloid leukemia patient. J Leukoc Biol 2021; 111:981-987. [PMID: 34622967 DOI: 10.1002/jlb.2a0720-441rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
ETO2 is a nuclear co-repressor, which plays a critical role in the regulation of the cell cycle, self-renewal capacity, and differentiation of hematopoietic progenitor cells. We identified novel fusion transcripts involving ETO2 and CTCF by RNA-seq in a multiple relapsed AML case. The CTCF-ETO2 and ETO2-CTCF chimeric genes were validated by RT-PCR and Sanger sequencing. In addition, both transcripts apparently promoted cell proliferation via JAK/STAT3 pathway that is sensitive to STAT3 inhibitors. The novel fusions may have prognostic value and pathogenic mechanisms in acute myeloid leukemia.
Collapse
Affiliation(s)
- Jiao Li
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, P. R. China.,Hematology Department, Yixing People's Hospital of Jiangsu Province, Yixing, Wuxi, P. R. China
| | - Zhen Shen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, P. R. China
| | - Zheng Wang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, P. R. China.,Suzhou Jsuniwell Medical Laboratory, Suzhou, P. R. China
| | - Hongying Chao
- Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, P. R. China
| | - Yi Xu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, P. R. China
| | - Zhao Zeng
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, P. R. China
| | - Xiaosen Bian
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P. R. China
| | - Jun Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, P. R. China
| | - Jinlan Pan
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, P. R. China
| | - Weiwei Miao
- Changshu No.1 People's Hospital, Suzhou, P. R. China
| | - Wenzhong Wu
- Hematology Department, Yixing People's Hospital of Jiangsu Province, Yixing, Wuxi, P. R. China
| | - Li Yao
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, P. R. China
| | - Suning Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, P. R. China.,Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P. R. China
| | - Lijun Wen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, P. R. China.,Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P. R. China
| |
Collapse
|
7
|
de Castro CPM, Cadefau M, Cuartero S. The Mutational Landscape of Myeloid Leukaemia in Down Syndrome. Cancers (Basel) 2021; 13:4144. [PMID: 34439298 PMCID: PMC8394284 DOI: 10.3390/cancers13164144] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 12/12/2022] Open
Abstract
Children with Down syndrome (DS) are particularly prone to haematopoietic disorders. Paediatric myeloid malignancies in DS occur at an unusually high frequency and generally follow a well-defined stepwise clinical evolution. First, the acquisition of mutations in the GATA1 transcription factor gives rise to a transient myeloproliferative disorder (TMD) in DS newborns. While this condition spontaneously resolves in most cases, some clones can acquire additional mutations, which trigger myeloid leukaemia of Down syndrome (ML-DS). These secondary mutations are predominantly found in chromatin and epigenetic regulators-such as cohesin, CTCF or EZH2-and in signalling mediators of the JAK/STAT and RAS pathways. Most of them are also found in non-DS myeloid malignancies, albeit at extremely different frequencies. Intriguingly, mutations in proteins involved in the three-dimensional organization of the genome are found in nearly 50% of cases. How the resulting mutant proteins cooperate with trisomy 21 and mutant GATA1 to promote ML-DS is not fully understood. In this review, we summarize and discuss current knowledge about the sequential acquisition of genomic alterations in ML-DS.
Collapse
Affiliation(s)
| | - Maria Cadefau
- Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, 08916 Badalona, Spain; (C.P.M.d.C); (M.C.)
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain
| | - Sergi Cuartero
- Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, 08916 Badalona, Spain; (C.P.M.d.C); (M.C.)
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain
| |
Collapse
|
8
|
Wee Y, Liu Y, Zhao M. Identification of consistent post-translational regulatory triplets related to oncogenic and tumour suppressive modulators in childhood acute lymphoblastic leukemia. PeerJ 2021; 9:e11803. [PMID: 34316412 PMCID: PMC8286060 DOI: 10.7717/peerj.11803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 06/26/2021] [Indexed: 11/24/2022] Open
Abstract
Background Acute lymphoblastic leukemia (ALL) is the most common type of childhood cancer. It can be caused by mutations that turn on oncogenes or turn off tumour suppressor genes. For instance, changes in certain genes including Rb and p53 are common in ALL cells. Oncogenes and TSGs may serve as a modulator gene to regulate the gene expression level via their respective target genes. To investigate the regulatory relationship between oncogenes, tumour suppressor genes and transcription factors at the post translational level in childhood ALL, we performed an integrative network analysis on the gene regulation in the post-translational level for childhood ALL based on many publicly available cancer gene expression data including TARGET and GEO database. Methods We collected 259 childhood ALL-related genes from the latest online leukemia database, Leukemia Gene Literature Database. These 259 genes were selected from a comprehensive systematic literature with experimental evidences. The identified and curated genes were also associated with patient survival cases and we incorporated this pediatric ALL-related gene list into our analysis. We extracted the known human TFs from the TRRUST database. Among 259 childhood ALL-related genes, 101 unique regulators were mapped to the list of oncogene and tumour suppressor genes (TSGs) from the ONGene and the TSGene databases, and these included 74 TSGs, 62 oncogenes and 46 TF genes. Results The resulted regulation was presented as a hierarchical regulatory network with transcription factors (TFs) as intermediate regulators connecting the top modulators (oncogene and TSGs) to the common target genes. Cross-validation was applied to the results from the TARGET dataset by identifying the consistent regulatory motifs based on three independent ALL expression datasets. A three-layer regulatory network of consistent positive modulators in childhood ALL was constructed in which 74 modulators (40 oncogenes, 34 TSGs) are considered as the most important regulators. The middle layer and the bottom layer contain 34 TFs and 176 target genes, respectively. Oncogenes mostly participated in positive regulation of gene expression and the transcription process of RNA II polymerase, while TSGs were mainly involved in the negative regulation of gene expression. In addition, the oncogene-specific targets were enriched with regulators of the MAPK cascade while tumour suppressor-specific targets were associated with cell death. Conclusion The results revealed that oncogenes and TSGs possess a different functional regulatory pattern with regard to not only their biological functions but also their specific target genes in childhood ALL cancer progression. Taken together, our findings could contribute to a better understanding of the important regulatory mechanisms and this method could be used to analyse the targeted genes at the post-translational level in childhood ALL through integrative network analysis.
Collapse
Affiliation(s)
- YongKiat Wee
- School of Science and Engineering, University of the Sunshine Coast, Sunshine Coast, QLD, Australia
| | - Yining Liu
- The School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Min Zhao
- School of Science and Engineering, University of the Sunshine Coast, Sunshine Coast, QLD, Australia
| |
Collapse
|
9
|
Varela T, Conceição N, Laizé V, Cancela ML. Transcriptional regulation of human DUSP4 gene by cancer-related transcription factors. J Cell Biochem 2021; 122:1556-1566. [PMID: 34254709 DOI: 10.1002/jcb.30078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 11/11/2022]
Abstract
Dual specificity phosphatase 4 (DUSP4), a member of the dual specificity phosphatase family, is responsible for the dephosphorylation and inactivation of ERK, JNK and p38, which are mitogen-activated protein kinases involved in cell proliferation, differentiation and apoptosis, but also in inflammation processes. Given its importance for cellular signalling, DUSP4 is subjected to a tight regulation and there is growing evidence that its expression is dysregulated in several tumours. However, the mechanisms underlying DUSP4 transcriptional regulation remain poorly understood. Here, we analysed the regulation of the human DUSP4 promoters 1 and 2, located upstream of exons 1 and 2, respectively, by the cancer-related transcription factors (TFs) STAT3, FOXA1, CTCF and YY1. The presence of binding sites for these TFs was predicted in both promoters through the in silico analysis of DUSP4, and their functionality was assessed through luciferase activity assays. Regulatory activity of the TFs tested was found to be promoter-specific. While CTCF stimulated the activity of promoter 2 that controls the transcription of variants 2 and X1, STAT3 stimulated the activity of promoter 1 that controls the transcription of variant 1. YY1 positively regulated both promoters, although to different extents. Through site-directed mutagenesis, the functionality of YY1 binding sites present in promoter 2 was confirmed. This study provides novel insights into the transcriptional regulation of DUSP4, contributing to a better comprehension of the mechanisms of its dysregulation observed in several types of cancer.
Collapse
Affiliation(s)
- Tatiana Varela
- Centre of Marine Sciences, University of Algarve, Faro, Portugal.,Faculty of Medicine and Biomedical Sciences, University of Algarve, Faro, Portugal
| | - Natércia Conceição
- Centre of Marine Sciences, University of Algarve, Faro, Portugal.,Faculty of Medicine and Biomedical Sciences, University of Algarve, Faro, Portugal.,Algarve Biomedical Center, University of Algarve, Faro, Portugal
| | - Vincent Laizé
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - M Leonor Cancela
- Centre of Marine Sciences, University of Algarve, Faro, Portugal.,Algarve Biomedical Center, University of Algarve, Faro, Portugal
| |
Collapse
|
10
|
AML displays increased CTCF occupancy associated with aberrant gene expression and transcription factor binding. Blood 2021; 136:339-352. [PMID: 32232485 DOI: 10.1182/blood.2019002326] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 03/01/2020] [Indexed: 12/11/2022] Open
Abstract
CCTC-binding factor (CTCF) is a key regulator of gene expression through organization of the chromatin structure. Still, it is unclear how CTCF binding is perturbed in leukemia or in cancer in general. We studied CTCF binding by chromatin immunoprecipitation sequencing in cells from patients with acute myeloid leukemia (AML) and in normal bone marrow (NBM) in the context of gene expression, DNA methylation, and azacitidine exposure. CTCF binding was increased in AML compared with NBM. Aberrant CTCF binding was enriched for motifs for key myeloid transcription factors such as CEBPA, PU.1, and RUNX1. AML with TET2 mutations was characterized by a particularly strong gain of CTCF binding, highly enriched for gain in promoter regions, while AML in general was enriched for changes at enhancers. There was a strong anticorrelation between CTCF binding and DNA methylation. Gain of CTCF occupancy was associated with increased gene expression; however, the genomic location (promoter vs distal regions) and enrichment of motifs (for repressing vs activating cofactors) were decisive for the gene expression pattern. Knockdown of CTCF in K562 cells caused loss of CTCF binding and transcriptional repression of genes with changed CTCF binding in AML, as well as loss of RUNX1 binding at RUNX1/CTCF-binding sites. In addition, CTCF knockdown caused increased differentiation. Azacitidine exposure caused major changes in CTCF occupancy in AML patient cells, partly by restoring a CTCF-binding pattern similar to NBM. We conclude that AML displays an aberrant increase in CTCF occupancy that targets key genes for AML development and impacts gene expression.
Collapse
|
11
|
Singbrant S, Mattebo A, Sigvardsson M, Strid T, Flygare J. Prospective isolation of radiation induced erythroid stress progenitors reveals unique transcriptomic and epigenetic signatures enabling increased erythroid output. Haematologica 2020; 105:2561-2571. [PMID: 33131245 PMCID: PMC7604643 DOI: 10.3324/haematol.2019.234542] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 01/02/2020] [Indexed: 11/09/2022] Open
Abstract
Massive expansion of erythroid progenitor cells is essential for surviving anemic stress. Research towards understanding this critical process, referred to as stress-erythropoiesis, has been hampered due to lack of specific marker-combinations enabling analysis of the distinct stress-progenitor cells capable of providing radioprotection and enhanced red blood cell production. Here we present a method for precise identification and in vivo validation of progenitor cells contributing to both steady-state and stress-erythropoiesis, enabling for the first time in-depth molecular characterization of these cells. Differential expression of surface markers CD150, CD9 and Sca1 defines a hierarchy of splenic stress-progenitors during irradiation-induced stress recovery in mice, and provides high-purity isolation of the functional stress-BFU-Es with a 100-fold improved enrichment compared to state-of-the-art. By transplanting purified stress-progenitors expressing the fluorescent protein Kusabira Orange, we determined their kinetics in vivo and demonstrated that CD150+CD9+Sca1- stress-BFU-Es provide a massive but transient radioprotective erythroid wave, followed by multi-lineage reconstitution from CD150+CD9+Sca1+ multi-potent stem/progenitor cells. Whole genome transcriptional analysis revealed that stress-BFU-Es express gene signatures more associated with erythropoiesis and proliferation compared to steady-state BFU-Es, and are BMP-responsive. Evaluation of chromatin accessibility through ATAC sequencing reveals enhanced and differential accessibility to binding sites of the chromatin-looping transcription factor CTCF in stress-BFU-Es compared to steady-state BFU-Es. Our findings offer molecular insight to the unique capacity of stress-BFU-Es to rapidly form erythroid cells in response to anemia and constitute an important step towards identifying novel erythropoiesis stimulating agents.
Collapse
Affiliation(s)
- Sofie Singbrant
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University
| | - Alexander Mattebo
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University
| | - Mikael Sigvardsson
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Tobias Strid
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Johan Flygare
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University
| |
Collapse
|
12
|
Sawaengdee W, Cui K, Zhao K, Hongeng S, Fucharoen S, Wongtrakoongate P. Genome-Wide Transcriptional Regulation of the Long Non-coding RNA Steroid Receptor RNA Activator in Human Erythroblasts. Front Genet 2020; 11:850. [PMID: 32849830 PMCID: PMC7431964 DOI: 10.3389/fgene.2020.00850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/13/2020] [Indexed: 01/21/2023] Open
Abstract
Erythropoiesis of human hematopoietic stem cells (HSCs) maintains generation of red blood cells throughout life. However, little is known how human erythropoiesis is regulated by long non-coding RNAs (lncRNAs). By using ChIRP-seq, we report here that the lncRNA steroid receptor RNA activator (SRA) occupies chromatin, and co-localizes with CTCF, H3K4me3, and H3K27me3 genome-wide in human erythroblast cell line K562. CTCF binding sites that are also occupied by SRA are enriched for either H3K4me3 or H3K27me3. Transcriptome-wide analyses reveal that SRA facilitates expression of erythroid-associated genes, while repressing leukocyte-associated genes in both K562 and CD36-positive primary human proerythroblasts derived from HSCs. We find that SRA-regulated genes are enriched by both CTCF and SRA bindings. Further, silencing of SRA decreases expression of the erythroid-specific markers TFRC and GYPA, and down-regulates expression of globin genes in both K562 and human proerythroblast cells. Taken together, our findings establish that the lncRNA SRA occupies chromatin, and promotes transcription of erythroid genes, therefore facilitating human erythroid transcriptional program.
Collapse
Affiliation(s)
- Waritta Sawaengdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kairong Cui
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Bangkok, Thailand
| | - Patompon Wongtrakoongate
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok, Thailand
| |
Collapse
|
13
|
Hyle J, Zhang Y, Wright S, Xu B, Shao Y, Easton J, Tian L, Feng R, Xu P, Li C. Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping. Nucleic Acids Res 2019; 47:6699-6713. [PMID: 31127282 PMCID: PMC6648894 DOI: 10.1093/nar/gkz462] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/12/2019] [Accepted: 05/14/2019] [Indexed: 12/11/2022] Open
Abstract
Numerous pieces of evidence support the complex, 3D spatial organization of the genome dictates gene expression. CTCF is essential to define topologically associated domain boundaries and to facilitate the formation of insulated chromatin loop structures. To understand CTCF's direct role in global transcriptional regulation, we integrated the miniAID-mClover3 cassette to the endogenous CTCF locus in a human pediatric B-ALL cell line, SEM, and an immortal erythroid precursor cell line, HUDEP-2, to allow for acute depletion of CTCF protein by the auxin-inducible degron system. In SEM cells, CTCF loss notably disrupted intra-TAD loops and TAD integrity in concurrence with a reduction in CTCF-binding affinity, while showing no perturbation to nuclear compartment integrity. Strikingly, the overall effect of CTCF's loss on transcription was minimal. Whole transcriptome analysis showed hundreds of genes differentially expressed in CTCF-depleted cells, among which MYC and a number of MYC target genes were specifically downregulated. Mechanically, acute depletion of CTCF disrupted the direct interaction between the MYC promoter and its distal enhancer cluster residing ∼1.8 Mb downstream. Notably, MYC expression was not profoundly affected upon CTCF loss in HUDEP-2 cells suggesting that CTCF could play a B-ALL cell line specific role in maintaining MYC expression.
Collapse
Affiliation(s)
- Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ying Shao
- Department of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ruopeng Feng
- Department of Hematology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Peng Xu
- Department of Hematology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| |
Collapse
|
14
|
Zhang B, Zhang Y, Zou X, Chan AW, Zhang R, Lee TKW, Liu H, Lau EYT, Ho NPY, Lai PB, Cheung YS, To KF, Wong HK, Choy KW, Keng VW, Chow LM, Chan KK, Cheng AS, Ko BC. The CCCTC-binding factor (CTCF)-forkhead box protein M1 axis regulates tumour growth and metastasis in hepatocellular carcinoma. J Pathol 2017; 243:418-430. [PMID: 28862757 PMCID: PMC5725705 DOI: 10.1002/path.4976] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 08/16/2017] [Accepted: 08/24/2017] [Indexed: 12/21/2022]
Abstract
CCCTC‐binding factor (CTCF) is a DNA‐binding protein that interacts with a large number of highly divergent target sequences throughout the genome. It is implicated in a variety of functions, including chromatin organization and transcriptional control. The functional role of CTCF in tumour pathogenesis remains elusive. We showed that CTCF is frequently upregulated in a subset of primary hepatocellular carcinomas (HCCs) as compared with non‐tumoural liver. Overexpression of CTCF was associated with shorter disease‐free survival of patients. Short hairpin RNA (shRNA)‐mediated suppression of CTCF inhibited cell proliferation, motility and invasiveness in HCC cell lines; these effects were correlated with prominent reductions in the expression of telomerase reverse transcriptase (TERT), the shelterin complex member telomerase repeat‐binding factor 1, and forkhead box protein M1 (FOXM1). In contrast, upregulation of CTCF was positively correlated with FOXM1 and TERT expression in clinical HCC biopsies. Depletion of CTCF resulted in reduced motility and invasiveness in HCC cells that could be reversed by ectopic expression of FOXM1, suggesting that FOXM1 is one of the important downstream effectors of CTCF in HCC. Reporter gene analysis suggested that depletion of CTCF is associated with reduced FOXM1 and TERT promoter activity. Chromatin immunoprecipitation (ChIP)–polymerase chain reaction (PCR) analysis further revealed occupancy of the FOXM1 promoter by CTCF in vivo. Importantly, depletion of CTCF by shRNA significantly inhibited tumour progression and metastasis in HCC mouse models. Our work uncovered a novel functional role of CTCF in HCC pathogenesis, which suggests that targeting CTCF could be further explored as a potential therapeutic strategy for HCC. © 2017 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Bin Zhang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, PR China
| | - Yajing Zhang
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, PR China.,Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China.,State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China
| | - Xiaoping Zou
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, PR China
| | - Anthony Wh Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, SAR, PR China
| | - Rui Zhang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China.,State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China
| | - Terence Kin-Wah Lee
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China.,State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China
| | - Hang Liu
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China
| | - Eunice Yuen-Ting Lau
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China
| | - Nicole Pui-Yu Ho
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China
| | - Paul Bs Lai
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, SAR, PR China
| | - Yue-Sun Cheung
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, SAR, PR China
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, SAR, PR China
| | - Hoi Kin Wong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, PR China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, PR China
| | - Vincent W Keng
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China
| | - Larry Mc Chow
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China.,State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China
| | - Kenrick Ky Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China
| | - Alfred S Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, PR China
| | - Ben Cb Ko
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, PR China.,Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China.,State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hong Kong, SAR, PR China
| |
Collapse
|
15
|
Kim TG, Kim S, Jung S, Kim M, Yang B, Lee MG, Kim HP. CCCTC-binding factor is essential to the maintenance and quiescence of hematopoietic stem cells in mice. Exp Mol Med 2017; 49:e371. [PMID: 28857086 PMCID: PMC5579513 DOI: 10.1038/emm.2017.124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/27/2017] [Accepted: 03/20/2017] [Indexed: 12/11/2022] Open
Abstract
Hematopoiesis involves a series of lineage differentiation programs initiated in hematopoietic stem cells (HSCs) found in bone marrow (BM). To ensure lifelong hematopoiesis, various molecular mechanisms are needed to maintain the HSC pool. CCCTC-binding factor (CTCF) is a DNA-binding, zinc-finger protein that regulates the expression of its target gene by organizing higher order chromatin structures. Currently, the role of CTCF in controlling HSC homeostasis is unknown. Using a tamoxifen-inducible CTCF conditional knockout mouse system, we aimed to determine whether CTCF regulates the homeostatic maintenance of HSCs. In adult mice, acute systemic CTCF ablation led to severe BM failure and the rapid shrinkage of multiple c-Kithi progenitor populations, including Sca-1+ HSCs. Similarly, hematopoietic system-confined CTCF depletion caused an acute loss of HSCs and highly increased mortality. Mixed BM chimeras reconstituted with supporting BM demonstrated that CTCF deficiency-mediated HSC depletion has both cell-extrinsic and cell-intrinsic effects. Although c-Kithi myeloid progenitor cell populations were severely reduced after ablating Ctcf, c-Kitint common lymphoid progenitors and their progenies were less affected by the lack of CTCF. Whole-transcriptome microarray and cell cycle analyses indicated that CTCF deficiency results in the enhanced expression of the cell cycle-promoting program, and that CTCF-depleted HSCs express higher levels of reactive oxygen species (ROS). Importantly, in vivo treatment with an antioxidant partially rescued c-Kithi cell populations and their quiescence. Altogether, our results suggest that CTCF is indispensable for maintaining adult HSC pools, likely by regulating ROS-dependent HSC quiescence.
Collapse
Affiliation(s)
- Tae-Gyun Kim
- Department of Environmental Medical Biology, Institute. of Tropical Medicine, Yonsei University College of Medicine, Seoul, Korea.,BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.,Department of Dermatology, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Sueun Kim
- Department of Environmental Medical Biology, Institute. of Tropical Medicine, Yonsei University College of Medicine, Seoul, Korea.,BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Soyeon Jung
- Department of Environmental Medical Biology, Institute. of Tropical Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Mikyoung Kim
- Department of Environmental Medical Biology, Institute. of Tropical Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Bobae Yang
- Department of Environmental Medical Biology, Institute. of Tropical Medicine, Yonsei University College of Medicine, Seoul, Korea.,BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Min-Geol Lee
- BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.,Department of Dermatology, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Hyoung-Pyo Kim
- Department of Environmental Medical Biology, Institute. of Tropical Medicine, Yonsei University College of Medicine, Seoul, Korea.,BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| |
Collapse
|
16
|
Wu J, Li PC, Pang JY, Liu GY, Xie XM, Li JY, Yin YC, Han JH, Guo XZ, Qiu L. CCCTC-binding factor inhibits breast cancer cell proliferation and metastasis via inactivation of the nuclear factor-kappaB pathway. Oncotarget 2017; 8:93516-93529. [PMID: 29212169 PMCID: PMC5706815 DOI: 10.18632/oncotarget.18977] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 06/18/2017] [Indexed: 11/25/2022] Open
Abstract
CCCTC-binding factor (CTCF) is an important epigenetic regulator implicated in multiple cellular processes, including growth, proliferation, differentiation, and apoptosis. Although CTCF deletion or mutation has been associated with human breast cancer, the role of CTCF in breast cancer is questionable. We investigated the biological functions of CTCF in breast cancer and the underlying mechanism. The results showed that CTCF expression in human breast cancer cells and tissues was significantly lower than that in normal breast cells and tissues. In addition, CTCF expression correlated significantly with cancer stage (P = 0.043) and pathological differentiation (P = 0.029). Furthermore, CTCF overexpression resulted in the inhibition of proliferation, migration, and invasion, while CTCF knockdown induced these processes in breast cancer cells. Transcriptome analysis and further experimental confirmation in MDA-MD-231 cells revealed that forced overexpression of CTCF might attenuate the DNA-binding ability of nuclear factor-kappaB (NF-κB) p65 subunit and inhibit activation of NF-κB and its target pro-oncogenes (tumor necrosis factor alpha-induced protein 3 [TNFAIP3]) and genes for growth-related proteins (early growth response protein 1 [EGR1] and growth arrest and DNA-damage-inducible alpha [GADD45a]). The present study provides a new insight into the tumor suppressor roles of CTCF in breast cancer development and suggests that the CTCF/NF-κB pathway is a potential target for breast cancer therapy.
Collapse
Affiliation(s)
- Jie Wu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, 100730, China
| | - Peng-Chang Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, 100730, China
| | - Jun-Yi Pang
- Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, 100730, China
| | - Guo-You Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Xue-Min Xie
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Jia-Yao Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, 100730, China
| | - Yi-Cong Yin
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, 100730, China
| | - Jian-Hua Han
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, 100730, China
| | - Xiu-Zhi Guo
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, 100730, China
| | - Ling Qiu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, 100730, China
| |
Collapse
|
17
|
Laitem C, Zaborowska J, Tellier M, Yamaguchi Y, Cao Q, Egloff S, Handa H, Murphy S. CTCF regulates NELF, DSIF and P-TEFb recruitment during transcription. Transcription 2015; 6:79-90. [PMID: 26399478 PMCID: PMC4802788 DOI: 10.1080/21541264.2015.1095269] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
CTCF is a versatile transcription factor with well-established roles in chromatin organization and insulator function. Recent findings also implicate CTCF in the control of elongation by RNA polymerase (RNAP) II. Here we show that CTCF knockdown abrogates RNAP II pausing at the early elongation checkpoint of c-myc by affecting recruitment of DRB-sensitivity-inducing factor (DSIF). CTCF knockdown also causes a termination defect on the U2 snRNA genes (U2), by affecting recruitment of negative elongation factor (NELF). In addition, CTCF is required for recruitment of positive elongation factor b (P-TEFb), which phosphorylates NELF, DSIF, and Ser2 of the RNAP II CTD to activate elongation of transcription of c-myc and recognition of the snRNA gene-specific 3' box RNA processing signal. These findings implicate CTCF in a complex network of protein:protein/protein:DNA interactions and assign a key role to CTCF in controlling RNAP II transcription through the elongation checkpoint of the protein-coding c-myc and the termination site of the non-coding U2, by regulating the recruitment and/or activity of key players in these processes.
Collapse
Affiliation(s)
- Clélia Laitem
- a Sir William Dunn School of Pathology; University of Oxford ; Oxford , UK.,e Current address: Immunocore Limited; Milton Park , Abingdon , Oxon , UK
| | - Justyna Zaborowska
- a Sir William Dunn School of Pathology; University of Oxford ; Oxford , UK
| | - Michael Tellier
- a Sir William Dunn School of Pathology; University of Oxford ; Oxford , UK
| | - Yuki Yamaguchi
- b Graduate School of Bioscience and Biotechnology; Tokyo Institute of Technology ; Yokohama , Japan
| | - Qingfu Cao
- b Graduate School of Bioscience and Biotechnology; Tokyo Institute of Technology ; Yokohama , Japan
| | - Sylvain Egloff
- c Université de Toulouse; UPS; Laboratoire de Biologie Moléculaire Eucaryote ; Toulouse , France
| | - Hiroshi Handa
- d Department of Nanoparticle Translational Research ; Tokyo Medical University ; Tokyo , Japan
| | - Shona Murphy
- a Sir William Dunn School of Pathology; University of Oxford ; Oxford , UK
| |
Collapse
|
18
|
The roles of SNF2/SWI2 nucleosome remodeling enzymes in blood cell differentiation and leukemia. BIOMED RESEARCH INTERNATIONAL 2015; 2015:347571. [PMID: 25789315 PMCID: PMC4348595 DOI: 10.1155/2015/347571] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 01/27/2015] [Indexed: 12/15/2022]
Abstract
Here, we review the role of sucrose nonfermenting (SNF2) family enzymes in blood cell development. The SNF2 family comprises helicase-like ATPases, originally discovered in yeast, that can remodel chromatin by changing chromatin structure and composition. The human genome encodes 30 different SNF2 enzymes. SNF2 family enzymes are often part of multisubunit chromatin remodeling complexes (CRCs), which consist of noncatalytic/auxiliary subunit along with the ATPase subunit. However, blood cells express a limited set of SNF2 ATPases that are necessary to maintain the pool of hematopoietic stem cells (HSCs) and drive normal blood cell development and differentiation. The composition of CRCs can be altered by the association of specific auxiliary subunits. Several auxiliary CRC subunits have specific functions in hematopoiesis. Aberrant expressions of SNF2 ATPases and/or auxiliary CRC subunit(s) are often observed in hematological malignancies. Using large-scale data from the International Cancer Genome Consortium (ICGC) we observed frequent mutations in genes encoding SNF2 helicase-like enzymes and auxiliary CRC subunits in leukemia. Hence, orderly function of SNF2 family enzymes is crucial for the execution of normal blood cell developmental program, and defects in chromatin remodeling caused by mutations or aberrant expression of these proteins may contribute to leukemogenesis.
Collapse
|
19
|
Schönheit J, Leutz A, Rosenbauer F. Chromatin Dynamics during Differentiation of Myeloid Cells. J Mol Biol 2015; 427:670-87. [DOI: 10.1016/j.jmb.2014.08.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 08/05/2014] [Accepted: 08/20/2014] [Indexed: 12/23/2022]
|
20
|
Abstract
DNA methylation and histone modification are epigenetic mechanisms that result in altered gene expression and cellular phenotype. The exact role of methylation in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) remains unclear. However, aberrations (e.g. loss-/gain-of-function or up-/down-regulation) in components of epigenetic transcriptional regulation in general, and of the methylation machinery in particular, have been implicated in the pathogenesis of these diseases. In addition, many of these components have been identified as therapeutic targets for patients with MDS/AML, and are also being assessed as potential biomarkers of response or resistance to hypomethylating agents (HMAs). The HMAs 5-azacitidine (AZA) and 2'-deoxy-5-azacitidine (decitabine, DAC) inhibit DNA methylation and have shown significant clinical benefits in patients with myeloid malignancies. Despite being viewed as mechanistically similar drugs, AZA and DAC have differing mechanisms of action. DAC is incorporated 100% into DNA, whereas AZA is incorporated into RNA (80-90%) as well as DNA (10-20%). As such, both drugs inhibit DNA methyltransferases (DNMTs; dependently or independently of DNA replication) resulting in the re-expression of tumor-suppressor genes; however, AZA also has an impact on mRNA and protein metabolism via its inhibition of ribonucleotide reductase, resulting in apoptosis. Herein, we first give an overview of transcriptional regulation, including DNA methylation, post-translational histone-tail modifications, the role of micro-RNA and long-range epigenetic gene silencing. We place special emphasis on epigenetic transcriptional regulation and discuss the implication of various components in the pathogenesis of MDS/AML, their potential as therapeutic targets, and their therapeutic modulation by HMAs and other substances (if known). The main focus of this review is laid on dissecting the rapidly evolving knowledge of AZA and DAC with a special focus on their differing mechanisms of action, and the effect of HMAs on transcriptional regulation.
Collapse
Affiliation(s)
- Lisa Pleyer
- 3rd Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Laboratory for Immunological and Molecular Cancer Research, Oncologic Center, Paracelsus Medical University Hospital Salzburg, Center for Clinical Cancer and Immunology Trials at Salzburg Cancer Research Institute , Salzburg , Austria
| | | |
Collapse
|
21
|
De Antonellis P, Carotenuto M, Vandenbussche J, De Vita G, Ferrucci V, Medaglia C, Boffa I, Galiero A, Di Somma S, Magliulo D, Aiese N, Alonzi A, Spano D, Liguori L, Chiarolla C, Verrico A, Schulte JH, Mestdagh P, Vandesompele J, Gevaert K, Zollo M. Early targets of miR-34a in neuroblastoma. Mol Cell Proteomics 2014; 13:2114-31. [PMID: 24912852 DOI: 10.1074/mcp.m113.035808] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Several genes encoding for proteins involved in proliferation, invasion, and apoptosis are known to be direct miR-34a targets. Here, we used proteomics to screen for targets of miR-34a in neuroblastoma (NBL), a childhood cancer that originates from precursor cells of the sympathetic nervous system. We examined the effect of miR-34a overexpression using a tetracycline inducible system in two NBL cell lines (SHEP and SH-SY5Y) at early time points of expression (6, 12, and 24 h). Proteome analysis using post-metabolic labeling led to the identification of 2,082 proteins, and among these 186 were regulated (112 proteins down-regulated and 74 up-regulated). Prediction of miR-34a targets via bioinformatics showed that 32 transcripts held miR-34a seed sequences in their 3'-UTR. By combining the proteomics data with Kaplan Meier gene-expression studies, we identified seven new gene products (ALG13, TIMM13, TGM2, ABCF2, CTCF, Ki67, and LYAR) that were correlated with worse clinical outcomes. These were further validated in vitro by 3'-UTR seed sequence regulation. In addition, Michigan Molecular Interactions searches indicated that together these proteins affect signaling pathways that regulate cell cycle and proliferation, focal adhesions, and other cellular properties that overall enhance tumor progression (including signaling pathways such as TGF-β, WNT, MAPK, and FAK). In conclusion, proteome analysis has here identified early targets of miR-34a with relevance to NBL tumorigenesis. Along with the results of previous studies, our data strongly suggest miR-34a as a useful tool for improving the chance of therapeutic success with NBL.
Collapse
Affiliation(s)
- Pasqualino De Antonellis
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Marianeve Carotenuto
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Jonathan Vandenbussche
- ‖Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; **Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Gennaro De Vita
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Veronica Ferrucci
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Chiara Medaglia
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Iolanda Boffa
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Alessandra Galiero
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Sarah Di Somma
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Daniela Magliulo
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Nadia Aiese
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Alessandro Alonzi
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Daniela Spano
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Lucia Liguori
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Cristina Chiarolla
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy
| | - Antonio Verrico
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy; ‡‡Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, 80131 Naples, Italy
| | | | - Pieter Mestdagh
- ¶¶Center for Medical Genetics, Ghent University Hospital, B-9000 Ghent, Belgium
| | - Jo Vandesompele
- ¶¶Center for Medical Genetics, Ghent University Hospital, B-9000 Ghent, Belgium
| | - Kris Gevaert
- ‖Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; **Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Massimo Zollo
- From the ‡Centro di Ingegneria Genetica e Biotecnologie Avanzate (CEINGE), 80145 Naples, Italy; §Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80131 Naples, Italy; ‖‖Centro di Medicina Trasfusionale, Azienda Ospedaliera Federico II, 80131 Naples, Italy
| |
Collapse
|
22
|
Kolodziej S, Kuvardina ON, Oellerich T, Herglotz J, Backert I, Kohrs N, Buscató EL, Wittmann SK, Salinas-Riester G, Bonig H, Karas M, Serve H, Proschak E, Lausen J. PADI4 acts as a coactivator of Tal1 by counteracting repressive histone arginine methylation. Nat Commun 2014; 5:3995. [PMID: 24874575 PMCID: PMC4050257 DOI: 10.1038/ncomms4995] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 04/28/2014] [Indexed: 01/26/2023] Open
Abstract
The transcription factor Tal1 is a
critical activator or repressor of gene expression in hematopoiesis and leukaemia.
The mechanism by which Tal1
differentially influences transcription of distinct genes is not fully understood.
Here we show that Tal1 interacts
with the peptidylarginine deiminase
IV (PADI4). We
demonstrate that PADI4 can act as
an epigenetic coactivator through influencing H3R2me2a. At the Tal1/PADI4 target gene IL6ST the repressive H3R2me2a mark triggered by
PRMT6 is counteracted by
PADI4, which augments the
active H3K4me3 mark and thus increases IL6ST expression. In contrast, at the CTCF promoter PADI4 acts as a repressor. We propose that
the influence of PADI4 on
IL6ST transcription
plays a role in the control of IL6ST expression during lineage differentiation of
hematopoietic stem/progenitor cells. These results open the possibility to
pharmacologically influence Tal1
in leukaemia. Peptidylarginine deiminase 4 (PADI4) is a transcriptional
co-regulator that converts arginine residues at histone tails to citrulline. The authors
show that PADI4 interacts with the central haematopoietic transcription factor TAL1 to
regulate gene expression in an erythroleukemia cell line.
Collapse
Affiliation(s)
- Stephan Kolodziej
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Strasse 42-44, D-60596 Frankfurt am Main, Germany
| | - Olga N Kuvardina
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Strasse 42-44, D-60596 Frankfurt am Main, Germany
| | - Thomas Oellerich
- Department of Medicine, Hematology/Oncology, Johann-Wolfgang-Goethe University, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany
| | - Julia Herglotz
- 1] Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Strasse 42-44, D-60596 Frankfurt am Main, Germany [2]
| | - Ingo Backert
- 1] Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Strasse 42-44, D-60596 Frankfurt am Main, Germany [2]
| | - Nicole Kohrs
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Strasse 42-44, D-60596 Frankfurt am Main, Germany
| | - Estel la Buscató
- Institute of Pharmaceutical Chemistry, Johann-Wolfgang-Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Sandra K Wittmann
- Institute of Pharmaceutical Chemistry, Johann-Wolfgang-Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Gabriela Salinas-Riester
- Medical-University Goettingen, Transcriptome Analysis Laboratory, Justus-von-Liebig-Weg 11, D-37077 Goettingen, Germany
| | - Halvard Bonig
- German Red Cross Blood Service and Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University, Sandhofstrasse 1, D-60528 Frankfurt am Main, Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry, Johann-Wolfgang-Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Hubert Serve
- 1] Department of Medicine, Hematology/Oncology, Johann-Wolfgang-Goethe University, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany [2] German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ewgenij Proschak
- 1] Institute of Pharmaceutical Chemistry, Johann-Wolfgang-Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany [2] German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Jörn Lausen
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Strasse 42-44, D-60596 Frankfurt am Main, Germany
| |
Collapse
|
23
|
A novel mechanism for CTCF in the epigenetic regulation of Bax in breast cancer cells. Neoplasia 2014; 15:898-912. [PMID: 23908591 DOI: 10.1593/neo.121948] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 04/23/2013] [Accepted: 05/03/2013] [Indexed: 01/20/2023] Open
Abstract
We previously reported the association of elevated levels of the multifunctional transcription factor, CCCTC binding factor (CTCF), in breast cancer cells with the specific anti-apoptotic function of CTCF. To understand the molecular mechanisms of this phenomenon, we investigated regulation of the human Bax gene by CTCF in breast and non-breast cells. Two CTCF binding sites (CTSs) within the Bax promoter were identified. In all cells, breast and non-breast, active histone modifications were present at these CTSs, DNA harboring this region was unmethylated, and levels of Bax mRNA and protein were similar. Nevertheless, up-regulation of Bax mRNA and protein and apoptotic cell death were observed only in breast cancer cells depleted of CTCF. We proposed that increased CTCF binding to the Bax promoter in breast cancer cells, by comparison with non-breast cells, may be mechanistically linked to the specific apoptotic phenotype in CTCF-depleted breast cancer cells. In this study, we show that CTCF binding was enriched at the Bax CTSs in breast cancer cells and tumors; in contrast, binding of other transcription factors (SP1, WT1, EGR1, and c-Myc) was generally increased in non-breast cells and normal breast tissues. Our findings suggest a novel mechanism for CTCF in the epigenetic regulation of Bax in breast cancer cells, whereby elevated levels of CTCF support preferential binding of CTCF to the Bax CTSs. In this context, CTCF functions as a transcriptional repressor counteracting influences of positive regulatory factors; depletion of breast cancer cells from CTCF therefore results in the activation of Bax and apoptosis.
Collapse
|
24
|
Dluhosova M, Curik N, Vargova J, Jonasova A, Zikmund T, Stopka T. Epigenetic control of SPI1 gene by CTCF and ISWI ATPase SMARCA5. PLoS One 2014; 9:e87448. [PMID: 24498324 PMCID: PMC3911986 DOI: 10.1371/journal.pone.0087448] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 12/24/2013] [Indexed: 01/08/2023] Open
Abstract
CCCTC-binding factor (CTCF) can both activate as well as inhibit transcription by forming chromatin loops between regulatory regions and promoters. In this regard, Ctcf binding on non-methylated DNA and its interaction with the Cohesin complex results in differential regulation of the H19/Igf2 locus. Similarly, a role for CTCF has been established in normal hematopoietic development; however its involvement in leukemia remains elusive. Here, we show that Ctcf binds to the imprinting control region of H19/Igf2 in AML blasts. We also demonstrate that Smarca5, which also associates with the Cohesin complex, facilitates Ctcf binding to its target sites on DNA. Furthermore, Smarca5 supports Ctcf functionally and is needed for enhancer-blocking effect at ICR. We next asked whether CTCF and SMARCA5 control the expression of key hematopoiesis regulators. In normally differentiating myeloid cells both CTCF and SMARCA5 together with members of the Cohesin complex are recruited to the SPI1 gene, a key hematopoiesis regulator and leukemia suppressor. Due to DNA methylation, CTCF binding to the SPI1 gene is blocked in AML blasts. Upon AZA-mediated DNA demethylation of human AML blasts, CTCF and SMARCA5 are recruited to the −14.4 Enhancer of SPI1 gene and block its expression. Our data provide new insight into complex SPI1 gene regulation now involving additional key epigenetic factors, CTCF and SMARCA5 that control PU.1 expression at the −14.4 Enhancer.
Collapse
MESH Headings
- Acute Disease
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Animals
- Azacitidine/pharmacology
- CCCTC-Binding Factor
- Cell Line, Tumor
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA Methylation/drug effects
- Epigenesis, Genetic
- Gene Expression Regulation, Neoplastic
- Genomic Imprinting
- HeLa Cells
- Humans
- Immunoblotting
- Insulin-Like Growth Factor II/genetics
- Insulin-Like Growth Factor II/metabolism
- K562 Cells
- Leukemia, Erythroblastic, Acute/genetics
- Leukemia, Erythroblastic, Acute/metabolism
- Leukemia, Erythroblastic, Acute/pathology
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/metabolism
- Leukemia, Myeloid/pathology
- Microscopy, Confocal
- Protein Binding
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA Interference
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Trans-Activators/genetics
- Trans-Activators/metabolism
Collapse
Affiliation(s)
- Martina Dluhosova
- Department of Pathophysiology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Nikola Curik
- Department of Pathophysiology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Jarmila Vargova
- Department of Pathophysiology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Anna Jonasova
- Department of Pathophysiology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- Department of Medicine - Hematology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Tomas Zikmund
- Department of Pathophysiology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Tomas Stopka
- Department of Pathophysiology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- Department of Medicine - Hematology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- * E-mail:
| |
Collapse
|
25
|
Zhang H, Zhu L, He H, Zhu S, Zhang W, Liu X, Zhao X, Gao C, Mei M, Bao S, Zheng H. NF-kappa B mediated up-regulation of CCCTC-binding factor in pediatric acute lymphoblastic leukemia. Mol Cancer 2014; 13:5. [PMID: 24393203 PMCID: PMC3928924 DOI: 10.1186/1476-4598-13-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 01/03/2014] [Indexed: 11/25/2022] Open
Abstract
Background Acute lymphoblastic leukemia (ALL) is the most frequently occurring malignant neoplasm in children. Despite advances in treatment and outcomes for ALL patients, the pathogenesis of the disease remains unclear. Microarray analysis of samples from 100 Chinese children with ALL revealed the up-regulation of CTCF (CCCTC binding factor). CTCF is a highly conserved 11-zinc finger protein that is involved in many human cancers; however, the biological function of CTCF in pediatric ALL is unknown. Methods The expression patterns of CTCF were evaluated in matched newly diagnosed (ND), complete remission (CR), and relapsed (RE) bone marrow samples from 28 patients. The potential oncogenic mechanism of CTCF and related pathways in leukemogenesis were investigated in leukemia cell lines. Results We identified significant up-regulation of CTCF in the ND samples. Importantly, the expression of CTCF returned to normal levels after CR but rebounded in the RE samples. In the pre-B ALL cell line Nalm-6, siRNA-mediated silencing of CTCF expression promoted cell apoptosis and reduced cell proliferation; accordingly, over-expression of a cDNA encoding full-length CTCF protected cells from apoptosis and enhanced cell proliferation. Furthermore, inhibition or activation of the nuclear factor-kappa B (NF-κB) pathway resulted in marked variations in the levels of CTCF mRNA and protein in leukemic cells, indicating that CTCF may be involved downstream of the NF-κB pathway. Moreover, inhibition of the NF-κB pathway increased cell apoptosis, which was partially rescued by ectopic over-expression of CTCF, suggesting that CTCF may play a significant role in the anti-apoptotic pathway mediated by NF-κB. Conclusions Our results indicate that CTCF serves as both an anti-apoptotic factor and a proliferative factor in leukemic cells. It potentially contributes to leukemogenesis through the NF-κB pathway in pediatric ALL patients.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Shilai Bao
- Beijing Key Laboratory of Pediatric Hematology Oncology; National Key Discipline of Pediatrics, Ministry of Education; Key Laboratory of Major Diseases in Children, Ministry of Education; Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, 56 Nanlishi Road, Beijing, 100045, China.
| | | |
Collapse
|
26
|
Batlle-López A, Cortiguera MG, Rosa-Garrido M, Blanco R, del Cerro E, Torrano V, Wagner SD, Delgado MD. Novel CTCF binding at a site in exon1A of BCL6 is associated with active histone marks and a transcriptionally active locus. Oncogene 2013; 34:246-56. [PMID: 24362533 DOI: 10.1038/onc.2013.535] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 10/01/2013] [Accepted: 11/01/2013] [Indexed: 12/14/2022]
Abstract
BCL6 is a zinc-finger transcriptional repressor, which is highly expressed in germinal centre B-cells and is essential for germinal centre formation and T-dependent antibody responses. Constitutive BCL6 expression is sufficient to produce lymphomas in mice. Deregulated expression of BCL6 due to chromosomal rearrangements, mutations of a negative autoregulatory site in the BCL6 promoter region and aberrant post-translational modifications have been detected in a number of human lymphomas. Tight lineage and temporal regulation of BCL6 is, therefore, required for normal immunity, and abnormal regulation occurs in lymphomas. CCCTC-binding factor (CTCF) is a multi-functional chromatin regulator, which has recently been shown to bind in a methylation-sensitive manner to sites within the BCL6 first intron. We demonstrate a novel CTCF-binding site in BCL6 exon1A within a potential CpG island, which is unmethylated both in cell lines and in primary lymphoma samples. CTCF binding, which was found in BCL6-expressing cell lines, correlated with the presence of histone variant H2A.Z and active histone marks, suggesting that CTCF induces chromatin modification at a transcriptionally active BCL6 locus. CTCF binding to exon1A was required to maintain BCL6 expression in germinal centre cells by avoiding BCL6-negative autoregulation. Silencing of CTCF in BCL6-expressing cells reduced BCL6 mRNA and protein expression, which is sufficient to induce B-cell terminal differentiation toward plasma cells. Moreover, lack of CTCF binding to exon1A shifts the BCL6 local chromatin from an active to a repressive state. This work demonstrates that, in contexts in which BCL6 is expressed, CTCF binding to BCL6 exon1A associates with epigenetic modifications indicative of transcriptionally open chromatin.
Collapse
Affiliation(s)
- A Batlle-López
- 1] Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) and Departamento de Biología Molecular, Universidad de Cantabria, CSIC, SODERCAN, Santander, Spain [2] Servicio de Hematología, Hospital U. Marqués de Valdecilla, and IFIMAV-FMV, Santander, Spain
| | - M G Cortiguera
- 1] Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) and Departamento de Biología Molecular, Universidad de Cantabria, CSIC, SODERCAN, Santander, Spain [2] Servicio de Hematología, Hospital U. Marqués de Valdecilla, and IFIMAV-FMV, Santander, Spain
| | - M Rosa-Garrido
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) and Departamento de Biología Molecular, Universidad de Cantabria, CSIC, SODERCAN, Santander, Spain
| | - R Blanco
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) and Departamento de Biología Molecular, Universidad de Cantabria, CSIC, SODERCAN, Santander, Spain
| | - E del Cerro
- Servicio de Hematología, Hospital U. Marqués de Valdecilla, and IFIMAV-FMV, Santander, Spain
| | - V Torrano
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) and Departamento de Biología Molecular, Universidad de Cantabria, CSIC, SODERCAN, Santander, Spain
| | - S D Wagner
- Department of Cancer Studies and Molecular Medicine and MRC Toxicology Unit, University of Leicester, Leicester, UK
| | - M D Delgado
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) and Departamento de Biología Molecular, Universidad de Cantabria, CSIC, SODERCAN, Santander, Spain
| |
Collapse
|
27
|
Plasschaert RN, Vigneau S, Tempera I, Gupta R, Maksimoska J, Everett L, Davuluri R, Mamorstein R, Lieberman PM, Schultz D, Hannenhalli S, Bartolomei MS. CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation. Nucleic Acids Res 2013; 42:774-89. [PMID: 24121688 PMCID: PMC3902912 DOI: 10.1093/nar/gkt910] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
CTCF (CCCTC-binding factor) is a highly conserved multifunctional DNA-binding protein with thousands of binding sites genome-wide. Our previous work suggested that differences in CTCF’s binding site sequence may affect the regulation of CTCF recruitment and its function. To investigate this possibility, we characterized changes in genome-wide CTCF binding and gene expression during differentiation of mouse embryonic stem cells. After separating CTCF sites into three classes (LowOc, MedOc and HighOc) based on similarity to the consensus motif, we found that developmentally regulated CTCF binding occurs preferentially at LowOc sites, which have lower similarity to the consensus. By measuring the affinity of CTCF for selected sites, we show that sites lost during differentiation are enriched in motifs associated with weaker CTCF binding in vitro. Specifically, enrichment for T at the 18th position of the CTCF binding site is associated with regulated binding in the LowOc class and can predictably reduce CTCF affinity for binding sites. Finally, by comparing changes in CTCF binding with changes in gene expression during differentiation, we show that LowOc and HighOc sites are associated with distinct regulatory functions. Our results suggest that the regulatory control of CTCF is dependent in part on specific motifs within its binding site.
Collapse
Affiliation(s)
- Robert N Plasschaert
- Department of Cell & Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA, Program of Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA, Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA and Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Ouboussad L, Kreuz S, Lefevre PF. CTCF depletion alters chromatin structure and transcription of myeloid-specific factors. J Mol Cell Biol 2013; 5:308-22. [PMID: 23933634 DOI: 10.1093/jmcb/mjt023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Differentiation is a multistep process tightly regulated and controlled by complex transcription factor networks. Here, we show that the rate of differentiation of common myeloid precursor cells increases after depletion of CTCF, a protein emerging as a potential key factor regulating higher-order chromatin structure. We identified CTCF binding in the vicinity of important transcription factors regulating myeloid differentiation and showed that CTCF depletion impacts on the expression of these genes in concordance with the observed acceleration of the myeloid commitment. Furthermore, we observed a loss of the histone variant H2A.Z within the selected promoter regions and an increase in non-coding RNA transcription upstream of these genes. Both abnormalities suggest a global chromatin structure destabilization and an associated increase of non-productive transcription in response to CTCF depletion but do not drive the CTCF-mediated transcription alterations of the neighbouring genes. Finally, we detected a transient eviction of CTCF at the Egr1 locus in correlation with Egr1 peak of expression in response to lipopolysaccharide (LPS) treatment in macrophages. This eviction is also correlated with the expression of an antisense non-coding RNA transcribing through the CTCF-binding region indicating that non-coding RNA transcription could be the cause and the consequence of CTCF eviction.
Collapse
Affiliation(s)
- Lylia Ouboussad
- Section of Experimental Haematology, Leeds Institute of Cancer Studies and Pathology, University of Leeds, Wellcome Trust Brenner Building, St. James's University Hospital, Leeds LS9 7TF, UK
| | | | | |
Collapse
|
29
|
Forn M, Muñoz M, Tauriello DVF, Merlos-Suárez A, Rodilla V, Bigas A, Batlle E, Jordà M, Peinado MA. Long range epigenetic silencing is a trans-species mechanism that results in cancer specific deregulation by overriding the chromatin domains of normal cells. Mol Oncol 2013; 7:1129-41. [PMID: 24035705 DOI: 10.1016/j.molonc.2013.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 01/08/2023] Open
Abstract
DNA methylation and chromatin remodeling are frequently implicated in the silencing of genes involved in carcinogenesis. Long Range Epigenetic Silencing (LRES) is a mechanism of gene inactivation that affects multiple contiguous CpG islands and has been described in different human cancer types. However, it is unknown whether there is a coordinated regulation of the genes embedded in these regions in normal cells and in early stages of tumor progression. To better characterize the molecular events associated with the regulation and remodeling of these regions we analyzed two regions undergoing LRES in human colon cancer in the mouse model. We demonstrate that LRES also occurs in murine cancer in vivo and mimics the molecular features of the human phenomenon, namely, downregulation of gene expression, acquisition of inactive histone marks, and DNA hypermethylation of specific CpG islands. The genes embedded in these regions showed a dynamic and autonomous regulation during mouse intestinal cell differentiation, indicating that, in the framework considered here, the coordinated regulation in LRES is restricted to cancer. Unexpectedly, benign adenomas in Apc(Min/+) mice showed overexpression of most of the genes affected by LRES in cancer, which suggests that the repressive remodeling of the region is a late event. Chromatin immunoprecipitation analysis of the transcriptional insulator CTCF in mouse colon cancer cells revealed disrupted chromatin domain boundaries as compared with normal cells. Malignant regression of cancer cells by in vitro differentiation resulted in partial reversion of LRES and gain of CTCF binding. We conclude that genes in LRES regions are plastically regulated in cell differentiation and hyperproliferation, but are constrained to a coordinated repression by abolishing boundaries and the autonomous regulation of chromatin domains in cancer cells.
Collapse
Affiliation(s)
- Marta Forn
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Huang K, Jia J, Wu C, Yao M, Li M, Jin J, Jiang C, Cai Y, Pei D, Pan G, Yao H. Ribosomal RNA gene transcription mediated by the master genome regulator protein CCCTC-binding factor (CTCF) is negatively regulated by the condensin complex. J Biol Chem 2013; 288:26067-26077. [PMID: 23884423 DOI: 10.1074/jbc.m113.486175] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CCCTC-binding factor (CTCF) is a ubiquitously expressed "master weaver" and plays multiple functions in the genome, including transcriptional activation/repression, chromatin insulation, imprinting, X chromosome inactivation, and high-order chromatin organization. It has been shown that CTCF facilitates the recruitment of the upstream binding factor onto ribosomal DNA (rDNA) and regulates the local epigenetic state of rDNA repeats. However, the mechanism by which CTCF modulates rRNA gene transcription has not been well understood. Here we found that wild-type CTCF augments the pre-rRNA level, cell size, and cell growth in cervical cancer cells. In contrast, RNA interference-mediated knockdown of CTCF reduced pre-rRNA transcription. CTCF positively regulates rRNA gene transcription in a RNA polymerase I-dependent manner. We identified an RRGR motif as a putative nucleolar localization sequence in the C-terminal region of CTCF that is required for activating rRNA gene transcription. Using mass spectrometry, we identified SMC2 and SMC4, two subunits of condensin complexes that interact with CTCF. Condensin negatively regulates CTCF-mediated rRNA gene transcription. Knockdown of SMC2 expression significantly facilitates the loading of CTCF and the upstream binding factor onto the rDNA locus and increases histone acetylation across the rDNA locus. Taken together, our study suggests that condensin competes with CTCF in binding to a specific rDNA locus and negatively regulates CTCF-mediated rRNA gene transcription.
Collapse
Affiliation(s)
- Kaimeng Huang
- From the Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,; the College of Life Science, Jilin University, Changchun, Jilin 130012, China, and
| | - Jinping Jia
- From the Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Changwei Wu
- From the Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Mingze Yao
- From the Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Min Li
- the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jingji Jin
- the College of Life Science, Jilin University, Changchun, Jilin 130012, China, and
| | - Cizhong Jiang
- the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yong Cai
- the College of Life Science, Jilin University, Changchun, Jilin 130012, China, and
| | - Duanqing Pei
- From the Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Guangjin Pan
- From the Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,.
| | - Hongjie Yao
- From the Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,.
| |
Collapse
|
31
|
Tiffen JC, Bailey CG, Marshall AD, Metierre C, Feng Y, Wang Q, Watson SL, Holst J, Rasko JEJ. The cancer-testis antigen BORIS phenocopies the tumor suppressor CTCF in normal and neoplastic cells. Int J Cancer 2013; 133:1603-13. [PMID: 23553099 DOI: 10.1002/ijc.28184] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/15/2013] [Indexed: 11/10/2022]
Abstract
BORIS and CTCF are paralogous, multivalent 11-zinc finger transcription factors that play important roles in organizing higher-order chromatin architecture. BORIS is a cancer-testis antigen with a poorly defined function in cancer, although it has been hypothesized to exhibit oncogenic properties. CTCF, however, has been postulated as a candidate tumor suppressor. We collated the genetic lesions in BORIS and CTCF from multiple cancers identified using high-throughput genomics. In BORIS, nonsense and missense mutations are evenly distributed. In CTCF, recurrent mutations are mostly clustered in the conserved zinc finger domain and at residues critical for contacting DNA and zinc ion co-ordination. Three missense mutations are common to both proteins. We used an inducible lentivector to express wildtype BORIS or CTCF in primary cells and cancer cell lines in order to define their functional differences. Both BORIS and CTCF caused a significant decrease in cell proliferation and clonogenic capacity, without alteration of specific cell cycle phases. Both BORIS and CTCF conferred protective effects in primary cells and some cancer cells during UV damage-induced apoptosis. Using a bioluminescent MCF-7 orthotopic breast cancer model in vivo, we demonstrated that CTCF and BORIS suppressed breast cancer growth. These findings provide further evidence that CTCF behaves as a tumor suppressor, and show BORIS has a similar growth inhibitory effect in vitro and in vivo. Hence, acquired zinc finger mutations may disrupt these functions, thereby contributing to tumor growth and development.
Collapse
Affiliation(s)
- Jessamy C Tiffen
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW 2050, Australia
| | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Grossmann V, Haferlach C, Weissmann S, Roller A, Schindela S, Poetzinger F, Stadler K, Bellos F, Kern W, Haferlach T, Schnittger S, Kohlmann A. The molecular profile of adult T-cell acute lymphoblastic leukemia: mutations in RUNX1 and DNMT3A are associated with poor prognosis in T-ALL. Genes Chromosomes Cancer 2013; 52:410-22. [PMID: 23341344 DOI: 10.1002/gcc.22039] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 11/02/2012] [Accepted: 11/20/2012] [Indexed: 12/15/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive and heterogeneous disease. The diagnosis is predominantly based on immunophenotyping. In addition to known cytogenetic abnormalities molecular mutations were recently identified. Here, 90 adult T-ALL cases were investigated for mutations in NOTCH1, FBXW7, PHF6, CDKN2A, DNMT3A, FLT3, PTEN, and RUNX1 using 454 next-generation amplicon sequencing and melting curve analyses. These data were further complemented by FISH, chromosome banding, array CGH, and CDKN2B promoter methylation analyses. NOTCH1 was the most frequently mutated gene with a 71.1% frequency followed by FBXW7 (18.9%), PHF6 (39.5%), DNMT3A (17.8%), RUNX1 (15.5%), PTEN (10.0%), CDKN2A (4.4%), FLT3-ITD (2.2%), and FLT3-TKD (1.1%). In total, 84/90 (93.3%) cases harbored at least one mutation. Combining these data with CDKN2A/B deletions and CDKN2B methylation status, we detected minimum one aberration in 89/90 (98.9%) patients. Survival analyses revealed the subtype as defined by the immunophenotype as the strongest independent prognostic factor. When restricting the survival analysis to the early T-ALL subtype, a strong association of RUNX1 (P = 0.027) and DNMT3A (P = 0.005) mutations with shorter overall survival was observed. In conclusion, RUNX1 and DNMT3A are frequently mutated in T-ALL and are associated with poor prognosis in early T-ALL.
Collapse
Affiliation(s)
- Vera Grossmann
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Lee BK, Iyer VR. Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation. J Biol Chem 2012; 287:30906-13. [PMID: 22952237 PMCID: PMC3438923 DOI: 10.1074/jbc.r111.324962] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Eukaryotic genomes are organized into higher order chromatin architectures by protein-mediated long-range interactions in the nucleus. CCCTC-binding factor (CTCF), a sequence-specific transcription factor, serves as a chromatin organizer in building this complex chromatin structure by linking chromosomal domains. Recent genome-wide studies mapping the binding sites of CTCF and its interacting partner, cohesin, using chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) revealded that CTCF globally co-localizes with cohesin. This partnership between CTCF and cohesin is emerging as a novel and perhaps pivotal aspect of gene regulatory mechanisms, in addition to playing a role in the organization of higher order chromatin architecture.
Collapse
Affiliation(s)
- Bum-Kyu Lee
- From the Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, Texas 78712
| | - Vishwanath R. Iyer
- From the Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, Texas 78712
| |
Collapse
|
34
|
Rosa-Garrido M, Ceballos L, Alonso-Lecue P, Abraira C, Delgado MD, Gandarillas A. A cell cycle role for the epigenetic factor CTCF-L/BORIS. PLoS One 2012; 7:e39371. [PMID: 22724006 PMCID: PMC3378572 DOI: 10.1371/journal.pone.0039371] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 05/19/2012] [Indexed: 11/19/2022] Open
Abstract
CTCF is a ubiquitous epigenetic regulator that has been proposed as a master keeper of chromatin organisation. CTCF-like, or BORIS, is thought to antagonise CTCF and has been found in normal testis, ovary and a large variety of tumour cells. The cellular function of BORIS remains intriguing although it might be involved in developmental reprogramming of gene expression patterns. We here unravel the expression of CTCF and BORIS proteins throughout human epidermis. While CTCF is widely distributed within the nucleus, BORIS is confined to the nucleolus and other euchromatin domains. Nascent RNA experiments in primary keratinocytes revealed that endogenous BORIS is present in active transcription sites. Interestingly, BORIS also localises to interphase centrosomes suggesting a role in the cell cycle. Blocking the cell cycle at S phase or mitosis, or causing DNA damage, produced a striking accumulation of BORIS. Consistently, ectopic expression of wild type or GFP- BORIS provoked a higher rate of S phase cells as well as genomic instability by mitosis failure. Furthermore, down-regulation of endogenous BORIS by specific shRNAs inhibited both RNA transcription and cell cycle progression. The results altogether suggest a role for BORIS in coordinating S phase events with mitosis.
Collapse
Affiliation(s)
- Manuel Rosa-Garrido
- Cell Cycle, Stem Cell Fate and Cancer Laboratory, Fundación Marqués de Valdecilla-Instituto de Formación e Investigación Marqués de Valdecilla, Santander, Spain
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, SODERCAN, Santander, Spain
| | - Laura Ceballos
- Cell Cycle, Stem Cell Fate and Cancer Laboratory, Fundación Marqués de Valdecilla-Instituto de Formación e Investigación Marqués de Valdecilla, Santander, Spain
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, SODERCAN, Santander, Spain
| | - Pilar Alonso-Lecue
- Cell Cycle, Stem Cell Fate and Cancer Laboratory, Fundación Marqués de Valdecilla-Instituto de Formación e Investigación Marqués de Valdecilla, Santander, Spain
| | - Cristina Abraira
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, SODERCAN, Santander, Spain
| | - M. Dolores Delgado
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, SODERCAN, Santander, Spain
| | - Alberto Gandarillas
- Cell Cycle, Stem Cell Fate and Cancer Laboratory, Fundación Marqués de Valdecilla-Instituto de Formación e Investigación Marqués de Valdecilla, Santander, Spain
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, SODERCAN, Santander, Spain
- Institut National de la Santé et de la Recherche Médicale, ADR Languedoc-Roussillon, Montpellier, France
| |
Collapse
|
35
|
Abstract
CTCF is an evolutionary conserved and ubiquitously expressed protein that binds thousands of sites in the human genome. Ectopic expression of CTCF in various normal and tumoral human cell lines inhibits cell division and clonogenicity, with the consequence to consider CTCF a potential tumor-suppressor factor. In this review article, we focused on the molecular mechanisms engaged by CTCF to modulate the expression of several key-regulators of differentiation, cellular senescence, cell cycle control and progression, whose expression is frequently altered in tumors. Moreover, we discussed common features of CTCF at each tumor-related DNA-binding sequence, such as protein-partners, post-translational modifications, and distinctive epigenetic marks establishment. The investigation of the molecular mechanisms engaged by CTCF to modulate tumor-related genes emphasizes the cell-type dependency of its tumor suppressor role. Indeed, the ability of CTCF to bind their promoters strictly depends by cell-type features as DNA methylation, BORIS-binding and post-translational modifications as PARYlation.
Collapse
Affiliation(s)
- Francesco Paolo Fiorentino
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
| | | |
Collapse
|
36
|
Maiques-Diaz A, Chou FS, Wunderlich M, Gómez-López G, Jacinto FV, Rodriguez-Perales S, Larrayoz MJ, Calasanz MJ, Mulloy JC, Cigudosa JC, Alvarez S. Chromatin modifications induced by the AML1-ETO fusion protein reversibly silence its genomic targets through AML1 and Sp1 binding motifs. Leukemia 2012; 26:1329-37. [DOI: 10.1038/leu.2011.376] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
37
|
Manavathi B, Lo D, Bugide S, Dey O, Imren S, Weiss MJ, Humphries RK. Functional regulation of pre-B-cell leukemia homeobox interacting protein 1 (PBXIP1/HPIP) in erythroid differentiation. J Biol Chem 2011; 287:5600-14. [PMID: 22187427 DOI: 10.1074/jbc.m111.289843] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pre-B-cell leukemia homeobox interacting protein 1 or human PBX1 interacting protein (PBXIP1/HPIP) is a co-repressor of pre-B-cell leukemia homeobox 1 (PBX1) and is also known to regulate estrogen receptor functions by associating with the microtubule network. Despite its initial discovery in the context of hematopoietic cells, little is yet known about the role of HPIP in hematopoiesis. Here, we show that lentivirus-mediated overexpression of HPIP in human CD34(+) cells enhances hematopoietic colony formation in vitro, whereas HPIP knockdown leads to a reduction in the number of such colonies. Interestingly, erythroid colony number was significantly higher in HPIP-overexpressing cells. In addition, forced expression of HPIP in K562 cells, a multipotent erythro-megakaryoblastic leukemia cell line, led to an induction of erythroid differentiation. HPIP overexpression in both CD34(+) and K562 cells was associated with increased activation of the PI3K/AKT pathway, and corresponding treatment with a PI3K-specific inhibitor, LY-294002, caused a reduction in clonogenic progenitor number in HPIP-expressing CD34(+) cells and decreased K562 cell differentiation. Combined, these findings point to an important role of the PI3K/AKT pathway in mediating HPIP-induced effects on the growth and differentiation of hematopoietic cells. Interestingly, HPIP gene expression was found to be induced in K562 cells in response to erythroid differentiation signals such as DMSO and erythropoietin. The erythroid lineage-specific transcription factor GATA1 binds to the HPIP promoter and activates HPIP gene transcription in a CCCTC-binding factor (CTCF)-dependent manner. Co-immunoprecipitation and co-localization experiments revealed the association of CTCF with GATA1 indicating the recruitment of CTCF/GATA1 transcription factor complex onto the HPIP promoter. Together, this study provides evidence that HPIP is a target of GATA1 and CTCF in erythroid cells and plays an important role in erythroid differentiation by modulating the PI3K/AKT pathway.
Collapse
Affiliation(s)
- Bramanandam Manavathi
- Molecular and Cellular Oncology Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad-500046, India.
| | | | | | | | | | | | | |
Collapse
|
38
|
Abstract
Chromatin insulators are DNA-protein complexes with broad functions in nuclear biology. Based on the ability of insulator proteins to interact with each other, it was originally found that insulators form loops that bring together distant regions of the genome. Data from genome-wide localization studies indicate that insulator proteins can be present in intergenic regions as well as at the 5', introns or 3' of genes, suggesting a variety of roles for insulator loops in chromosome biology. Recent results suggest that insulators mediate intra- and interchromosomal interactions to affect transcription, imprinting, and recombination. Cells have developed mechanisms to control insulator activity by recruiting specialized proteins or by covalent modification of core components. It is then possible that insulator-mediated interactions set up cell-specific blueprints of nuclear organization that may contribute to the establishment of different patterns of gene expression during cell differentiation and development. As a consequence, disruption of insulator activity could result in the development of cancer or other disease states.
Collapse
Affiliation(s)
- Jingping Yang
- Department of Biology, Emory University, Atlanta, GA, USA
| | | |
Collapse
|
39
|
Recillas-Targa F, de la Rosa-Velázquez IA, Soto-Reyes E. Insulation of tumor suppressor genes by the nuclear factor CTCF. Biochem Cell Biol 2011; 89:479-88. [PMID: 21846316 DOI: 10.1139/o11-031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
One of the most outstanding nuclear factors, which has chromatin insulator and transcriptional properties and also contribute to genomic organization, is the zinc-finger protein CCCTC-binding factor (CTCF). Among its multiple functions, a growing amount of evidence implicates CTCF in the epigenetic regulation of genes responsible for the control of the cell cycle, and its mis-regulation can lead to aberrant epigenetic silencing of genes involved in cancer development. Detailed studies are now revealing that CTCF can serve as a barrier against the spread of DNA methylation and histone repressive marks over promoter regions of tumor suppressor genes. Moreover, new evidences points out to the capacity of CTCF to be covalently modified, in particular, through poly(ADP-ribosyl)ation with regulatory consequences. An unexplored aspect of CTCF is its intergenic and intragenic distribution in certain loci. Such distribution seems to facilitate the formation of an optimal chromatin structure and the recruitment of chromatin remodelers with the possible incorporation of RNA polymerase II. Therefore, in the context of tumor suppressor genes and cancer development, CTCF appears to play a relevant role by incorporating a combination of mechanisms involved in the protection against epigenetic silencing components and the maintenance of optimal higher-order organization of the corresponding loci.
Collapse
Affiliation(s)
- Félix Recillas-Targa
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México D.F. 04510, México.
| | | | | |
Collapse
|
40
|
Nikolaev LG, Akopov SB, Didych DA, Sverdlov ED. Vertebrate Protein CTCF and its Multiple Roles in a Large-Scale Regulation of Genome Activity. Curr Genomics 2011; 10:294-302. [PMID: 20119526 PMCID: PMC2729993 DOI: 10.2174/138920209788921038] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 06/15/2009] [Accepted: 06/18/2009] [Indexed: 11/24/2022] Open
Abstract
The CTCF transcription factor is an 11 zinc fingers multifunctional protein that uses different zinc finger combinations to recognize and bind different sites within DNA. CTCF is thought to participate in various gene regulatory networks including transcription activation and repression, formation of independently functioning chromatin domains and regulation of imprinting. Sequencing of human and other genomes opened up a possibility to ascertain the genomic distribution of CTCF binding sites and to identify CTCF-dependent cis-regulatory elements, including insulators. In the review, we summarized recent data on genomic distribution of CTCF binding sites in the human and other genomes within a framework of the loop domain hypothesis of large-scale regulation of the genome activity. We also tried to formulate possible lines of studies on a variety of CTCF functions which probably depend on its ability to specifically bind DNA, interact with other proteins and form di- and multimers. These three fundamental properties allow CTCF to serve as a transcription factor, an insulator and a constitutive dispersed genome-wide demarcation tool able to recruit various factors that emerge in response to diverse external and internal signals, and thus to exert its signal-specific function(s).
Collapse
Affiliation(s)
- L G Nikolaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya, 117997, Moscow, Russia
| | | | | | | |
Collapse
|
41
|
van de Nobelen S, Rosa-Garrido M, Leers J, Heath H, Soochit W, Joosen L, Jonkers I, Demmers J, van der Reijden M, Torrano V, Grosveld F, Delgado MD, Renkawitz R, Galjart N, Sleutels F. CTCF regulates the local epigenetic state of ribosomal DNA repeats. Epigenetics Chromatin 2010; 3:19. [PMID: 21059229 PMCID: PMC2993708 DOI: 10.1186/1756-8935-3-19] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 11/08/2010] [Indexed: 02/06/2023] Open
Abstract
Background CCCTC binding factor (CTCF) is a highly conserved zinc finger protein, which is involved in chromatin organization, local histone modifications, and RNA polymerase II-mediated gene transcription. CTCF may act by binding tightly to DNA and recruiting other proteins to mediate its various functions in the nucleus. To further explore the role of this essential factor, we used a mass spectrometry-based approach to screen for novel CTCF-interacting partners. Results Using biotinylated CTCF as bait, we identified upstream binding factor (UBF) and multiple other components of the RNA polymerase I complex as potential CTCF-interacting partners. Interestingly, CTCFL, the testis-specific paralog of CTCF, also binds UBF. The interaction between CTCF(L) and UBF is direct, and requires the zinc finger domain of CTCF(L) and the high mobility group (HMG)-box 1 and dimerization domain of UBF. Because UBF is involved in RNA polymerase I-mediated ribosomal (r)RNA transcription, we analyzed CTCF binding to the rDNA repeat. We found that CTCF bound to a site upstream of the rDNA spacer promoter and preferred non-methylated over methylated rDNA. DNA binding by CTCF in turn stimulated binding of UBF. Absence of CTCF in cultured cells resulted in decreased association of UBF with rDNA and in nucleolar fusion. Furthermore, lack of CTCF led to reduced binding of RNA polymerase I and variant histone H2A.Z near the rDNA spacer promoter, a loss of specific histone modifications, and diminished transcription of non-coding RNA from the spacer promoter. Conclusions UBF is the first common interaction partner of CTCF and CTCFL, suggesting a role for these proteins in chromatin organization of the rDNA repeats. We propose that CTCF affects RNA polymerase I-mediated events globally by controlling nucleolar number, and locally by regulating chromatin at the rDNA spacer promoter, similar to RNA polymerase II promoters. CTCF may load UBF onto rDNA, thereby forming part of a network that maintains rDNA genes poised for transcription.
Collapse
|
42
|
Farrar D, Rai S, Chernukhin I, Jagodic M, Ito Y, Yammine S, Ohlsson R, Murrell A, Klenova E. Mutational analysis of the poly(ADP-ribosyl)ation sites of the transcription factor CTCF provides an insight into the mechanism of its regulation by poly(ADP-ribosyl)ation. Mol Cell Biol 2010; 30:1199-216. [PMID: 20038529 PMCID: PMC2820893 DOI: 10.1128/mcb.00827-09] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Revised: 08/02/2009] [Accepted: 12/10/2009] [Indexed: 12/13/2022] Open
Abstract
Poly(ADP-ribosyl)ation of the conserved multifunctional transcription factor CTCF was previously identified as important to maintain CTCF insulator and chromatin barrier functions. However, the molecular mechanism of this regulation and also the necessity of this modification for other CTCF functions remain unknown. In this study, we identified potential sites of poly(ADP-ribosyl)ation within the N-terminal domain of CTCF and generated a mutant deficient in poly(ADP-ribosyl)ation. Using this CTCF mutant, we demonstrated the requirement of poly(ADP-ribosyl)ation for optimal CTCF function in transcriptional activation of the p19ARF promoter and inhibition of cell proliferation. By using a newly generated isogenic insulator reporter cell line, the CTCF insulator function at the mouse Igf2-H19 imprinting control region (ICR) was found to be compromised by the CTCF mutation. The association and simultaneous presence of PARP-1 and CTCF at the ICR, confirmed by single and serial chromatin immunoprecipitation assays, were found to be independent of CTCF poly(ADP-ribosyl)ation. These results suggest a model of CTCF regulation by poly(ADP-ribosyl)ation whereby CTCF and PARP-1 form functional complexes at sites along the DNA, producing a dynamic reversible modification of CTCF. By using bioinformatics tools, numerous sites of CTCF and PARP-1 colocalization were demonstrated, suggesting that such regulation of CTCF may take place at the genome level.
Collapse
Affiliation(s)
- Dawn Farrar
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Sushma Rai
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Igor Chernukhin
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Maja Jagodic
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Yoko Ito
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Samer Yammine
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Rolf Ohlsson
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Adele Murrell
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Elena Klenova
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden
| |
Collapse
|
43
|
Abstract
CTCF is a highly conserved zinc finger protein implicated in diverse regulatory functions, including transcriptional activation/repression, insulation, imprinting, and X chromosome inactivation. Here we re-evaluate data supporting these roles in the context of mechanistic insights provided by recent genome-wide studies and highlight evidence for CTCF-mediated intra- and interchromosomal contacts at several developmentally regulated genomic loci. These analyses support a primary role for CTCF in the global organization of chromatin architecture and suggest that CTCF may be a heritable component of an epigenetic system regulating the interplay between DNA methylation, higher-order chromatin structure, and lineage-specific gene expression.
Collapse
|
44
|
Charles PC, Alder BD, Hilliard EG, Schisler JC, Lineberger RE, Parker JS, Mapara S, Wu SS, Portbury A, Patterson C, Stouffer GA. Tobacco use induces anti-apoptotic, proliferative patterns of gene expression in circulating leukocytes of Caucasian males. BMC Med Genomics 2008; 1:38. [PMID: 18710571 PMCID: PMC2531187 DOI: 10.1186/1755-8794-1-38] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Accepted: 08/18/2008] [Indexed: 01/03/2023] Open
Abstract
Background Strong epidemiologic evidence correlates tobacco use with a variety of serious adverse health effects, but the biological mechanisms that produce these effects remain elusive. Results We analyzed gene transcription data to identify expression spectra related to tobacco use in circulating leukocytes of 67 Caucasian male subjects. Levels of cotinine, a nicotine metabolite, were used as a surrogate marker for tobacco exposure. Significance Analysis of Microarray and Gene Set Analysis identified 109 genes in 16 gene sets whose transcription levels were differentially regulated by nicotine exposure. We subsequently analyzed this gene set by hyperclustering, a technique that allows the data to be clustered by both expression ratio and gene annotation (e.g. Gene Ontologies). Conclusion Our results demonstrate that tobacco use affects transcription of groups of genes that are involved in proliferation and apoptosis in circulating leukocytes. These transcriptional effects include a repertoire of transcriptional changes likely to increase the incidence of neoplasia through an altered expression of genes associated with transcription and signaling, interferon responses and repression of apoptotic pathways.
Collapse
Affiliation(s)
- Peter C Charles
- Carolina Cardiovascular Biology Center, University of North Carolina at Chapel Hill, Chapel Hill, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Gao J, Li T, Lu L. Functional role of CCCTC binding factor in insulin-stimulated cell proliferation. Cell Prolif 2007; 40:795-808. [PMID: 18021171 DOI: 10.1111/j.1365-2184.2007.00472.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES CCCTC binding factor (CTCF) is a nuclear protein containing an 11-zinc-finger DNA-binding domain. CTCF plays important roles in the regulation of epigenetics and gene transcription. As a multifunctional protein, CTCF is also involved in the regulation of cell proliferation and of apoptosis. However, mechanisms underlining the regulatory function of CTCF in mediating growth factor- and cytokine-stimulated cell fate are largely unknown. MATERIALS AND METHODS The effect of CTCF on insulin-induced ML-1 cell proliferation was investigated by studying insulin-stimulated extracellular signal-regulated kinase (Erk) and Akt signalling pathways, and the alterations of CTCF activity in these cells. RESULTS The present study demonstrates that insulin-induced human haematopoietic myeloblastic ML-1 cell proliferation requires increased CTCF expression. Inhibition of Erk and Akt pathways with specific blockers or by dominantly negative expression of Erk and Akt mutants markedly suppressed expression of CTCF and resulted in retardation of cell proliferation. Furthermore, insulin-induced ML-1 cell proliferation was significantly enhanced by overexpression of cDNA encoding full-length CTCF. In contrast, ML-1 cell proliferation was inhibited by knocking down CTCF mRNA using specific small interference RNA. CONCLUSIONS Our results indicate that CTCF is indeed a protein with multifunctional activity that plays a significant role in modulating signalling pathways to mediate insulin-induced ML-1 cell proliferation.
Collapse
Affiliation(s)
- J Gao
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Torrance, CA 90502, USA
| | | | | |
Collapse
|
46
|
Li T, Lu L. Functional role of CCCTC binding factor (CTCF) in stress-induced apoptosis. Exp Cell Res 2007; 313:3057-65. [PMID: 17583694 PMCID: PMC2706011 DOI: 10.1016/j.yexcr.2007.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 05/02/2007] [Accepted: 05/17/2007] [Indexed: 10/23/2022]
Abstract
CTCF, a nuclear transcriptional factor, is a multifunctional protein and involves regulation of growth factor- and cytokine-induced cell proliferation/differentiation. In the present study, we investigated the role of CTCF in protecting stress-induced apoptosis in various human cell types. We found that UV irradiation and hyper-osmotic stress induced human corneal epithelial (HCE) and hematopoietic myeloid cell apoptosis detected by significantly increased caspase 3 activity and decreased cell viability. The stress-induced apoptotic response in these cells requires down-regulation of CTCF at both mRNA and protein levels, suggesting that CTCF may play an important role in downstream events of stress-induced signaling pathways. Inhibition of NFkappaB activity prevented stress-induced down-regulation of CTCF and increased cell viability against stress-induced apoptosis. The anti-apoptotic effect of CTCF was further studied by manipulating CTCF activities in HCE and hematopoietic cells. Transient transfection of cDNAs encoding full-length human CTCF markedly suppressed stress-induced apoptosis in these cells. In contrast, knocking down of CTCF mRNA using siRNA specific to CTCF significantly promoted stress-induced apoptosis. Thus, our results reveal that CTCF is a down stream target of stress-induced signaling cascades and it plays a significant anti-apoptotic role in regulation of stress-induced cellular responses in HCE and hematopoietic myeloid cells.
Collapse
Affiliation(s)
| | - Luo Lu
- Address correspondence to: Luo Lu, Division of Molecular Medicine, UCLA School of Medicine, Harbor-UCLA Medical Center, 1124 W. Carson Street, C-2, Torrance, CA 90502, Tel. 310 787-6853, Fax. 310 222-3781, E-mail:
| |
Collapse
|
47
|
Kantidze OL, Iarovaia OV, Philonenko ES, Yakutenko II, Razin SV. Unusual compartmentalization of CTCF and other transcription factors in the course of terminal erythroid differentiation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1773:924-33. [PMID: 17467075 DOI: 10.1016/j.bbamcr.2007.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Revised: 03/06/2007] [Accepted: 03/21/2007] [Indexed: 01/31/2023]
Abstract
It is demonstrated that in chicken embryonic and mature erythrocyte nuclei the distribution of a versatile transcription factor CTCF differs drastically from its distribution in nuclei of proliferating erythroid and non-erythroid cells. In the latter case CTCF was distributed throughout the whole nucleus volume, being concentrated in many small compartments (punctuate nuclear staining). In contrast, in embryonic and mature erythrocytes CTCF was concentrated in a limited number of large compartments. These large CTCF-containing compartments were not observed in other cells. Occasionally, but not in all cells, some of these compartments were localized close to nucleoli but did not colocalize with them. In mature erythrocytes a clear exclusion of CTCF-containing compartments from the chromatin domain was observed. This exclusion correlated with a tight association of CTCF with the nuclear matrix. Concentration in relatively large compartments and exclusion from the chromatin domain in nuclei of mature erythrocytes were also observed for RNA polymerase II and several transcription factors. The data are discussed in the context of a hypothesis postulating that relocalization of different components of the transcriptional machinery from the chromatin domain into the interchromatin compartment is an important step of the terminal inactivation of chicken erythrocyte nuclei.
Collapse
Affiliation(s)
- Omar L Kantidze
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology RAS, 34/5 Vavilov Street, 119334 Moscow, Russia
| | | | | | | | | |
Collapse
|
48
|
Koesters C, Unger B, Bilic I, Schmidt U, Bluml S, Lichtenberger B, Schreiber M, Stockl J, Ellmeier W. Regulation of dendritic cell differentiation and subset distribution by the zinc finger protein CTCF. Immunol Lett 2007; 109:165-74. [PMID: 17368809 DOI: 10.1016/j.imlet.2007.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Revised: 02/11/2007] [Accepted: 02/11/2007] [Indexed: 11/28/2022]
Abstract
The molecular mechanisms that regulate DC differentiation and subset distribution are largely unknown. In this study we report the identification of the C(2)H(2) zinc finger transcription factors (TF) CTCF as a regulator of DC differentiation. CTCF was expressed in human and murine DC and its expression was downregulated during the differentiation of human monocyte-derived DC. Enforced expression of CTCF during the differentiation of murine BM-derived DC (BMDC) caused increased apoptosis and reduced proliferation leading to a dramatically reduced number of CTCF transduced DC. The CTCF expressing BMDC that developed had a more immature phenotype than control cells, and showed defects in maturation upon TLR stimulation. Furthermore, in vivo expression of CTCF led to an increase in the percentage of plasmacytoid DC (pDC) within the DC lineage. Our data provide new insight into molecular mechanisms regulating DC differentiation and subset development and identify CTCF as a factor involved in the regulation of these important processes.
Collapse
Affiliation(s)
- Christina Koesters
- Institute of Immunology, Medical University of Vienna, Lazarettgasse 19, A-1090 Vienna, Austria
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Recillas-Targa F, De La Rosa-Velázquez IA, Soto-Reyes E, Benítez-Bribiesca L. Epigenetic boundaries of tumour suppressor gene promoters: the CTCF connection and its role in carcinogenesis. J Cell Mol Med 2007; 10:554-68. [PMID: 16989720 PMCID: PMC3933142 DOI: 10.1111/j.1582-4934.2006.tb00420.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Genetic and epigenetic regulations are essential mechanisms that ensure proper early and subsequent mammalian programming of diverse cellular processes. These mechanisms affect transcriptional regulation, stem cell determination and cell cycle control, including senescence and aging. It is not surprising that perturbation of the exquisite balance between genetic and epigenetic regulation can lead to diverse diseases, including cancer. Histone covalent modifications and DNA methylation do not explain all epigenetic phenomena. We describe a previously unsuspected epigenetic factor and propose the incorporation of the 11-zinc finger CCCTC-binding factor, known as CTCF as a novel and multifunctional epigenetic regulator.
Collapse
Affiliation(s)
- Felix Recillas-Targa
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, México.
| | | | | | | |
Collapse
|
50
|
Chernukhin I, Shamsuddin S, Kang SY, Bergström R, Kwon YW, Yu W, Whitehead J, Mukhopadhyay R, Docquier F, Farrar D, Morrison I, Vigneron M, Wu SY, Chiang CM, Loukinov D, Lobanenkov V, Ohlsson R, Klenova E. CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide. Mol Cell Biol 2007; 27:1631-48. [PMID: 17210645 PMCID: PMC1820452 DOI: 10.1128/mcb.01993-06] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
CTCF is a transcription factor with highly versatile functions ranging from gene activation and repression to the regulation of insulator function and imprinting. Although many of these functions rely on CTCF-DNA interactions, it is an emerging realization that CTCF-dependent molecular processes involve CTCF interactions with other proteins. In this study, we report the association of a subpopulation of CTCF with the RNA polymerase II (Pol II) protein complex. We identified the largest subunit of Pol II (LS Pol II) as a protein significantly colocalizing with CTCF in the nucleus and specifically interacting with CTCF in vivo and in vitro. The role of CTCF as a link between DNA and LS Pol II has been reinforced by the observation that the association of LS Pol II with CTCF target sites in vivo depends on intact CTCF binding sequences. "Serial" chromatin immunoprecipitation (ChIP) analysis revealed that both CTCF and LS Pol II were present at the beta-globin insulator in proliferating HD3 cells but not in differentiated globin synthesizing HD3 cells. Further, a single wild-type CTCF target site (N-Myc-CTCF), but not the mutant site deficient for CTCF binding, was sufficient to activate the transcription from the promoterless reporter gene in stably transfected cells. Finally, a ChIP-on-ChIP hybridization assay using microarrays of a library of CTCF target sites revealed that many intergenic CTCF target sequences interacted with both CTCF and LS Pol II. We discuss the possible implications of our observations with respect to plausible mechanisms of transcriptional regulation via a CTCF-mediated direct link of LS Pol II to the DNA.
Collapse
Affiliation(s)
- Igor Chernukhin
- Department of Biological Sciences, Central Campus, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|