1
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Li K, Liu Y, Ding Y, Zhang Z, Feng J, Hu J, Chen J, Lian Z, Chen Y, Hu K, Chen Z, Cai Z, Liu M, Pang X. BCL6 is regulated by the MAPK/ELK1 axis and promotes KRAS-driven lung cancer. J Clin Invest 2022; 132:161308. [PMID: 36377663 PMCID: PMC9663163 DOI: 10.1172/jci161308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Mutational activation of KRAS is a common oncogenic event in lung cancer, yet effective therapies are still lacking. Here, we identify B cell lymphoma 6 (BCL6) as a lynchpin in KRAS-driven lung cancer. BCL6 expression was increased upon KRAS activation in lung tumor tissue in mice and was positively correlated with the expression of KRAS-GTP, the active form of KRAS, in various human cancer cell lines. Moreover, BCL6 was highly expressed in human KRAS-mutant lung adenocarcinomas and was associated with poor patient survival. Mechanistically, the MAPK/ERK/ELK1 signaling axis downstream of mutant KRAS directly regulated BCL6 expression. BCL6 maintained the global expression of prereplication complex components; therefore, BCL6 inhibition induced stalling of the replication fork, leading to DNA damage and growth arrest in KRAS-mutant lung cancer cells. Importantly, BCL6-specific knockout in lungs significantly reduced the tumor burden and mortality in the LSL-KrasG12D/+ lung cancer mouse model. Likewise, pharmacological inhibition of BCL6 significantly impeded the growth of KRAS-mutant lung cancer cells both in vitro and in vivo. In summary, our findings reveal a crucial role of BCL6 in promoting KRAS-addicted lung cancer and suggest BCL6 as a therapeutic target for the treatment of this intractable disease.
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Affiliation(s)
- Kun Li
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
- Joint Translational Science and Technology Research Institute, East China Normal University, Shanghai, China
- Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yanan Liu
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Yi Ding
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Zhengwei Zhang
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Juanjuan Feng
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Jiaxin Hu
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Jiwei Chen
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Zhengke Lian
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Yiliang Chen
- Department of Biochemistry and Molecular Biology, School of Medicine, Tongji University, Shanghai, China
| | - Kewen Hu
- Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhi Chen
- Medical Research Institute, Wuhan University, Wuhan, China
| | - Zhenyu Cai
- Department of Biochemistry and Molecular Biology, School of Medicine, Tongji University, Shanghai, China
| | - Mingyao Liu
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Xiufeng Pang
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
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2
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Cheng X, Joseph A, Castro V, Chen-Liaw A, Skidmore Z, Ueno T, Fujisawa JI, Rauch DA, Challen GA, Martinez MP, Green P, Griffith M, Payton JE, Edwards JR, Ratner L. Epigenomic regulation of human T-cell leukemia virus by chromatin-insulator CTCF. PLoS Pathog 2021; 17:e1009577. [PMID: 34019588 PMCID: PMC8174705 DOI: 10.1371/journal.ppat.1009577] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 06/03/2021] [Accepted: 04/22/2021] [Indexed: 11/30/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus that causes an aggressive T-cell malignancy and a variety of inflammatory conditions. The integrated provirus includes a single binding site for the epigenomic insulator, CCCTC-binding protein (CTCF), but its function remains unclear. In the current study, a mutant virus was examined that eliminates the CTCF-binding site. The mutation did not disrupt the kinetics and levels of virus gene expression, or establishment of or reactivation from latency. However, the mutation disrupted the epigenetic barrier function, resulting in enhanced DNA CpG methylation downstream of the CTCF binding site on both strands of the integrated provirus and H3K4Me3, H3K36Me3, and H3K27Me3 chromatin modifications both up- and downstream of the site. A majority of clonal cell lines infected with wild type HTLV-1 exhibited increased plus strand gene expression with CTCF knockdown, while expression in mutant HTLV-1 clonal lines was unaffected. These findings indicate that CTCF binding regulates HTLV-1 gene expression, DNA and histone methylation in an integration site dependent fashion. Human T-cell leukemia virus type 1 (HTLV-1) is a cause of leukemia and lymphoma as well as several inflammatory medical disorders. The virus integrates in the host cell DNA, and it has a single binding site for a protein designated CTCF. This protein is important in the regulation of many DNA viruses, as well as many properties of normal and malignant cells. In order to define the role of CTCF binding to HTLV, we analyzed a mutant virus lacking the binding site. We found that this mutation variably affected gene expression, DNA and histone modification, suggesting a key role in regulation of virus replication in infected cells.
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Affiliation(s)
- Xiaogang Cheng
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Ancy Joseph
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Victor Castro
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Alice Chen-Liaw
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Zachary Skidmore
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Takaharu Ueno
- Department of Microbiology, Kansai Medical University, Osaka, Japan
| | | | - Daniel A. Rauch
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Grant A. Challen
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Michael P. Martinez
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, United States of America
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Patrick Green
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, United States of America
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Malachi Griffith
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jacqueline E. Payton
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - John R. Edwards
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Phamacogenomics, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Lee Ratner
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
- * E-mail:
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3
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Rogers KJ, Vijay R, Butler NS. Anti-malarial humoral immunity: the long and short of it. Microbes Infect 2021; 23:104807. [PMID: 33684519 DOI: 10.1016/j.micinf.2021.104807] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/28/2021] [Accepted: 02/28/2021] [Indexed: 12/17/2022]
Abstract
Humoral immunity is critical for limiting Plasmodium parasite infections and the severity of malaria. Naturally acquired immunity against malaria occurs inefficiently and protection is relatively short-lived. Here we review recent advances and explore emerging hypotheses regarding the molecular and cellular pathways that regulate Plasmodium parasite-specific B cell responses and durable anti-malarial humoral immunity.
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Affiliation(s)
- Kai J Rogers
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Rahul Vijay
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Noah S Butler
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA; Interdisciplinary Graduate Program in Immunology, The University of Iowa, Iowa City, IA, USA.
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4
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Lai Q, Li Q, He C, Fang Y, Lin S, Cai J, Ding J, Zhong Q, Zhang Y, Wu C, Wang X, He J, Liu Y, Yan Q, Li A, Liu S. CTCF promotes colorectal cancer cell proliferation and chemotherapy resistance to 5-FU via the P53-Hedgehog axis. Aging (Albany NY) 2020; 12:16270-16293. [PMID: 32688344 PMCID: PMC7485712 DOI: 10.18632/aging.103648] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/19/2020] [Indexed: 12/15/2022]
Abstract
CTCF is overexpressed in several cancers and plays crucial roles in regulating aggressiveness, but little is known about whether CTCF drives colorectal cancer progression. Here, we identified a tumor-promoting role for CTCF in colorectal cancer. Our study demonstrated that CTCF was upregulated in colorectal cancer specimens compared with adjacent noncancerous colorectal tissues. The overexpression of CTCF promoted colorectal cancer cell proliferation and tumor growth, while the opposite effects were observed in CTCF knockdown cells. Increased GLI1, Shh, PTCH1, and PTCH2 levels were observed in CTCF-overexpressing cells using western blot analyses. CCK-8 and apoptosis assays revealed that 5-fluorouracil chemosensitivity was negatively associated with CTCF expression. Furthermore, we identified that P53 is a direct transcriptional target gene of CTCF in colorectal cancer. Western blot and nuclear extract assays showed that inhibition of P53 can counteract Hedgehog signaling pathway repression induced by CTCF knockdown. In conclusion, we uncovered a crucial role for CTCF regulation that possibly involves the P53-Hedgehog axis and highlighted the clinical utility of colorectal cancer-specific potential therapeutic target as disease progression or clinical response biomarkers.
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Affiliation(s)
- Qiuhua Lai
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Qingyuan Li
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Chengcheng He
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuxin Fang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Simin Lin
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jianqun Cai
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jian Ding
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Qian Zhong
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yue Zhang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Changjie Wu
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xinke Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Juan He
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yongfeng Liu
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Qun Yan
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Aimin Li
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Side Liu
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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5
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Suppression of BCL6 function by HDAC inhibitor mediated acetylation and chromatin modification enhances BET inhibitor effects in B-cell lymphoma cells. Sci Rep 2019; 9:16495. [PMID: 31712669 PMCID: PMC6848194 DOI: 10.1038/s41598-019-52714-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
Multiple genetic aberrations in the regulation of BCL6, including in acetyltransferase genes, occur in clinically aggressive B-cell lymphomas and lead to higher expression levels and activity of this transcriptional repressor. BCL6 is, therefore, an attractive target for therapy in aggressive lymphomas. In this study romidepsin, a potent histone deacetylase inhibitor (HDACi), induced apoptosis and cell cycle arrest in Burkitt and diffuse large B-cell lymphoma cell lines, which are model cells for studying the mechanism of action of BCL6. Romidepsin caused BCL6 acetylation at early timepoints inhibiting its function, while at later timepoints BCL6 expression was reduced and target gene expression increased due to chromatin modification. MYC contributes to poor prognosis in aggressive lymphoma. MYC function is reduced by inhibition of chromatin readers of the bromodomain and extra-terminal repeat (BET) family, which includes BRD4. The novel combination of romidepsin and JQ1, a BRD4 inhibitor was investigated and showed synergy. Collectively we suggest that the combination of HDACi and BRD4i should be pursued in further pre-clinical testing.
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6
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van Meurs JB, Boer CG, Lopez-Delgado L, Riancho JA. Role of Epigenomics in Bone and Cartilage Disease. J Bone Miner Res 2019; 34:215-230. [PMID: 30715766 DOI: 10.1002/jbmr.3662] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/03/2018] [Accepted: 01/02/2019] [Indexed: 12/14/2022]
Abstract
Phenotypic variation in skeletal traits and diseases is the product of genetic and environmental factors. Epigenetic mechanisms include information-containing factors, other than DNA sequence, that cause stable changes in gene expression and are maintained during cell divisions. They represent a link between environmental influences, genome features, and the resulting phenotype. The main epigenetic factors are DNA methylation, posttranslational changes of histones, and higher-order chromatin structure. Sometimes non-coding RNAs, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are also included in the broad term of epigenetic factors. There is rapidly expanding experimental evidence for a role of epigenetic factors in the differentiation of bone cells and the pathogenesis of skeletal disorders, such as osteoporosis and osteoarthritis. However, different from genetic factors, epigenetic signatures are cell- and tissue-specific and can change with time. Thus, elucidating their role has particular difficulties, especially in human studies. Nevertheless, epigenomewide association studies are beginning to disclose some disease-specific patterns that help to understand skeletal cell biology and may lead to development of new epigenetic-based biomarkers, as well as new drug targets useful for treating diffuse and localized disorders. Here we provide an overview and update of recent advances on the role of epigenomics in bone and cartilage diseases. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
| | - Cindy G Boer
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Laura Lopez-Delgado
- Department of Internal Medicine, Hospital U M Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - Jose A Riancho
- Department of Internal Medicine, Hospital U M Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
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7
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Pantoja-Escobar G, Morales-Martínez M, Vega GG, Castro-Escarpulli G, Vega MI. Cytotoxic effect caspase activation dependent of a genetically engineered fusion protein with a CD154 peptide mimetic (OmpC-CD154 p) on B-NHL cell lines is mediated by the inhibition of bcl-6 and YY1 through MAPK p38 activation. Leuk Lymphoma 2018; 60:1062-1070. [PMID: 30277117 DOI: 10.1080/10428194.2018.1516286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The interaction between CD40, and its ligand, CD154, is essential for the development of humoral and cellular immune responses. The selective inhibition or activation of this pathway forms the basis for the development of new therapeutics against immunologically based diseases and malignancies. We are developing a gene fusion of Salmonella typhi OmpC protein expressing the CD154 Tyr140-Ser-149 amino acid strand. This OmpC-CD154 binds CD40 and activates B cells. In this study, we demonstrate that OmpC-CD154p treatment inhibits cell growth, proliferation and induced apoptosis in the B-NHL cell lines Raji and Ramos. The Bcl-2 family proteins were regulated and the Bcl-6 and YY1 oncoproteins were inhibited. p38 MAPK activation is an important mechanism underlying the effect on proliferation and apoptosis mediated by this fusion protein. This study establishes a basis for the possible use of fusion protein OmpC-CD154 as an alternative treatment for B-NHL.
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Affiliation(s)
- Gerardo Pantoja-Escobar
- a Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas , Laboratorio de Investigación Clínica y Ambiental , Mexico City , Mexico.,b Molecular Signal Pathways in Cancer Laboratory , UIMEO, Oncology Hospital, Siglo XXI National Medical Center, IMSS , Mexico City , Mexico
| | - Mario Morales-Martínez
- b Molecular Signal Pathways in Cancer Laboratory , UIMEO, Oncology Hospital, Siglo XXI National Medical Center, IMSS , Mexico City , Mexico
| | - Gabriel G Vega
- b Molecular Signal Pathways in Cancer Laboratory , UIMEO, Oncology Hospital, Siglo XXI National Medical Center, IMSS , Mexico City , Mexico
| | - Graciela Castro-Escarpulli
- a Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas , Laboratorio de Investigación Clínica y Ambiental , Mexico City , Mexico
| | - Mario I Vega
- b Molecular Signal Pathways in Cancer Laboratory , UIMEO, Oncology Hospital, Siglo XXI National Medical Center, IMSS , Mexico City , Mexico.,c Department of Medicine , Hematology-Oncology Division VA West Los Angeles Medical Center BBRI UCLA Medical Center Jonsson Comprehensive Cancer Center , Los Angeles , CA , USA
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8
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Affiliation(s)
- Rebecca J Leeman-Neill
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
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9
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Méndez A, Mendoza L. A Network Model to Describe the Terminal Differentiation of B Cells. PLoS Comput Biol 2016; 12:e1004696. [PMID: 26751566 PMCID: PMC4720151 DOI: 10.1371/journal.pcbi.1004696] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 12/07/2015] [Indexed: 01/31/2023] Open
Abstract
Terminal differentiation of B cells is an essential process for the humoral immune response in vertebrates and is achieved by the concerted action of several transcription factors in response to antigen recognition and extracellular signals provided by T-helper cells. While there is a wealth of experimental data regarding the molecular and cellular signals involved in this process, there is no general consensus regarding the structure and dynamical properties of the underlying regulatory network controlling this process. We developed a dynamical model of the regulatory network controlling terminal differentiation of B cells. The structure of the network was inferred from experimental data available in the literature, and its dynamical behavior was analyzed by modeling the network both as a discrete and a continuous dynamical systems. The steady states of these models are consistent with the patterns of activation reported for the Naive, GC, Mem, and PC cell types. Moreover, the models are able to describe the patterns of differentiation from the precursor Naive to any of the GC, Mem, or PC cell types in response to a specific set of extracellular signals. We simulated all possible single loss- and gain-of-function mutants, corroborating the importance of Pax5, Bcl6, Bach2, Irf4, and Blimp1 as key regulators of B cell differentiation process. The model is able to represent the directional nature of terminal B cell differentiation and qualitatively describes key differentiation events from a precursor cell to terminally differentiated B cells. Generation of antibody-producing cells through terminal B cell differentiation represents a good model to study the formation of multiple effector cells from a progenitor cell type. This process is controlled by the action of several molecules that maintain cell type specific programs in response to cytokines, antigen recognition and the direct contact with T helper cells, forming a complex regulatory network. While there is a large body of experimental data regarding some of the key molecules involved in this process and there have been several efforts to reconstruct the underlying regulatory network, a general consensus about the structure and dynamical behavior of this network is lacking. Moreover, it is not well understood how this network controls the establishment of specific B cell expression patterns and how it responds to specific external signals. We present a model of the regulatory network controlling terminal B cell differentiation and analyze its dynamical behavior under normal and mutant conditions. The model recovers the patterns of differentiation of B cells and describes a large set of gain- and loss-of-function mutants. This model provides an unified framework to generate qualitative descriptions to interpret the role of intra- and extracellular regulators of B cell differentiation.
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Affiliation(s)
- Akram Méndez
- Programa de Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Ciudad de México, México
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
- C3, Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, México
- * E-mail:
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10
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Marina RJ, Sturgill D, Bailly MA, Thenoz M, Varma G, Prigge MF, Nanan KK, Shukla S, Haque N, Oberdoerffer S. TET-catalyzed oxidation of intragenic 5-methylcytosine regulates CTCF-dependent alternative splicing. EMBO J 2015; 35:335-55. [PMID: 26711177 DOI: 10.15252/embj.201593235] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/25/2015] [Indexed: 01/09/2023] Open
Abstract
Intragenic 5-methylcytosine and CTCF mediate opposing effects on pre-mRNA splicing: CTCF promotes inclusion of weak upstream exons through RNA polymerase II pausing, whereas 5-methylcytosine evicts CTCF, leading to exon exclusion. However, the mechanisms governing dynamic DNA methylation at CTCF-binding sites were unclear. Here, we reveal the methylcytosine dioxygenases TET1 and TET2 as active regulators of CTCF-mediated alternative splicing through conversion of 5-methylcytosine to its oxidation derivatives. 5-hydroxymethylcytosine and 5-carboxylcytosine are enriched at an intragenic CTCF-binding sites in the CD45 model gene and are associated with alternative exon inclusion. Reduced TET levels culminate in increased 5-methylcytosine, resulting in CTCF eviction and exon exclusion. In vitro analyses establish the oxidation derivatives are not sufficient to stimulate splicing, but efficiently promote CTCF association. We further show genomewide that reciprocal exchange of 5-hydroxymethylcytosine and 5-methylcytosine at downstream CTCF-binding sites is a general feature of alternative splicing in naïve and activated CD4(+) T cells. These findings significantly expand our current concept of the pre-mRNA "splicing code" to include dynamic intragenic DNA methylation catalyzed by the TET proteins.
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Affiliation(s)
- Ryan J Marina
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - David Sturgill
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Marc A Bailly
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Morgan Thenoz
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Garima Varma
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Maria F Prigge
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Kyster K Nanan
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Sanjeev Shukla
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Nazmul Haque
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Shalini Oberdoerffer
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
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11
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Kang JY, Song SH, Yun J, Jeon MS, Kim HP, Han SW, Kim TY. Disruption of CTCF/cohesin-mediated high-order chromatin structures by DNA methylation downregulates PTGS2 expression. Oncogene 2015; 34:5677-84. [PMID: 25703332 DOI: 10.1038/onc.2015.17] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/15/2014] [Accepted: 01/16/2015] [Indexed: 12/25/2022]
Abstract
The CCCTC-binding factor (CTCF)/cohesin complex regulates gene transcription via high-order chromatin organization of the genome. De novo methylation of CpG islands in the promoter region is an epigenetic hallmark of gene silencing in cancer. Although the CTCF/cohesin complex preferentially targets hypomethylated DNA, it remains unclear whether the CTCF/cohesin-mediated high-order chromatin structure is affected by DNA methylation during tumorigenesis. We found that DNA methylation downregulates the expression of prostaglandin-endoperoxide synthase 2 (PTGS2), which is an inducible, rate-limiting enzyme for prostaglandin synthesis, by disrupting CTCF/cohesin-mediated chromatin looping. We show that the CTCF/cohesin complex is enriched near a CpG island associated with PTGS2 and that the PTGS2 locus forms chromatin loops through methylation-sensitive binding of the CTCF/cohesin complex. DNA methylation abolishes the association of the CTCF/cohesin complex with the PTGS2 CpG island. Disruption of chromatin looping by DNA methylation abrogates the enrichment of transcriptional components, such as positive elongation factor b, at the transcriptional start site of the PTGS2 locus. These alterations result in the downregulation of PTGS2. Our results provide evidence that CTCF/cohesin-mediated chromatin looping of the PTGS2 locus is dynamically influenced by the DNA methylation status.
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Affiliation(s)
- J Y Kang
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - S H Song
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - J Yun
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - M S Jeon
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - H P Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - S W Han
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - T Y Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
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12
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Victoria-Acosta G, Vazquez-Santillan K, Jimenez-Hernandez L, Muñoz-Galindo L, Maldonado V, Martinez-Ruiz GU, Melendez-Zajgla J. Epigenetic silencing of the XAF1 gene is mediated by the loss of CTCF binding. Sci Rep 2015; 5:14838. [PMID: 26443201 PMCID: PMC4595840 DOI: 10.1038/srep14838] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/07/2015] [Indexed: 12/15/2022] Open
Abstract
XAF1 is a tumour suppressor gene that compromises cell viability by modulating different cellular events such as mitosis, cell cycle progression and apoptosis. In cancer, the XAF1 gene is commonly silenced by CpG-dinucleotide hypermethylation of its promoter. DNA demethylating agents induce transcriptional reactivation of XAF1, sensitizing cancer cells to therapy. The molecular mechanisms that mediate promoter CpG methylation have not been previously studied. Here, we demonstrate that CTCF interacts with the XAF1 promoter in vivo in a methylation-sensitive manner. By transgene assays, we demonstrate that CTCF mediates the open-chromatin configuration of the XAF1 promoter, inhibiting both CpG-dinucleotide methylation and repressive histone posttranslational modifications. In addition, the absence of CTCF in the XAF1 promoter inhibits transcriptional activation induced by well-known apoptosis activators. We report for the first time that epigenetic silencing of the XAF1 gene is a consequence of the loss of CTCF binding.
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Affiliation(s)
- Georgina Victoria-Acosta
- Functional Cancer Genomics Laboratory, National Institute of Genomic Medicine, Mexico D.F., 14610, Mexico
| | | | - Luis Jimenez-Hernandez
- Epigenetics Laboratory, National Institute of Genomic Medicine, Mexico D.F., 14610, México
| | - Laura Muñoz-Galindo
- Epigenetics Laboratory, National Institute of Genomic Medicine, Mexico D.F., 14610, México
| | - Vilma Maldonado
- Epigenetics Laboratory, National Institute of Genomic Medicine, Mexico D.F., 14610, México
| | - Gustavo Ulises Martinez-Ruiz
- Functional Cancer Genomics Laboratory, National Institute of Genomic Medicine, Mexico D.F., 14610, Mexico.,Unit of Investigative Research on Oncological Disease, Children's Hospital of Mexico "Federico Gomez", Mexico City, Mexico
| | - Jorge Melendez-Zajgla
- Functional Cancer Genomics Laboratory, National Institute of Genomic Medicine, Mexico D.F., 14610, Mexico
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13
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Batlle-López A, Cortiguera MG, Delgado MD. The epigenetic regulator CTCF modulates BCL6 in lymphoma. Oncoscience 2015; 2:783-4. [PMID: 26682243 PMCID: PMC4671918 DOI: 10.18632/oncoscience.239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 09/12/2015] [Indexed: 12/12/2022] Open
Affiliation(s)
- Ana Batlle-López
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-Universidad de Cantabria) Santander, Spain
| | - María G Cortiguera
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-Universidad de Cantabria) Santander, Spain
| | - M Dolores Delgado
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-Universidad de Cantabria) Santander, Spain
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14
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Epigenetic Control of B Cell Development and B-Cell-Related Immune Disorders. Clin Rev Allergy Immunol 2015; 50:301-11. [DOI: 10.1007/s12016-015-8494-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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