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Zhang X, Wang H, Zhang Y, Wang X. Advances in epigenetic alterations of chronic lymphocytic leukemia: from pathogenesis to treatment. Clin Exp Med 2024; 24:54. [PMID: 38492089 PMCID: PMC10944427 DOI: 10.1007/s10238-023-01268-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: 05/05/2023] [Accepted: 12/01/2023] [Indexed: 03/18/2024]
Abstract
Chronic lymphocytic leukemia (CLL) is a heterogeneous disease with alterations in genetic expression and epigenetic modifications. In recent years, the new insight into epigenetics in the pathogenesis of CLL has been developed considerably, including DNA methylation, histone modification, RNA methylation, non-coding RNAs as well as chromatin remodeling. Epigenetic modification regulates various processes such as stem cell biology, cell growth, and tumorigenesis without altering gene sequence. Growing evidence indicates that the disturbance of gene expression profiles which were regulated by epigenetic modifications exerts vital roles in the development and progress in CLL, which provides novel perspectives to explore the etiology of CLL. In addition, the integration with epigenetic therapeutic targets and the in-depth understanding of epigenetic therapy contribute to develop new therapeutic strategies for CLL. Herein, the present review discusses the advances of epigenetic alterations in the pathogenesis, diagnosis, and prognostic assessment of CLL patients and also highlights existing and emerging agents targeting epigenetic regulators.
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Affiliation(s)
- Xin Zhang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Hua Wang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Ya Zhang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China.
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
- Taishan Scholars Program of Shandong Province, Jinan, 250021, Shandong, China.
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China.
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
- Taishan Scholars Program of Shandong Province, Jinan, 250021, Shandong, China.
- Branch of National Clinical Research Center for Hematologic Diseases, Jinan, 250021, Shandong, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China.
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Chatzidavid S, Kontandreopoulou CN, Giannakopoulou N, Diamantopoulos PT, Stafylidis C, Kyrtsonis MC, Dimou M, Panayiotidis P, Viniou NA. The Role of Methylation in Chronic Lymphocytic Leukemia and Its Prognostic and Therapeutic Impacts in the Disease: A Systematic Review. Adv Hematol 2024; 2024:1370364. [PMID: 38435839 PMCID: PMC10907108 DOI: 10.1155/2024/1370364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 03/05/2024] Open
Abstract
Epigenetic regulation has been thoroughly investigated in recent years and has emerged as an important aspect of chronic lymphocytic leukemia (CLL) biology. Characteristic aberrant features such as methylation patterns and global DNA hypomethylation were the early findings of the research during the last decades. The investigation in this field led to the identification of a large number of genes where methylation features correlated with important clinical and laboratory parameters. Gene-specific analyses investigated methylation in the gene body enhancer regions as well as promoter regions. The findings included genes and proteins involved in key pathways that play central roles in the pathophysiology of the disease. Τhe application of these findings beyond the theoretical understanding can not only lead to the creation of prognostic and predictive models and scores but also to the design of novel therapeutic agents. The following is a review focusing on the present knowledge about single gene/gene promoter methylation or mRNA expression in CLL cases as well as records of older data that have been published in past papers.
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Affiliation(s)
- Sevastianos Chatzidavid
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
- Thalassemia and Sickle Cell Disease Center, Laikon General Hospital, Athens, Greece
| | - Christina-Nefeli Kontandreopoulou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Panagiotis T. Diamantopoulos
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos Stafylidis
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Marie-Christine Kyrtsonis
- Hematology Section of the First Department of Propaedeutic Internal Medicine, Laikon University Hospital, Athens, Greece
| | - Maria Dimou
- Hematology Section of the First Department of Propaedeutic Internal Medicine, Laikon University Hospital, Athens, Greece
| | - Panayiotis Panayiotidis
- Department of Hematology and Bone Marrow Transplantation Unit, National and Kapodistrian University of Athens, School of Medicine, Laikon General Hospital, Athens, Greece
| | - Nora-Athina Viniou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
- Hematology Department, Iatriko Kentro Palaiou Falirou, Athens, Greece
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3
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Radhakrishnan K, Truong L, Carmichael CL. An "unexpected" role for EMT transcription factors in hematological development and malignancy. Front Immunol 2023; 14:1207360. [PMID: 37600794 PMCID: PMC10435889 DOI: 10.3389/fimmu.2023.1207360] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/14/2023] [Indexed: 08/22/2023] Open
Abstract
The epithelial to mesenchymal transition (EMT) is a fundamental developmental process essential for normal embryonic development. It is also important during various pathogenic processes including fibrosis, wound healing and epithelial cancer cell metastasis and invasion. EMT is regulated by a variety of cell signalling pathways, cell-cell interactions and microenvironmental cues, however the key drivers of EMT are transcription factors of the ZEB, TWIST and SNAIL families. Recently, novel and unexpected roles for these EMT transcription factors (EMT-TFs) during normal blood cell development have emerged, which appear to be largely independent of classical EMT processes. Furthermore, EMT-TFs have also begun to be implicated in the development and pathogenesis of malignant hematological diseases such as leukemia and lymphoma, and now present themselves or the pathways they regulate as possible new therapeutic targets within these malignancies. In this review, we discuss the ZEB, TWIST and SNAIL families of EMT-TFs, focusing on what is known about their normal roles during hematopoiesis as well as the emerging and "unexpected" contribution they play during development and progression of blood cancers.
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Affiliation(s)
- Karthika Radhakrishnan
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Lynda Truong
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Catherine L. Carmichael
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Monash University, Faculty of Medicine, Nursing and Health Sciences, Clayton, VIC, Australia
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4
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Paul P, Stüssi G, Bruscaggin A, Rossi D. Genetics and epigenetics of CLL. Leuk Lymphoma 2023; 64:551-563. [PMID: 36503384 DOI: 10.1080/10428194.2022.2153359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chronic lymphocytic leukemia (CLL) has a heterogeneous biological behavior, which is highly influenced by its immunogenetic, epigenetic, and genomic properties. The remarkably variable clinical course of the disease has been associated with genetic features such as chromosomal abnormalities, the presence of either high or low numbers of somatic hypermutations (SHM) in the variable region of the immunoglobulin heavy chain locus (IGHV), and somatic mutations of several specific driver genes. Next-generation sequencing (NGS) technologies have provided a comprehensive characterization of the genomic and epigenomic landscape in CLL, elucidating important underlying mechanisms of the disease's biology. The scope of this review is to summarize the most recent discoveries about novel genetic and epigenetic alterations, discussing their impact on clinical outcomes and response to currently available therapy.
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Affiliation(s)
- Pamella Paul
- Department of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Georg Stüssi
- Department of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Alessio Bruscaggin
- Laboratory of Experimental Hematology, Institute of Oncology of Southern Switzerland, Institute of Oncology Research, Bellinzona, Switzerland
| | - Davide Rossi
- Department of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Laboratory of Experimental Hematology, Institute of Oncology of Southern Switzerland, Institute of Oncology Research, Bellinzona, Switzerland
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5
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Chatzidavid S, Kontandreopoulou CN, Diamantopoulos PT, Giannakopoulou N, Katsiampoura P, Stafylidis C, Dryllis G, Kyrtsonis MC, Dimou M, Panayiotidis P, Viniou NA. The Clinical and Prognostic Significance of Ribonucleotide Reductase Subunits RRM1 and RRM2 mRNA Levels in Patients with Chronic Lymphocytic Leukemia. Clin Hematol Int 2023:10.1007/s44228-023-00033-x. [PMID: 36811764 DOI: 10.1007/s44228-023-00033-x] [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: 11/03/2022] [Accepted: 01/25/2023] [Indexed: 02/24/2023] Open
Abstract
Ribonucleotide Reductase (RNR) converts ribonucleotides to deoxyribonucleotides required for DNA replication and repair. RNR consists of subunits M1 and M2. It has been studied as a prognostic factor in several solid tumors and in chronic hematological malignancies, but not in chronic lymphocytic leukemia (CLL). Peripheral blood samples were collected from 135 CLL patients. M1/M2 gene mRNA levels were measured and expressed as a RRM1-2/GAPDH ratio. M1 gene promoter methylation was studied in a patients' subgroup. M1 mRNA expression was higher in patients without anemia (p = 0.026), without lymphadenopathy (p = 0.005) and 17p gene deletion (p = 0.031). Abnormal LDH (p = 0.022) and higher Rai stage (p = 0.019) were associated with lower M1 mRNA levels. Higher M2 mRNA levels were found in patients without lymphadenopathy (p = .048), Rai stage 0 (p = 0.025) and Trisomy 12 (p = 0.025). The correlation between RNR subunits and clinic-biological characteristics in CLL patients demonstrate RNR's potential role as a prognostic factor.
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Affiliation(s)
- Sevastianos Chatzidavid
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece.
| | - Christina-Nefeli Kontandreopoulou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece
| | - Panagiotis T Diamantopoulos
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece
| | - Nefeli Giannakopoulou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece
| | - Panagiota Katsiampoura
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece
| | - Christos Stafylidis
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece
| | - Georgios Dryllis
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece
| | - Marie-Christine Kyrtsonis
- Hematology Section of the First Department of Propaedeutic Internal Medicine, Laikon University Hospital, Athens, Greece
| | - Maria Dimou
- Hematology Section of the First Department of Propaedeutic Internal Medicine, Laikon University Hospital, Athens, Greece
| | - Panayiotis Panayiotidis
- Department of Hematology and Bone Marrow Transplantation Unit, National and Kapodistrian University of Athens, School of Medicine, Laikon General Hospital, Athens, Greece
| | - Nora-Athina Viniou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece
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6
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Targeting DNA Methylation in Leukemia, Myelodysplastic Syndrome, and Lymphoma: A Potential Diagnostic, Prognostic, and Therapeutic Tool. Int J Mol Sci 2022; 24:ijms24010633. [PMID: 36614080 PMCID: PMC9820560 DOI: 10.3390/ijms24010633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022] Open
Abstract
DNA methylation represents a crucial mechanism of epigenetic regulation in hematologic malignancies. The methylation process is controlled by specific DNA methyl transferases and other regulators, which are often affected by genetic alterations. Global hypomethylation and hypermethylation of tumor suppressor genes are associated with hematologic cancer development and progression. Several epi-drugs have been successfully implicated in the treatment of hematologic malignancies, including the hypomethylating agents (HMAs) decitabine and azacytidine. However, combinations with other treatment modalities and the discovery of new molecules are still the subject of research to increase sensitivity to anti-cancer therapies and improve patient outcomes. In this review, we summarized the main functions of DNA methylation regulators and genetic events leading to changes in methylation landscapes. We provide current knowledge about target genes with aberrant methylation levels in leukemias, myelodysplastic syndromes, and malignant lymphomas. Moreover, we provide an overview of the clinical trials, focused mainly on the combined therapy of HMAs with other treatments and its impact on adverse events, treatment efficacy, and survival rates among hematologic cancer patients. In the era of precision medicine, a transition from genes to their regulation opens up the possibility of an epigenetic-based approach as a diagnostic, prognostic, and therapeutic tool.
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Bloehdorn J, Braun A, Taylor-Weiner A, Jebaraj BMC, Robrecht S, Krzykalla J, Pan H, Giza A, Akylzhanova G, Holzmann K, Scheffold A, Johnston HE, Yeh RF, Klymenko T, Tausch E, Eichhorst B, Bullinger L, Fischer K, Weisser M, Robak T, Schneider C, Gribben J, Dahal LN, Carter MJ, Elemento O, Landau DA, Neuberg DS, Cragg MS, Benner A, Hallek M, Wu CJ, Döhner H, Stilgenbauer S, Mertens D. Multi-platform profiling characterizes molecular subgroups and resistance networks in chronic lymphocytic leukemia. Nat Commun 2021; 12:5395. [PMID: 34518531 PMCID: PMC8438057 DOI: 10.1038/s41467-021-25403-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 08/03/2021] [Indexed: 02/07/2023] Open
Abstract
Knowledge of the genomic landscape of chronic lymphocytic leukemia (CLL) grows increasingly detailed, providing challenges in contextualizing the accumulated information. To define the underlying networks, we here perform a multi-platform molecular characterization. We identify major subgroups characterized by genomic instability (GI) or activation of epithelial-mesenchymal-transition (EMT)-like programs, which subdivide into non-inflammatory and inflammatory subtypes. GI CLL exhibit disruption of genome integrity, DNA-damage response and are associated with mutagenesis mediated through activation-induced cytidine deaminase or defective mismatch repair. TP53 wild-type and mutated/deleted cases constitute a transcriptionally uniform entity in GI CLL and show similarly poor progression-free survival at relapse. EMT-like CLL exhibit high genomic stability, reduced benefit from the addition of rituximab and EMT-like differentiation is inhibited by induction of DNA damage. This work extends the perspective on CLL biology and risk categories in TP53 wild-type CLL. Furthermore, molecular targets identified within each subgroup provide opportunities for new treatment approaches.
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Affiliation(s)
| | - Andrejs Braun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | | | - Sandra Robrecht
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Julia Krzykalla
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Heng Pan
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Adam Giza
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Gulnara Akylzhanova
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Annika Scheffold
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Harvey E Johnston
- Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
| | - Ru-Fang Yeh
- Biostatistics, Genentech Inc., South San Francisco, CA, USA
| | - Tetyana Klymenko
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Eugen Tausch
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Barbara Eichhorst
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Lars Bullinger
- Medical Clinic for Hematology, Oncology and Tumor Biology, Charité University Hospital, Berlin, Germany
| | - Kirsten Fischer
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Martin Weisser
- Roche Pharma Research and Early Development, Penzberg, Germany
| | - Tadeusz Robak
- Department of Hematology, Medical University of Lodz, Lodz, Poland
| | | | - John Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lekh N Dahal
- Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
- Department of Pharmacology and Therapeutics, Faculty of Life and Health Sciences, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Mathew J Carter
- Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Dan A Landau
- Cancer Genomics and Evolutionary Dynamics, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Donna S Neuberg
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark S Cragg
- Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Michael Hallek
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Catherine J Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Hartmut Döhner
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | | | - Daniel Mertens
- Department of Internal Medicine III, University of Ulm, Ulm, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
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8
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Wierzbinska JA, Toth R, Ishaque N, Rippe K, Mallm JP, Klett LC, Mertens D, Zenz T, Hielscher T, Seifert M, Küppers R, Assenov Y, Lutsik P, Stilgenbauer S, Roessner PM, Seiffert M, Byrd J, Oakes CC, Plass C, Lipka DB. Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL. Genome Med 2020; 12:29. [PMID: 32188505 PMCID: PMC7081711 DOI: 10.1186/s13073-020-00724-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/11/2020] [Indexed: 02/07/2023] Open
Abstract
Background In cancer, normal epigenetic patterns are disturbed and contribute to gene expression changes, disease onset, and progression. The cancer epigenome is composed of the epigenetic patterns present in the tumor-initiating cell at the time of transformation, and the tumor-specific epigenetic alterations that are acquired during tumor initiation and progression. The precise dissection of these two components of the tumor epigenome will facilitate a better understanding of the biological mechanisms underlying malignant transformation. Chronic lymphocytic leukemia (CLL) originates from differentiating B cells, which undergo extensive epigenetic programming. This poses the challenge to precisely determine the epigenomic ground state of the cell-of-origin in order to identify CLL-specific epigenetic aberrations. Methods We developed a linear regression model, methylome-based cell-of-origin modeling (Methyl-COOM), to map the cell-of-origin for individual CLL patients based on the continuum of epigenomic changes during normal B cell differentiation. Results Methyl-COOM accurately maps the cell-of-origin of CLL and identifies CLL-specific aberrant DNA methylation events that are not confounded by physiologic epigenetic B cell programming. Furthermore, Methyl-COOM unmasks abnormal action of transcription factors, altered super-enhancer activities, and aberrant transcript expression in CLL. Among the aberrantly regulated transcripts were many genes that have previously been implicated in T cell biology. Flow cytometry analysis of these markers confirmed their aberrant expression on malignant B cells at the protein level. Conclusions Methyl-COOM analysis of CLL identified disease-specific aberrant gene regulation. The aberrantly expressed genes identified in this study might play a role in immune-evasion in CLL and might serve as novel targets for immunotherapy approaches. In summary, we propose a novel framework for in silico modeling of reference DNA methylomes and for the identification of cancer-specific epigenetic changes, a concept that can be broadly applied to other human malignancies. Electronic supplementary material Supplementary information accompanies this paper at 10.1186/s13073-020-00724-7.
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Affiliation(s)
- Justyna A Wierzbinska
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,The German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Reka Toth
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Naveed Ishaque
- The German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Karsten Rippe
- The German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Chromatin Networks, DKFZ, Heidelberg, Germany
| | - Jan-Philipp Mallm
- The German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Chromatin Networks, DKFZ, Heidelberg, Germany
| | - Lara C Klett
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Division of Chromatin Networks, DKFZ, Heidelberg, Germany
| | - Daniel Mertens
- The German Cancer Consortium (DKTK), Heidelberg, Germany.,Mechanisms of Leukemogenesis, DKFZ, Heidelberg, Germany
| | - Thorsten Zenz
- Experimental Hematology Lab, University Hospital Zurich, Zurich, Switzerland
| | | | - Marc Seifert
- Group Molecular Genetics, Essen University Hospital, Essen, Germany
| | - Ralf Küppers
- Group Molecular Genetics, Essen University Hospital, Essen, Germany
| | - Yassen Assenov
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | | | | | | | - John Byrd
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, USA
| | - Christopher C Oakes
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, USA
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany. .,The German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Daniel B Lipka
- The German Cancer Consortium (DKTK), Heidelberg, Germany. .,Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany. .,National Center for Tumor Diseases (NCT), Heidelberg, Germany. .,Faculty of Medicine, Medical Center, Otto-von-Guericke-University, 39120, Magdeburg, Germany.
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9
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Zhao C, Zhang W, Zhu X, Xu Y, Yang K, Wei D, Liang S, Zhao F, Zhang Y, Chen X, Sun L, Yuan H, Shi X, Wang X, Liu M, Yang F, Wang J, Yang Z. TWIST2: A new candidate tumor suppressor in prostate cancer. Prostate 2019; 79:1647-1657. [PMID: 31433071 PMCID: PMC6771699 DOI: 10.1002/pros.23889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/16/2019] [Indexed: 01/22/2023]
Abstract
BACKGROUND Prostate cancer (PCa) is a leading cause of cancer morbidity and mortality in men worldwide; however, PCa incidence and mortality rates vary widely across geographic regions and ethnic groups. The current study was designed to elucidate the pivotal factors involved in PCa occurrence and development. METHODS We performed RNA sequencing on the prostate tumor and adjacent normal tissues from Chinese PCa patients. Genes identified via genome-wide expression profile analysis were validated by quantitative reverse-transcription polymerase chain reaction and immunohistochemistry. Hypermethylation of CpG islands was assessed by nested methylation-specific PCR. Whole genome microarray analysis was performed using an Affymetrix GeneChip. RESULTS We identified nine possible abnormally expressed genes (P < .05) and then revealed TWIST2 as having strikingly lower expression in tumors than in control tissues (P < .01). Low messenger RNA expression levels of TWIST2 were associated with hypermethylation of CpG islands in its promoter region. In accordance with these findings, PCa tumor tissues showed markedly decreased TWIST2 protein expression compared to that in both normal and prostatic intraepithelial neoplasia tissues by immunohistochemical staining. Ectopic expression of TWIST2 in LNCap cells not only inhibited cell proliferation and colony formation in vitro and tumor growth in vivo but also induced transcriptional repression of a cell proliferation-related gene cohort, including androgen receptor signaling mediators, cyclins, homeobox genes, forkhead box genes, and SOX2. CONCLUSIONS Our results suggest that TWIST2 could function as a tumor suppressor involved in the pathogenesis of PCa by influencing the expression of target genes and that hypermethylation of the TWIST2 promoter in prostate tumors may be an underlying mechanism for TWIST2 transcriptional silencing.
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Affiliation(s)
- Chengxiao Zhao
- School of Pharmaceutical ScienceShanxi Medical UniversityTaiyuanShanxiChina
- The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of GeriatricsMinistry of HealthBeijingChina
| | - Wei Zhang
- Department of PathologyBeijing HospitalBeijingChina
| | - Xiaoquan Zhu
- The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of GeriatricsMinistry of HealthBeijingChina
| | - Yong Xu
- Department of UrologyThe Second Hospital of Tianjin Medical UniversityTianjinChina
| | - Kuo Yang
- Department of UrologyThe Second Hospital of Tianjin Medical UniversityTianjinChina
| | - Dong Wei
- Department of UrologyBeijing HospitalBeijingChina
| | - Siying Liang
- The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of GeriatricsMinistry of HealthBeijingChina
| | - Fan Zhao
- The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of GeriatricsMinistry of HealthBeijingChina
| | | | - Xin Chen
- Department of UrologyBeijing HospitalBeijingChina
| | - Liang Sun
- The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of GeriatricsMinistry of HealthBeijingChina
| | - Huiping Yuan
- The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of GeriatricsMinistry of HealthBeijingChina
| | - Xiaohong Shi
- The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of GeriatricsMinistry of HealthBeijingChina
| | - Xin Wang
- Department of UrologyBeijing HospitalBeijingChina
| | - Ming Liu
- School of Basic Medical ScienceShanxi Medical UniversityTaiyuanShanxiChina
| | - Fan Yang
- The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of GeriatricsMinistry of HealthBeijingChina
| | - Jianye Wang
- Department of UrologyBeijing HospitalBeijingChina
| | - Ze Yang
- The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of GeriatricsMinistry of HealthBeijingChina
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10
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Crassini K, Stevenson WS, Mulligan SP, Best OG. Molecular pathogenesis of chronic lymphocytic leukaemia. Br J Haematol 2019; 186:668-684. [DOI: 10.1111/bjh.16102] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kyle Crassini
- Northern Blood Research Centre Kolling Institute of Medical Research SydneyNSWAustralia
| | - William S. Stevenson
- Northern Blood Research Centre Kolling Institute of Medical Research SydneyNSWAustralia
| | - Stephen P. Mulligan
- Northern Blood Research Centre Kolling Institute of Medical Research SydneyNSWAustralia
- School of Life and Environmental Science University of Sydney Sydney NSW Australia
| | - O. Giles Best
- Northern Blood Research Centre Kolling Institute of Medical Research SydneyNSWAustralia
- School of Life and Environmental Science University of Sydney Sydney NSW Australia
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11
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Gaiti F, Chaligne R, Gu H, Brand RM, Kothen-Hill S, Schulman R, Grigorev K, Risso D, Kim KT, Pastore A, Huang KY, Alonso A, Sheridan C, Omans ND, Biederstedt E, Clement K, Wang L, Felsenfeld JA, Bhavsar EB, Aryee MJ, Allan JN, Furman R, Gnirke A, Wu CJ, Meissner A, Landau DA. Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia. Nature 2019; 569:576-580. [PMID: 31092926 PMCID: PMC6533116 DOI: 10.1038/s41586-019-1198-z] [Citation(s) in RCA: 167] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/12/2019] [Indexed: 11/22/2022]
Abstract
Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of cancer1. Chronic lymphocytic leukaemia (CLL) is a highly informative model for cancer evolution as it undergoes substantial genetic diversification and evolution after therapy2,3. The CLL epigenome is also an important disease-defining feature4,5, and growing populations of cells in CLL diversify by stochastic changes in DNA methylation known as epimutations6. However, previous studies using bulk sequencing methods to analyse the patterns of DNA methylation were unable to determine whether epimutations affect CLL populations homogeneously. Here, to measure the epimutation rate at single-cell resolution, we applied multiplexed single-cell reduced-representation bisulfite sequencing to B cells from healthy donors and patients with CLL. We observed that the common clonal origin of CLL results in a consistently increased epimutation rate, with low variability in the cell-to-cell epimutation rate. By contrast, variable epimutation rates across healthy B cells reflect diverse evolutionary ages across the trajectory of B cell differentiation, consistent with epimutations serving as a molecular clock. Heritable epimutation information allowed us to reconstruct lineages at high-resolution with single-cell data, and to apply this directly to patient samples. The CLL lineage tree shape revealed earlier branching and longer branch lengths than in normal B cells, reflecting rapid drift after the initial malignant transformation and a greater proliferative history. Integration of single-cell bisulfite sequencing analysis with single-cell transcriptomes and genotyping confirmed that genetic subclones mapped to distinct clades, as inferred solely on the basis of epimutation information. Finally, to examine potential lineage biases during therapy, we profiled serial samples during ibrutinib-associated lymphocytosis, and identified clades of cells that were preferentially expelled from the lymph node after treatment, marked by distinct transcriptional profiles. The single-cell integration of genetic, epigenetic and transcriptional information thus charts the lineage history of CLL and its evolution with therapy.
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Affiliation(s)
- Federico Gaiti
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Ronan Chaligne
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Ryan Matthew Brand
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Steven Kothen-Hill
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Rafael Schulman
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | | | - Davide Risso
- Weill Cornell Medicine, New York, NY, 10021, USA,Department of Statistical Sciences, University of Padova, Padova, 35121, Italy
| | - Kyu-Tae Kim
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Alessandro Pastore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Kevin Y. Huang
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | | | | | - Nathaniel D. Omans
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Evan Biederstedt
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Kendell Clement
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Lili Wang
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA,Beckman Research Institute, City of Hope, Monrovia, CA, 91016, USA
| | | | | | - Martin J. Aryee
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | | | | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catherine J. Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA,Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Dan A. Landau
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA,Corresponding author: Dan A. Landau, MD, PhD, Weill Cornell Medicine, Belfer Research Building, 413 East 69th Street, New York, NY 10021,
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12
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Mansouri L, Wierzbinska JA, Plass C, Rosenquist R. Epigenetic deregulation in chronic lymphocytic leukemia: Clinical and biological impact. Semin Cancer Biol 2018; 51:1-11. [PMID: 29427646 DOI: 10.1016/j.semcancer.2018.02.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 12/12/2017] [Accepted: 02/05/2018] [Indexed: 01/01/2023]
Abstract
Deregulated transcriptional control caused by aberrant DNA methylation and/or histone modifications is a hallmark of cancer cells. In chronic lymphocytic leukemia (CLL), the most common adult leukemia, the epigenetic 'landscape' has added a new layer of complexity to our understanding of this clinically and biologically heterogeneous disease. Early studies identified aberrant DNA methylation, often based on single gene promoter analysis with both biological and clinical impact. Subsequent genome-wide profiling studies revealed differential DNA methylation between CLLs and controls and in prognostics subgroups of the disease. From these studies, it became apparent that DNA methylation in regions outside of promoters, such as enhancers, is important for the regulation of coding genes as well as for the regulation of non-coding RNAs. Although DNA methylation profiles are reportedly stable over time and in relation to therapy, a higher epigenetic heterogeneity or 'burden' is seen in more aggressive CLL subgroups, albeit as non-recurrent 'passenger' events. More recently, DNA methylation profiles in CLL analyzed in relation to differentiating normal B-cell populations revealed that the majority of the CLL epigenome reflects the epigenomes present in the cell of origin and that only a small fraction of the epigenetic alterations represents truly CLL-specific changes. Furthermore, CLL patients can be grouped into at least three clinically relevant epigenetic subgroups, potentially originating from different cells at various stages of differentiation and associated with distinct outcomes. In this review, we summarize the current understanding of the DNA methylome in CLL, the role of histone modifying enzymes, highlight insights derived from animal models and attempts made to target epigenetic regulators in CLL along with the future directions of this rapidly advancing field.
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Affiliation(s)
- Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Sweden
| | - Justyna Anna Wierzbinska
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Sweden.
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13
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Mesenchymal Stem Cells in Myeloid Malignancies: A Focus on Immune Escaping and Therapeutic Implications. Stem Cells Int 2017; 2017:6720594. [PMID: 28947904 PMCID: PMC5602646 DOI: 10.1155/2017/6720594] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/06/2017] [Accepted: 07/20/2017] [Indexed: 01/07/2023] Open
Abstract
The importance of the bone marrow microenvironment forming the so-called niche in physiologic hemopoiesis is largely known, and recent evidences support the presence of stromal alterations from the molecular to the cytoarchitectural level in hematologic malignancies. Various alterations in cell adhesion, metabolism, cytokine signaling, autophagy, and methylation patterns of tumor-derived mesenchymal stem cells have been demonstrated, contributing to the genesis of a leukemic permissive niche. This niche allows both the ineffective haematopoiesis typical of myelodysplastic syndromes and the differentiation arrest, proliferation advantage, and clone selection which is the hallmark of acute myeloid leukemia. Furthermore, the immune system, both adaptive and innate, encompassing mesenchymal-derived cells, has been shown to take part to the leukemic niche. Here, we critically review the state of art about mesenchymal stem cell role in myelodysplastic syndromes and acute myeloid leukemia, focusing on immune escaping mechanisms as a target for available and future anticancer therapies.
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14
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Kahlert UD, Joseph JV, Kruyt FAE. EMT- and MET-related processes in nonepithelial tumors: importance for disease progression, prognosis, and therapeutic opportunities. Mol Oncol 2017; 11:860-877. [PMID: 28556516 PMCID: PMC5496495 DOI: 10.1002/1878-0261.12085] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 12/21/2022] Open
Abstract
The epithelial-to mesenchymal (EMT) process is increasingly recognized for playing a key role in the progression, dissemination, and therapy resistance of epithelial tumors. Accumulating evidence suggests that EMT inducers also lead to a gain in mesenchymal properties and promote malignancy of nonepithelial tumors. In this review, we present and discuss current findings, illustrating the importance of EMT inducers in tumors originating from nonepithelial/mesenchymal tissues, including brain tumors, hematopoietic malignancies, and sarcomas. Among these tumors, the involvement of mesenchymal transition has been most extensively investigated in glioblastoma, providing proof for cell autonomous and microenvironment-derived stimuli that provoke EMT-like processes that regulate stem cell, invasive, and immunogenic properties as well as therapy resistance. The involvement of prominent EMT transcription factor families, such as TWIST, SNAI, and ZEB, in promoting therapy resistance and tumor aggressiveness has also been reported in lymphomas, leukemias, and sarcomas. A reverse process, resembling mesenchymal-to-epithelial transition (MET), seems particularly relevant for sarcomas, where (partial) epithelial differentiation is linked to less aggressive tumors and a better patient prognosis. Overall, a hybrid model in which more stable epithelial and mesenchymal intermediates exist likely extends to the biology of tumors originating from sources other than the epithelium. Deeper investigation and understanding of the EMT/MET machinery in nonepithelial tumors will shed light on the pathogenesis of these tumors, potentially paving the way toward the identification of clinically relevant biomarkers for prognosis and future therapeutic targets.
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Affiliation(s)
- Ulf D Kahlert
- Department of Neurosurgery, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | | | - Frank A E Kruyt
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, The Netherlands
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15
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Rani L, Mathur N, Gupta R, Gogia A, Kaur G, Dhanjal JK, Sundar D, Kumar L, Sharma A. Genome-wide DNA methylation profiling integrated with gene expression profiling identifies PAX9 as a novel prognostic marker in chronic lymphocytic leukemia. Clin Epigenetics 2017; 9:57. [PMID: 28572861 PMCID: PMC5450117 DOI: 10.1186/s13148-017-0356-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 05/18/2017] [Indexed: 12/22/2022] Open
Abstract
Background In chronic lymphocytic leukemia (CLL), epigenomic and genomic studies have expanded the existing knowledge about the disease biology and led to the identification of potential biomarkers relevant for implementation of personalized medicine. In this study, an attempt has been made to examine and integrate the global DNA methylation changes with gene expression profile and their impact on clinical outcome in early stage CLL patients. Results The integration of DNA methylation profile (n = 14) with the gene expression profile (n = 21) revealed 142 genes as hypermethylated-downregulated and; 62 genes as hypomethylated-upregulated in early stage CLL patients compared to CD19+ B-cells from healthy individuals. The mRNA expression levels of 17 genes identified to be differentially methylated and/or differentially expressed was further examined in early stage CLL patients (n = 93) by quantitative real time PCR (RQ-PCR). Significant differences were observed in the mRNA expression of MEIS1, PMEPA1, SOX7, SPRY1, CDK6, TBX2, and SPRY2 genes in CLL cells as compared to B-cells from healthy individuals. The analysis in the IGHV mutation based categories (Unmutated = 39, Mutated = 54) revealed significantly higher mRNA expression of CRY1 and PAX9 genes in the IGHV unmutated subgroup (p < 0.001). The relative risk of treatment initiation was significantly higher among patients with high expression of CRY1 (RR = 1.91, p = 0.005) or PAX9 (RR = 1.87, p = 0.001). High expression of CRY1 (HR: 3.53, p < 0.001) or PAX9 (HR: 3.14, p < 0.001) gene was significantly associated with shorter time to first treatment. The high expression of PAX9 gene (HR: 3.29, 95% CI 1.172–9.272, p = 0.016) was also predictive of shorter overall survival in CLL. Conclusions The DNA methylation changes associated with mRNA expression of CRY1 and PAX9 genes allow risk stratification of early stage CLL patients. This comprehensive analysis supports the concept that the epigenetic changes along with the altered expression of genes have the potential to predict clinical outcome in early stage CLL patients. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0356-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lata Rani
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Nitin Mathur
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Ajay Gogia
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Gurvinder Kaur
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Jaspreet Kaur Dhanjal
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory of Advanced Biomedicine (DAILAB), Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110016 India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory of Advanced Biomedicine (DAILAB), Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110016 India
| | - Lalit Kumar
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Atul Sharma
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
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16
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Kim MS, Jeong J, Seo J, Kim HS, Kim SJ, Jin W. Dysregulated JAK2 expression by TrkC promotes metastasis potential, and EMT program of metastatic breast cancer. Sci Rep 2016; 6:33899. [PMID: 27654855 PMCID: PMC5032000 DOI: 10.1038/srep33899] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 09/02/2016] [Indexed: 12/22/2022] Open
Abstract
Metastatic breast cancers are aggressive tumors associated with high levels of epithelial-mesenchymal transition (EMT) markers, activation of IL6/JAK2/STAT3 and PI3K/AKT pathways for cell growth, mobility, invasion, metastasis, and CSC status. We identified a new molecular and functional network present in metastasis that regulates and coordinates with TrkC. Inhibition of SOCS3-mediated JAK2 degradation by TrkC increases total JAK2/STAT3 expression, and then leads to upregulation of Twist-1 through activation of JAK2/STAT3 cascade. Also, TrkC increases secretion and expression of IL-6, suggesting that this autocrine loop generated by TrkC maintains the mesenchymal state by continued activation of the JAK2/STAT3 cascade and upregulation of Twist expression. Moreover, TrkC interacts with the c-Src/Jak2 complex, which increases Twist-1 and Twist-2 levels via regulation of JAK2/STAT3 activation and JAK2/STAT3 expression. Furthermore, TrkC enhances metastatic potential of breast cancer via induction of EMT by upregulating Twist-1 and Twist-2. Additionally, TrkC significantly enhances the ability of breast cancer cells to form pulmonary metastases and primary tumor formation. Unexpectedly, we found that TrkC expression and clinical breast tumor pathological phenotypes show significant correlation. These findings suggest that TrkC plays a central role in tumorigenicity, metastasis, and self-renewal traits of metastatic breast cancer.
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Affiliation(s)
- Min Soo Kim
- Laboratory of Molecular Disease and Cell Regulation, Department of Biochemistry, School of Medicine, Gachon University, Incheon 406-840, Korea
| | - Joon Jeong
- Department of Surgery, Gangnam Severance Hospital, Yonsei University Medical College, 712 Eonjuro, Gangnam-Gu, Seoul, 135-720, Korea
| | - Jeongbeob Seo
- Medicinal Chemistry, CMG Pharma, 335, CHA Bio Complex, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13488, Korea
| | - Hae-Suk Kim
- TheragenEtex Bio Institute, TheragenEtex Co., Suwon, Gyeonggi-do 16229, Republic of Korea
| | - Seong-Jin Kim
- Nano-Bio Medicine Research Center, Advanced Institutes of Convergence Technology, and Department of Transdisciplinary Studies, Graduate School of Convergence Science and Technology, Seoul National University, Suwon, Kyunggi-do 16229, Republic of Korea
| | - Wook Jin
- Laboratory of Molecular Disease and Cell Regulation, Department of Biochemistry, School of Medicine, Gachon University, Incheon 406-840, Korea.,Gachon Medical Research Institute, Gil Medical Center, Incheon, 405-760, Korea
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17
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Kim MS, Lee WS, Jeong J, Kim SJ, Jin W. Induction of metastatic potential by TrkB via activation of IL6/JAK2/STAT3 and PI3K/AKT signaling in breast cancer. Oncotarget 2016; 6:40158-71. [PMID: 26515594 PMCID: PMC4741886 DOI: 10.18632/oncotarget.5522] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 10/08/2015] [Indexed: 02/06/2023] Open
Abstract
In metastatic breast cancers, the acquisition of metastatic ability, which leads to clinically incurable disease and poor survival, has been associated with acquisition of epithelial-mesenchymal transition (EMT) program and self-renewing trait (CSCs) via activation of PI3K/AKT and IL6/JAK2/STAT3 signaling pathways. We found that TrkB is a key regulator of PI3K/AKT and JAK/STAT signal pathway-mediated tumor metastasis and EMT program. Here, we demonstrated that TrkB activates AKT by directly binding to c-Src, leading to increased proliferation. Also, TrkB increases Twist-1 and Twist-2 expression through activation of JAK2/STAT3 by inducing c-Src-JAK2 complex formation. Furthermore, TrkB in the absence of c-Src binds directly to JAK2 and inhibits SOCS3-mediated JAK2 degradation, resulting in increased total JAK2 and STAT3 levels, which subsequently leads to JAK2/STAT3 activation and Twist-1 upregulation. Additionally, activation of the JAK2/STAT3 pathway via induction of IL-6 secretion by TrkB enables induction of activation of the EMT program via induction of STAT3 nuclear translocation. These observations suggest that TrkB is a promising target for future intervention strategies to prevent tumor metastasis, EMT program and self-renewing trait in breast cancer.
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Affiliation(s)
- Min Soo Kim
- Laboratory of Molecular Disease and Cell Regulation, Department of Molecular Medicine, School of Medicine, Gachon University, Incheon 406-840, Korea
| | - Won Sung Lee
- Laboratory of Molecular Disease and Cell Regulation, Department of Molecular Medicine, School of Medicine, Gachon University, Incheon 406-840, Korea
| | - Joon Jeong
- Department of Surgery, Kangnam Severance Hospital, Yonsei University, Kangnam, Seoul 146-92, Korea
| | - Seong-Jin Kim
- CHA Cancer Institute, CHA University, Seongnam-si, Kyunggi-do 463-400, Korea
| | - Wook Jin
- Laboratory of Molecular Disease and Cell Regulation, Department of Molecular Medicine, School of Medicine, Gachon University, Incheon 406-840, Korea.,Gachon Medical Research Institute, Gil Medical Center, Gachon University, Incheon 405-760, Korea
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18
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Kushwaha G, Dozmorov M, Wren JD, Qiu J, Shi H, Xu D. Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia. Hum Genomics 2016; 10 Suppl 2:18. [PMID: 27461342 PMCID: PMC4965721 DOI: 10.1186/s40246-016-0071-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Methylation changes are frequent in cancers, but understanding how hyper- and hypomethylated region changes coordinate, associate with genomic features, and affect gene expression is needed to better understand their biological significance. The functional significance of hypermethylation is well studied, but that of hypomethylation remains limited. Here, with paired expression and methylation samples gathered from a patient/control cohort, we attempt to better characterize the gene expression and methylation changes that take place in cancer from B cell chronic lymphocyte leukemia (B-CLL) samples. Results Across the dataset, we found that consistent differentially hypomethylated regions (C-DMRs) across samples were relatively few compared to the many poorly consistent hypo- and highly conserved hyper-DMRs. However, genes in the hypo-C-DMRs tended to be associated with functions antagonistic to those in the hyper-C-DMRs, like differentiation, cell-cycle regulation and proliferation, suggesting coordinated regulation of methylation changes. Hypo-C-DMRs in B-CLL were found enriched in key signaling pathways like B cell receptor and p53 pathways and genes/motifs essential for B lymphopoiesis. Hypo-C-DMRs tended to be proximal to genes with elevated expression in contrast to the transcription silencing-mechanism imposed by hypermethylation. Hypo-C-DMRs tended to be enriched in the regions of activating H4K4me1/2/3, H3K79me2, and H3K27ac histone modifications. In comparison, the polycomb repressive complex 2 (PRC2) signature, marked by EZH2, SUZ12, CTCF binding-sites, repressive H3K27me3 marks, and “repressed/poised promoter” states were associated with hyper-C-DMRs. Most hypo-C-DMRs were found in introns (36 %), 3′ untranslated regions (29 %), and intergenic regions (24 %). Many of these genic regions also overlapped with enhancers. The methylation of CpGs from 3′UTR exons was found to have weak but positive correlation with gene expression. In contrast, methylation in the 5′UTR was negatively correlated with expression. To better characterize the overlap between methylation and expression changes, we identified correlation modules that associate with “apoptosis” and “leukocyte activation”. Conclusions Despite clinical heterogeneity in disease presentation, a number of methylation changes, both hypo and hyper, appear to be common in B-CLL. Hypomethylation appears to play an active, targeted, and complementary role in cancer progression, and it interplays with hypermethylation in a coordinated fashion in the cancer process. Electronic supplementary material The online version of this article (doi:10.1186/s40246-016-0071-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Garima Kushwaha
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.,Informatics Institute, University of Missouri, Columbia, MO, 65211, USA
| | - Mikhail Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23225, USA
| | - Jonathan D Wren
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Jing Qiu
- Department of Applied Economics & Statistics, University of Delaware, Newark, DE, 19716, USA
| | - Huidong Shi
- GRU Cancer Center, Georgia Regents University, Augusta, GA, 30912, USA. .,Department of Biochemistry and Molecular Biology, Georgia Regents University, Augusta, GA, 30912, USA.
| | - Dong Xu
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA. .,Informatics Institute, University of Missouri, Columbia, MO, 65211, USA. .,Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA.
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19
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Pleyer L, Valent P, Greil R. Mesenchymal Stem and Progenitor Cells in Normal and Dysplastic Hematopoiesis-Masters of Survival and Clonality? Int J Mol Sci 2016; 17:ijms17071009. [PMID: 27355944 PMCID: PMC4964385 DOI: 10.3390/ijms17071009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 05/20/2016] [Accepted: 06/08/2016] [Indexed: 02/07/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are malignant hematopoietic stem cell disorders that have the capacity to progress to acute myeloid leukemia (AML). Accumulating evidence suggests that the altered bone marrow (BM) microenvironment in general, and in particular the components of the stem cell niche, including mesenchymal stem cells (MSCs) and their progeny, play a pivotal role in the evolution and propagation of MDS. We here present an overview of the role of MSCs in the pathogenesis of MDS, with emphasis on cellular interactions in the BM microenvironment and related stem cell niche concepts. MSCs have potent immunomodulatory capacities and communicate with diverse immune cells, but also interact with various other cellular components of the microenvironment as well as with normal and leukemic stem and progenitor cells. Moreover, compared to normal MSCs, MSCs in MDS and AML often exhibit altered gene expression profiles, an aberrant phenotype, and abnormal functional properties. These alterations supposedly contribute to the “reprogramming” of the stem cell niche into a disease-permissive microenvironment where an altered immune system, abnormal stem cell niche interactions, and an impaired growth control lead to disease progression. The current article also reviews molecular targets that play a role in such cellular interactions and possibilities to interfere with abnormal stem cell niche interactions by using specific targeted drugs.
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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 Salzburg, 5020 Salzburg, Austria.
- Center for Clinical Cancer and Immunology Trials at Salzburg Cancer Research Institute, 5020 Salzburg, Austria.
- 3rd Medical Department, Cancer Cluster Salzburg, 5020 Salzburg, Austria.
| | - Peter Valent
- Department of Internal Medicine I, Division of Hematology and Hemostaseology & Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, 1090 Vienna, Austria.
| | - Richard Greil
- 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 Salzburg, 5020 Salzburg, Austria.
- Center for Clinical Cancer and Immunology Trials at Salzburg Cancer Research Institute, 5020 Salzburg, Austria.
- 3rd Medical Department, Cancer Cluster Salzburg, 5020 Salzburg, Austria.
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20
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Bhoi S, Ljungström V, Baliakas P, Mattsson M, Smedby KE, Juliusson G, Rosenquist R, Mansouri L. Prognostic impact of epigenetic classification in chronic lymphocytic leukemia: The case of subset #2. Epigenetics 2016; 11:449-55. [PMID: 27128508 DOI: 10.1080/15592294.2016.1178432] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Based on the methylation status of 5 single CpG sites, a novel epigenetic classification of chronic lymphocytic leukemia (CLL) was recently proposed, classifying CLL patients into 3 clinico-biological subgroups with different outcome, termed memory like CLL (m-CLL), naïve like CLL (n-CLL), and a third intermediate CLL subgroup (i-CLL). While m-CLL and n-CLL patients at large corresponded to patients carrying mutated and unmutated IGHV genes, respectively, limited information exists regarding the less defined i-CLL group. Using pyrosequencing, we investigated the prognostic impact of the proposed 5 CpG signature in a well-characterized CLL cohort (135 cases), including IGHV-mutated and unmutated patients as well as clinically aggressive stereotyped subset #2 patients. Overall, we confirmed the signature's association with established prognostic markers. Moreover, in the presence of the IGHV mutational status, the epigenetic signature remained independently associated with both time-to-first-treatment and overall survival in multivariate analyses. As a prime finding, we observed that subset #2 patients were predominantly classified as i-CLL, probably reflecting their borderline IGHV mutational status (97-99% germline identity), though having a similarly poor prognosis as n-CLL patients. In summary, we validated the epigenetic classifier as an independent factor in CLL prognostication and provide further evidence that subset #2 is a member of the i-CLL group, hence supporting the existence of a third, intermediate epigenetic subgroup.
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Affiliation(s)
- Sujata Bhoi
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
| | - Viktor Ljungström
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
| | - Panagiotis Baliakas
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
| | - Mattias Mattsson
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden.,b Department of Medical Sciences , Uppsala University , Uppsala , Sweden
| | - Karin E Smedby
- c Department of Medicine Solna , Clinical Epidemiology Unit, Karolinska Institutet , Stockholm , Sweden
| | - Gunnar Juliusson
- d Department of Laboratory Medicine , Stem Cell Center, Hematology and Transplantation, Lund University , Lund , Sweden
| | - Richard Rosenquist
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
| | - Larry Mansouri
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
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21
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Norozi F, Ahmadzadeh A, Shahjahani M, Shahrabi S, Saki N. Twist as a new prognostic marker in hematological malignancies. Clin Transl Oncol 2015. [DOI: 10.1007/s12094-015-1357-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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22
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Guo Y, Lee JH, Shu L, Huang Y, Li W, Zhang C, Yang AY, Boyanapalli SS, Perekatt A, Hart RP, Verzi M, Kong ANT. Association of aberrant DNA methylation in Apc(min/+) mice with the epithelial-mesenchymal transition and Wnt/β-catenin pathways: genome-wide analysis using MeDIP-seq. Cell Biosci 2015; 5:24. [PMID: 26101583 PMCID: PMC4476183 DOI: 10.1186/s13578-015-0013-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/11/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Aberrant DNA methylation at the 5-carbon on cytosine residues (5mC) in CpG dinucleotides is probably the most extensively characterized epigenetic modification in colon cancer. It has been suggested that the loss of adenomatous polyposis coli (APC) function initiates tumorigenesis and that additional genetic and epigenetic events are involved in colon cancer progression. We aimed to study the genome-wide DNA methylation profiles of intestinal tumorigenesis in Apc(min/+) mice. RESULTS Methylated DNA immunoprecipitation (MeDIP) followed by next-generation sequencing was used to determine the global profile of DNA methylation changes in Apc(min/+) mice. DNA was extracted from adenomatous polyps from Apc(min/+) mice and from normal intestinal tissue from age-matched Apc(+/+) littermates, and the MeDIP-seq assay was performed. Ingenuity Pathway Analysis (IPA) software was used to analyze the data for gene interactions. A total of 17,265 differentially methylated regions (DMRs) displayed a ≥ 2-fold change (log2) in methylation in Apc(min/+) mice; among these DMRs, 9,078 (52.6 %) and 8,187 (47.4 %) exhibited increased and decreased methylation, respectively. Genes with altered methylation patterns were mainly mapped to networks and biological functions associated with cancer and gastrointestinal diseases. Among these networks, several canonical pathways, such as the epithelial-mesenchymal transition (EMT) and Wnt/β-catenin pathways, were significantly associated with genome-wide methylation changes in polyps from Apc(min/+) mice. The identification of certain differentially methylated molecules in the EMT and Wnt/β-catenin pathways, such as APC2 (adenomatosis polyposis coli 2), SFRP2 (secreted frizzled-related protein 2), and DKK3 (dickkopf-related protein 3), was consistent with previous publications. CONCLUSIONS Our findings indicated that Apc(min/+) mice exhibited extensive aberrant DNA methylation that affected certain signaling pathways, such as the EMT and Wnt/β-catenin pathways. The genome-wide DNA methylation profile of Apc(min/+) mice is informative for future studies investigating epigenetic gene regulation in colon tumorigenesis and the prevention of colon cancer.
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Affiliation(s)
- Yue Guo
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Jong Hun Lee
- Department of Food Science and Biotechnology, College of Life Science, CHA University, Gyeonggi-do, 463-400 South Korea
| | - Limin Shu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Ying Huang
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Wenji Li
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Chengyue Zhang
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Anne Yuqing Yang
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Sarandeep Ss Boyanapalli
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Ansu Perekatt
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Michael Verzi
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Ah-Ng Tony Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
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23
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Zhang X, Ma W, Cui J, Yao H, Zhou H, Ge Y, Xiao L, Hu X, Liu BH, Yang J, Li YY, Chen S, Eaves CJ, Wu D, Zhao Y. Regulation of p21 by TWIST2 contributes to its tumor-suppressor function in human acute myeloid leukemia. Oncogene 2014; 34:3000-10. [DOI: 10.1038/onc.2014.241] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 06/08/2014] [Accepted: 06/15/2014] [Indexed: 12/18/2022]
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24
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Gautrey HE, van Otterdijk SD, Cordell HJ, Mathers JC, Strathdee G. DNA methylation abnormalities at gene promoters are extensive and variable in the elderly and phenocopy cancer cells. FASEB J 2014; 28:3261-72. [PMID: 24858281 DOI: 10.1096/fj.13-246173] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Abnormal patterns of DNA methylation are one of the hallmarks of cancer cells. The process of aging has also been associated with similar, albeit less dramatic, changes in methylation patterns, leading to the hypothesis that age-related changes in DNA methylation may partially underlie the increased risk of cancer in the elderly. Here we studied 377 participants aged 85 yr from the Newcastle 85+ Study to investigate the extent of, and interindividual variation in, age-related changes in DNA methylation at specific CpG islands. Using highly quantitative pyrosequencing analysis, we found extensive and highly variable methylation of promoter-associated CpG islands with levels ranging from 4% to 35%, even at known tumor suppressor genes such as TWIST2. Furthermore, the interindividual differences in methylation seen across this elderly population phenocopies multiple features of the altered methylation patterns seen in cancer cells. Both aging- and cancer-related methylation can occur at similar sets of genes, both result in the formation of densely methylated, and likely transcriptionally repressed, alleles, and both exhibit coordinate methylation across multiple loci. In addition, high methylation levels were associated with subsequent diagnosis of leukemia or lymphoma during a 3-yr follow-up period (P=0.00008). These data suggest that the accumulation of age-related changes in promoter-associated CpG islands may contribute to the increased cancer risk seen during aging.-Gautrey, H. E., van Otterdijk, S. D., Cordell, H. J., Newcastle 85+ study core team, Mathers, J. C., Strathdee, G. DNA methylation abnormalities at gene promoters are extensive and variable in the elderly and phenocopy cancer cells.
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Affiliation(s)
| | | | | | | | - John C Mathers
- Human Nutrition Research Centre, Institute for Ageing and Health, Campus for Ageing and Vitality, Newcastle University, Newcastle Upon Tyne, UK; and
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25
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Merindol N, Riquet A, Szablewski V, Eliaou JF, Puisieux A, Bonnefoy N. The emerging role of Twist proteins in hematopoietic cells and hematological malignancies. Blood Cancer J 2014; 4:e206. [PMID: 24769647 PMCID: PMC4003416 DOI: 10.1038/bcj.2014.22] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 03/17/2014] [Indexed: 02/03/2023] Open
Abstract
Twist1 and Twist2 (Twist1–2) are two transcription factors, members of the basic helix-loop-helix family, that have been well established as master transcriptional regulators of embryogenesis and developmental programs of mesenchymal cell lineages. Their role in oncogenesis in epithelium-derived cancer and in epithelial-to-mesenchymal transition has also been thoroughly characterized. Recently, emerging evidence also suggests a key role for Twist1–2 in the function and development of hematopoietic cells, as well as in survival and development of numerous hematological malignancies. In this review, we summarize the latest data that depict the role of Twist1–2 in monocytes, T cells and B lymphocyte activation, and in associated hematological malignancies.
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Affiliation(s)
- N Merindol
- Université de Lyon and INSERM U1111, Lyon, France
| | - A Riquet
- Université de Lyon and INSERM U1111, Lyon, France
| | - V Szablewski
- 1] IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U896, Université Montpellier 1, Montpellier, France [2] Département de Biopathologie, Centre Hospitalier Régional Universitaire de Montpellier et Faculté de Médecine, Université Montpellier 1, Montpellier, France
| | - J-F Eliaou
- 1] IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U896, Université Montpellier 1, Montpellier, France [2] Département d'Immunologie, Centre Hospitalier Régional Universitaire de Montpellier et Faculté de Médecine, Université Montpellier 1, Montpellier, France
| | - A Puisieux
- Centre de Receherche en Cancérologie de Lyon, INSERM UMR-S1052, Centre Léon Bérard, Lyon, France
| | - N Bonnefoy
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U896, Université Montpellier 1, Montpellier, France
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26
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Abstract
The myelodysplastic syndrome (MDS) is a clonal hematologic disorder that frequently evolves to acute myeloid leukemia (AML). Its pathogenesis remains unclear, but mutations in epigenetic modifiers are common and the disease often responds to DNA methylation inhibitors. We analyzed DNA methylation in the bone marrow and spleen in two mouse models of MDS/AML, the NUP98-HOXD13 (NHD13) mouse and the RUNX1 mutant mouse model. Methylation array analysis showed an average of 512/3445 (14.9%) genes hypermethylated in NHD13 MDS, and 331 (9.6%) genes hypermethylated in RUNX1 MDS. Thirty-two percent of genes in common between the two models (2/3 NHD13 mice and 2/3 RUNX1 mice) were also hypermethylated in at least two of 19 human MDS samples. Detailed analysis of 41 genes in mice showed progressive drift in DNA methylation from young to old normal bone marrow and spleen; to MDS, where we detected accelerated age-related methylation; and finally to AML, which markedly extends DNA methylation abnormalities. Most of these genes showed similar patterns in human MDS and AML. Repeat element hypomethylation was rare in MDS but marked the transition to AML in some cases. Our data show consistency in patterns of aberrant DNA methylation in human and mouse MDS and suggest that epigenetically, MDS displays an accelerated aging phenotype.
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27
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Wang LQ, Kwong YL, Kho CSB, Wong KF, Wong KY, Ferracin M, Calin GA, Chim CS. Epigenetic inactivation of miR-9 family microRNAs in chronic lymphocytic leukemia--implications on constitutive activation of NFκB pathway. Mol Cancer 2013; 12:173. [PMID: 24373626 PMCID: PMC3877874 DOI: 10.1186/1476-4598-12-173] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 12/20/2013] [Indexed: 01/12/2023] Open
Abstract
Background The miR-9 family microRNAs have been identified as a tumor suppressor miRNA in cancers. We postulated that miR-9-1, miR-9-2 and miR-9-3 might be inactivated by DNA hypermethylation in chronic lymphocytic leukemia (CLL). Methods Methylation of miR-9-1, miR-9-2 and miR-9-3 was studied in eight normal controls including normal bone marrow, buffy coat, and CD19-sorted peripheral blood B-cells from healthy individuals, seven CLL cell lines, and seventy-eight diagnostic CLL samples by methylation-specific polymerase chain reaction. Results The promoters of miR-9-3 and miR-9-1 were both unmethylated in normal controls, but methylated in five (71.4%) and one of seven CLL cell lines respectively. However, miR-9-2 promoter was methylated in normal controls including CD19 + ve B-cells, hence suggestive of a tissue-specific but not tumor-specific methylation, and thus not further studied. Different MSP statuses of miR-9-3, including complete methylation, partial methylation, and complete unmethylation, were verified by quantitative bisulfite methylation analysis. 5-Aza-2′-deoxycytidine treatment resulted in miR-9-3 promoter demethylation and re-expression of pri-miR-9-3 in I83-E95 and WAC3CD5+ cells, which were homozygously methylated for miR-9-3. Moreover, overexpression of miR-9 led to suppressed cell proliferation and enhanced apoptosis together with downregulation of NFκB1 in I83-E95 cells, supporting a tumor suppressor role of miR-9-3 in CLL. In primary CLL samples, miR-9-3 was detected in 17% and miR-9-1 methylation in none of the patients at diagnosis. Moreover, miR-9-3 methylation was associated with advanced Rai stage (≥ stage 2) (P = 0.04). Conclusions Of the miR-9 family, miR-9-3 is a tumor suppressor miRNA relatively frequently methylated, and hence silenced in CLL; whereas miR-9-1 methylation is rare in CLL. The role of miR-9-3 methylation in the constitutive activation of NFκB signaling pathway in CLL warrants further study.
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Affiliation(s)
| | | | | | | | | | | | | | - Chor Sang Chim
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China.
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28
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Khan MA, Chen HC, Zhang D, Fu J. Twist: a molecular target in cancer therapeutics. Tumour Biol 2013; 34:2497-506. [PMID: 23873099 DOI: 10.1007/s13277-013-1002-x] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 07/04/2013] [Indexed: 01/28/2023] Open
Abstract
Twist, the basic helix-loop-helix transcription factor, is involved in the process of epithelial to mesenchymal transitions (EMTs), which play an essential role in cancer metastasis. Overexpression of Twist or its promoter methylation is a common scenario in metastatic carcinomas. Twist is activated by a variety of signal transduction pathways, including Akt, signal transducer and activator of transcription 3, mitogen-activated protein kinase, Ras, and Wnt signaling. Activated Twist upregulates N-cadherin and downregulates E-cadherin, which are the hallmarks of EMT. Moreover, Twist plays an important role in some physiological processes involved in metastasis, like angiogenesis, invadopodia, extravasation, and chromosomal instability. Twist also protects cancer cells from apoptotic cell death. In addition, Twist is responsible for the stemness of cancer cells and the generation of drug resistance. Recently, targeting Twist has gained significant interests in cancer therapeutics. The inactivation of Twist by small RNA technology or chemotherapeutic approach has been proved successful. Moreover, several inhibitors which are antagonistic to the upstream or downstream molecules of Twist signaling pathways have also been identified. Development of potential treatment strategies by targeting Twist has a great promise in cancer therapeutics.
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Affiliation(s)
- Md Asaduzzaman Khan
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Luzhou Medical College, 3-319 Zhongshan Road, Luzhou, Sichuan, 646000, China
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Martinelli S, Kanduri M, Maffei R, Fiorcari S, Bulgarelli J, Marasca R, Rosenquist R. ANGPT2 promoter methylation is strongly associated with gene expression and prognosis in chronic lymphocytic leukemia. Epigenetics 2013; 8:720-9. [PMID: 23803577 PMCID: PMC3781191 DOI: 10.4161/epi.24947] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/30/2013] [Accepted: 05/05/2013] [Indexed: 01/20/2023] Open
Abstract
Increasing evidence suggests a key role for angiopoietin-2 (ANGPT2) in influencing the aggressiveness of chronic lymphocytic leukemia (CLL). In the presence of vascular endothelial growth factor (VEGF), ANGPT2 causes vessel destabilization leading to neoangiogenesis. Accordingly, high expression levels of ANGPT2 and high degree of angiogenesis have consistently been associated with poor prognosis in CLL; however, the molecular mechanisms behind the variability in ANGPT2 expression are still to be discovered. Here, for the first time, we investigated the DNA methylation status of the ANGPT2 promoter in a large CLL cohort (n = 88) using pyrosequencing and correlated methylation data with ANGPT2 expression levels, prognostic factors and outcome. Importantly, methylation levels of the ANGPT2 gene correlated inversely with its mRNA expression levels (p<0.001). Moreover, low ANGPT2 methylation status was highly associated with adverse prognostic markers, shorter time to first treatment and overall survival. Finally, treatment with methyl inhibitors induced re-expression of ANGPT2 in two B-cell lymphoma cell lines, underscoring the importance of DNA methylation in regulating transcriptional silencing of this gene. In conclusion, we believe that the known variability in ANGPT2 expression among CLL patients could be explained by differential promoter DNA methylation and that low methylation levels of the ANGPT2 promoter have an adverse prognostic impact in CLL.
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Affiliation(s)
- Silvia Martinelli
- Hematology Unit; Department of Medical and Surgical Sciences; University of Modena and Reggio Emilia; Modena, Italy
| | - Meena Kanduri
- Institute of Biomedicine; Department of Clinical Chemistry and Transfusion Medicine; Sahlgrenska University Hospital; Gothenburg, Sweden
| | - Rossana Maffei
- Hematology Unit; Department of Medical and Surgical Sciences; University of Modena and Reggio Emilia; Modena, Italy
| | - Stefania Fiorcari
- Hematology Unit; Department of Medical and Surgical Sciences; University of Modena and Reggio Emilia; Modena, Italy
| | - Jenny Bulgarelli
- Hematology Unit; Department of Medical and Surgical Sciences; University of Modena and Reggio Emilia; Modena, Italy
| | - Roberto Marasca
- Hematology Unit; Department of Medical and Surgical Sciences; University of Modena and Reggio Emilia; Modena, Italy
| | - Richard Rosenquist
- Department of Immunology; Genetics and Pathology; Science for Life Laboratory; Uppsala University, Uppsala, Sweden
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Ishikawa T, Shimizu T, Ueki A, Yamaguchi SI, Onishi N, Sugihara E, Kuninaka S, Miyamoto T, Morioka H, Nakayama R, Kobayashi E, Toyama Y, Mabuchi Y, Matsuzaki Y, Yamaguchi R, Miyano S, Saya H. Twist2 functions as a tumor suppressor in murine osteosarcoma cells. Cancer Sci 2013; 104:880-8. [PMID: 23557174 DOI: 10.1111/cas.12163] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 03/13/2013] [Accepted: 03/16/2013] [Indexed: 01/13/2023] Open
Abstract
The epithelial-mesenchymal transition (EMT) contributes to the malignant progression of cancer cells including acquisition of the ability to undergo metastasis. However, whereas EMT-related transcription factors (EMT-TF) are known to play an important role in the malignant progression of epithelial tumors, their role in mesenchymal tumors remains largely unknown. We show that expression of the gene for Twist2 is downregulated in human osteosarcoma and correlates inversely with tumorigenic potential in mouse osteosarcoma. Forced expression of Twist2 in highly tumorigenic murine osteosarcoma cells induced a slight inhibition of cell growth in vitro but markedly suppressed tumor formation in vivo. Conversely, knockdown of Twist2 in osteosarcoma cells with a low tumorigenic potential promoted tumor formation in vivo, suggesting that Twist2 functions as a tumor suppressor in osteosarcoma cells. Furthermore, Twist2 induced expression of fibulin-5, which has been reported as a tumor suppressor. Medium conditioned by mouse osteosarcoma cells overexpressing Twist2 inhibited expression of the MMP9 gene as well as invasion in mouse embryonic fibroblasts, and forced expression of Twist2 in osteosarcoma cells suppressed MMP9 gene expression in tumor tissue. Data from the present study suggest that Twist2 inhibits formation of a microenvironment conducive to tumor growth and thereby attenuates tumorigenesis in osteosarcoma.
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Affiliation(s)
- Tomoki Ishikawa
- Division of Gene Regulation, Institute for Advanced Medical Research, School of Medicine, Keio University, Tokyo, Japan
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Yu H, Jin GZ, Liu K, Dong H, Yu H, Duan JC, Li Z, Dong W, Cong WM, Yang JH. Twist2 is a valuable prognostic biomarker for colorectal cancer. World J Gastroenterol 2013; 19:2404-2411. [PMID: 23613636 PMCID: PMC3631994 DOI: 10.3748/wjg.v19.i15.2404] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/15/2013] [Accepted: 02/06/2013] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the significance of Twist2 for colorectal cancer (CRC).
METHODS: In this study, 93 CRC patients were included who received curative surgery in Eastern Hepatobiliary Surgery Hospital from January 1999 to December 2010. Records of patients’ clinicopathological characteristics and follow up data were reviewed. Formalin-fixed, paraffin-embedded tissue blocks were used to observe the protein expression of Twist2 and E-cadherin by immunohistochemistry. Two independent pathologists who were blinded to the clinical information performed semiquantitative scoring of immunostaining. A total score of 3-6 (sum of extent + intensity) was considered as Twist2-positive expression. The expression of E-cadherin was divided into two levels (preserved and reduced). An exploratory statistical analysis was conducted to determine the association between Twist2 expression and clinicopathological parameters, as well as E-cadherin expression. Furthermore, the variables associated with prognosis were analyzed by Cox’s proportional hazards model. Kaplan-Meier analysis was used to plot survival curves according to different expression levels of Twist2.
RESULTS: Twist2-positive expression was observed in 66 (71.0%) samples and mainly located in the cytoplasm. Forty-three (46.2%) samples showed reduced expression of E-cadherin. There were no significant correlations between Twist2 expression and any of the clinicopathological parameters. However, Twist2-positive expression was significantly associated with reduced expression of E-cadherin (P = 0.040). Multivariate analysis revealed that bad M-stage [hazard ratio (HR) = 7.694, 95%CI: 2.927-20.224, P < 0.001] and Twist2-positive (HR = 5.744, 95%CI: 1.347-24.298, P = 0.018) were the independent risk factors for poor overall survival (OS), while Twist2-positive (HR = 3.264, 95%CI: 1.455-7.375, P = 0.004), bad N-stage (HR = 2.149, 95%CI: 1.226-3.767, P = 0.008) and bad M-stage (HR = 10.907, 95%CI: 4.937-24.096, P < 0.001) were independently associated with poor disease-free survival (DFS). Survival curves showed a definite trend for Twist2-negative patients to have longer OS and DFS than Twist2-negative patients, not only overall, but also for patients in different stages, especially for DFS of patients in stage III (P = 0.033) and IV (P = 0.026).
CONCLUSION: Our data suggests, for the first time, that Twist2 is a valuable prognostic biomarker for CRC, particularly for patients in stage III and IV.
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Rodríguez-Vicente AE, Díaz MG, Hernández-Rivas JM. Chronic lymphocytic leukemia: a clinical and molecular heterogenous disease. Cancer Genet 2013; 206:49-62. [DOI: 10.1016/j.cancergen.2013.01.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 01/21/2013] [Accepted: 01/24/2013] [Indexed: 12/11/2022]
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Cahill N, Rosenquist R. Uncovering the DNA methylome in chronic lymphocytic leukemia. Epigenetics 2013; 8:138-48. [PMID: 23321535 DOI: 10.4161/epi.23439] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Over the past two decades, aberrant DNA methylation has emerged as a key player in the pathogenesis of chronic lymphocytic leukemia (CLL), and knowledge regarding its biological and clinical consequences in this disease has evolved rapidly. Since the initial studies relating DNA hypomethylation to genomic instability in CLL, a plethora of reports have followed showing the impact of DNA hypermethylation in silencing vital single gene promoters and the reversible nature of DNA methylation through inhibitor drugs. With the recognition that DNA hypermethylation events could potentially act as novel prognostic and treatment targets in CLL, the search for aberrantly methylated genes, gene families and pathways has ensued. Subsequently, the advent of microarray and next-generation sequencing technologies has supported the hunt for such targets, allowing exploration of the methylation landscape in CLL at an unprecedented scale. In light of these analyses, we now understand that different CLL prognostic subgroups are characterized by differential methylation profiles; we recognize DNA methylation of a number of signaling pathways genes to be altered in CLL, and acknowledge the role of DNA methylation outside of traditional CpG island promoters as fundamental players in the regulation of gene expression. Today, the significance and timing of altered DNA methylation within the complex epigenetic network of concomitant epigenetic messengers such as histones and miRNAs is an intensive area of research. In CLL, it appears that DNA methylation is a rather stable epigenetic mark occurring rather early in the disease pathogenesis. However, other consequences, such as how and why aberrant methylation marks occur, are less explored. In this review, we will not only provide a comprehensive summary of the current literature within the epigenetics field of CLL, but also highlight some of the novel findings relating to when, where, why and how altered DNA methylation materializes in CLL.
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Affiliation(s)
- Nicola Cahill
- Department of Immunology, Genetics and Pathology; Uppsala University; Uppsala, Sweden
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Kanduri M, Marincevic M, Halldórsdóttir AM, Mansouri L, Junevik K, Ntoufa S, Kultima HG, Isaksson A, Juliusson G, Andersson PO, Ehrencrona H, Stamatopoulos K, Rosenquist R. Distinct transcriptional control in major immunogenetic subsets of chronic lymphocytic leukemia exhibiting subset-biased global DNA methylation profiles. Epigenetics 2012; 7:1435-42. [PMID: 23154584 DOI: 10.4161/epi.22901] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) can be divided into prognostic subgroups based on the IGHV gene mutational status, and is further characterized by multiple subsets of cases with quasi-identical or stereotyped B cell receptors that also share clinical and biological features. We recently reported differential DNA methylation profiles in IGHV-mutated and IGHV-unmutated CLL subgroups. For the first time, we here explore the global methylation profiles of stereotyped subsets with different prognosis, by applying high-resolution methylation arrays on CLL samples from three major stereotyped subsets: the poor-prognostic subsets #1 (n = 15) and #2 (n = 9) and the favorable-prognostic subset #4 (n = 15). Overall, the three subsets exhibited significantly different methylation profiles, which only partially overlapped with those observed in our previous study according to IGHV gene mutational status. Specifically, gene ontology analysis of the differentially methylated genes revealed a clear enrichment of genes involved in immune response, such as B cell activation (e.g., CD80, CD86 and IL10), with higher methylation levels in subset #1 than subsets #2 and #4. Accordingly, higher expression of the co-stimulatory molecules CD80 and CD86 was demonstrated in subset #4 vs. subset #1, pointing to a key role for these molecules in the crosstalk of CLL subset #4 cells with the microenvironment. In summary, investigation of three prototypic, stereotyped CLL subsets revealed distinct DNA methylation profiles for each subset, which suggests subset-biased patterns of transcriptional control and highlights a key role for epigenetics during leukemogenesis.
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Affiliation(s)
- Meena Kanduri
- Institute of Biomedicine, Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
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35
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Cahill N, Bergh AC, Kanduri M, Göransson-Kultima H, Mansouri L, Isaksson A, Ryan F, Smedby KE, Juliusson G, Sundström C, Rosén A, Rosenquist R. 450K-array analysis of chronic lymphocytic leukemia cells reveals global DNA methylation to be relatively stable over time and similar in resting and proliferative compartments. Leukemia 2012; 27:150-8. [DOI: 10.1038/leu.2012.245] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Shinawi T, Hill V, Dagklis A, Baliakas P, Stamatopoulos K, Agathanggelou A, Stankovic T, Maher ER, Ghia P, Latif F. KIBRA gene methylation is associated with unfavorable biological prognostic parameters in chronic lymphocytic leukemia. Epigenetics 2012; 7:211-5. [PMID: 22430796 DOI: 10.4161/epi.7.3.19222] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Ras-association domain family (RASSF) members are a family of genes containing an RA domain in either the C-terminus (RASSF1-RASSF6) or in the N-terminus (RASSF7-RASSF10). Members of this gene family are core members of the Salvador/Warts/Hippo (SWH) tumor suppressor network and have been shown to be involved in human tumorigenesis. Among the RASSF genes, RASSF1A is one of the most frequently methylated genes in a wide range of epithelial cancers, and we previously demonstrated that RASSF6 and RASSF10 genes are frequently epigenetically inactivated in acute leukemias, particularly in those of the B cell type. We here determined the methylation profiles of all members of the RASSF gene family as well as two recently identified (KIBRA, CRB3) upstream members of the SWH pathway in the leukemic B cells obtained from a well-characterized cohort of 95 patients with chronic lymphocytic leukemia (CLL). Among the RASSF genes, RASSF10 (50%) was the most frequently methylated gene, followed by RASSF6 (16%). The remaining RASSF genes were either unmethylated or showed a frequency of methylation < 10%. The upstream SWH member KIBRA was also frequently methylated in CLL (35%) in contrast to CRB3. Interestingly, the analysis of clinical-pathological parameters showed that KIBRA methylation was associated with unfavorable biological prognostic parameters, including unmutated IGHV genes (p = 0.007) and high CD38 expression (p < 0.05).
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Affiliation(s)
- Thoraia Shinawi
- University of Birmingham, College of Medical and Dental Sciences, School of Clinical and Experimental Medicine, Medical and Molecular Genetics, Edgbaston, Birmingham, UK
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Rahmatpanah FB, Carstens S, Hooshmand SI, Welsh EC, Sjahputera O, Taylor KH, Bennett LB, Shi H, Davis JW, Arthur GL, Shanafelt TD, Kay NE, Wooldridge JE, Caldwell CW. Large-scale analysis of DNA methylation in chronic lymphocytic leukemia. Epigenomics 2012; 1:39-61. [PMID: 20495622 DOI: 10.2217/epi.09.10] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
AIMS B-cell chronic lymphocytic leukemia (CLL) is a heterogeneous malignancy that clinically ranges from indolent to rapidly progressive. CLL, like other cancers, can be affected by epigenetic alterations. MATERIALS & METHODS A microarray discovery-based study was initiated to determine DNA methylation in CLL cases with a range of CD38 expression (1–92%). RESULTS Many loci were either methylated or unmethylated across all CD38 levels, but differential methylation was also observed for some genes. Genomic sequencing of DLEU7 confirmed extensive cytosine methylation preferentially in patient samples with low CD38 expression, whereas NRP2, SFRP2 and ADAM12 were more commonly methylated in those with high CD38 expression. CONCLUSION This study demonstrates that CLL is affected by CpG island methylation in some genes that segregate with CD38 expression levels, while most others show similar methylation patterns across all levels. The CpG island methylation in certain functional gene groups and pathway-associated genes that are known to be deregulated in CLL provides additional insights into the CLL methylome and epigenetic contribution to cellular dysfunction. It will now be useful to investigate the effectiveness of epigenetic therapeutic reversal of these alterations to develop effective treatments for the disease.
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Affiliation(s)
- Farahnaz B Rahmatpanah
- Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, Missouri 65212, USA
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Moskalev EA, Luckert K, Vorobjev IA, Mastitsky SE, Gladkikh AA, Stephan A, Schrenk M, Kaplanov KD, Kalashnikova OB, Pötz O, Joos TO, Hoheisel JD. Concurrent epigenetic silencing of wnt/β-catenin pathway inhibitor genes in B cell chronic lymphocytic leukaemia. BMC Cancer 2012; 12:213. [PMID: 22672427 PMCID: PMC3489542 DOI: 10.1186/1471-2407-12-213] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 06/06/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The Wnt/β-catenin signalling is aberrantly activated in primary B cell chronic lymphocytic leukaemia (CLL). Epigenetic silencing of pathway inhibitor genes may be a mechanism for its activation. In this study, we investigated systematically and quantitatively the methylation status of 12 Wnt/β-catenin pathway inhibitor genes - CDH1, DACT1, DKK1, DKK2, DKK3, DKK4, SFRP1, SFRP2, SFRP3, SFRP4, SFRP5 and WIF1 - in the cell lines EHEB and MEC-1 as well as patient samples. METHODS Quantification of DNA methylation was performed by means of bisulphite pyrosequencing and confirmed by bisulphite Sanger sequencing. Gene expression was analysed by qPCR using GAPDH as internal control. E-cadherin and β-catenin protein quantification was carried out by microsphere-based immunoassays. Methylation differences observed between the patient and control groups were tested using generalised least squares models. RESULTS For 10 genes, a higher methylation level was observed in tumour material. Only DKK4 exhibited similarly high methylation levels in both tumour and normal specimens, while DACT1 was always essentially unmethylated. However, also for these inhibitors, treatment of cells with the demethylating agent 5-aza-2´-deoxycytidine resulted in an induction of their expression, as shown by quantitative PCR, suggesting an indirect epigenetic control of activity. While the degree of demethylation and its transcriptional consequences differed between the genes, there was an overall high correlation of demethylation and increased activity. Protein expression studies revealed that no constitutive Wnt/β-catenin signalling occurred in the cell lines, which is in discrepancy with results from primary CLL. However, treatment with 5-aza-2´-deoxycytidine caused accumulation of β-catenin. Simultaneously, E-cadherin expression was strongly induced, leading to the formation of a complex with β-catenin and thus demonstrating its epigenetically regulated inhibition effect. CONCLUSIONS The results suggest an epigenetic silencing mechanism of the Wnt/β-catenin pathway inhibitor genes in CLL. Hypermethylation and silencing of functionally related genes may not be completely stochastic but result from the tumour epigenome reprogramming orchestrated by Polycomb-group repressive complexes. The data are of interest in the context of epigenetic-based therapy.
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MESH Headings
- Antimetabolites, Antineoplastic/pharmacology
- Azacitidine/pharmacology
- Cadherins/metabolism
- Cell Line, Tumor
- Chromosome Mapping
- CpG Islands
- DNA Methylation
- Epigenesis, Genetic
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Silencing
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Protein Binding
- Signal Transduction
- Wnt Proteins/metabolism
- beta Catenin/metabolism
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Affiliation(s)
- Evgeny A Moskalev
- Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Diagnostic Molecular Pathology, Institute of Pathology, University of Erlangen-Nürnberg, Krankenhausstr. 8-10, 91054, Erlangen, Germany
| | - Katrin Luckert
- Biochemistry Department, NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Ivan A Vorobjev
- Functional Morphology of Hemablastoses, National Hematology Research Centre of Russian Academy of Medical Sciences, Novy Zykovsky passage 4a, 125167, Moscow, Russia
- A.N. Belozersky Institute and Biological Faculty, Moscow State University, Leninskie Gory 1, 119991, Moscow, Russia
| | - Sergey E Mastitsky
- Theoretical Bioinformatics, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Aleena A Gladkikh
- Functional Morphology of Hemablastoses, National Hematology Research Centre of Russian Academy of Medical Sciences, Novy Zykovsky passage 4a, 125167, Moscow, Russia
| | - Achim Stephan
- Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Marita Schrenk
- Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Kamil D Kaplanov
- Department of Haematology, Volgograd Regional Clinical Oncological Dispensary No.1, Zemlyachki str. 78, 400138, Volgograd, Russia
| | - Olga B Kalashnikova
- Department of Haematology, Volgograd Regional Clinical Oncological Dispensary No.1, Zemlyachki str. 78, 400138, Volgograd, Russia
| | - Oliver Pötz
- Biochemistry Department, NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Thomas O Joos
- Biochemistry Department, NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Jörg D Hoheisel
- Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
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Pei L, Choi JH, Liu J, Lee EJ, McCarthy B, Wilson JM, Speir E, Awan F, Tae H, Arthur G, Schnabel JL, Taylor KH, Wang X, Xu D, Ding HF, Munn DH, Caldwell C, Shi H. Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia. Epigenetics 2012; 7:567-78. [PMID: 22534504 DOI: 10.4161/epi.20237] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We conducted a genome-wide DNA methylation analysis in CD19 (+) B-cells from chronic lymphocytic leukemia (CLL) patients and normal control samples using reduced representation bisulfite sequencing (RRBS). The methylation status of 1.8-2.3 million CpGs in the CLL genome was determined; about 45% of these CpGs were located in more than 23,000 CpG islands (CGIs). While global CpG methylation was similar between CLL and normal B-cells, 1764 gene promoters were identified as being differentially methylated in at least one CLL sample when compared with normal B-cell samples. Nineteen percent of the differentially methylated genes were involved in transcriptional regulation. Aberrant hypermethylation was found in all HOX gene clusters and a significant number of WNT signaling pathway genes. Hypomethylation occurred more frequently in the gene body including introns, exons, and 3'-UTRs in CLL. The NFATc1 P2 promoter and first intron was found to be hypomethylated and correlated with upregulation of both NFATc1 RNA and protein expression levels in CLL suggesting that an epigenetic mechanism is involved in the constitutive activation of NFAT activity in CLL cells. This comprehensive DNA methylation analysis will further our understanding of the epigenetic contribution to cellular dysfunction in CLL.
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Affiliation(s)
- Lirong Pei
- GHSU Cancer Center; Georgia Health Sciences University; Augusta, GA, USA
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40
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Florean C, Schnekenburger M, Grandjenette C, Dicato M, Diederich M. Epigenomics of leukemia: from mechanisms to therapeutic applications. Epigenomics 2012; 3:581-609. [PMID: 22126248 DOI: 10.2217/epi.11.73] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Leukemogenesis is a multistep process in which successive transformational events enhance the ability of a clonal population arising from hematopoietic progenitor cells to proliferate, differentiate and survive. Clinically and pathologically, leukemia is subdivided into four main categories: chronic lymphocytic leukemia, chronic myeloid leukemia, acute lymphocytic leukemia and acute myeloid leukemia. Leukemia has been previously considered only as a genetic disease. However, in recent years, significant advances have been made in the elucidation of the leukemogenesis-associated processes. Thus, we have come to understand that epigenetic alterations including DNA methylation, histone modifications and miRNA are involved in the permanent changes of gene expression controlling the leukemia phenotype. In this article, we will focus on the epigenetic defects associated with leukemia and their implications as biomarkers for diagnostic, prognostic and therapeutic applications.
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Affiliation(s)
- Cristina Florean
- Laboratoire de Biologie Moléculaire et Cellulaire de Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg
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41
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Thathia SH, Ferguson S, Gautrey HE, van Otterdijk SD, Hili M, Rand V, Moorman AV, Meyer S, Brown R, Strathdee G. Epigenetic inactivation of TWIST2 in acute lymphoblastic leukemia modulates proliferation, cell survival and chemosensitivity. Haematologica 2011; 97:371-8. [PMID: 22058208 DOI: 10.3324/haematol.2011.049593] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Altered regulation of many transcription factors has been shown to be important in the development of leukemia. TWIST2 modulates the activity of a number of important transcription factors and is known to be a regulator of hematopoietic differentiation. Here, we investigated the significance of epigenetic regulation of TWIST2 in the control of cell growth and survival and in response to cytotoxic agents in acute lymphoblastic leukemia. DESIGN AND METHODS TWIST2 promoter methylation status was assessed quantitatively, by combined bisulfite and restriction analysis (COBRA) and pyrosequencing assays, in multiple types of leukemia and TWIST2 expression was determined by quantitative reverse transcriptase polymerase chain reaction analysis. The functional role of TWIST2 in cell proliferation, survival and response to chemotherapy was assessed in transient and stable expression systems. RESULTS We found that TWIST2 was inactivated in more than 50% of cases of childhood and adult acute lymphoblastic leukemia through promoter hypermethylation and that this epigenetic regulation was especially prevalent in RUNX1-ETV6-driven cases. Re-expression of TWIST2 in cell lines resulted in a dramatic reduction in cell growth and induction of apoptosis in the Reh cell line. Furthermore, re-expression of TWIST2 resulted in increased sensitivity to the chemotherapeutic agents etoposide, daunorubicin and dexamethasone and TWIST2 hypermethylation was almost invariably found in relapsed adult acute lymphoblastic leukemia (91% of samples hypermethylated). CONCLUSIONS This study suggests a dual role for epigenetic inactivation of TWIST2 in acute lymphoblastic leukemia, initially through altering cell growth and survival properties and subsequently by increasing resistance to chemotherapy.
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Affiliation(s)
- Shabnam H Thathia
- Crucible Laboratory, Institute for Ageing and Health, Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, UK
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42
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Gunnarsson R, Rosenquist R. New insights into the pathobiology of chronic lymphocytic leukemia. J Hematop 2011. [DOI: 10.1007/s12308-011-0091-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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43
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Irving L, Mainou-Fowler T, Parker A, Ibbotson RE, Oscier DG, Strathdee G. Methylation markers identify high risk patients in IGHV mutated chronic lymphocytic leukemia. Epigenetics 2011; 6:300-6. [PMID: 21051931 DOI: 10.4161/epi.6.3.14038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) exhibits a very variable clinical course. Altered DNA methylation of genes has shown promise as a source of novel prognostic makers in a number of cancers. Here we have studied the potential utility of a panel of methylation markers (CD38, HOXA4 and BTG4) in 118 CLL patients. Each of the three loci assessed exhibited frequent methylation, as determined by COBRA analysis, and individually correlated with either good (CD38, BTG4 methylation) or poor (HOXA4 methylation) prognosis. Using a combined approach to produce an overall methylation score, we found that methylation score was significantly associated with time to first treatment in CLL patients. Multivariate Cox regression analysis revealed that methylation score was the strongest predictor of time to first treatment, and was independent of IGHV gene mutational status and CD38 expression. This study provides proof of principle that a panel of methylation markers can be used for additional risk stratification of CLL patients.
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Affiliation(s)
- Laura Irving
- Crucible Laboratory, Institute for Ageing and Health, Newcastle University, UK
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44
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Zenz T, Fröhling S, Mertens D, Döhner H, Stilgenbauer S. Moving from prognostic to predictive factors in chronic lymphocytic leukaemia (CLL). Best Pract Res Clin Haematol 2011; 23:71-84. [PMID: 20620972 DOI: 10.1016/j.beha.2009.12.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Many prognostic factors have been identified in chronic lymphocytic leukaemia (CLL). Based on the assessment of B cell receptor (BCR) structure and function, a subdivision into subtypes is possible (e.g., immunoglobulin heavy chain variable gene segment (IGHV) unmutated and mutated, V3-21 usage) with distinct biological and clinical characteristics. Recurrent genomic aberrations (i.e., 11q and 17p deletion) and gene mutations (i.e., TP53 and ATM) help to define biological and clinical subgroups. In addition, serum markers (e.g., thymidine kinase (TK) and beta2-microglobulin (beta2-MG)), cellular markers (e.g., CD38 and ZAP70) and clinical staging have an impact on outcome in CLL. The biological characterisation of CLL has not only led to progress in outcome prediction but also has begun to be translated into novel treatment strategies. Nonetheless, most factors associated with prognosis have not been thoroughly interrogated for their predictive value in the light of different therapeutic approaches. With a growing number of agents acting on specific biological targets and being used in different clinical situations, the future is likely to bring the identification of predictive factors in CLL.
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MESH Headings
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Predictive Value of Tests
- Prognosis
- Receptors, Antigen, B-Cell/immunology
- Risk Factors
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Affiliation(s)
- Thorsten Zenz
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
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45
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Deregulation of TWIST-1 in the CD34+ compartment represents a novel prognostic factor in chronic myeloid leukemia. Blood 2010; 117:1673-6. [PMID: 21123820 DOI: 10.1182/blood-2009-11-254680] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The mechanisms of resistance to tyrosine kinase inhibitors (TKIs) in chronic myeloid leukemia (CML) often remain obscure. Analysis of patient samples during disease progression revealed the up-regulation of the oncogene TWIST-1, also measured in primary samples from TKI-resistant patients. Moreover, we found that TWIST-1 was overexpressed in CML diagnostic samples of patients who later developed cytogenetic resistance to imatinib, even those without any detectable resistance mechanism. We confirmed the up-regulation of TWIST-1 at both RNA and protein levels in imatinib-resistant cell lines, irrespective of any other resistance mechanism. Analysis with specific small interfering RNA suggested TWIST-1 involvement in the resistance phenotype. Finally, the kinetics of TWIST-1 expression during the individual medical histories of CML patients indicated that TWIST-1 expression is down-regulated by TKIs and up-regulated with TKI resistance. We hypothesize that the overexpression of the TWIST-1 oncogene represents a novel key prognostic factor potentially useful for optimizing CML management in the TKI era.
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46
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Tong WG, Wierda WG, Lin E, Kuang SQ, Bekele BN, Estrov Z, Wei Y, Yang H, Keating MJ, Garcia-Manero G. Genome-wide DNA methylation profiling of chronic lymphocytic leukemia allows identification of epigenetically repressed molecular pathways with clinical impact. Epigenetics 2010; 5:499-508. [PMID: 20484983 PMCID: PMC3322493 DOI: 10.4161/epi.5.6.12179] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We performed a genome-wide analysis of aberrant DNA methylation in chronic lymphocytic leukemia (CLL) using methylated CpG island amplification (MCA) coupled with a promoter microarray. We identified 280 potential targets of aberrant DNA methylation in CLL. These genes were located more frequently in chromosomes 19 (16%, p=0.001), 16 (11%, p=0.001), 17 (10%, p=0.02) and 11 (9%, p=0.02) and could be grouped in several functional networks. Methylation status was confirmed for 22 of these genes (SOX11, DLX1, FAM62C, SOX14, RSPO1, ADCY5, HAND2,SPOCK, MLL, ING1, PRIMA1, BCL11B, LTBP2, BNC1, NR2F2, SALL1, GALGT2, LHX1, DLX4, KLK10, TFAP2 and APP) in 78 CLL patients by pyrosequencing. As a proof of principle, we analyzed the expression of 2 genes, PRIMA1 and APP, in primary cells and of GALGT2, TFAP2C and PRIMA1 in leukemia cells. There was an inverse association between methylation and gene expression. This could be reversed by treatment with 5-aza-2'-deoxycytidine in cell lines. Treatment in a clinical trial with 5-azacitidine resulted in decreased methylation of LINE, DLX4 and SALL1 in the peripheral blood B-cells of patients with CLL. IgVH mutational status or ZAP-70 expression were not associated with specific methylation profiles. By multivariate analysis, methylation of LINE and APP was associated with shorter overall survival (p = 0.045 and 0.0035, respectively). This study demonstrates that aberrant DNA methylation is common and has potential prognostic and therapeutic value in CLL.
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Affiliation(s)
- Wei-Gang Tong
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - William G. Wierda
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - E. Lin
- Department of Biostatistics; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Shao-Qing Kuang
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - B. Nebiyou Bekele
- Department of Biostatistics; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Zeev Estrov
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Yue Wei
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Hui Yang
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Michael J Keating
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Guillermo Garcia-Manero
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
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Blum KA, Liu Z, Lucas DM, Chen P, Xie Z, Baiocchi R, Benson DM, Devine SM, Jones J, Andritsos L, Flynn J, Plass C, Marcucci G, Chan KK, Grever MR, Byrd JC. Phase I trial of low dose decitabine targeting DNA hypermethylation in patients with chronic lymphocytic leukaemia and non-Hodgkin lymphoma: dose-limiting myelosuppression without evidence of DNA hypomethylation. Br J Haematol 2010; 150:189-95. [PMID: 20456354 DOI: 10.1111/j.1365-2141.2010.08213.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Targeting aberrant DNA hypermethylation in chronic lymphocytic leukaemia (CLL) and non-Hodgkin lymphoma (NHL) with decitabine may reverse epigenetic silencing in B-cell malignancies. Twenty patients were enrolled in two phase I trials to determine the minimum effective pharmacological dose of decitabine in patients with relapsed/refractory CLL (n = 16) and NHL (n = 4). Patients received 1-3 cycles of decitabine. Dose-limiting toxicity (DLT) was observed in 2 of 4 CLL and 2 of 2 NHL patients receiving decitabine at 15 mg/m(2) per d days 1-10, consisting of grade 3-4 thrombocytopenia and hyperbilirubinaemia. Six patients with CLL received decitabine at 10 mg/m(2) per d days 1-10 without DLT; however, re-expression of methylated genes or changes in global DNA methylation were not observed. Therefore, a 5-day decitabine schedule was examined. With 15 mg/m(2) per d decitabine days 1-5, DLT occurred in 2 of 6 CLL and 2 of 2 NHL patients, consisting of grade 3-4 neutropenia, thrombocytopenia, and febrile neutropenia. Eight patients had stable disease. In 17 patients, there were no significant changes in genome-wide methylation or in target gene re-expression. In conclusion, dose-limiting myelosuppression and infectious complications prevented dose escalation of decitabine to levels associated with changes in global methylation or gene re-expression in CLL and NHL.
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Affiliation(s)
- Kristie A Blum
- Division of Hematology-Oncology, Department of Internal Medicine, The Arthur G. James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
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48
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Butler T, Gribben JG. Biologic and clinical significance of molecular profiling in Chronic Lymphocytic Leukemia. Blood Rev 2010; 24:135-41. [PMID: 20398985 DOI: 10.1016/j.blre.2010.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
CLL is extremely heterogeneous in its clinical course, with some patients living decades with no need for treatment whilst others have a rapidly aggressive clinical course. A major focus of research has been to try to identify those biological factors that influence this heterogeneity. The goal of therapy has been to maintain the best quality of life and treat only when patients become symptomatic from their disease. For the majority of patients this means following a "watch and wait" approach to determine the rate of progression of the disease and assess for development of symptoms. Any alteration to this approach will require identification of criteria that define patients sufficiently "high-risk" that they gain benefit by introduction of early therapy. The use of molecular profiling to suggest particular therapies is currently appropriate only in defining the treatment of the minority of patients with 17p deletions or p53 mutations and in all other circumstances remains a clinical trial question.
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Affiliation(s)
- Tom Butler
- Medical Oncology, Institute of Cancer, Barts and London School of Medicine, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom.
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Chen SS, Sherman MH, Hertlein E, Johnson AJ, Teitell MA, Byrd JC, Plass C. Epigenetic alterations in a murine model for chronic lymphocytic leukemia. Cell Cycle 2010; 8:3663-7. [PMID: 19901553 DOI: 10.4161/cc.8.22.9957] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Early stages in the development of chronic lymphocytic leukemia (CLL) have not been explored mainly due to the inability to study normal B-cells en route to transformation. In order to determine such early events of leukemogenesis, we have used a well established mouse model for CLL. Over-expression of human TCL1, a known CLL oncogene in murine B-cells leads to the development of mature CD19+/CD5+/IgM+ clonal leukemia with a disease phenotype similar to that seen in human CLL. Herein, we review our recent study using this TCL1-driven mouse model for CLL and corresponding human CLL samples in a cross-species epigenomics approach to address the timing and relevance of epigenetic events occurring during leukemogenesis. We demonstrated that the mouse model recapitulates the epigenetic events that have been reported for human CLL, affirming the power and validity of this mouse model to study early epigenetic events in cancer progression. Epigenetic alterations are detected as early as three months after birth, far before disease manifests at about 11 months of age. These mice undergo NFkappaB repressor complex mediated inactivation of the transcription factor Foxd3, whose targets become aberrantly methylated and silenced in mouse and human CLL. Overall, our data suggest the accumulated epigenetic alterations during CLL pathogenesis as a consequence of gene silencing through TCL1 and NFkappaB repressor complex, suggesting the relevance for NFkappaB as a therapeutic target in CLL.
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Affiliation(s)
- Shih-Shih Chen
- Laboratory of Experimental Immunology, Feinstein Institute for Medical Research, Manhasset, NY, USA
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Differential genome-wide array-based methylation profiles in prognostic subsets of chronic lymphocytic leukemia. Blood 2009; 115:296-305. [PMID: 19897574 DOI: 10.1182/blood-2009-07-232868] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Global hypomethylation and regional hypermethylation are well-known epigenetic features of cancer; however, in chronic lymphocytic leukemia (CLL), studies on genome-wide epigenetic modifications are limited. Here, we analyzed the global methylation profiles in CLL, by applying high-resolution methylation microarrays (27,578 CpG sites) to 23 CLL samples, belonging to the immunoglobulin heavy-chain variable (IGHV) mutated (favorable) and IGHV unmutated/IGHV3-21 (poor-prognostic) subsets. Overall, results demonstrated significant differences in methylation patterns between these subgroups. Specifically, in IGHV unmutated CLL, we identified methylation of 7 known or candidate tumor suppressor genes (eg, VHL, ABI3, and IGSF4) as well as 8 unmethylated genes involved in cell proliferation and tumor progression (eg, ADORA3 and PRF1 enhancing the nuclear factor-kappaB and mitogen-activated protein kinase pathways, respectively). In contrast, these latter genes were silenced by methylation in IGHV mutated patients. The array data were validated for selected genes using methylation-specific polymerase chain reaction, quantitative reverse transcriptase-polymerase chain reaction, and bisulfite sequencing. Finally, the significance of DNA methylation in regulating gene promoters was shown by reinducing 4 methylated tumor suppressor genes (eg, VHL and ABI3) in IGHV unmutated samples using the methyl-inhibitor 5-aza-2'-deoxycytidine. Taken together, our data for the first time reveal differences in global methylation profiles between prognostic subsets of CLL, which may unfold epigenetic silencing mechanisms involved in CLL pathogenesis.
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