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Yurttaş NÖ, Eşkazan AE. Clinical Application of Biomarkers for Hematologic Malignancies. Biomark Med 2022. [DOI: 10.2174/9789815040463122010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Over the last decade, significant advancements have been made in the
molecular mechanisms, diagnostic methods, prognostication, and treatment options in
hematologic malignancies. As the treatment landscape continues to expand,
personalized treatment is much more important.
With the development of new technologies, more sensitive evaluation of residual
disease using flow cytometry and next generation sequencing is possible nowadays.
Although some conventional biomarkers preserve their significance, novel potential
biomarkers accurately detect the mutational landscape of different cancers, and also,
serve as prognostic and predictive biomarkers, which can be used in evaluating therapy
responses and relapses. It is likely that we will be able to offer a more targeted and
risk-adapted therapeutic approach to patients with hematologic malignancies guided by
these potential biomarkers. This chapter summarizes the biomarkers used (or proposed
to be used) in the diagnosis and/or monitoring of hematologic neoplasms.;
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Affiliation(s)
- Nurgül Özgür Yurttaş
- Division of Hematology, Department of Internal Medicine, Cerrahpasa Faculty of Medicine,
Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ahmet Emre Eşkazan
- Division of Hematology, Department of Internal Medicine, Cerrahpasa Faculty of Medicine,
Istanbul University-Cerrahpasa, Istanbul, Turkey
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2
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Minson A, Tam C, Dickinson M, Seymour JF. Targeted Agents in the Treatment of Indolent B-Cell Non-Hodgkin Lymphomas. Cancers (Basel) 2022; 14:1276. [PMID: 35267584 PMCID: PMC8908980 DOI: 10.3390/cancers14051276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/24/2022] [Accepted: 02/27/2022] [Indexed: 02/01/2023] Open
Abstract
Targeted therapies continue to change the landscape of lymphoma treatment, resulting in improved therapy options and patient outcomes. Numerous agents are now approved for use in the indolent lymphomas and many others under development demonstrate significant promise. In this article, we review the landscape of targeted agents that apply to the indolent lymphomas, predominantly follicular lymphoma, lymphoplasmacytic lymphoma/Waldenstrom macroglobulinaemia and marginal zone lymphoma. The review covers small molecule inhibitors, immunomodulators and targeted immunotherapies, as well as presenting emerging and promising combination therapies.
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Affiliation(s)
- Adrian Minson
- Peter MacCallum Cancer Centre & Royal Melbourne Hospital, Melbourne, VIC 3000, Australia; (C.T.); (M.D.); (J.F.S.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Constantine Tam
- Peter MacCallum Cancer Centre & Royal Melbourne Hospital, Melbourne, VIC 3000, Australia; (C.T.); (M.D.); (J.F.S.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael Dickinson
- Peter MacCallum Cancer Centre & Royal Melbourne Hospital, Melbourne, VIC 3000, Australia; (C.T.); (M.D.); (J.F.S.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - John F. Seymour
- Peter MacCallum Cancer Centre & Royal Melbourne Hospital, Melbourne, VIC 3000, Australia; (C.T.); (M.D.); (J.F.S.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
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3
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Gemović B, Perović V, Davidović R, Drljača T, Veljkovic N. Alignment-free method for functional annotation of amino acid substitutions: Application on epigenetic factors involved in hematologic malignancies. PLoS One 2021; 16:e0244948. [PMID: 33395407 PMCID: PMC7781373 DOI: 10.1371/journal.pone.0244948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 12/21/2020] [Indexed: 11/19/2022] Open
Abstract
For the last couple of decades, there has been a significant growth in sequencing data, leading to an extraordinary increase in the number of gene variants. This places a challenge on the bioinformatics research community to develop and improve computational tools for functional annotation of new variants. Genes coding for epigenetic regulators have important roles in cancer pathogenesis and mutations in these genes show great potential as clinical biomarkers, especially in hematologic malignancies. Therefore, we developed a model that specifically focuses on these genes, with an assumption that it would outperform general models in predicting the functional effects of amino acid substitutions. EpiMut is a standalone software that implements a sequence based alignment-free method. We applied a two-step approach for generating sequence based features, relying on the biophysical and biochemical indices of amino acids and the Fourier Transform as a sequence transformation method. For each gene in the dataset, the machine learning algorithm-Naïve Bayes was used for building a model for prediction of the neutral or disease-related status of variants. EpiMut outperformed state-of-the-art tools used for comparison, PolyPhen-2, SIFT and SNAP2. Additionally, EpiMut showed the highest performance on the subset of variants positioned outside conserved functional domains of analysed proteins, which represents an important group of cancer-related variants. These results imply that EpiMut can be applied as a first choice tool in research of the impact of gene variants in epigenetic regulators, especially in the light of the biomarker role in hematologic malignancies. EpiMut is freely available at https://www.vin.bg.ac.rs/180/tools/epimut.php.
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Affiliation(s)
- Branislava Gemović
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
- * E-mail:
| | - Vladimir Perović
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Radoslav Davidović
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Tamara Drljača
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Nevena Veljkovic
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
- Heliant d.o.o., Belgrade, Serbia
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4
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Zuo W, Zhu Y, Liu Z, Xia Y, Xu Y, Peng C, Yu L, Wang N. BRD4 inhibition sensitizes aggressive non-Hodgkin lymphomas to PI3Kδ inhibitors by suppressing PI3K reactivation and c-MYC expression. Am J Cancer Res 2021; 11:215-235. [PMID: 33520370 PMCID: PMC7840716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023] Open
Abstract
Targeting phosphatidylinositol 3-kinase δ (PI3Kδ) is an important therapeutic strategy for indolent non-Hodgkin lymphomas (NHLs). However, we previously observed reactivation of phosphatidylinositol 3-kinase (PI3K) pathways in aggressive NHL cell lines following continuous exposure to PI3Kδ inhibitors (PI3Kδi), which limited their efficacy and suggests that more studies should be focused on this reactivation to improve current PI3Kδi-based treatments. Herein we conducted a drug synergy screening that combined a marketed PI3Kδi, idelalisib, with 14 well-characterized epigenetic drugs across several types of aggressive NHL cell lines. We identified BRD4 inhibitors (BRD4i) as potent partners that, in combination with idelalisib, were capable of synergistically exerting anti-proliferative activity and inducing cell apoptosis in a panel of aggressive NHL cell lines through continuous suppression of PI3K pathways. More importantly, the combination of BRD4i and PI3Kδi simultaneously inhibited transcription and translation of the oncogenic transcription factor c-MYC, downregulating the expression of c-MYC and continuously suppressing the proliferation of cancer cells in vitro, as well as the growth of tumors in vivo even after drug withdrawal. This study, thus, reveals the potential of simultaneously targeting PI3Kδ and BRD4 as a new therapeutic strategy for aggressive forms of NHL.
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Affiliation(s)
- Weiqiong Zuo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Collaborative Innovation Center for BiotherapyChengdu 610041, China
| | - Yongxia Zhu
- Department of Clinical Pharmacy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of ChinaChengdu 610041, China
| | - Zhihao Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Collaborative Innovation Center for BiotherapyChengdu 610041, China
| | - Yong Xia
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Collaborative Innovation Center for BiotherapyChengdu 610041, China
| | - Ying Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Collaborative Innovation Center for BiotherapyChengdu 610041, China
| | - Cuiting Peng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Collaborative Innovation Center for BiotherapyChengdu 610041, China
| | - Luoting Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Collaborative Innovation Center for BiotherapyChengdu 610041, China
| | - Ningyu Wang
- School of Life Science and Engineering, Southwest Jiaotong UniversityChengdu 610031, China
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5
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Targeting BCL-2 in B-cell malignancies and overcoming therapeutic resistance. Cell Death Dis 2020; 11:941. [PMID: 33139702 PMCID: PMC7608616 DOI: 10.1038/s41419-020-03144-y] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022]
Abstract
Defects in apoptosis can promote tumorigenesis and impair responses of malignant B cells to chemotherapeutics. Members of the B-cell leukemia/lymphoma-2 (BCL-2) family of proteins are key regulators of the intrinsic, mitochondrial apoptotic pathway. Overexpression of antiapoptotic BCL-2 family proteins is associated with treatment resistance and poor prognosis. Thus, inhibition of BCL-2 family proteins is a rational therapeutic option for malignancies that are dependent on antiapoptotic BCL-2 family proteins. Venetoclax (ABT-199, GDC-0199) is a highly selective BCL-2 inhibitor that represents the first approved agent of this class and is currently widely used in the treatment of chronic lymphocytic leukemia (CLL) as well as acute myeloid leukemia (AML). Despite impressive clinical activity, venetoclax monotherapy for a prolonged duration can lead to drug resistance or loss of dependence on the targeted protein. In this review, we provide an overview of the mechanism of action of BCL-2 inhibition and the role of this approach in the current treatment paradigm of B-cell malignancies. We summarize the drivers of de novo and acquired resistance to venetoclax that are closely associated with complex clonal shifts, interplay of expression and interactions of BCL-2 family members, transcriptional regulators, and metabolic modulators. We also examine how tumors initially resistant to venetoclax become responsive to it following prior therapies. Here, we summarize preclinical data providing a rationale for efficacious combination strategies of venetoclax to overcome therapeutic resistance by a targeted approach directed against alternative antiapoptotic BCL-2 family proteins (MCL-1, BCL-xL), compensatory prosurvival pathways, epigenetic modifiers, and dysregulated cellular metabolism/energetics for durable clinical remissions.
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6
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Moubadder L, McCullough LE, Flowers CR, Koff JL. Linking Environmental Exposures to Molecular Pathogenesis in Non-Hodgkin Lymphoma Subtypes. Cancer Epidemiol Biomarkers Prev 2020; 29:1844-1855. [PMID: 32727723 DOI: 10.1158/1055-9965.epi-20-0228] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/27/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022] Open
Abstract
Non-Hodgkin lymphoma comprises a heterogeneous group of hematologic malignancies, with about 60 subtypes that arise via various pathogenetic mechanisms. Although establishing etiology for specific NHL subtypes has been historically difficult given their relative rarity, environmental exposures have been repeatedly implicated as risk factors across many subtypes. Large-scale epidemiologic investigations have pinpointed chemical exposures in particular, but causality has not been established, and the exact biologic mechanisms underpinning these associations are unclear. Here we review chemical exposures that have been associated with development of NHL subtypes and discuss their biologic plausibility based on current research.
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Affiliation(s)
- Leah Moubadder
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Lauren E McCullough
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Christopher R Flowers
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jean L Koff
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia.
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Abstract
Introduction: T-cell lymphomas represent a broad group of malignant T-cell neoplasms with marked molecular, clinical, and biologic heterogeneity. Survival rates after conventional chemotherapy regimens are poor for most subtypes and new therapies are needed. Rapidly expanding knowledge in the field of epigenomics and the development of an increasing number of epigenetic-modifying agents have created new opportunities for epigenetic therapies for patients with this complex group of diseases.Areas covered: The present review summarizes current knowledge on epigenetic alterations in T-cell lymphomas, availability, and mechanisms of action of epigenetic-modifying agents, results of clinical trials of epigenetic therapies in T-cell lymphomas, status of FDA approval, and biomarker approaches to guide therapy. Promising future directions are discussed.Expert opinion: Mutations in epigenetic-modifying genes are among the most common genetic alterations in T-cell lymphomas, highlighting the potential for epigenetic therapies to improve management of this group of diseases. Single-agent efficacy is well documented, leading to FDA approval for several indications, but overall response rates and durability of responses remain modest. Critical next steps for the field include optimizing combination therapies that incorporate epigenetic-modifying agents and developing predictive biomarkers that help guide patient and drug selection.
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Affiliation(s)
- Nada Ahmed
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.,Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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8
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Rahmani M, Fardi M, Farshdousti Hagh M, Hosseinpour Feizi AA, Talebi M, Solali S. An investigation of methylation pattern changes in the IKZF1 promoter in patients with childhood B-cell acute lymphoblastic leukemia. Blood Res 2019; 54:144-148. [PMID: 31309094 PMCID: PMC6614096 DOI: 10.5045/br.2019.54.2.144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/09/2019] [Accepted: 04/04/2019] [Indexed: 11/29/2022] Open
Abstract
Background Ikaros family zinc finger 1 (IKZF1) is a transcription factor with an important role in controlling hematopoietic proliferation and function, particularly lymphoid cell differentiation. It was previously shown that various mechanisms and expression patterns of Ikaros are linked to a variety of cancers. We hypothesized that aberrant methylation (hypomethylation) of the IKZF1 promoter region might be one of the causes of B-cell acute lymphoblastic leukemia (B-ALL). In B-ALL patients, an increased expression of this gene is a potential cause of B-cell differentiation arrest and proliferation induction. Therefore, as more than 90% of patients with ALL are <15 years old, we investigated the methylation pattern of the IKZF1 promoter in childhood B-ALL. Methods Twenty-five newly diagnosed B-ALL cases were included (all younger than 15 yr). In addition, we selected 25 healthy age- and sex-matched children as the control group. We collected the blood samples in EDTA-containing tubes and isolated lymphocytes from whole blood using Ficoll 1.077 Lymphosep. Next, we extracted genomic DNA with the phenol/chloroform method. Two microgram of DNA per sample was treated with sodium bisulfite using the EpiTect Bisulfite Kit, followed by an assessment of DNA methylation by polymerase chain reaction (PCR) analysis of the bisulfite-modified genomic DNA. Results Our data highlighted a hypomethylated status of the IKZF1 promoter in the ALL cases (96% of the cases were unmethylated). In contrast, the control group samples were partially methylated (68%). Conclusion This study demonstrated a hypomethylated pattern of the IKZF1 promoter region in childhood B-ALL, which might underlie the aberrant Ikaros expression patterns that were previously linked to this malignancy.
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Affiliation(s)
- Mina Rahmani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoumeh Fardi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Mehdi Talebi
- Immunology Department, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Solali
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Division of Hematology and Transfusion Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Gaudio E, Tarantelli C, Ponzoni M, Odore E, Rezai K, Bernasconi E, Cascione L, Rinaldi A, Stathis A, Riveiro E, Cvitkovic E, Zucca E, Bertoni F. Bromodomain inhibitor OTX015 (MK-8628) combined with targeted agents shows strong in vivo antitumor activity in lymphoma. Oncotarget 2018; 7:58142-58147. [PMID: 27494885 PMCID: PMC5295419 DOI: 10.18632/oncotarget.10983] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/07/2016] [Indexed: 11/25/2022] Open
Abstract
The bromodomain inhibitor OTX015 (MK-8628) has shown anti-lymphoma activity as a single agent in both the preclinical and clinical settings, as well as in vitro synergism with several anticancer agents. Here, we report in vivo data for OTX015 in combination with the histone deacetylase inhibitor vorinostat, the Bruton's tyrosine kinase inhibitor ibrutinib, the anti-CD20 monoclonal antibody rituximab, and the mTOR inhibitor everolimus in a diffuse large B cell lymphoma model. The antitumor effect of OTX015-containing combinations in SU-DHL-2 xenografts in mice was much stronger than the activity of the corresponding single agents with almost complete tumor eradication for all four combinations. Pharmacokinetic analyses showed similar OTX015 levels in plasma and tumor samples of approximately 1.5 μM, which is equivalent to the concentration showing strong in vitro activity. For all four combinations, mean terminal levels of the bromodomain inhibitor differed from those in mice exposed to single agent OTX015, indicating a need for thorough pharmacokinetic investigations in phase I combination studies. In conclusion, our results provide a strong rationale to explore OTX015-containing combinations in the clinical lymphoma setting.
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Affiliation(s)
- Eugenio Gaudio
- Lymphoma and Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland
| | - Chiara Tarantelli
- Lymphoma and Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland
| | | | - Elodie Odore
- Institut Curie, Hôpital René Huguenin, Saint-Cloud, France
| | - Keyvan Rezai
- Institut Curie, Hôpital René Huguenin, Saint-Cloud, France
| | - Elena Bernasconi
- Lymphoma and Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland
| | - Luciano Cascione
- Lymphoma and Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland.,Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
| | - Andrea Rinaldi
- Lymphoma and Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland
| | - Anastasios Stathis
- Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
| | | | | | - Emanuele Zucca
- Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
| | - Francesco Bertoni
- Lymphoma and Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland.,Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
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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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11
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Rossmann MP, Orkin SH, Chute JP. Hematopoietic Stem Cell Biology. Hematology 2018. [DOI: 10.1016/b978-0-323-35762-3.00009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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12
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DNA methylation profiling reveals common signatures of tumorigenesis and defines epigenetic prognostic subtypes of canine Diffuse Large B-cell Lymphoma. Sci Rep 2017; 7:11591. [PMID: 28912427 PMCID: PMC5599585 DOI: 10.1038/s41598-017-11724-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/29/2017] [Indexed: 02/06/2023] Open
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13
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Rahmani T, Azad M, Chahardouli B, Nasiri H, Vatanmakanian M, Kaviani S. Patterns of DNMT1 Promoter Methylation in Patients with Acute Lymphoblastic Leukemia. Int J Hematol Oncol Stem Cell Res 2017; 11:172-177. [PMID: 28989582 PMCID: PMC5625466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Background: Acute lymphoblastic leukemia (ALL) is a clonal malignant disorder characterized by an uncontrolled proliferation of immature T or B lymphocytes. Extensive studies have shown that the epigenetic changes, especially modified DNA methylation patterns in the regulatory regions through the DNA methyltransferase (DNMTs), play an important role in the development of genetic disorders and abnormal growth and maturation capacity of leukemic stem cells (LSCs).The aim of this study was to evaluate the changes in DNMT1 promoter methylation and its expression pattern in patients with ALL. Materials and Methods: In this experimental study, methylation specific PCR (MSP) was used to assess the methylation status of DNMT1 promoter regions in samples collected from ALL patients (n=45) and healthy control subjects. According to this method, un-methylated cytosine nucleotides are converted to uracil by sodium bisulfite and the proliferation of methylated and un-methylated regions are performed using specific primers for target sequences. Results: None of the patients with B and T-ALL showed methylated promoter regions of the DNMT1 gene, while the methylation pattern of both pre-B ALL patients and the control group showed a relative promoter methylation. Conclusion: Analysis of promoter methylation patterns in various subgroups of ALL has revealed the importance of DNMT1 in the regulation of gene expression. Likewise, extensive data have also highlighted the methylation-based mechanisms exerted by DNAM1 as one of the main participants regulating gene expression in B-ALL and T-ALL patients. Investigation of the overall DNA methylation pattern offers significant improvements in the prediction of disease prognosis and treatment response.
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Affiliation(s)
- Tirdad Rahmani
- Department of Hematology, School of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehdi Azad
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Bahram Chahardouli
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hajar Nasiri
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran,Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mousa Vatanmakanian
- Department of Hematology, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeid Kaviani
- Department of Hematology, School of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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14
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Stevens WBC, Mendeville M, Redd R, Clear AJ, Bladergroen R, Calaminici M, Rosenwald A, Hoster E, Hiddemann W, Gaulard P, Xerri L, Salles G, Klapper W, Pfreundschuh M, Jack A, Gascoyne RD, Natkunam Y, Advani R, Kimby E, Sander B, Sehn LH, Hagenbeek A, Raemaekers J, Gribben J, Kersten MJ, Ylstra B, Weller E, de Jong D. Prognostic relevance of CD163 and CD8 combined with EZH2 and gain of chromosome 18 in follicular lymphoma: a study by the Lunenburg Lymphoma Biomarker Consortium. Haematologica 2017; 102:1413-1423. [PMID: 28411252 PMCID: PMC6643731 DOI: 10.3324/haematol.2017.165415] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/11/2017] [Indexed: 01/25/2023] Open
Abstract
In follicular lymphoma, studies addressing the prognostic value of microenvironment-related immunohistochemical markers and tumor cell-related genetic markers have yielded conflicting results, precluding implementation in practice. Therefore, the Lunenburg Lymphoma Biomarker Consortium performed a validation study evaluating published markers. To maximize sensitivity, an end of spectrum design was applied for 122 uniformly immunochemotherapy-treated follicular lymphoma patients retrieved from international trials and registries. The criteria were: early failure, progression or lymphoma-related death <2 years versus long remission, response duration of >5 years. Immunohistochemical staining for T cells and macrophages was performed on tissue microarrays from initial biopsies and scored with a validated computer-assisted protocol. Shallow whole-genome and deep targeted sequencing was performed on the same samples. The 96/122 cases with complete molecular and immunohistochemical data were included in the analysis. EZH2 wild-type (P=0.006), gain of chromosome 18 (P=0.002), low percentages of CD8+ cells (P=0.011) and CD163+ areas (P=0.038) were associated with early failure. No significant differences in other markers were observed, thereby refuting previous claims of their prognostic significance. Using an optimized study design, this Lunenburg Lymphoma Biomarker Consortium study substantiates wild-type EZH2 status, gain of chromosome 18, low percentages of CD8+ cells and CD163+ area as predictors of early failure to immunochemotherapy in follicular lymphoma treated with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP [-like]), while refuting the prognostic impact of various other markers.
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Affiliation(s)
| | - Matias Mendeville
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Robert Redd
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrew J Clear
- Centre for Haemato-Oncology, Barts Cancer Institute, University of London, UK
| | - Reno Bladergroen
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Maria Calaminici
- Centre for Haemato-Oncology, Barts Cancer Institute, University of London, UK
| | - Andreas Rosenwald
- Institute of Pathology, Comprehensive Cancer Center Mainfranken, University of Würzburg, Germany
| | - Eva Hoster
- Department of Medicine III, University Hospital Grosshadern, Munich, Germany
| | - Wolfgang Hiddemann
- Department of Medicine III, University Hospital Grosshadern, Munich, Germany
| | - Philippe Gaulard
- Department of Pathology and Inserm U955, Hôpital Henri Mondor, University Paris-Est, Créteil, France
| | - Luc Xerri
- Département de Biopathologie, Institut Paoli-Calmettes, Marseille, France
| | - Gilles Salles
- Service d'Hématologie,Hospices Civils de Lyon & Université Claude Bernard Lyon-1, UMR CNRS 5239, France
| | - Wolfram Klapper
- Institute of Pathology, University of Schleswig-Holstein, Kiel, Germany
| | | | - Andrew Jack
- Haematological Malignancy Diagnostic Service, St James's University Hospital, Leeds, UK
| | - Randy D Gascoyne
- Department of Pathology & Medical Oncology, Centre for Lymphoid Cancer, British Columbia Cancer Agency, University of British Columbia, Vancouver, Canada
| | - Yasodha Natkunam
- Department of Pathology, Stanford University School of Medicine, CA, USA
| | - Ranjana Advani
- Department of Hematology, Stanford University School of Medicine, CA, USA
| | - Eva Kimby
- Department of Medicine, Division of Hematology, Karolinska Institute, Stockholm, Sweden
| | - Birgitta Sander
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Laurie H Sehn
- Department of Pathology & Medical Oncology, Centre for Lymphoid Cancer, British Columbia Cancer Agency, University of British Columbia, Vancouver, Canada
| | - Anton Hagenbeek
- Department of Hematology, Academic Medical Center, Amsterdam, the Netherlands
| | - John Raemaekers
- Department of Hematology, Radboudumc, Nijmegen, the Netherlands
| | - John Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, University of London, UK
| | - Marie José Kersten
- Department of Hematology, Academic Medical Center, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Edie Weller
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Daphne de Jong
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
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15
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Arribas AJ, Bertoni F. Methylation patterns in marginal zone lymphoma. Best Pract Res Clin Haematol 2016; 30:24-31. [PMID: 28288713 DOI: 10.1016/j.beha.2016.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 09/16/2016] [Accepted: 09/19/2016] [Indexed: 02/07/2023]
Abstract
Promoter DNA methylation is a major regulator of gene expression and transcription. The identification of methylation changes is important for understanding disease pathogenesis, for identifying prognostic markers and can drive novel therapeutic approaches. In this review we summarize the current knowledge regarding DNA methylation in MALT lymphoma, splenic marginal zone lymphoma, nodal marginal zone lymphoma. Despite important differences in the study design for different publications and the existence of a sole large and genome-wide methylation study for splenic marginal zone lymphoma, it is clear that DNA methylation plays an important role in marginal zone lymphomas, in which it contributes to the inactivation of tumor suppressors but also to the expression of genes sustaining tumor cell survival and proliferation. Existing preclinical data provide the rationale to target the methylation machinery in these disorders.
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Affiliation(s)
- Alberto J Arribas
- Lymphoma & Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland.
| | - Francesco Bertoni
- Lymphoma & Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland; Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland.
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16
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Karrman K, Johansson B. Pediatric T-cell acute lymphoblastic leukemia. Genes Chromosomes Cancer 2016; 56:89-116. [PMID: 27636224 DOI: 10.1002/gcc.22416] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/06/2016] [Indexed: 12/29/2022] Open
Abstract
The most common pediatric malignancy is acute lymphoblastic leukemia (ALL), of which T-cell ALL (T-ALL) comprises 10-15% of cases. T-ALL arises in the thymus from an immature thymocyte as a consequence of a stepwise accumulation of genetic and epigenetic aberrations. Crucial biological processes, such as differentiation, self-renewal capacity, proliferation, and apoptosis, are targeted and deranged by several types of neoplasia-associated genetic alteration, for example, translocations, deletions, and mutations of genes that code for proteins involved in signaling transduction, epigenetic regulation, and transcription. Epigenetically, T-ALL is characterized by gene expression changes caused by hypermethylation of tumor suppressor genes, histone modifications, and miRNA and lncRNA abnormalities. Although some genetic and gene expression patterns have been associated with certain clinical features, such as immunophenotypic subtype and outcome, none has of yet generally been implemented in clinical routine for treatment decisions. The recent advent of massive parallel sequencing technologies has dramatically increased our knowledge of the genetic blueprint of T-ALL, revealing numerous fusion genes as well as novel gene mutations. The challenges now are to integrate all genetic and epigenetic data into a coherent understanding of the pathogenesis of T-ALL and to translate the wealth of information gained in the last few years into clinical use in the form of improved risk stratification and targeted therapies. Here, we provide an overview of pediatric T-ALL with an emphasis on the acquired genetic alterations that result in this disease. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Kristina Karrman
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden.,Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Bertil Johansson
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden.,Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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17
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Sun R, Medeiros LJ, Young KH. Diagnostic and predictive biomarkers for lymphoma diagnosis and treatment in the era of precision medicine. Mod Pathol 2016; 29:1118-42. [PMID: 27363492 DOI: 10.1038/modpathol.2016.92] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/13/2016] [Accepted: 04/14/2016] [Indexed: 02/07/2023]
Abstract
Lymphomas are a group of hematological malignancies derived from lymphocytes. Lymphomas are clinically and biologically heterogeneous and have overlapping diagnostic features. With the advance of new technologies and the application of efficient and feasible detection platforms, an unprecedented number of novel biomarkers have been discovered or are under investigation at the genetic, epigenetic, and protein level as well as the tumor microenvironment. These biomarkers have enabled new clinical and pathological insights into the mechanisms underlying lymphomagenesis and also have facilitated improvements in the diagnostic workup, sub-classification, outcome stratification, and personalized therapy for lymphoma patients. However, integrating these biomarkers into clinical practice effectively and precisely in daily practice is challenging. More in-depth studies are required to further validate these novel biomarkers and to assess other parameters that can affect the reproducibility of these biomarkers such as the selection of detection methods, biological reagents, interpretation of data, and cost efficiency. Despite these challenges, there are many reasons to be optimistic that novel biomarkers will facilitate better algorithms and strategies as we enter a new era of precision medicine to better refine diagnosis, prognostication, and rational treatment design for patients with lymphomas.
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Affiliation(s)
- Ruifang Sun
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Pathology, Shanxi Cancer Hospital, Shanxi, China
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ken H Young
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,The University of Texas Graduate School of Biomedical Science, Houston, TX, USA
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18
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Dupéré-Richer D, Kinal M, Pettersson F, Emond A, Calvo-Vidal MN, Nichol JN, Guilbert C, Plourde D, Klein Oros K, Nielsen TH, Ezponda T, Licht JD, Johnson NA, Assouline S, Cerchietti L, Miller WH, Mann KK. Increased protein processing gene signature in HDACi-resistant cells predicts response to proteasome inhibitors. Leuk Lymphoma 2016; 58:218-221. [PMID: 27185211 DOI: 10.1080/10428194.2016.1180684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Daphné Dupéré-Richer
- a Segal Cancer Center, Lady Davis Institute for Medical Research , McGill University , Montréal , QC , Canada
| | - Mena Kinal
- a Segal Cancer Center, Lady Davis Institute for Medical Research , McGill University , Montréal , QC , Canada
| | - Filippa Pettersson
- a Segal Cancer Center, Lady Davis Institute for Medical Research , McGill University , Montréal , QC , Canada
| | - Audrey Emond
- a Segal Cancer Center, Lady Davis Institute for Medical Research , McGill University , Montréal , QC , Canada
| | - M Nieves Calvo-Vidal
- b Division of Hematology and Oncology, Department of Medicine , Cornell University , New York , NY, USA
| | - Jessica N Nichol
- a Segal Cancer Center, Lady Davis Institute for Medical Research , McGill University , Montréal , QC , Canada
| | - Cynthia Guilbert
- a Segal Cancer Center, Lady Davis Institute for Medical Research , McGill University , Montréal , QC , Canada
| | - Dany Plourde
- a Segal Cancer Center, Lady Davis Institute for Medical Research , McGill University , Montréal , QC , Canada
| | - Kathleen Klein Oros
- a Segal Cancer Center, Lady Davis Institute for Medical Research , McGill University , Montréal , QC , Canada
| | - Torsten H Nielsen
- a Segal Cancer Center, Lady Davis Institute for Medical Research , McGill University , Montréal , QC , Canada
| | - Teresa Ezponda
- c Division of Hematology/Oncology , Robert. H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine , Chicago , IL, USA
| | - Jonathan D Licht
- c Division of Hematology/Oncology , Robert. H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine , Chicago , IL, USA
| | - Nathalie A Johnson
- a Segal Cancer Center, Lady Davis Institute for Medical Research , McGill University , Montréal , QC , Canada
| | - Sarit Assouline
- a Segal Cancer Center, Lady Davis Institute for Medical Research , McGill University , Montréal , QC , Canada
| | - Leandro Cerchietti
- b Division of Hematology and Oncology, Department of Medicine , Cornell University , New York , NY, USA
| | - Wilson H Miller
- a Segal Cancer Center, Lady Davis Institute for Medical Research , McGill University , Montréal , QC , Canada
| | - Koren K Mann
- a Segal Cancer Center, Lady Davis Institute for Medical Research , McGill University , Montréal , QC , Canada
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19
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van Doorn R, Slieker RC, Boonk SE, Zoutman WH, Goeman JJ, Bagot M, Michel L, Tensen CP, Willemze R, Heijmans BT, Vermeer MH. Epigenomic Analysis of Sézary Syndrome Defines Patterns of Aberrant DNA Methylation and Identifies Diagnostic Markers. J Invest Dermatol 2016; 136:1876-1884. [PMID: 27113428 DOI: 10.1016/j.jid.2016.03.042] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/09/2016] [Accepted: 03/29/2016] [Indexed: 11/28/2022]
Abstract
Sézary syndrome (Sz) is a malignancy of skin-homing CD4(+) memory T cells that is clinically characterized by erythroderma, lymphadenopathy, and blood involvement. Distinction of Sz from erythroderma secondary to inflammatory skin diseases (erythrodermic inflammatory dermatosis [EID]) is often challenging. Recent studies identified recurrent mutations in epigenetic enzymes involved in DNA modification in Sz. Here we defined the DNA methylomes of purified CD4(+) T cells from patients with Sz, EID, and healthy control subjects. Sz showed extensive global DNA methylation alterations, with 7.8% of 473,921 interrogated autosomal CpG sites showing hypomethylation and 3.2% hypermethylation. Promoter CpG islands were markedly enriched for hypermethylation. The 126 genes with recurrent promoter hypermethylation in Sz included multiple candidate tumor suppressors that showed transcriptional repression, implicating aberrant methylation in the pathogenesis of Sz. Validation in an independent sample set showed promoter hypermethylation of CMTM2, C2orf40, G0S2, HSPB6, PROM1, and PAM in 94-100% of Sz samples but not in EID samples. Notably, promoter hypermethylation of a single gene, the chemokine-like factor CMTM2, was sufficient to accurately distinguish Sz from EID in all cases. This study shows that Sz is characterized by widespread yet distinct DNA methylation alterations, which can be used clinically as epigenetic diagnostic markers.
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Affiliation(s)
- Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Roderick C Slieker
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Stéphanie E Boonk
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Willem H Zoutman
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jelle J Goeman
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Martine Bagot
- Institut National de la Santé et de la Recherche Médicale U976, Onco-Dermatology, Immunology and Cutaneous Stem Cells, Paris, France; University Paris Diderot, Sorbonne Paris Cité, Paris, France; Assistance Publique-Hôpitaux de Paris, Saint Louis Hospital, Department of Dermatology, Paris, France
| | - Laurence Michel
- Institut National de la Santé et de la Recherche Médicale U976, Onco-Dermatology, Immunology and Cutaneous Stem Cells, Paris, France; University Paris Diderot, Sorbonne Paris Cité, Paris, France; Assistance Publique-Hôpitaux de Paris, Saint Louis Hospital, Department of Dermatology, Paris, France
| | - Cornelis P Tensen
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rein Willemze
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Bas T Heijmans
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Maarten H Vermeer
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
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20
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Fernández-Rodríguez C, Salar A, Navarro A, Gimeno E, Pairet S, Camacho L, Ferraro M, Serrano S, Besses C, Bellosillo B, Sanchez-Gonzalez B. Anti-tumor activity of the combination of bendamustine with vorinostat in diffuse large B-cell lymphoma cells. Leuk Lymphoma 2016; 57:692-9. [DOI: 10.3109/10428194.2015.1063143] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
| | - Antonio Salar
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Servei d’Hematologia, Hospital del Mar, Barcelona, Spain
| | - Alfons Navarro
- Human Anatomy Unit, School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Eva Gimeno
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Servei d’Hematologia, Hospital del Mar, Barcelona, Spain
| | - Silvia Pairet
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | - Laura Camacho
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | | | - Sergi Serrano
- Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | - Carles Besses
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Servei d’Hematologia, Hospital del Mar, Barcelona, Spain
| | - Beatriz Bellosillo
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Servei de Patologia, Hospital del Mar, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Blanca Sanchez-Gonzalez
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Servei d’Hematologia, Hospital del Mar, Barcelona, Spain
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21
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Boi M, Gaudio E, Bonetti P, Kwee I, Bernasconi E, Tarantelli C, Rinaldi A, Testoni M, Cascione L, Ponzoni M, Mensah AA, Stathis A, Stussi G, Riveiro ME, Herait P, Inghirami G, Cvitkovic E, Zucca E, Bertoni F. The BET Bromodomain Inhibitor OTX015 Affects Pathogenetic Pathways in Preclinical B-cell Tumor Models and Synergizes with Targeted Drugs. Clin Cancer Res 2015; 21:1628-38. [PMID: 25623213 DOI: 10.1158/1078-0432.ccr-14-1561] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/19/2015] [Indexed: 12/19/2022]
Abstract
PURPOSE In cancer cells, the epigenome is often deregulated, and inhibition of the bromodomain and extra-terminal (BET) family of bromodomain-containing proteins is a novel epigenetic therapeutic approach. Preliminary results of an ongoing phase I trial have reported promising activity and tolerability with the new BET bromodomain inhibitor OTX015. EXPERIMENTAL DESIGN We assessed the preclinical activity of OTX015 as single agent and in combination in mature B-cell lymphoma models and performed in vitro and in vivo experiments to identify the mechanism of action and the genetic features associated with sensitivity to the compound. RESULTS OTX015 showed antiproliferative activity in a large panel of cell lines derived from mature B-cell lymphoid tumors with median IC50 of 240 nmol/L, without significant differences among the different histotypes. In vitro and in vivo experiments showed that OTX015 targeted NFKB/TLR/JAK/STAT signaling pathways, MYC- and E2F1-regulated genes, cell-cycle regulation, and chromatin structure. OTX015 presented in vitro synergism with several anticancer agents, especially with mTOR and BTK inhibitors. Gene expression signatures associated with different degrees of sensitivity to OTX015 were identified. Although OTX015 was mostly cytostatic, the compound induced apoptosis in a genetically defined subgroup of cells, derived from activated B-cell-like diffuse large B-cell lymphoma, bearing wtTP53, mutations in MYD88, and CD79B or CARD11. CONCLUSIONS Together with the data coming from the ongoing phase I study, the in vitro and in vivo data presented here provide the basis for further clinical investigation of OTX015 as single agent and in combination therapies.
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Affiliation(s)
- Michela Boi
- Lymphoma and Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland
| | - Eugenio Gaudio
- Lymphoma and Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland
| | - Paola Bonetti
- Lymphoma and Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland
| | - Ivo Kwee
- Lymphoma and Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland. Dalle Molle Institute for Artificial Intelligence (IDSIA), Manno, Switzerland. Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Elena Bernasconi
- Lymphoma and Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland
| | - Chiara Tarantelli
- Lymphoma and Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland
| | - Andrea Rinaldi
- Lymphoma and Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland
| | - Monica Testoni
- Lymphoma and Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland
| | - Luciano Cascione
- Lymphoma and Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland. IOSI Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Maurilio Ponzoni
- Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy
| | - Afua Adjeiwaa Mensah
- Lymphoma and Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland
| | - Anastasios Stathis
- IOSI Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Georg Stussi
- IOSI Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | | | | | - Giorgio Inghirami
- Department of Pathology and Center for Experimental Research and Medical Studies (CeRMS), University of Turin, Turin, Italy. Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York. Department of Pathology and NYU Cancer Center, New York University School of Medicine, New York, New York
| | - Esteban Cvitkovic
- OTD Oncology Therapeutic Development, Clichy, France. Oncoethix, Lausanne, Switzerland
| | - Emanuele Zucca
- IOSI Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Francesco Bertoni
- Lymphoma and Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland. IOSI Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.
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22
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DNA methylation profiling identifies two splenic marginal zone lymphoma subgroups with different clinical and genetic features. Blood 2015; 125:1922-31. [PMID: 25612624 DOI: 10.1182/blood-2014-08-596247] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Splenic marginal zone lymphoma is a rare lymphoma. Loss of 7q31 and somatic mutations affecting the NOTCH2 and KLF2 genes are the commonest genomic aberrations. Epigenetic changes can be pharmacologically reverted; therefore, identification of groups of patients with specific epigenomic alterations might have therapeutic relevance. Here we integrated genome-wide DNA-promoter methylation profiling with gene expression profiling, and clinical and biological variables. An unsupervised clustering analysis of a test series of 98 samples identified 2 clusters with different degrees of promoter methylation. The cluster comprising samples with higher-promoter methylation (High-M) had a poorer overall survival compared with the lower (Low-M) cluster. The prognostic relevance of the High-M phenotype was confirmed in an independent validation set of 36 patients. In the whole series, the High-M phenotype was associated with IGHV1-02 usage, mutations of NOTCH2 gene, 7q31-32 loss, and histologic transformation. In the High-M set, a number of tumor-suppressor genes were methylated and repressed. PRC2 subunit genes and several prosurvival lymphoma genes were unmethylated and overexpressed. A model based on the methylation of 3 genes (CACNB2, HTRA1, KLF4) identified a poorer-outcome patient subset. Exposure of splenic marginal zone lymphoma cell lines to a demethylating agent caused partial reversion of the High-M phenotype and inhibition of proliferation.
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23
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Abstract
The pathogenesis of diffuse large B-cell lymphoma (DLBCL) is strongly linked to perturbation of epigenetic mechanisms. The germinal center (GC) B cells from which DLBCLs arise are prone to instability in their cytosine methylation patterns. DLBCLs inherit this epigenetic instability and display variable degrees of epigenetic heterogeneity. Greater epigenetic heterogeneity is linked with poor clinical outcome. Somatic mutations of histone-modifying proteins have also emerged as a hallmark of DLBCL. The effect of these somatic mutations may be to disrupt epigenetic switches that control the GC phenotype and "lock in" certain oncogenic features of GC B cells, resulting in malignant transformation. DNA methyltransferase and histone methyltransferase inhibitors are emerging as viable therapeutic approaches to erase aberrant epigenetic programming, suppress DLBCL growth, and overcome chemotherapy resistance. This review will discuss these recent advances and their therapeutic implications.
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Affiliation(s)
- Yanwen Jiang
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Ari Melnick
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA.
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24
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Libby EN, Becker PS, Burwick N, Green DJ, Holmberg L, Bensinger WI. Panobinostat: a review of trial results and future prospects in multiple myeloma. Expert Rev Hematol 2014; 8:9-18. [PMID: 25410127 DOI: 10.1586/17474086.2015.983065] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Multiple myeloma is an incurable often devastating disease that is responsible for 1-2% of all cancers. Multiple myeloma is the second most common hematologic malignancy. Over the past two decades, advances in therapy have doubled life expectancy. Unfortunately, all patients ultimately relapse. Novel agents (immunomodulatory drugs and proteasome inhibitors) have changed the outlook for patients, but further breakthroughs are needed. Epigenetic treatments offer potential for advancing therapy by modifying oncogene responses. The acetylation status of various proteins can affect the availability of chromatin for transcription. This response may be modulated epigenetically to advantage using histone deacetylase inhibitors like panobinostat.
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Affiliation(s)
- Edward N Libby
- University of Washington School of Medicine - Medical Oncology, 825 Eastlake Ave E, Seattle, WA 98109, USA
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25
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Zhao X, Yang F, Li S, Liu M, Ying S, Jia X, Wang X. CpG island methylator phenotype of myelodysplastic syndrome identified through genome-wide profiling of DNA methylation and gene expression. Br J Haematol 2014; 165:649-58. [PMID: 24601943 DOI: 10.1111/bjh.12811] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 01/10/2014] [Indexed: 12/13/2022]
Abstract
The CpG island methylator phenotype (CIMP) is an epigenetic phenomenon and plays an important role in tumourigenesis in various cancers. The identification of aberrant DNA methylation can be exploited for early diagnosis and risk assessment of patients. We identified a CIMP in myelodysplastic syndrome (MDS). Genes were screened for hypermethylation and transcription downregulation through genome-wide DNA methylation profiling and gene expression microarrays. Methylation-specific, real-time, and bisulfite-sequencing polymerase chain reaction were performed to validate selected genes. The hypermethylation of genes as a diagnostic tool for the detection of MDS was evaluated. Kaplan-Meier survival analysis and Cox regression were performed. A draft of an MDS CIMP was established and revised to 6 genes after validation in 20 patients and 20 controls. Further large-scale analysis showed that the majority of 211 MDS patients were hypermethylated in 6 genes. The area under the curve of CIMP was 0·9768 (95% confidence interval 0·9609-0·9928). A combination of 5 or more of the methylated genes showed a specificity of 95% and sensitivity of 91% for the diagnosis of MDS. We found CIMP positivity to be a significantly unfavourable prognostic factor for MDS. These results indicate that the newly established CIMP may improve diagnostic accuracy and prognosis assessment in MDS.
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Affiliation(s)
- Xiaoli Zhao
- Department of Haematology, Huashan Hospital, Fudan University, Shanghai, China
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26
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Humphries LA, Godbersen JC, Danilova OV, Kaur P, Christensen BC, Danilov AV. Pro-apoptotic TP53 homolog TAp63 is repressed via epigenetic silencing and B-cell receptor signalling in chronic lymphocytic leukaemia. Br J Haematol 2013; 163:590-602. [PMID: 24117128 DOI: 10.1111/bjh.12580] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 08/21/2013] [Indexed: 02/05/2023]
Abstract
Chronic lymphocytic leukaemia (CLL) is an accumulative disorder marked by deficient apoptosis. The TP53 homolog TAp63 promotes apoptosis and chemosensitivity in solid tumours and its deregulation may contribute to CLL cell survival. We found that TAp63α was the most prevalent TP63 isoform in CLL. Compared to healthy B cells, TAp63 mRNA was repressed in 55·7% of CLL samples. TP63 promoter methylation was high in CLL and inversely correlated with TP63 protein expression in B-cell lymphoma cell lines. siRNA-mediated knockdown of TP63 resulted in partial protection from spontaneous apoptosis accompanied by reductions in PMAIP1 (NOXA), BBC3 (PUMA), and BAX mRNA in CLL cells and increased proliferation of Raji lymphoma cells. TAp63 mRNA levels were higher in CLL with unmutated IGHV. B-cell receptor (BCR) engagement led to repression of TP63 mRNA expression in malignant B cells, while pharmacological inhibition of BCR signalling prevented TP63 downregulation. MIR21, known to target TAp63, correlated inversely with TAp63 expression in CLL, and BCR-mediated downregulation of TP63 was accompanied by MIR21 upregulation in most CLL samples. Our data illustrate the pro-apoptotic function of TP63, provide insights into the mechanisms of BCR-targeting agents, and establish a rationale for designing novel approaches to induce TP63 in CLL and B-cell lymphoma.
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Abstract
Genetic analysis of hematologic malignancies over the past 5 years has revealed abundant mutations in epigenetic regulators in all classes of disorders. Here, we summarize the observations made within our review series on the role of epigenetics in hematology. We highlight the clinical implications of mutations in epigenetic regulators and outline what we envision are some of the major areas that merit future research. Recent findings may have immediate prognostic value, but also offer new targets for drug development. However, the pleiotropic action of these regulators indicates caution is warranted and argues for investment in understanding of their underlying mechanisms of action as we proceed to exploit these findings for the benefit of patients.
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