51
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The Role of Nucleosomes in Epigenetic Gene Regulation. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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52
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Abstract
Immunoglobulin (IG) gene remodeling by V(D)J recombination plays a central role in the generation of normal B cells, and somatic hypermutation and class switching of IG genes are key processes during antigen-driven B cell differentiation. However, errors of these processes are involved in the development of B cell lymphomas. IG locus-associated translocations of proto-oncogenes are a hallmark of many B cell malignancies. Additional transforming events include inactivating mutations in various tumor suppressor genes and also latent infection of B cells with viruses, such as Epstein-Barr virus. Many B cell lymphomas require B cell antigen receptor expression, and in several instances, chronic antigenic stimulation plays a role in lymphoma development and/or sustaining tumor growth. Often, survival and proliferation signals provided by other cells in the microenvironment are a further critical factor in lymphoma development and pathophysiology. Many B cell malignancies derive from germinal center B cells, most likely because of the high proliferation rate of these cells and the high activity of mutagenic processes.
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53
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Vogt J, Wagener R, Montesinos-Rongen M, Ammerpohl O, Paulus W, Deckert M, Siebert R. Array-based profiling of the lymphoma cell DNA methylome does not unequivocally distinguish primary lymphomas of the central nervous system from non-CNS diffuse large B-cell lymphomas. Genes Chromosomes Cancer 2018; 58:66-69. [PMID: 30284345 DOI: 10.1002/gcc.22687] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/25/2018] [Accepted: 09/25/2018] [Indexed: 02/02/2023] Open
Abstract
Primary lymphomas of the central nervous system (PCNSL) are diffuse large B-cell lymphomas (DLBCLs) confined to the central nervous system (CNS). We here performed array-based DNA methylation analyses of 26 PCNSL and 78 DLBCL and validated our findings in an independent dataset. We identified 2847 CpGs differentially methylated between PCNSL and non-CNS-DLBCL. Neither a supervised analysis using these CpGs nor application of 3 CpG classifiers selected for class separation unambiguously separated PCNSL from non-CNS-DLBCL. Remarkably, 6/78 non-CNS-DLBCL consistently segregated with PCNSL, which displayed molecular features typical for PCNSL. Our findings suggest that a subset of non-CNS-DLBCL exists which molecularly resembles PCNSL.
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Affiliation(s)
- Julia Vogt
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Rabea Wagener
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Martina Deckert
- Institute of Neuropathology, University Hospital of Cologne, Cologne, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
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54
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Desmots F, Roussel M, Pangault C, Llamas-Gutierrez F, Pastoret C, Guiheneuf E, Le Priol J, Camara-Clayette V, Caron G, Henry C, Belaud-Rotureau MA, Godmer P, Lamy T, Jardin F, Tarte K, Ribrag V, Fest T. Pan-HDAC Inhibitors Restore PRDM1 Response to IL21 in CREBBP-Mutated Follicular Lymphoma. Clin Cancer Res 2018; 25:735-746. [DOI: 10.1158/1078-0432.ccr-18-1153] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/26/2018] [Accepted: 10/17/2018] [Indexed: 11/16/2022]
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55
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Ma KF, Zhang QX, Cheng TR, Yan XL, Pan HT, Wang J. Substantial Epigenetic Variation Causing Flower Color Chimerism in the Ornamental Tree Prunus mume Revealed by Single Base Resolution Methylome Detection and Transcriptome Sequencing. Int J Mol Sci 2018; 19:E2315. [PMID: 30087265 PMCID: PMC6121637 DOI: 10.3390/ijms19082315] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/29/2018] [Accepted: 08/02/2018] [Indexed: 01/03/2023] Open
Abstract
Epigenetic changes caused by methylcytosine modification participate in gene regulation and transposable element (TE) repression, resulting in phenotypic variation. Although the effects of DNA methylation and TE repression on flower, fruit, seed coat, and leaf pigmentation have been investigated, little is known about the relationship between methylation and flower color chimerism. In this study, we used a comparative methylomic⁻transcriptomic approach to explore the molecular mechanism responsible for chimeric flowers in Prunus mume "Danban Tiaozhi". High-performance liquid chromatography-electrospray ionization mass spectrometry revealed that the variation in white (WT) and red (RT) petal tissues in this species is directly due to the accumulation of anthocyanins, i.e., cyanidin 3,5-O-diglucoside, cyanidin 3-O-glucoside, and peonidin 3-O-glucoside. We next mapped the first-ever generated methylomes of P. mume, and found that 11.29⁻14.83% of the genomic cytosine sites were methylated. We also determined that gene expression was negatively correlated with methylcytosine level in general, and uncovered significant epigenetic variation between WT and RT. Furthermore, we detected differentially methylated regions (DMRs) and DMR-related genes between WT and RT, and concluded that many of these genes, including differentially expressed genes (DEGs) and transcription factor genes, are critical participants in the anthocyanin regulatory pathway. Importantly, some of the associated DEGs harbored TE insertions that were also modified by methylcytosine. The above evidence suggest that flower color chimerism in P. mume is induced by the DNA methylation of critical genes and TEs.
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Affiliation(s)
- Kai-Feng Ma
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
| | - Qi-Xiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
| | - Tang-Ren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
| | - Xiao-Lan Yan
- Mei Research Center of China, Wuhan 430074, China.
| | - Hui-Tang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
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56
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Shen L, Zhu J, Robert Li SY, Fan X. Detect differentially methylated regions using non-homogeneous hidden Markov model for methylation array data. Bioinformatics 2018; 33:3701-3708. [PMID: 29036320 DOI: 10.1093/bioinformatics/btx467] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 07/18/2017] [Indexed: 12/12/2022] Open
Abstract
Motivation DNA methylation is an important epigenetic mechanism in gene regulation and the detection of differentially methylated regions (DMRs) is enthralling for many disease studies. There are several aspects that we can improve over existing DMR detection methods: (i) methylation statuses of nearby CpG sites are highly correlated, but this fact has seldom been modelled rigorously due to the uneven spacing; (ii) it is practically important to be able to handle both paired and unpaired samples; and (iii) the capability to detect DMRs from a single pair of samples is demanded. Results We present DMRMark (DMR detection based on non-homogeneous hidden Markov model), a novel Bayesian framework for detecting DMRs from methylation array data. It combines the constrained Gaussian mixture model that incorporates the biological knowledge with the non-homogeneous hidden Markov model that models spatial correlation. Unlike existing methods, our DMR detection is achieved without predefined boundaries or decision windows. Furthermore, our method can detect DMRs from a single pair of samples and can also incorporate unpaired samples. Both simulation studies and real datasets from The Cancer Genome Atlas showed the significant improvement of DMRMark over other methods. Availability and implementation DMRMark is freely available as an R package at the CRAN R package repository. Contact xfan@cuhk.edu.hk. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Linghao Shen
- Department of Information Engineering, The Chinese University of Hong Kong, Hong Kong
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York University, New York, NY, USA
| | - Shuo-Yen Robert Li
- University of Electronic Science and Technology of China, Sichuan, China
| | - Xiaodan Fan
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong
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57
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Insight into origins, mechanisms, and utility of DNA methylation in B-cell malignancies. Blood 2018; 132:999-1006. [PMID: 30037886 DOI: 10.1182/blood-2018-02-692970] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/15/2018] [Indexed: 12/12/2022] Open
Abstract
Understanding how tumor cells fundamentally alter their identity is critical to identify specific vulnerabilities for use in precision medicine. In B-cell malignancy, knowledge of genetic changes has resulted in great gains in our understanding of the biology of tumor cells, impacting diagnosis, prognosis, and treatment. Despite this knowledge, much remains to be explained as genetic events do not completely explain clinical behavior and outcomes. Many patients lack recurrent driver mutations, and said drivers can persist in nonmalignant cells of healthy individuals remaining cancer-free for decades. Epigenetics has emerged as a valuable avenue to further explain tumor phenotypes. The epigenetic landscape is the software that powers and stabilizes cellular identity by abridging a broad genome into the essential information required per cell. A genome-level view of B-cell malignancies reveals complex but recurrent epigenetic patterns that define tumor types and subtypes, permitting high-resolution classification and novel insight into tumor-specific mechanisms. Epigenetic alterations are guided by distinct cellular processes, such as polycomb-based silencing, transcription, signaling pathways, and transcription factor activity, and involve B-cell-specific aspects, such as activation-induced cytidine deaminase activity and germinal center-specific events. Armed with a detailed knowledge of the epigenetic events that occur across the spectrum of B-cell differentiation, B-cell tumor-specific aberrations can be detected with improved accuracy and serve as a model for identification of tumor-specific events in cancer. Insight gained through recent efforts may prove valuable in guiding the use of both epigenetic- and nonepigenetic-based therapies.
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58
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Nair SS, Luu PL, Qu W, Maddugoda M, Huschtscha L, Reddel R, Chenevix-Trench G, Toso M, Kench JG, Horvath LG, Hayes VM, Stricker PD, Hughes TP, White DL, Rasko JEJ, Wong JJL, Clark SJ. Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten. Epigenetics Chromatin 2018; 11:24. [PMID: 29807544 PMCID: PMC5971424 DOI: 10.1186/s13072-018-0194-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/21/2018] [Indexed: 12/24/2022] Open
Abstract
Background Comprehensive genome-wide DNA methylation profiling is critical to gain insights into epigenetic reprogramming during development and disease processes. Among the different genome-wide DNA methylation technologies, whole genome bisulphite sequencing (WGBS) is considered the gold standard for assaying genome-wide DNA methylation at single base resolution. However, the high sequencing cost to achieve the optimal depth of coverage limits its application in both basic and clinical research. To achieve 15× coverage of the human methylome, using WGBS, requires approximately three lanes of 100-bp-paired-end Illumina HiSeq 2500 sequencing. It is important, therefore, for advances in sequencing technologies to be developed to enable cost-effective high-coverage sequencing. Results In this study, we provide an optimised WGBS methodology, from library preparation to sequencing and data processing, to enable 16–20× genome-wide coverage per single lane of HiSeq X Ten, HCS 3.3.76. To process and analyse the data, we developed a WGBS pipeline (METH10X) that is fast and can call SNPs. We performed WGBS on both high-quality intact DNA and degraded DNA from formalin-fixed paraffin-embedded tissue. First, we compared different library preparation methods on the HiSeq 2500 platform to identify the best method for sequencing on the HiSeq X Ten. Second, we optimised the PhiX and genome spike-ins to achieve higher quality and coverage of WGBS data on the HiSeq X Ten. Third, we performed integrated whole genome sequencing (WGS) and WGBS of the same DNA sample in a single lane of HiSeq X Ten to improve data output. Finally, we compared methylation data from the HiSeq 2500 and HiSeq X Ten and found high concordance (Pearson r > 0.9×). Conclusions Together we provide a systematic, efficient and complete approach to perform and analyse WGBS on the HiSeq X Ten. Our protocol allows for large-scale WGBS studies at reasonable processing time and cost on the HiSeq X Ten platform. Electronic supplementary material The online version of this article (10.1186/s13072-018-0194-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shalima S Nair
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Phuc-Loi Luu
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Wenjia Qu
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Madhavi Maddugoda
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Lily Huschtscha
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Roger Reddel
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | | | | | - James G Kench
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Lisa G Horvath
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia.,Clinical Prostate Cancer Research, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Chris O'Brien Lifehouse, Camperdown, NSW, Australia
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Phillip D Stricker
- Department of Urology, St. Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Timothy P Hughes
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,Australian Leukaemia and Lymphoma Group, Melbourne, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia.,Department of Haematology, SA Pathology, Adelaide, SA, Australia
| | - Deborah L White
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,Australian Leukaemia and Lymphoma Group, Melbourne, Australia.,Faculty of Health Science and Faculty of Science, University of Adelaide, Adelaide, SA, Australia.,Australian Genomic Health Alliance, Melbourne, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, Australia
| | - Justin J-L Wong
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Susan J Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia. .,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia. .,Epigenetics Research Program, The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW, 2010, Australia.
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59
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Critical influences on the pathogenesis of follicular lymphoma. Blood 2018; 131:2297-2306. [PMID: 29666116 DOI: 10.1182/blood-2017-11-764365] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/28/2017] [Indexed: 12/15/2022] Open
Abstract
The development of follicular lymphoma (FL) from a founder B cell with an upregulation of B-cell lymphoma 2 (BCL2), via the t(14;18) translocation, to a proliferating clone, poised to undergo further transformation to an aggressive lymphoma, illustrates the opportunistic Darwinian process of tumorigenesis. Protection against apoptosis allows an innocent cell to persist and divide, with dangerous accumulation of further mutational changes, commonly involving inactivation of chromatin-modifying genes. But this is not all. FL cells reflect normal B cells in relying on expression of surface immunoglobulin. In doing so, they add another supportive mechanism by exploiting the natural process of somatic hypermutation of the IGV genes. Positive selection of motifs for addition of glycan into the antigen-binding sites of virtually all cases, and the placement of unusual mannoses in those sites, reveals a posttranslational strategy to engage the microenvironment. A bridge between mannosylated surface immunoglobulin of FL cells and macrophage-expressed dendritic cell-specific ICAM-3-grabbing nonintegrin produces a persistent low-level signal that appears essential for life in the hostile germinal center. Early-stage FL therefore requires a triad of changes: protection from apoptosis, mutations in chromatin modifiers, and an ability to interact with lectin-expressing macrophages. These changes are common and persistent. Genetic/epigenetic analysis is providing important data but investigation of the posttranslational landscape is the next challenge. We have one glimpse of its operation via the influence of added glycan on the B-cell receptor of FL. The consequential interaction with environmental lectins illustrates how posttranslational modifications can be exploited by tumor cells, and could lead to new approaches to therapy.
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60
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Pidsley R, Lawrence MG, Zotenko E, Niranjan B, Statham A, Song J, Chabanon RM, Qu W, Wang H, Richards M, Nair SS, Armstrong NJ, Nim HT, Papargiris M, Balanathan P, French H, Peters T, Norden S, Ryan A, Pedersen J, Kench J, Daly RJ, Horvath LG, Stricker P, Frydenberg M, Taylor RA, Stirzaker C, Risbridger GP, Clark SJ. Enduring epigenetic landmarks define the cancer microenvironment. Genome Res 2018; 28:625-638. [PMID: 29650553 PMCID: PMC5932604 DOI: 10.1101/gr.229070.117] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 03/27/2018] [Indexed: 12/21/2022]
Abstract
The growth and progression of solid tumors involves dynamic cross-talk between cancer epithelium and the surrounding microenvironment. To date, molecular profiling has largely been restricted to the epithelial component of tumors; therefore, features underpinning the persistent protumorigenic phenotype of the tumor microenvironment are unknown. Using whole-genome bisulfite sequencing, we show for the first time that cancer-associated fibroblasts (CAFs) from localized prostate cancer display remarkably distinct and enduring genome-wide changes in DNA methylation, significantly at enhancers and promoters, compared to nonmalignant prostate fibroblasts (NPFs). Differentially methylated regions associated with changes in gene expression have cancer-related functions and accurately distinguish CAFs from NPFs. Remarkably, a subset of changes is shared with prostate cancer epithelial cells, revealing the new concept of tumor-specific epigenome modifications in the tumor and its microenvironment. The distinct methylome of CAFs provides a novel epigenetic hallmark of the cancer microenvironment and promises new biomarkers to improve interpretation of diagnostic samples.
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Affiliation(s)
- Ruth Pidsley
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales 2010, Australia.,St. Vincent's Clinical School, UNSW Sydney, New South Wales 2052, Australia
| | - Mitchell G Lawrence
- Prostate Research Group, Cancer Program-Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Victoria 3800, Australia.,Prostate Cancer Translational Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Elena Zotenko
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales 2010, Australia.,St. Vincent's Clinical School, UNSW Sydney, New South Wales 2052, Australia
| | - Birunthi Niranjan
- Prostate Research Group, Cancer Program-Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Victoria 3800, Australia
| | - Aaron Statham
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Jenny Song
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Roman M Chabanon
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Wenjia Qu
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Hong Wang
- Prostate Research Group, Cancer Program-Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Victoria 3800, Australia
| | - Michelle Richards
- Prostate Research Group, Cancer Program-Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Victoria 3800, Australia
| | - Shalima S Nair
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales 2010, Australia.,St. Vincent's Clinical School, UNSW Sydney, New South Wales 2052, Australia
| | - Nicola J Armstrong
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales 2010, Australia.,Mathematics and Statistics, Murdoch University, Perth, Western Australia 6150, Australia
| | - Hieu T Nim
- Prostate Research Group, Cancer Program-Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Victoria 3800, Australia.,Faculty of Information Technology, Monash University, Clayton, Victoria 3800, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Melissa Papargiris
- Prostate Research Group, Cancer Program-Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Victoria 3800, Australia
| | - Preetika Balanathan
- Prostate Research Group, Cancer Program-Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Victoria 3800, Australia
| | - Hugh French
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Timothy Peters
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Sam Norden
- Tissupath Pathology, Mount Waverley, Victoria 3149, Australia
| | - Andrew Ryan
- Tissupath Pathology, Mount Waverley, Victoria 3149, Australia
| | - John Pedersen
- Prostate Research Group, Cancer Program-Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Victoria 3800, Australia.,Tissupath Pathology, Mount Waverley, Victoria 3149, Australia
| | - James Kench
- Cancer Research Division, Garvan Institute of Medical Research/The Kinghorn Cancer Centre, Darlinghurst, New South Wales 2010, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, Sydney, New South Wales 2050, Australia
| | - Roger J Daly
- Signalling Network Laboratory, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Victoria 3800, Australia
| | - Lisa G Horvath
- Cancer Research Division, Garvan Institute of Medical Research/The Kinghorn Cancer Centre, Darlinghurst, New South Wales 2010, Australia.,Chris O'Brien Lifehouse, Missenden Road, Camperdown, New South Wales 2050, Australia.,University of Sydney, Sydney, New South Wales 2050, Australia
| | - Phillip Stricker
- Cancer Research Division, Garvan Institute of Medical Research/The Kinghorn Cancer Centre, Darlinghurst, New South Wales 2010, Australia.,Department of Urology, St. Vincent's Prostate Cancer Centre, Sydney, New South Wales 2050, Australia
| | - Mark Frydenberg
- Prostate Research Group, Cancer Program-Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Victoria 3800, Australia
| | - Renea A Taylor
- Prostate Cancer Translational Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,Prostate Research Group, Cancer Program-Biomedicine Discovery Institute Department of Physiology, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Melbourne, Victoria 3800, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales 2010, Australia.,St. Vincent's Clinical School, UNSW Sydney, New South Wales 2052, Australia
| | - Gail P Risbridger
- Prostate Research Group, Cancer Program-Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash Partners Comprehensive Cancer Consortium, Monash University, Clayton, Victoria 3800, Australia.,Prostate Cancer Translational Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales 2010, Australia.,St. Vincent's Clinical School, UNSW Sydney, New South Wales 2052, Australia
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61
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Huet S, Sujobert P, Salles G. From genetics to the clinic: a translational perspective on follicular lymphoma. Nat Rev Cancer 2018; 18:224-239. [PMID: 29422597 DOI: 10.1038/nrc.2017.127] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Follicular lymphoma (FL) is the most frequent indolent B cell lymphoma and is still considered to be incurable. In recent years, whole-exome sequencing studies of large cohorts of patients have greatly improved our knowledge of the FL mutational landscape. Moreover, the prolonged evolution of this disease has enabled some insights regarding the early pre-lymphoma lesions as well as the clonal evolution after treatment, allowing an evolutionary perspective on lymphomagenesis. Deciphering the earliest initiating lesions and identifying the molecular alterations leading to disease progression currently represent important goals; accomplishing these could help identify the most relevant targets for precision therapy.
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Affiliation(s)
- Sarah Huet
- Cancer Research Center of Lyon, INSERM 1052 CNRS5286, 'Clinical and experimental models of lymphomagenesis' Team, Equipe labellisée Ligue Contre le Cancer Oullins, France
- Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, 165 chemin du Grand Revoyet, Pierre Bénite 69495, France
- Université Lyon-1, ISPB-Faculté de Pharmacie de Lyon, Lyon, France
| | - Pierre Sujobert
- Cancer Research Center of Lyon, INSERM 1052 CNRS5286, 'Clinical and experimental models of lymphomagenesis' Team, Equipe labellisée Ligue Contre le Cancer Oullins, France
- Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, 165 chemin du Grand Revoyet, Pierre Bénite 69495, France
- Université Lyon-1, Faculté de Médecine et de Maïeutique Lyon-Sud Charles Mérieux, Oullins, France
| | - Gilles Salles
- Cancer Research Center of Lyon, INSERM 1052 CNRS5286, 'Clinical and experimental models of lymphomagenesis' Team, Equipe labellisée Ligue Contre le Cancer Oullins, France
- Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, 165 chemin du Grand Revoyet, Pierre Bénite 69495, France
- Université Lyon-1, Faculté de Médecine et de Maïeutique Lyon-Sud Charles Mérieux, Oullins, France
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62
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Miousse IR, Ewing LE, Kutanzi KR, Griffin RJ, Koturbash I. DNA Methylation in Radiation-Induced Carcinogenesis: Experimental Evidence and Clinical Perspectives. Crit Rev Oncog 2018; 23:1-11. [PMID: 29953365 PMCID: PMC6369919 DOI: 10.1615/critrevoncog.2018025687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ionizing radiation is a valuable tool in many spheres of human life. At the same time, it is a genotoxic agent with a well-established carcinogenic potential. Progress achieved in the last two decades has demonstrated convincingly that ionizing radiation can also target the cellular epigenome. Epigenetics is defined as heritable changes in the expression of genes that are not due to alterations of DNA sequence but consist of specific covalent modifications of chromatin components, such as methylation of DNA, histone modifications, and control performed by non-coding RNAs. Accumulating evidence suggests that DNA methylation, a key epigenetic mechanism involved in the control of expression of genetic information, may serve as one of the driving mechanisms of radiation-induced carcinogenesis. Here, we review the literature on the effects of ionizing radiation on DNA methylation in various biological systems, discuss the role of DNA methylation in radiation carcinogenesis, and provide our opinion on the potential utilization of this knowledge in radiation oncology.
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Affiliation(s)
- Isabelle R. Miousse
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Laura E. Ewing
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Kristy R. Kutanzi
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Robert J. Griffin
- Department of Radiation Oncology, Radiation Biology Division, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Igor Koturbash
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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63
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Oduor CI, Kaymaz Y, Chelimo K, Otieno JA, Ong’echa JM, Moormann AM, Bailey JA. Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma. BMC Cancer 2017; 17:761. [PMID: 29132323 PMCID: PMC5683570 DOI: 10.1186/s12885-017-3711-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 10/30/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Burkitt lymphoma (BL) is characterized by overexpression of the c-myc oncogene, which in the vast majority of cases is a consequence of an IGH/MYC translocation. While myc is the seminal event, BL is a complex amalgam of genetic and epigenetic changes causing dysregulation of both coding and non-coding transcripts. Emerging evidence suggest that abnormal modulation of mRNA transcription via miRNAs might be a significant factor in lymphomagenesis. However, the alterations in these miRNAs and their correlations to their putative mRNA targets have not been extensively studied relative to normal germinal center (GC) B cells. METHODS Using more sensitive and specific transcriptome deep sequencing, we compared previously published small miRNA and long mRNA of a set of GC B cells and eBL tumors. MiRWalk2.0 was used to identify the validated target genes for the deregulated miRNAs, which would be important for understanding the regulatory networks associated with eBL development. RESULTS We found 211 differentially expressed (DE) genes (79 upregulated and 132 downregulated) and 49 DE miRNAs (22 up-regulated and 27 down-regulated). Gene Set enrichment analysis identified the enrichment of a set of MYC regulated genes. Network propagation-based method and correlated miRNA-mRNA expression analysis identified dysregulated miRNAs, including miR-17~95 cluster members and their target genes, which have diverse oncogenic properties to be critical to eBL lymphomagenesis. Central to all these findings, we observed the downregulation of ATM and NLK genes, which represent important regulators in response to DNA damage in eBL tumor cells. These tumor suppressors were targeted by multiple upregulated miRNAs (miR-19b-3p, miR-26a-5p, miR-30b-5p, miR-92a-5p and miR-27b-3p) which could account for their aberrant expression in eBL. CONCLUSION Combined loss of p53 induction and function due to miRNA-mediated regulation of ATM and NLK, together with the upregulation of TFAP4, may be a central role for human miRNAs in eBL oncogenesis. This facilitates survival of eBL tumor cells with the IGH/MYC chromosomal translocation and promotes MYC-induced cell cycle progression, initiating eBL lymphomagenesis. This characterization of miRNA-mRNA interactions in eBL relative to GC B cells provides new insights on miRNA-mediated transcript regulation in eBL, which are potentially useful for new improved therapeutic strategies.
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Affiliation(s)
- Cliff I. Oduor
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Yasin Kaymaz
- Department of Bioinformatics & Integrative Biology, University of Massachusetts Medical School, Worcester, MA USA
| | - Kiprotich Chelimo
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Juliana A. Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Ministry of Health, Kisumu, Kenya
| | | | - Ann M. Moormann
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA USA
| | - Jeffrey A. Bailey
- Department of Bioinformatics & Integrative Biology, University of Massachusetts Medical School, Worcester, MA USA
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, 368 Plantation St. Albert Sherman Building 41077, Worcester, MA 01605 USA
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64
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Pathogenesis of follicular lymphoma. Best Pract Res Clin Haematol 2017; 31:2-14. [PMID: 29452662 DOI: 10.1016/j.beha.2017.10.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/23/2017] [Indexed: 12/21/2022]
Abstract
Follicular lymphoma (FL) is presented as a germinal centre B cell lymphoma that is characterized by an indolent clinical course, but remains - paradoxically - largely incurable to date. The last years have seen significant progress in our understanding of FL lymphomagenesis, which is a multi-step process beginning in the bone marrow with the hallmark t(14;18)(q32;q21) translocation. The pathobiology of FL is complex and combines broad somatic changes at the level of both the genome and the epigenome, the latter evidenced by highly recurrent mutations in chromatin-modifying genes such as KMT2D and CREBBP. While the importance of the FL microenvironment has since long been well understood, it has become evident that somatic lesions within tumour cells re-educate normal immune and stromal cells to their advantage. Enhanced understanding of FL pathogenesis is currently leading to refined therapeutic targeting of perturbed biology, paving the way for precision medicine in this lymphoma subtype.
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65
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Shosaku J. Genome-wide DNA methylation analysis of senescence in repetitively infected memory cytotoxic T lymphocytes. Immunology 2017; 153:253-267. [PMID: 28898397 DOI: 10.1111/imm.12840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/21/2017] [Accepted: 09/06/2017] [Indexed: 02/06/2023] Open
Abstract
The immune system including antigen-specific CD8 T cells, which are cytotoxic T lymphocytes (CTLs), can acquire the potential for more effective elimination of the pathogen at re-infection. As memory CTLs could exert protective immunity after the next response, we aimed to elucidate the substantial change of repetitively infected memory CTLs. Currently, DNA methylation status in repetitively infected memory CTLs is unknown, so we performed next-generation sequencing to evaluate methylation status and transcriptional regulation of naive, primary and secondary memory CD8 T cells on the basis of transcription start sites (TSS). Notably, total CpG sites in the entire regions of all genes were significantly unmethylated in primary memory CTLs (young memory CTLs) and even more unmethylated in secondary memory CTLs (old memory CTLs). However, total proximal regions from TSS, which cover transcriptional promoters, were steadily methylated with repeated infections. In contrast, distal regions from TSS, which are the majority of entire regions and include transcriptional enhancers, were extensively unmethylated by infections. In association between transcriptional and methylation changes, accompanied by genes characteristic of the immune response, natural killer cell signature genes, known to be expressed in senescent CD8 T cells, were transcriptionally up-regulated and unmethylated in young memory CTLs, and more so in old memory CTLs, whereas ribosomal proteins were transcriptionally down-regulated and methylated in proximal region from the TSS by infections. Our results suggest that epigenetically augmented enhancers and suppressed promoters, which could consequently lead to global decline of transcription and translation, could represent the senescence of memory CTLs.
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Affiliation(s)
- Jumpei Shosaku
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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66
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Glaser LV, Rieger S, Thumann S, Beer S, Kuklik-Roos C, Martin DE, Maier KC, Harth-Hertle ML, Grüning B, Backofen R, Krebs S, Blum H, Zimmer R, Erhard F, Kempkes B. EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells. PLoS Pathog 2017; 13:e1006664. [PMID: 28968461 PMCID: PMC5638620 DOI: 10.1371/journal.ppat.1006664] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 10/12/2017] [Accepted: 09/22/2017] [Indexed: 12/26/2022] Open
Abstract
Epstein-Barr virus (EBV) infection converts resting human B cells into permanently proliferating lymphoblastoid cell lines (LCLs). The Epstein-Barr virus nuclear antigen 2 (EBNA2) plays a key role in this process. It preferentially binds to B cell enhancers and establishes a specific viral and cellular gene expression program in LCLs. The cellular DNA binding factor CBF1/CSL serves as a sequence specific chromatin anchor for EBNA2. The ubiquitous expression of this highly conserved protein raises the question whether additional cellular factors might determine EBNA2 chromatin binding selectively in B cells. Here we used CBF1 deficient B cells to identify cellular genes up or downregulated by EBNA2 as well as CBF1 independent EBNA2 chromatin binding sites. Apparently, CBF1 independent EBNA2 target genes and chromatin binding sites can be identified but are less frequent than CBF1 dependent EBNA2 functions. CBF1 independent EBNA2 binding sites are highly enriched for EBF1 binding motifs. We show that EBNA2 binds to EBF1 via its N-terminal domain. CBF1 proficient and deficient B cells require EBF1 to bind to CBF1 independent binding sites. Our results identify EBF1 as a co-factor of EBNA2 which conveys B cell specificity to EBNA2. Epstein-Barr virus (EBV) infection is closely linked to cancer development. At particular risk are immunocompromised individuals like post-transplant patients which can develop B cell lymphomas. In healthy individuals EBV preferentially infects B cells and establishes a latent infection without causing apparent clinical symptoms in most cases. Upon infection, Epstein-Barr virus nuclear antigen 2 (EBNA2) initiates a B cell specific gene expression program that causes activation and proliferation of the infected cells. EBNA2 is a transcription factor well known to use a cellular protein, CBF1/CSL, as a DNA adaptor. CBF1/CSL is a sequence specific DNA binding protein robustly expressed in all tissues. Here we show that EBNA2 can form complexes with early B cell factor 1 (EBF1), a B cell specific DNA binding transcription factor, and EBF1 stabilizes EBNA2 chromatin binding. This EBNA2/EBF1 complex might serve as a novel target to develop future small molecule strategies that act as antivirals in latent B cell infection.
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Affiliation(s)
- Laura V Glaser
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
| | - Simone Rieger
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
| | - Sybille Thumann
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
| | - Sophie Beer
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
| | | | | | | | | | - Björn Grüning
- Bioinformatics, Institute for Informatics, Albert-Ludwigs-University, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics, Institute for Informatics, Albert-Ludwigs-University, Freiburg, Germany
| | - Stefan Krebs
- Gene Center, Ludwig-Maximilians-University, Munich, Germany
| | - Helmut Blum
- Gene Center, Ludwig-Maximilians-University, Munich, Germany
| | - Ralf Zimmer
- Teaching and Research Unit Bioinformatics, Institute of Informatics, Ludwig-Maximilians-University, Munich, Germany
| | - Florian Erhard
- Teaching and Research Unit Bioinformatics, Institute of Informatics, Ludwig-Maximilians-University, Munich, Germany
| | - Bettina Kempkes
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
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67
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Schlosberg CE, VanderKraats ND, Edwards JR. Modeling complex patterns of differential DNA methylation that associate with gene expression changes. Nucleic Acids Res 2017; 45:5100-5111. [PMID: 28168293 PMCID: PMC5435975 DOI: 10.1093/nar/gkx078] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/26/2017] [Indexed: 12/15/2022] Open
Abstract
Numerous genomic studies are underway to determine which genes are abnormally regulated by DNA methylation in disease. However, we have a poor understanding of how disease-specific methylation changes affect expression. We thus developed an integrative analysis tool, Methylation-based Gene Expression Classification (ME-Class), to explain specific variation in methylation that associates with expression change. This model captures the complexity of methylation changes around a gene promoter. Using 17 whole-genome bisulfite sequencing and RNA-seq datasets from different tissues from the Roadmap Epigenomics Project, ME-Class significantly outperforms standard methods using methylation to predict differential gene expression change. To demonstrate its utility, we used ME-Class to analyze 32 datasets from different hematopoietic cell types from the Blueprint Epigenome project. Expression-associated methylation changes were predominantly found when comparing cells from distantly related lineages, implying that changes in the cell's transcriptional program precede associated methylation changes. Training ME-Class on normal-tumor pairs from The Cancer Genome Atlas indicated that cancer-specific expression-associated methylation changes differ from tissue-specific changes. We further show that ME-Class can detect functionally relevant cancer-specific, expression-associated methylation changes that are reversed upon the removal of methylation. ME-Class is thus a powerful tool to identify genes that are dysregulated by DNA methylation in disease.
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Affiliation(s)
- Christopher E Schlosberg
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Nathan D VanderKraats
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - John R Edwards
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
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68
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Kretzmer H, Otto C, Hoffmann S. BAT: Bisulfite Analysis Toolkit: BAT is a toolkit to analyze DNA methylation sequencing data accurately and reproducibly. It covers standard processing and analysis steps from raw read mapping up to annotation data integration and calculation of correlating DMRs. F1000Res 2017; 6:1490. [PMID: 28979767 PMCID: PMC5590080 DOI: 10.12688/f1000research.12302.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/11/2017] [Indexed: 11/20/2022] Open
Abstract
Here, we present
BAT, a modular bisulfite analysis toolkit, that facilitates the analysis of bisulfite sequencing data. It covers the essential analysis steps of read alignment, quality control, extraction of methylation information, and calling of differentially methylated regions, as well as biologically relevant downstream analyses, such as data integration with gene expression, histone modification data, or transcription factor binding site annotation.
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Affiliation(s)
- Helene Kretzmer
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, 04109, Germany.,Transcriptome Bioinformatics, Research Center for Civilization Diseases (LIFE), University of Leipzig, Leipzig, 04109, Germany
| | - Christian Otto
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, 04109, Germany.,Transcriptome Bioinformatics, Research Center for Civilization Diseases (LIFE), University of Leipzig, Leipzig, 04109, Germany.,ecSeq GmbH, Leipzig, 04275, Germany
| | - Steve Hoffmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, 04109, Germany.,Transcriptome Bioinformatics, Research Center for Civilization Diseases (LIFE), University of Leipzig, Leipzig, 04109, Germany
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69
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Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma. Sci Rep 2017; 7:7040. [PMID: 28765546 PMCID: PMC5539289 DOI: 10.1038/s41598-017-07226-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/27/2017] [Indexed: 02/02/2023] Open
Abstract
The contribution of mutations in regulatory regions to tumorigenesis has been the subject of many recent studies. We propose a new framework for integrative analysis of genome-wide sequencing data by considering diverse genetic information. This approach is applied to study follicular lymphoma (FL), a disease for which little is known about the contribution of regulatory gene mutations. Results from a test FL cohort revealed three novel highly recurrent regulatory mutation blocks near important genes implicated in FL, BCL6 and BCL2. Similar findings were detected in a validation FL cohort. We also found transcription factors (TF) whose binding may be disturbed by these mutations in FL: disruption of FOX TF family near the BCL6 promoter may result in reduced BCL6 expression, which then increases BCL2 expression over that caused by BCL2 gene translocation. Knockdown experiments of two TF hits (FOXD2 or FOXD3) were performed in human B lymphocytes verifying that they modulate BCL6/BCL2 according to the computationally predicted effects of the SNVs on TF binding. Overall, our proposed integrative analysis facilitates non-coding driver identification and the new findings may enhance the understanding of FL.
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70
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Ushmorov A, Wirth T. FOXO in B-cell lymphopoiesis and B cell neoplasia. Semin Cancer Biol 2017; 50:132-141. [PMID: 28774833 DOI: 10.1016/j.semcancer.2017.07.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/17/2017] [Accepted: 07/30/2017] [Indexed: 12/31/2022]
Abstract
FOX O family transcription factors are important for differentiation and function of multiple cell types. In B lymphocytes they play a critical role. The activity of FOXOs is directly regulated both by signaling from B cell receptor (BCR) and cytokine receptors. FOXO1 action controls the transition between differentiation stages of B cell development. In comparison to other FOXO family members, FOXO1 plays a superior role in the regulation of early stages of B-cell differentiation. Although being known as a negative regulator of cell proliferation and therefore potential tumor suppressor, FOXO1 is downregulated only in Hodgkin lymphoma (HL) subtypes. In non-Hodgkin lymphoma (NHL) entities its expression is maintained at significant levels, raising the question on the role of FOXO-transcription factors in the proliferation and survival programs in the process of B cell differentiation as well as their contribution to the oncogenic programs of B-cell lymphomas. In particular, we discuss molecular mechanisms that might determine the switch between pro-apoptotic and pro-survival effects of FOXO1 and their interplay with specific differentiation programs.
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Affiliation(s)
- Alexey Ushmorov
- Institute of Physiological Chemistry, University of Ulm, Ulm, Germany
| | - Thomas Wirth
- Institute of Physiological Chemistry, University of Ulm, Ulm, Germany.
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71
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Giulino-Roth L, van Besien HJ, Dalton T, Totonchy JE, Rodina A, Taldone T, Bolaender A, Erdjument-Bromage H, Sadek J, Chadburn A, Barth MJ, Dela Cruz FS, Rainey A, Kung AL, Chiosis G, Cesarman E. Inhibition of Hsp90 Suppresses PI3K/AKT/mTOR Signaling and Has Antitumor Activity in Burkitt Lymphoma. Mol Cancer Ther 2017; 16:1779-1790. [PMID: 28619753 DOI: 10.1158/1535-7163.mct-16-0848] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 05/08/2017] [Accepted: 06/08/2017] [Indexed: 12/15/2022]
Abstract
Hsp90 is a molecular chaperone that protects proteins, including oncogenic signaling complexes, from proteolytic degradation. PU-H71 is a next-generation Hsp90 inhibitor that preferentially targets the functionally distinct pool of Hsp90 present in tumor cells. Tumors that are driven by the MYC oncoprotein may be particularly sensitive to PU-H71 due to the essential role of Hsp90 in the epichaperome, which maintains the malignant phenotype in the setting of MYC. Burkitt lymphoma (BL) is an aggressive B-cell lymphoma characterized by MYC dysregulation. In this study, we evaluated Hsp90 as a potential therapeutic target in BL. We found that primary BL tumors overexpress Hsp90 and that Hsp90 inhibition has antitumor activity in vitro and in vivo, including potent activity in a patient-derived xenograft model of BL. To evaluate the targets of PU-H71 in BL, we performed high-affinity capture followed by proteomic analysis using mass spectrometry. We found that Hsp90 inhibition targets multiple components of PI3K/AKT/mTOR signaling, highlighting the importance of this pathway in BL. Finally, we found that the anti-lymphoma activity of PU-H71 is synergistic with dual PI3K/mTOR inhibition in vitro and in vivo Overall, this work provides support for Hsp90 as a therapeutic target in BL and suggests the potential for combination therapy with PU-H71 and inhibitors of PI3K/mTOR. Mol Cancer Ther; 16(9); 1779-90. ©2017 AACR.
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Affiliation(s)
- Lisa Giulino-Roth
- Department of Pediatrics, Weill Cornell Medical College, New York, New York. .,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Herman J van Besien
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Tanner Dalton
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Jennifer E Totonchy
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Anna Rodina
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tony Taldone
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Bolaender
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jouliana Sadek
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Matthew J Barth
- Department of Pediatrics, Roswell Park Cancer Institute, Buffalo, New York
| | - Filemon S Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Allison Rainey
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gabriela Chiosis
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
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72
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A DNA methylation map of human cancer at single base-pair resolution. Oncogene 2017; 36:5648-5657. [PMID: 28581523 PMCID: PMC5633654 DOI: 10.1038/onc.2017.176] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 03/21/2017] [Accepted: 05/04/2017] [Indexed: 12/19/2022]
Abstract
Although single base-pair resolution DNA methylation landscapes for embryonic and different somatic cell types provided important insights into epigenetic dynamics and cell-type specificity, such comprehensive profiling is incomplete across human cancer types. This prompted us to perform genome-wide DNA methylation profiling of 22 samples derived from normal tissues and associated neoplasms, including primary tumors and cancer cell lines. Unlike their invariant normal counterparts, cancer samples exhibited highly variable CpG methylation levels in a large proportion of the genome, involving progressive changes during tumor evolution. The whole-genome sequencing results from selected samples were replicated in a large cohort of 1112 primary tumors of various cancer types using genome-scale DNA methylation analysis. Specifically, we determined DNA hypermethylation of promoters and enhancers regulating tumor-suppressor genes, with potential cancer-driving effects. DNA hypermethylation events showed evidence of positive selection, mutual exclusivity and tissue specificity, suggesting their active participation in neoplastic transformation. Our data highlight the extensive changes in DNA methylation that occur in cancer onset, progression and dissemination.
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73
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Abstract
Next-generation sequencing has revealed that more than 50% of human cancers harbour mutations in enzymes that are involved in chromatin organization. Tumour cells not only are activated by genetic and epigenetic alterations, but also routinely use epigenetic processes to ensure their escape from chemotherapy and host immune surveillance. Hence, a growing emphasis of recent drug discovery efforts has been on targeting the epigenome, including DNA methylation and histone modifications, with several new drugs being tested and some already approved by the US Food and Drug Administration (FDA). The future will see the increasing success of combining epigenetic drugs with other therapies. As epigenetic drugs target the epigenome as a whole, these true 'genomic medicines' lessen the need for precision approaches to individualized therapies.
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Affiliation(s)
- Peter A Jones
- Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Stephen Baylin
- Van Andel Research Institute, Grand Rapids, Michigan 49503, USA.,Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland 21287, USA
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74
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Establishment of a Strong Link Between Smoking and Cancer Pathogenesis through DNA Methylation Analysis. Sci Rep 2017; 7:1811. [PMID: 28500316 PMCID: PMC5431893 DOI: 10.1038/s41598-017-01856-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 04/03/2017] [Indexed: 12/21/2022] Open
Abstract
Smoking is a well-documented risk factor in various cancers, especially lung cancer. In the current study, we tested the hypothesis that abnormal DNAm loci associated with smoking are enriched in genes and pathways that convey a risk of cancer by determining whether smoking-related methylated genes led to enrichment in cancer-related pathways. We analyzed two sets of smoking-related methylated genes from 28 studies originating from blood and buccal samples. By analyzing 320 methylated genes from 26 studies on blood samples (N = 17,675), we found 57 enriched pathways associated with different types of cancer (FDR < 0.05). Of these, 11 were also significantly overrepresented in the 661 methylated genes from two studies of buccal samples (N = 1,002). We further found the aryl hydrocarbon receptor signaling pathway plays an important role in the initiation of smoking-attributable cancer. Finally, we constructed a subnetwork of genes important for smoking-attributable cancer from the 48 non-redundant genes in the 11 oncogenic pathways. Of these, genes such as DUSP4 and AKT3 are well documented as being involved in smoking-related lung cancer. In summary, our findings provide robust and systematic evidence in support of smoking’s impact on the epigenome, which may be an important contributor to cancer.
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75
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Korfi K, Ali S, Heward JA, Fitzgibbon J. Follicular lymphoma, a B cell malignancy addicted to epigenetic mutations. Epigenetics 2017; 12:370-377. [PMID: 28106467 PMCID: PMC5453190 DOI: 10.1080/15592294.2017.1282587] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 01/07/2023] Open
Abstract
While follicular lymphoma (FL) is exquisitely responsive to immuno-chemotherapy, many patients follow a relapsing remitting clinical course driven in part by a common precursor cell (CPC) population. Advances in next generation sequencing have provided valuable insights into the genetic landscape of FL and its clonal evolution in response to therapy, implicating perturbations of epigenetic regulators as a hallmark of the disease. Recurrent mutations of histone modifiers KMT2D, CREBBP, EP300, EZH2, ARIDIA, and linker histones are likely early events arising in the CPC pool, rendering epigenetic based therapies conceptually attractive for treatment of indolent and transformed FL. This review provides a synopsis of the main epigenetic aberrations and the current efforts in development and testing of epigenetic therapies in this B cell malignancy.
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Affiliation(s)
- Koorosh Korfi
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Sara Ali
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - James A. Heward
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jude Fitzgibbon
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
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76
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Genome-wide DNA methylation profiles reveal novel candidate genes associated with meat quality at different age stages in hens. Sci Rep 2017; 7:45564. [PMID: 28378745 PMCID: PMC5381223 DOI: 10.1038/srep45564] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/27/2017] [Indexed: 01/18/2023] Open
Abstract
Poultry meat quality is associated with breed, age, tissue and other factors. Many previous studies have focused on distinct breeds; however, little is known regarding the epigenetic regulatory mechanisms in different age stages, such as DNA methylation. Here, we compared the global DNA methylation profiles between juvenile (20 weeks old) and later laying-period (55 weeks old) hens and identified candidate genes related to the development and meat quality of breast muscle using whole-genome bisulfite sequencing. The results showed that the later laying-period hens, which had a higher intramuscular fat (IMF) deposition capacity and water holding capacity (WHC) and less tenderness, exhibited higher global DNA methylation levels than the juvenile hens. A total of 2,714 differentially methylated regions were identified in the present study, which corresponded to 378 differentially methylated genes, mainly affecting muscle development, lipid metabolism, and the ageing process. Hypermethylation of the promoters of the genes ABCA1, COL6A1 and GSTT1L and the resulting transcriptional down-regulation in the later laying-period hens may be the reason for the significant difference in the meat quality between the juvenile and later laying-period hens. These findings contribute to a better understanding of epigenetic regulation in the skeletal muscle development and meat quality of chicken.
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77
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Tessoulin B, Eveillard M, Lok A, Chiron D, Moreau P, Amiot M, Moreau-Aubry A, Le Gouill S, Pellat-Deceunynck C. p53 dysregulation in B-cell malignancies: More than a single gene in the pathway to hell. Blood Rev 2017; 31:251-259. [PMID: 28284458 DOI: 10.1016/j.blre.2017.03.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 03/02/2017] [Indexed: 12/31/2022]
Abstract
TP53 deletion or mutation is frequent in B-cell malignancies and is associated with a low response rate. We describe here the p53 landscape in B-cell malignancies, from B-Acute Lymphoblastic Leukemia to Plasma Cell Leukemia, by analyzing incidence of gain or loss of function of actors both upstream and within the p53 pathway, namely MYC, RAS, ARF, MDM2, ATM and TP53. Abnormalities are not equally distributed and their incidence is highly variable among malignancies. Deletion and mutation, usually associated, of ATM or TP53 are frequent in Diffuse Large B-Cell Lymphoma and Mantle Cell Lymphoma. MYC gain, absent in post-GC malignancies, is frequent in B-Prolymphocytic-Leukemia, Multiple Myeloma and Plasma Cell Leukemias. RAS mutations are rare except in MM and PCL. Multiple Factorial Analysis notes that MYC deregulation is closely related to TP53 status. Moreover, MYC gain, TP53 deletion and RAS mutations are inversely correlated with survival. Based on this landscape, we further propose targeted therapeutic approaches for the different B-cell malignancies.
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Affiliation(s)
- B Tessoulin
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Nantes, France; Department of Hematology, Nantes University Hospital, Nantes, France.
| | - M Eveillard
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Nantes, France; Hematology Biology Department, Nantes University Hospital, Nantes, France
| | - A Lok
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Nantes, France; Department of Hematology, Nantes University Hospital, Nantes, France
| | - D Chiron
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Nantes, France
| | - P Moreau
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Nantes, France; Department of Hematology, Nantes University Hospital, Nantes, France
| | - M Amiot
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Nantes, France
| | - A Moreau-Aubry
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Nantes, France
| | - S Le Gouill
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Nantes, France; Department of Hematology, Nantes University Hospital, Nantes, France
| | - C Pellat-Deceunynck
- CRCINA, INSERM, CNRS, Université de Nantes, Université d'Angers, Nantes, France.
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78
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Rohde M, Bonn BR, Zimmermann M, Lange J, Möricke A, Klapper W, Oschlies I, Szczepanowski M, Nagel I, Schrappe M, Loeffler M, Siebert R, Reiter A, Burkhardt B. Relevance of ID3-TCF3-CCND3 pathway mutations in pediatric aggressive B-cell lymphoma treated according to the non-Hodgkin Lymphoma Berlin-Frankfurt-Münster protocols. Haematologica 2017; 102:1091-1098. [PMID: 28209658 PMCID: PMC5451341 DOI: 10.3324/haematol.2016.156885] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 02/07/2017] [Indexed: 11/18/2022] Open
Abstract
Mature B-cell non-Hodgkin lymphoma is the most common subtype of non-Hodgkin lymphoma in childhood and adolescence. B-cell non-Hodgkin lymphomas are further classified into histological subtypes, with Burkitt lymphoma and Diffuse large B-cell lymphoma being the most common subgroups in pediatric patients. Translocations involving the MYC oncogene are known as relevant but not sufficient for Burkitt lymphoma pathogenesis. Recently published large-scale next-generation sequencing studies unveiled sets of additional recurrently mutated genes in samples of pediatric and adult B-cell non-Hodgkin lymphoma patients. ID3, TCF3 and CCND3 are potential drivers of Burkitt lymphomagenesis. In the study herein, frequency and clinical relevance of mutations in ID3, TCF3 and CCND3 were analyzed within a well-defined cohort of 84 uniformly diagnosed and treated pediatric B-cell non-Hodgkin lymphoma patients of the Berlin-Frankfurt-Münster group. Mutation frequency was 78% (ID3), 13% (TCF3) and 36% (CCND3) in Burkitt lymphoma (including Burkitt leukemia). ID3 and CCND3 mutations were associated with more advanced stages of the disease in MYC rearrangement positive Burkitt lymphoma. In conclusion, ID3-TCF3-CCND3 pathway genes are mutated in more than 88% of MYC-rearranged pediatric B-cell non-Hodgkin lymphoma and the pathway may represent a highly relevant second hit of Burkitt lymphoma pathogenesis, especially in children and adolescents.
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Affiliation(s)
- Marius Rohde
- Department of Pediatric Hematology and Oncology, Justus-Liebig-University Giessen, Germany
| | - Bettina R Bonn
- Department of Pediatric Hematology and Oncology, Justus-Liebig-University Giessen, Germany
| | - Martin Zimmermann
- Department of Pediatric Hematology and Oncology, Justus-Liebig-University Giessen, Germany
| | - Jonas Lange
- Pediatric Hematology and Oncology, University Hospital Münster, Germany.,Translational Oncology, Department of Medicine A, University Hospital Münster; Cluster of Excellence EXC 1003, Cells in Motion, Münster, Germany
| | - Anja Möricke
- Pediatric Hematology and Oncology, University Medical Center Schleswig-Holstein, Campus Kiel, Germany
| | - Wolfram Klapper
- Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
| | - Ilske Oschlies
- Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
| | - Monika Szczepanowski
- Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, Kiel, Germany
| | - Inga Nagel
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Germany
| | - Martin Schrappe
- Pediatric Hematology and Oncology, University Medical Center Schleswig-Holstein, Campus Kiel, Germany
| | | | | | - Markus Loeffler
- Institute for Medical Informatics Statistics and Epidemiology, University Leipzig, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Germany.,Institute of Human Genetics, University of Ulm and University Medical Center Ulm, Germany
| | - Alfred Reiter
- Department of Pediatric Hematology and Oncology, Justus-Liebig-University Giessen, Germany
| | - Birgit Burkhardt
- Pediatric Hematology and Oncology, University Hospital Münster, Germany
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79
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Siebert R, Gerhäuser C, Simon R, Wagener R, Weber UD, Sauter G, Plass C, Lichter P. Internationales Krebsgenomkonsortium (ICGC). MED GENET-BERLIN 2017. [DOI: 10.1007/s11825-017-0117-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Zusammenfassung
Die Katalogisierung genomischer, epigenetischer und transkriptioneller Veränderungen in Tumorzellen sowie die Integration disponierender oder klinisch relevanter Keimbahnvarianten ist die Voraussetzung für die zukünftige Anwendung präzisionsmedizinischer Ansätze in der Onkologie. Das Internationale Krebsgenomkonsortium (International Cancer Genome Consortium, ICGC) hat sich deshalb zum Ziel gesetzt, auf verschiedenen OMICs-Ebenen die wesentlichen Aberrationen in den 50 häufigsten und sozioökonomisch relevanten Tumorentitäten zu beschreiben. Dazu werden die Tumoren nach standardisierten Protokollen mittels sequenzierungsbasierter Verfahren analysiert. Die erhobenen Daten sind unter bestimmten Bedingungen auch Wissenschaftlern außerhalb des ICGC zugänglich. Auch wenn die Datensammlung noch nicht abgeschlossen ist, konnten entitätenspezifische und -übergreifende Analysen u. a. bereits Mutationssignaturen oder neue Driververänderungen und pathogene Signalwege identifizieren.
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Affiliation(s)
- Reiner Siebert
- Aff1 0000 0004 1936 9748 grid.6582.9 Institut für Humangenetik Universität Ulm & Universitätsklinikum Ulm Albert-Einstein-Allee 11 89081 Ulm Deutschland
| | - Clarissa Gerhäuser
- Aff2 0000 0004 0492 0584 grid.7497.d Deutsches Krebsforschungszentrum (DKFZ) Heidelberg Deutschland
| | - Ronald Simon
- Aff3 0000 0001 2180 3484 grid.13648.38 Universitätsklinikum Hamburg-Eppendorf Hamburg Deutschland
| | - Rabea Wagener
- Aff1 0000 0004 1936 9748 grid.6582.9 Institut für Humangenetik Universität Ulm & Universitätsklinikum Ulm Albert-Einstein-Allee 11 89081 Ulm Deutschland
| | - Ursula D. Weber
- Aff2 0000 0004 0492 0584 grid.7497.d Deutsches Krebsforschungszentrum (DKFZ) Heidelberg Deutschland
| | - Guido Sauter
- Aff3 0000 0001 2180 3484 grid.13648.38 Universitätsklinikum Hamburg-Eppendorf Hamburg Deutschland
| | - Christoph Plass
- Aff2 0000 0004 0492 0584 grid.7497.d Deutsches Krebsforschungszentrum (DKFZ) Heidelberg Deutschland
| | - Peter Lichter
- Aff2 0000 0004 0492 0584 grid.7497.d Deutsches Krebsforschungszentrum (DKFZ) Heidelberg Deutschland
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80
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Das Tumorepigenom – von der Genregulation über die Tumorklassifikation zum Therapietarget. MED GENET-BERLIN 2017. [DOI: 10.1007/s11825-016-0115-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Zusammenfassung
Epigenetische Regulationsmechanismen sind essenziell für den koordinierten Ablauf zahlreicher zellulärer Prozesse wie die Differenzierung und Entwicklung oder auch die Anpassung der Genaktivität an die herrschenden Umweltbedingungen. Insbesondere Tumorerkrankungen gehen mit oftmals umfangreichen Alterationen im Epigenom einher. Diese Veränderungen sind dabei vielfach charakteristisch entweder für die Tumorentität, das Stadium der Erkrankung oder aber das klinische Ansprechen des Tumors auf eine Therapie und damit die individuelle Prognose des Patienten. Nach einer kurzen Darstellung epigenetischer Marker und ihrer Bedeutung bei malignen Erkrankungen werden in diesem Artikel Alterationen im Tumorepigenom und ihre Nutzbarkeit im Rahmen einer individualisierten Medizin exemplarisch vorgestellt.
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81
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Abstract
Epstein-Barr virus (EBV) infection is associated with several distinct hematological and epithelial malignancies, e.g., Burkitt lymphoma, Hodgkin lymphoma, nasopharyngeal carcinoma, gastric carcinoma, and others. The association with several malignant tumors of local and worldwide distribution makes EBV one of the most important tumor viruses. Furthermore, because EBV can cause posttransplant lymphoproliferative disease, transplant medicine has to deal with EBV as a major pathogenic virus second only to cytomegalovirus. In this review, we summarize briefly the natural history of EBV infection and outline some of the recent advances in the pathogenesis of the major EBV-associated neoplasms. We present alternative scenarios and discuss them in the light of most recent experimental data. Emerging research areas including EBV-induced patho-epigenetic alterations in host cells and the putative role of exosome-mediated information transfer in disease development are also within the scope of this review. This book contains an in-depth description of a series of modern methodologies used in EBV research. In this introductory chapter, we thoroughly refer to the applications of these methods and demonstrate how they contributed to the understanding of EBV-host cell interactions. The data gathered using recent technological advancements in molecular biology and immunology as well as the application of sophisticated in vitro and in vivo experimental models certainly provided deep and novel insights into the pathogenetic mechanisms of EBV infection and EBV-associated tumorigenesis. Furthermore, the development of adoptive T cell immunotherapy has provided a novel approach to the therapy of viral disease in transplant medicine and hematology.
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Affiliation(s)
- Janos Minarovits
- Faculty of Dentistry, Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza Lajos krt. 64, H-6720, Szeged, Hungary.
| | - Hans Helmut Niller
- Institute of Medical Microbiology and Hygiene, University of Regensburg, D-93053, Regensburg, Germany
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82
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Lange J, Lenz G, Burkhardt B. Mature aggressive B-cell lymphoma across age groups - molecular advances and therapeutic implications. Expert Rev Hematol 2016; 10:123-135. [PMID: 27936978 DOI: 10.1080/17474086.2017.1271318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Mature B-cell lymphoma represents the most common type of Non-Hodgkin lymphoma, and different subtypes prevail at different patient ages. Areas covered: We review recent data on differences and commonalities in mature B-cell lymphoma occurring in adult and pediatric patients, with a special emphasis on molecular advances and therapeutic implications. To this end, we will discuss knowledge on diffuse large B-cell lymphoma and Burkitt lymphoma/leukemia, which are the most frequent subtypes in adult and pediatric patients, respectively, and on primary mediastinal B-cell lymphoma, which is a subtype of mature B-cell lymphoma occurring mainly in adolescents and young adults with a female predominance. Expert commentary: Molecular profiling has revealed molecular alterations that can be used to further classify the subtypes of mature B-cell lymphoma. These new subgroups frequently respond differentially to targeted therapeutic strategies. Future clinical trials utilizing new drugs will address this issue by combining clinical data and response assessment with a molecular workup of the corresponding lymphomas.
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Affiliation(s)
- Jonas Lange
- a Pediatric Hematology and Oncology , University Hospital Muenster , Muenster , Germany.,b Translational Oncology, Department of Medicine A , University Hospital Muenster, Muenster, Germany; Cluster of Excellence EXC 1003, Cells in Motion , Muenster , Germany
| | - Georg Lenz
- b Translational Oncology, Department of Medicine A , University Hospital Muenster, Muenster, Germany; Cluster of Excellence EXC 1003, Cells in Motion , Muenster , Germany
| | - Birgit Burkhardt
- a Pediatric Hematology and Oncology , University Hospital Muenster , Muenster , Germany
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83
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Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers. Sci Rep 2016; 6:38133. [PMID: 27924834 PMCID: PMC5141443 DOI: 10.1038/srep38133] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/07/2016] [Indexed: 01/12/2023] Open
Abstract
Follicular lymphoma (FL) is an uncurable cancer characterized by progressive severity of relapses. We analyzed sequence context specificity of mutations in the B cells from a large cohort of FL patients. We revealed substantial excess of mutations within a novel hybrid nucleotide motif: the signature of somatic hypermutation (SHM) enzyme, Activation Induced Deaminase (AID), which overlaps the CpG methylation site. This finding implies that in FL the SHM machinery acts at genomic sites containing methylated cytosine. We identified the prevalence of this hybrid mutational signature in many other types of human cancer, suggesting that AID-mediated, CpG-methylation dependent mutagenesis is a common feature of tumorigenesis.
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84
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Epigenetic Impact on EBV Associated B-Cell Lymphomagenesis. Biomolecules 2016; 6:biom6040046. [PMID: 27886133 PMCID: PMC5197956 DOI: 10.3390/biom6040046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/02/2016] [Accepted: 11/07/2016] [Indexed: 01/09/2023] Open
Abstract
Epigenetic modifications leading to either transcriptional repression or activation, play an indispensable role in the development of human cancers. Epidemiological study revealed that approximately 20% of all human cancers are associated with tumor viruses. Epstein-Barr virus (EBV), the first human tumor virus, demonstrates frequent epigenetic alterations on both viral and host genomes in associated cancers—both of epithelial and lymphoid origin. The cell type-dependent different EBV latent gene expression patterns appear to be determined by the cellular epigenetic machinery and similarly viral oncoproteins recruit epigenetic regulators in order to deregulate the cellular gene expression profile resulting in several human cancers. This review elucidates the epigenetic consequences of EBV–host interactions during development of multiple EBV-induced B-cell lymphomas, which may lead to the discovery of novel therapeutic interventions against EBV-associated B-cell lymphomas by alteration of reversible patho-epigenetic markings.
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85
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Bernhart SH, Kretzmer H, Holdt LM, Jühling F, Ammerpohl O, Bergmann AK, Northoff BH, Doose G, Siebert R, Stadler PF, Hoffmann S. Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer. Sci Rep 2016; 6:37393. [PMID: 27876760 PMCID: PMC5120258 DOI: 10.1038/srep37393] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/27/2016] [Indexed: 02/08/2023] Open
Abstract
Bivalent (poised or paused) chromatin comprises activating and repressing histone modifications at the same location. This combination of epigenetic marks at promoter or enhancer regions keeps genes expressed at low levels but poised for rapid activation. Typically, DNA at bivalent promoters is only lowly methylated in normal cells, but frequently shows elevated methylation levels in cancer samples. Here, we developed a universal classifier built from chromatin data that can identify cancer samples solely from hypermethylation of bivalent chromatin. Tested on over 7,000 DNA methylation data sets from several cancer types, it reaches an AUC of 0.92. Although higher levels of DNA methylation are often associated with transcriptional silencing, counter-intuitive positive statistical dependencies between DNA methylation and expression levels have been recently reported for two cancer types. Here, we re-analyze combined expression and DNA methylation data sets, comprising over 5,000 samples, and demonstrate that the conjunction of hypermethylation of bivalent chromatin and up-regulation of the corresponding genes is a general phenomenon in cancer. This up-regulation affects many developmental genes and transcription factors, including dozens of homeobox genes and other genes implicated in cancer. Thus, we reason that the disturbance of bivalent chromatin may be intimately linked to tumorigenesis.
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Affiliation(s)
- Stephan H Bernhart
- Leipzig University, Chair of Bioinformatics, Leipzig, 04107, Germany.,Leipzig University, Transcriptome Bioinformatics Group - Interdisciplinary Center for Bioinformatics, Leipzig, 04107, Germany
| | - Helene Kretzmer
- Leipzig University, Chair of Bioinformatics, Leipzig, 04107, Germany.,Leipzig University, Transcriptome Bioinformatics Group - Interdisciplinary Center for Bioinformatics, Leipzig, 04107, Germany
| | - Lesca M Holdt
- Ludwig-Maximilians-University, Institute of Laboratory Medicine, Munich, 81377, Germany
| | - Frank Jühling
- Leipzig University, Chair of Bioinformatics, Leipzig, 04107, Germany.,Leipzig University, Transcriptome Bioinformatics Group - Interdisciplinary Center for Bioinformatics, Leipzig, 04107, Germany.,Inserm, U1110 - Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, 67000, France.,Université de Strasbourg, Strasbourg, 67000, France
| | - Ole Ammerpohl
- Christian Albrechts University &University Hospital Schleswig-Holstein - Campus Kiel, Institute of Human Genetics, Kiel, 24105, Germany
| | - Anke K Bergmann
- Christian Albrechts University &University Hospital Schleswig-Holstein - Campus Kiel, Institute of Human Genetics, Kiel, 24105, Germany.,Christian Albrechts University Kiel &University Hospital Schleswig-Holstein - Campus Kiel, Department of Pediatrics, Kiel, 24105, Germany
| | - Bernd H Northoff
- Ludwig-Maximilians-University, Institute of Laboratory Medicine, Munich, 81377, Germany
| | - Gero Doose
- Leipzig University, Chair of Bioinformatics, Leipzig, 04107, Germany.,Leipzig University, Transcriptome Bioinformatics Group - Interdisciplinary Center for Bioinformatics, Leipzig, 04107, Germany
| | - Reiner Siebert
- Christian Albrechts University &University Hospital Schleswig-Holstein - Campus Kiel, Institute of Human Genetics, Kiel, 24105, Germany.,Ulm University &Ulm University Medical Center, Institute for Human Genetics, Ulm, 89081, Germany
| | - Peter F Stadler
- Leipzig University, Chair of Bioinformatics, Leipzig, 04107, Germany.,Leipzig University, Transcriptome Bioinformatics Group - Interdisciplinary Center for Bioinformatics, Leipzig, 04107, Germany.,Leipzig University, LIFE - Leipzig Research Center for Civilization Diseases, Leipzig, 04107, Germany.,University of Vienna, Department of Theoretical Chemistry, Vienna, 1090, Austria.,Max-Planck-Institute for Mathematics in Sciences, Leipzig, 04103, Germany.,Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Steve Hoffmann
- Leipzig University, Chair of Bioinformatics, Leipzig, 04107, Germany.,Leipzig University, Transcriptome Bioinformatics Group - Interdisciplinary Center for Bioinformatics, Leipzig, 04107, Germany.,Leipzig University, LIFE - Leipzig Research Center for Civilization Diseases, Leipzig, 04107, Germany
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86
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Dirks RAM, Stunnenberg HG, Marks H. Genome-wide epigenomic profiling for biomarker discovery. Clin Epigenetics 2016; 8:122. [PMID: 27895806 PMCID: PMC5117701 DOI: 10.1186/s13148-016-0284-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/02/2016] [Indexed: 12/24/2022] Open
Abstract
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery. Recent years saw great progress in miniaturization of genome-wide epigenomic profiling, enabling large-scale epigenetic biomarker screens for disease diagnosis, prognosis, and stratification on patient-derived samples. All main genome-wide profiling technologies have now been scaled down and/or are compatible with single-cell readout, including: (i) Bisulfite sequencing to determine DNA methylation at base-pair resolution, (ii) ChIP-Seq to identify protein binding sites on the genome, (iii) DNaseI-Seq/ATAC-Seq to profile open chromatin, and (iv) 4C-Seq and HiC-Seq to determine the spatial organization of chromosomes. In this review we provide an overview of current genome-wide epigenomic profiling technologies and main technological advances that allowed miniaturization of these assays down to single-cell level. For each of these technologies we evaluate their application for future biomarker discovery. We will focus on (i) compatibility of these technologies with methods used for clinical sample preservation, including methods used by biobanks that store large numbers of patient samples, and (ii) automation of these technologies for robust sample preparation and increased throughput.
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Affiliation(s)
- René A M Dirks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
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87
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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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88
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Kaz AM, Wong CJ, Varadan V, Willis JE, Chak A, Grady WM. Global DNA methylation patterns in Barrett's esophagus, dysplastic Barrett's, and esophageal adenocarcinoma are associated with BMI, gender, and tobacco use. Clin Epigenetics 2016; 8:111. [PMID: 27795744 PMCID: PMC5082363 DOI: 10.1186/s13148-016-0273-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/29/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The risk of developing Barrett's esophagus (BE) and/or esophageal adenocarcinoma (EAC) is associated with specific demographic and behavioral factors, including gender, obesity/elevated body mass index (BMI), and tobacco use. Alterations in DNA methylation, an epigenetic modification that can affect gene expression and that can be influenced by environmental factors, is frequently present in both BE and EAC and is believed to play a role in the formation of BE and its progression to EAC. It is currently unknown whether obesity or tobacco smoking influences the risk of developing BE/EAC via the induction of alterations in DNA methylation. To investigate this possibility, we assessed the genome-wide methylation status of 81 esophageal tissues, including BE, dysplastic BE, and EAC epithelia using HumanMethylation450 BeadChips (Illumina). RESULTS We found numerous differentially methylated loci in the esophagus tissues when comparing males to females, obese to lean individuals, and smokers to nonsmokers. Differences in DNA methylation between these groups were seen in a variety of functional genomic regions and both within and outside of CpG islands. Several cancer-related pathways were found to have differentially methylated genes between these comparison groups. CONCLUSIONS Our findings suggest obesity and tobacco smoking may influence DNA methylation in the esophagus and raise the possibility that these risk factors affect the development of BE, dysplastic BE, and EAC through influencing the epigenetic status of specific loci that have a biologically plausible role in cancer formation.
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Affiliation(s)
- Andrew M. Kaz
- Gastroenterology Section, VA Puget Sound Health Care System, Seattle, WA 98108 USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195 USA
| | - Chao-Jen Wong
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Vinay Varadan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Joseph E. Willis
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - Amitabh Chak
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106 USA
- Division of Gastroenterology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195 USA
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89
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Knittel G, Liedgens P, Korovkina D, Pallasch CP, Reinhardt HC. Rewired NFκB signaling as a potentially actionable feature of activated B-cell-like diffuse large B-cell lymphoma. Eur J Haematol 2016; 97:499-510. [DOI: 10.1111/ejh.12792] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Gero Knittel
- Department I of Internal Medicine; University Hospital of Cologne; Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
| | - Paul Liedgens
- Department I of Internal Medicine; University Hospital of Cologne; Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
| | - Darya Korovkina
- Department I of Internal Medicine; University Hospital of Cologne; Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
| | - Christian P. Pallasch
- Department I of Internal Medicine; University Hospital of Cologne; Cologne Germany
- Center of Integrated Oncology (CIO); University Hospital of Cologne; Cologne Germany
| | - Hans Christian Reinhardt
- Department I of Internal Medicine; University Hospital of Cologne; Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
- Center of Integrated Oncology (CIO); University Hospital of Cologne; Cologne Germany
- Center of Molecular Medicine; University of Cologne; Cologne Germany
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90
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Ho C, Kluk MJ. Molecular Pathology: Predictive, Prognostic, and Diagnostic Markers in Lymphoid Neoplasms. Surg Pathol Clin 2016; 9:489-521. [PMID: 27523974 DOI: 10.1016/j.path.2016.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Lymphoid neoplasms show great diversity in morphology, immunophenotypic profile, and postulated cells of origin, which also reflects the variety of genetic alterations within this group of tumors. This review discusses many of the currently known genetic alterations in selected mature B-cell and T-cell lymphoid neoplasms, and their significance as diagnostic, prognostic, and therapeutic markers. Given the rapidly increasing number of genetic alterations that have been described in this group of tumors, and that the clinical significance of many is still being studied, this is not an entirely exhaustive review of all of the genetic alterations that have been reported.
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Affiliation(s)
- Caleb Ho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Michael J Kluk
- Department of Pathology, Weill Cornell Medical College, 525 East 68th Street, Mailbox #79, F-540, New York, NY 10065, USA.
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91
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Frazzi R, Auffray C, Ferrari A, Filippini P, Rutella S, Cesario A. Integrative systems medicine approaches to identify molecular targets in lymphoid malignancies. J Transl Med 2016; 14:252. [PMID: 27580852 PMCID: PMC5007715 DOI: 10.1186/s12967-016-1018-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/18/2016] [Indexed: 12/22/2022] Open
Abstract
Although survival rates for lymphoproliferative disorders are steadily increasing both in the US and in Europe, there is need for optimizing front-line therapies and developing more effective salvage strategies. Recent advances in molecular genetics have highlighted the biological diversity of lymphoproliferative disorders. In particular, integrative approaches including whole genome sequencing, whole exome sequencing, and transcriptome or RNA sequencing have been instrumental to the identification of molecular targets for treatment. Herein, we will discuss how genomic, epigenomic and proteomic approaches in lymphoproliferative disorders have supported the discovery of molecular lesions and their therapeutic targeting in the clinic.
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Affiliation(s)
- Raffaele Frazzi
- Laboratory of Translational Research, IRCCS "Arcispedale S. Maria Nuova", Reggio Emilia, Italy
| | - Charles Auffray
- European Institute for Systems Biology and Medicine (EISBM), Paris, France
| | - Angela Ferrari
- Division of Hematology, IRCCS "Arcispedale S. Maria Nuova", Reggio Emilia, Italy
| | - Perla Filippini
- Division of Translational Medicine, Sidra Medical and Research Centre, Doha, Qatar
| | - Sergio Rutella
- John van Geest Cancer Research Centre, College of Science and Technology, Nottingham Trent University, Clifton Campus, Nottingham, NG11 8NS, UK.
| | - Alfredo Cesario
- Clinical Governance and International Research Activities, Fondazione Policlinico Gemelli, Rome, Italy.,Division of Thoracic Surgery, Università Cattolica del Sacro Cuore, Rome, Italy.,European Association of Systems Medicine, Aachen, Germany
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92
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Ammerpohl O, Scheufele S, Siebert R. Analysen epigenetischer Marker aus Liquid Biopsies: Informationen von jenseits des Genoms. MED GENET-BERLIN 2016. [DOI: 10.1007/s11825-016-0093-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Zusammenfassung
Die Analyse epigenetischer Marker aus Liquid Biopsies erlaubt Einblicke in physiologische und pathologische Prozesse im Körper einer Person, die über die reine Sequenzinformation hinausgehen. Insbesondere das DNA-Methylierungsmuster sowie die Expressionsmuster von mRNA und ncRNA sind aus Liquid Biopsies erfassbar. Damit werden ganze Gruppen neuer potenzieller Biomarker einer nicht invasiven und ökonomischen Diagnostik zugänglich. Darüber hinaus und im Gegensatz zur reinen DNA-Sequenzanalyse von Liquid Biopsies erlaubt die hohe Gewebespezifität epigenetischer Marker auch die Bestimmung der Herkunft der analysierten Nukleinsäuren z. B. in Bezug auf ein betroffenes Organ. Angesichts der fallenden Kosten für Sequenzierungen und des technologischen Fortschritts, der die Nachweisgrenzen immer weiter zu immer sensitiveren Anwendungen verschiebt, könnten epigenetische Untersuchungen aus Liquid Biopsies den Trend zu einer Individualisierung in der Medizin weiter forcieren.
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Affiliation(s)
- Ole Ammerpohl
- Aff1 grid.9764.c 0000000121539986 Institut für Humangenetik Christian‑Albrechts‑Universität zu Kiel Schwanenweg 24 24105 Kiel Deutschland
- Aff2 grid.412468.d 0000000406462097 Universitätsklinikum Schleswig-Holstein Campus Kiel Kiel Deutschland
- Aff3 grid.452624.3 Airway Research Center North (ARCN) German Center for Lung Research (DZL) Gießen Deutschland
| | - Swetlana Scheufele
- Aff1 grid.9764.c 0000000121539986 Institut für Humangenetik Christian‑Albrechts‑Universität zu Kiel Schwanenweg 24 24105 Kiel Deutschland
- Aff2 grid.412468.d 0000000406462097 Universitätsklinikum Schleswig-Holstein Campus Kiel Kiel Deutschland
- Aff3 grid.452624.3 Airway Research Center North (ARCN) German Center for Lung Research (DZL) Gießen Deutschland
| | - Reiner Siebert
- Aff3 grid.452624.3 Airway Research Center North (ARCN) German Center for Lung Research (DZL) Gießen Deutschland
- Aff4 grid.6582.9 0000000419369748 Institut für Humangenetik Universität Ulm Albert-Einstein-Allee 11 89081 Ulm Deutschland
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93
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Wurster KD, Hummel F, Richter J, Giefing M, Hartmann S, Hansmann ML, Kreher S, Köchert K, Krappmann D, Klapper W, Hummel M, Wenzel SS, Lenz G, Janz M, Dörken B, Siebert R, Mathas S. Inactivation of the putative ubiquitin-E3 ligase PDLIM2 in classical Hodgkin and anaplastic large cell lymphoma. Leukemia 2016; 31:602-613. [PMID: 27538486 PMCID: PMC5339435 DOI: 10.1038/leu.2016.238] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 08/02/2016] [Accepted: 08/09/2016] [Indexed: 12/12/2022]
Abstract
Apart from its unique histopathological appearance with rare tumor cells embedded in an inflammatory background of bystander cells, classical Hodgkin lymphoma (cHL) is characterized by an unusual activation of a broad range of signaling pathways involved in cellular activation. This includes constitutive high-level activity of nuclear factor-κB (NF-κB), Janus kinase/signal transducer and activator of transcription (JAK/STAT), activator protein-1 (AP-1) and interferon regulatory factor (IRF) transcription factors (TFs) that are physiologically only transiently activated. Here, we demonstrate that inactivation of the putative ubiquitin E3-ligase PDLIM2 contributes to this TF activation. PDLIM2 expression is lost at the mRNA and protein levels in the majority of cHL cell lines and Hodgkin and Reed–Sternberg (HRS) cells of nearly all cHL primary samples. This loss is associated with PDLIM2 genomic alterations, promoter methylation and altered splicing. Reconstitution of PDLIM2 in HRS cell lines inhibits proliferation, blocks NF-κB transcriptional activity and contributes to cHL-specific gene expression. In non-Hodgkin B-cell lines, small interfering RNA-mediated PDLIM2 knockdown results in superactivation of TFs NF-κB and AP-1 following phorbol 12-myristate 13-acetate (PMA) stimulation. Furthermore, expression of PDLIM2 is lost in anaplastic large cell lymphoma (ALCL) that shares key biological aspects with cHL. We conclude that inactivation of PDLIM2 is a recurrent finding in cHL and ALCL, promotes activation of inflammatory signaling pathways and thereby contributes to their pathogenesis.
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Affiliation(s)
- K D Wurster
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - F Hummel
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - J Richter
- Institute of Human Genetics, Christian-Albrechts University Kiel, Kiel, Germany
| | - M Giefing
- Institute of Human Genetics, Christian-Albrechts University Kiel, Kiel, Germany.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - S Hartmann
- Dr Senckenberg Institute of Pathology, University of Frankfurt, Medical School, Frankfurt, Germany
| | - M-L Hansmann
- Dr Senckenberg Institute of Pathology, University of Frankfurt, Medical School, Frankfurt, Germany
| | - S Kreher
- Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - K Köchert
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - D Krappmann
- Research Unit Cellular Signal Integration, Helmholtz Zentrum München für Gesundheit und Umwelt, Neuherberg, Germany
| | - W Klapper
- Department of Pathology, Haematopathology Section and Lymph Node Registry, Christian-Albrechts University Kiel, Kiel, Germany
| | - M Hummel
- Institute of Pathology, Charité-Universitätsmedzin Berlin, Berlin, Germany
| | - S-S Wenzel
- Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - G Lenz
- Division of Translational Oncology, Department of Medicine A, University Hospital Münster, and Cluster of Excellence EXC 1003, Cells in Motion, Münster, Germany
| | - M Janz
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - B Dörken
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - R Siebert
- Institute of Human Genetics, Christian-Albrechts University Kiel, Kiel, Germany.,Institute of Human Genetics, University Hospital Ulm, Ulm, Germany
| | - S Mathas
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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94
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DNA methylation in hematopoietic development and disease. Exp Hematol 2016; 44:783-790. [PMID: 27178734 DOI: 10.1016/j.exphem.2016.04.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 12/28/2022]
Abstract
DNA methylation is an important epigenetic modification that can have profound and widespread effects on gene expression and on cellular fate and function. Recent work has indicated that DNA methylation plays a critical role in hematopoietic development and hematopoietic disease. DNA methyltransferases and Ten-eleven translocation enzymes are required to add and remove methyl "marks" from DNA, respectively, and both sets of genes have been found necessary for proper formation and maintenance of hematopoietic stem cells and for differentiation of downstream hematopoietic lineages during development. DNA methylation and demethylation enzymes have also been implicated in hematopoietic disorders such as acute myeloid leukemia and myelodysplastic syndrome. Here, we review some of the recent literature regarding the role of DNA methylation in hematopoietic health and disease.
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95
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Gu Z, Eils R, Schlesner M. gtrellis: an R/Bioconductor package for making genome-level Trellis graphics. BMC Bioinformatics 2016; 17:169. [PMID: 27089965 PMCID: PMC4835841 DOI: 10.1186/s12859-016-1051-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 04/13/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trellis graphics are a visualization method that splits data by one or more categorical variables and displays subsets of the data in a grid of panels. Trellis graphics are broadly used in genomic data analysis to compare statistics over different categories in parallel and reveal multivariate relationships. However, current software packages to produce Trellis graphics have not been designed with genomic data in mind and lack some functionality that is required for effective visualization of genomic data. RESULTS Here we introduce the gtrellis package which provides an efficient and extensible way to visualize genomic data in a Trellis layout. gtrellis provides highly flexible Trellis layouts which allow efficient arrangement of genomic categories on the plot. It supports multiple-track visualization, which makes it straightforward to visualize several properties of genomic data in parallel to explain complex relationships. In addition, gtrellis provides an extensible framework that allows adding user-defined graphics. CONCLUSIONS The gtrellis package provides an easy and effective way to visualize genomic data and reveal high dimensional relationships on a genome-wide scale. gtrellis can be flexibly extended and thus can also serve as a base package for highly specific purposes. gtrellis makes it easy to produce novel visualizations, which can lead to the discovery of previously unrecognized patterns in genomic data.
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Affiliation(s)
- Zuguang Gu
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant Center, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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96
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B-cell-specific conditional expression of Myd88p.L252P leads to the development of diffuse large B-cell lymphoma in mice. Blood 2016; 127:2732-41. [PMID: 27048211 DOI: 10.1182/blood-2015-11-684183] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/30/2016] [Indexed: 12/20/2022] Open
Abstract
The adaptor protein MYD88 is critical for relaying activation of Toll-like receptor signaling to NF-κB activation. MYD88 mutations, particularly the p.L265P mutation, have been described in numerous distinct B-cell malignancies, including diffuse large B-cell lymphoma (DLBCL). Twenty-nine percent of activated B-cell-type DLBCL (ABC-DLBCL), which is characterized by constitutive activation of the NF-κB pathway, carry the p.L265P mutation. In addition, ABC-DLBCL frequently displays focal copy number gains affecting BCL2 Here, we generated a novel mouse model in which Cre-mediated recombination, specifically in B cells, leads to the conditional expression of Myd88(p.L252P) (the orthologous position of the human MYD88(p.L265P) mutation) from the endogenous locus. These mice develop a lymphoproliferative disease and occasional transformation into clonal lymphomas. The clonal disease displays the morphologic and immunophenotypical characteristics of ABC-DLBCL. Lymphomagenesis can be accelerated by crossing in a further novel allele, which mediates conditional overexpression of BCL2 Cross-validation experiments in human DLBCL samples revealed that both MYD88 and CD79B mutations are substantially enriched in ABC-DLBCL compared with germinal center B-cell DLBCL. Furthermore, analyses of human DLBCL genome sequencing data confirmed that BCL2 amplifications frequently co-occurred with MYD88 mutations, further validating our approach. Finally, in silico experiments revealed that MYD88-mutant ABC-DLBCL cells in particular display an actionable addiction to BCL2. Altogether, we generated a novel autochthonous mouse model of ABC-DLBCL that could be used as a preclinical platform for the development and validation of novel therapeutic approaches for the treatment of ABC-DLBCL.
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97
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Vercelli D. Does epigenetics play a role in human asthma? Allergol Int 2016; 65:123-126. [PMID: 26778244 DOI: 10.1016/j.alit.2015.12.001] [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] [Received: 12/01/2015] [Revised: 12/04/2015] [Accepted: 12/07/2015] [Indexed: 02/02/2023] Open
Abstract
Asthma and other allergic diseases are among the most prevalent chronic non-communicable diseases of childhood. According to the World Health Organization, asthma affects >7.0 million children under 18 in the United States, with an economic burden that is estimated to exceed that of tuberculosis and HIV/AIDS combined. Despite much research, the natural history of asthma and its pathogenesis are still in many ways elusive. This review discusses our current understanding of the role epigenetic processes play in asthma pathogenesis, focusing on genome-wide, population-based studies.
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98
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Giulino-Roth L, Goldman S. Recent molecular and therapeutic advances in B-cell non-Hodgkin lymphoma in children. Br J Haematol 2016; 173:531-44. [DOI: 10.1111/bjh.13969] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Lisa Giulino-Roth
- Department of Pediatrics; Weill Cornell Medical College; New York NY USA
| | - Stanton Goldman
- Department of Pediatrics; Medical City Children's Hospital and Texas Oncology; Dallas TX USA
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99
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Szczepanowski M, Masqué-Soler N, Schlesner M, Haake A, Richter J, Wagener R, Burkhardt B, Kreuz M, Siebert R, Klapper W. Immunohistochemical detection of inhibitor of DNA binding 3 mutational variants in mature aggressive B-cell lymphoma. Haematologica 2016; 101:e259-61. [PMID: 26992947 DOI: 10.3324/haematol.2015.138701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Monika Szczepanowski
- Institute of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein Campus Kiel, Christian-Albrechts University Kiel, Germany
| | - Neus Masqué-Soler
- Institute of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein Campus Kiel, Christian-Albrechts University Kiel, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Germany
| | - Andrea Haake
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Müenster, Germany
| | - Julia Richter
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Müenster, Germany
| | - Rabea Wagener
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Müenster, Germany
| | - Birgit Burkhardt
- NHL-BFM Study Center and Department of Pediatric Hematology and Oncology, University Children's Hospital, Müenster, Germany
| | - Markus Kreuz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Müenster, Germany
| | | | - Wolfram Klapper
- Institute of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein Campus Kiel, Christian-Albrechts University Kiel, Germany
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100
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Miles RR, Shah RK, Frazer JK. Molecular genetics of childhood, adolescent and young adult non-Hodgkin lymphoma. Br J Haematol 2016; 173:582-96. [PMID: 26969846 DOI: 10.1111/bjh.14011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular genetic abnormalities are ubiquitous in non-Hodgkin lymphoma (NHL), but genetic changes are not yet used to define specific lymphoma subtypes. Certain recurrent molecular genetic abnormalities in NHL underlie molecular pathogenesis and/or are associated with prognosis or represent potential therapeutic targets. Most molecular genetic studies of B- and T-NHL have been performed on adult patient samples, and the relevance of many of these findings for childhood, adolescent and young adult NHL remains to be demonstrated. In this review, we focus on NHL subtypes that are most common in young patients and emphasize features actually studied in younger NHL patients. This approach highlights what is known about NHL genetics in young patients but also points to gaps that remain, which will require cooperative efforts to collect and share biological specimens for genomic and genetic analyses in order to help predict outcomes and guide therapy in the future.
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Affiliation(s)
- Rodney R Miles
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Rikin K Shah
- Jimmy Everest Section of Pediatric Hematology-Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - J Kimble Frazer
- E.L. and Thelma Gaylord Chair in Pediatric Oncology, Jimmy Everest Section of Pediatric Hematology-Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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