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Chiarella SE, Grammer LC. Immune deficiency in chronic rhinosinusitis: screening and treatment. Expert Rev Clin Immunol 2016; 13:117-123. [PMID: 27500811 DOI: 10.1080/1744666x.2016.1216790] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Chronic rhinosinusitis (CRS) is a prevalent disease with a high annual cost of treatment. Immune deficiencies are more common in individuals with CRS and should be especially considered in those patients who are refractory to medical and surgical therapy. Areas covered: We performed a literature search in PubMed of the terms "immunodeficiency" and "sinusitis" or "rhinosinusitis" from 2006 through March 2016. All abstracts were reviewed to determine if they pertained to human disease; relevant articles were evaluated in their entirety and included in this review. Expert commentary: CRS is a common disease; in those patients with frequent exacerbations or who are refractory to treatment, an immunodeficiency evaluation should be considered. Treatment includes vaccination, antibiotic therapy, immunoglobulin replacement and surgery.
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Affiliation(s)
- Sergio E Chiarella
- a Division of Allergy-Immunology, Department of Medicine , Northwestern University Feinberg School of Medicine , Chicago , IL , USA
| | - Leslie C Grammer
- a Division of Allergy-Immunology, Department of Medicine , Northwestern University Feinberg School of Medicine , Chicago , IL , USA
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52
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Kim S, Eliot M, Koestler DC, Houseman EA, Wetmur JG, Wiencke JK, Kelsey KT. Enlarged leukocyte referent libraries can explain additional variance in blood-based epigenome-wide association studies. Epigenomics 2016; 8:1185-92. [PMID: 27529193 DOI: 10.2217/epi-2016-0037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM We examined whether variation in blood-based epigenome-wide association studies could be more completely explained by augmenting existing reference DNA methylation libraries. MATERIALS & METHODS We compared existing and enhanced libraries in predicting variability in three publicly available 450K methylation datasets that collected whole-blood samples. Models were fit separately to each CpG site and used to estimate the additional variability when adjustments for cell composition were made with each library. RESULTS Calculation of the mean difference in the CpG-specific residual sums of squares error between models for an arthritis, aging and metabolic syndrome dataset, indicated that an enhanced library explained significantly more variation across all three datasets (p < 10(-3)). CONCLUSION Pathologically important immune cell subtypes can explain important variability in epigenome-wide association studies done in blood.
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Affiliation(s)
- Stephanie Kim
- Department of Epidemiology, Brown University School of Public Health, Providence, RI 02912, USA.,Department of Environmental Health, Boston University School of Public Health, Boston, MA 02118, USA
| | - Melissa Eliot
- Department of Epidemiology, Brown University School of Public Health, Providence, RI 02912, USA
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KA 66160, USA
| | - Eugene A Houseman
- Oregon State University College of Public Health & Human Sciences, Corvallis, OR 97331, USA
| | - James G Wetmur
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University School of Public Health, Providence, RI 02912, USA.,Department of Laboratory Medicine & Pathology, Brown University, Providence, RI 02912, USA
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Almamun M, Levinson BT, van Swaay AC, Johnson NT, McKay SD, Arthur GL, Davis JW, Taylor KH. Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia. Epigenetics 2016; 10:882-90. [PMID: 26308964 PMCID: PMC4622668 DOI: 10.1080/15592294.2015.1078050] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer diagnosed in children under the age of 15. In addition to genetic aberrations, epigenetic modifications such as DNA methylation are altered in cancer and impact gene expression. To identify epigenetic alterations in ALL, genome-wide methylation profiles were generated using the methylated CpG island recovery assay followed by next-generation sequencing. More than 25,000 differentially methylated regions (DMR) were observed in ALL patients with ∼90% present within intronic or intergenic regions. To determine the regulatory potential of the DMR, whole-transcriptome analysis was performed and integrated with methylation data. Aberrant promoter methylation was associated with the altered expression of genes involved in transcriptional regulation, apoptosis, and proliferation. Novel enhancer-like sequences were identified within intronic and intergenic DMR. Aberrant methylation in these regions was associated with the altered expression of neighboring genes involved in cell cycle processes, lymphocyte activation and apoptosis. These genes include potential epi-driver genes, such as SYNE1, PTPRS, PAWR, HDAC9, RGCC, MCOLN2, LYN, TRAF3, FLT1, and MELK, which may provide a selective advantage to leukemic cells. In addition, the differential expression of epigenetic modifier genes, pseudogenes, and non-coding RNAs was also observed accentuating the role of erroneous epigenetic gene regulation in ALL.
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Affiliation(s)
- Md Almamun
- a Department of Pathology and Anatomical Sciences ; University of Missouri-Columbia ; Columbia , MO USA
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54
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Köhrer S, Havranek O, Seyfried F, Hurtz C, Coffey GP, Kim E, Hacken ET, Jäger U, Vanura K, O’Brien S, Thomas DA, Kantarjian H, Ghosh D, Wang Z, Zhang M, Ma W, Jumaa H, Debatin KM, Müschen M, Meyer LH, Davis RE, Burger JA. Pre-BCR signaling in precursor B-cell acute lymphoblastic leukemia regulates PI3K/AKT, FOXO1 and MYC, and can be targeted by SYK inhibition. Leukemia 2016; 30:1246-54. [PMID: 26847027 PMCID: PMC5459356 DOI: 10.1038/leu.2016.9] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/20/2015] [Accepted: 12/23/2015] [Indexed: 12/11/2022]
Abstract
Precursor-B-cell receptor (pre-BCR) signaling and spleen tyrosine kinase (SYK) recently were introduced as therapeutic targets for patients with B-cell acute lymphoblastic leukemia (B-ALL), but the importance of this pathway in B-ALL subsets and mechanism of downstream signaling have not fully been elucidated. Here, we provide new detailed insight into the mechanism of pre-BCR signaling in B-ALL. We compared the effects of pharmacological and genetic disruption of pre-BCR signaling in vitro and in mouse models for B-ALL, demonstrating exquisite dependency of pre-BCR(+) B-ALL, but not other B-ALL subsets, on this signaling pathway. We demonstrate that SYK, PI3K/AKT, FOXO1 and MYC are important downstream mediators of pre-BCR signaling in B-ALL. Furthermore, we define a characteristic immune phenotype and gene expression signature of pre-BCR(+) ALL to distinguish them from other B-ALL subsets. These data provide comprehensive new insight into pre-BCR signaling in B-ALL and corroborate pre-BCR signaling and SYK as promising new therapeutic targets in pre-BCR(+) B-ALL.
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Affiliation(s)
- Stefan Köhrer
- Department of Leukemia, Unit 428, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States, 77030
| | - Ondrej Havranek
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States, 77030
| | - Felix Seyfried
- Ulm University Medical Center, Department of Pediatrics and Adolescent Medicine, Ulm, Germany
| | - Christian Hurtz
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143
| | | | - Ekaterina Kim
- Department of Leukemia, Unit 428, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States, 77030
| | - Elisa ten Hacken
- Department of Leukemia, Unit 428, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States, 77030
| | - Ulrich Jäger
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Katrina Vanura
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Susan O’Brien
- Department of Leukemia, Unit 428, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States, 77030
| | - Deborah A. Thomas
- Department of Leukemia, Unit 428, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States, 77030
| | - Hagop Kantarjian
- Department of Leukemia, Unit 428, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States, 77030
| | - Dipanjan Ghosh
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States, 77030
| | - Zhiqiang Wang
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States, 77030
| | - Min Zhang
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States, 77030
| | - Wencai Ma
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States, 77030
| | - Hassan Jumaa
- Ulm University, Department of Immunology, Ulm, Germany
| | - Klaus-Michael Debatin
- Ulm University Medical Center, Department of Pediatrics and Adolescent Medicine, Ulm, Germany
| | - Markus Müschen
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143
| | - Lüder H. Meyer
- Ulm University Medical Center, Department of Pediatrics and Adolescent Medicine, Ulm, Germany
| | - R. Eric Davis
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States, 77030
| | - Jan A. Burger
- Department of Leukemia, Unit 428, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States, 77030
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Epigenetics in Kidney Transplantation: Current Evidence, Predictions, and Future Research Directions. Transplantation 2016; 100:23-38. [PMID: 26356174 DOI: 10.1097/tp.0000000000000878] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Epigenetic modifications are changes to the genome that occur without any alteration in DNA sequence. These changes include cytosine methylation of DNA at cytosine-phosphate diester-guanine dinucleotides, histone modifications, microRNA interactions, and chromatin remodeling complexes. Epigenetic modifications may exert their effect independently or complementary to genetic variants and have the potential to modify gene expression. These modifications are dynamic, potentially heritable, and can be induced by environmental stimuli or drugs. There is emerging evidence that epigenetics play an important role in health and disease. However, the impact of epigenetic modifications on the outcomes of kidney transplantation is currently poorly understood and deserves further exploration. Kidney transplantation is the best treatment option for end-stage renal disease, but allograft loss remains a significant challenge that leads to increased morbidity and return to dialysis. Epigenetic modifications may influence the activation, proliferation, and differentiation of the immune cells, and therefore may have a critical role in the host immune response to the allograft and its outcome. The epigenome of the donor may also impact kidney graft survival, especially those epigenetic modifications associated with early transplant stressors (e.g., cold ischemia time) and donor aging. In the present review, we discuss evidence supporting the role of epigenetic modifications in ischemia-reperfusion injury, host immune response to the graft, and graft response to injury as potential new tools for the diagnosis and prediction of graft function, and new therapeutic targets for improving outcomes of kidney transplantation.
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Rodríguez-Cortez VC, Del Pino-Molina L, Rodríguez-Ubreva J, López-Granados E, Ballestar E. Dissecting Epigenetic Dysregulation of Primary Antibody Deficiencies. J Clin Immunol 2016; 36 Suppl 1:48-56. [PMID: 26984849 DOI: 10.1007/s10875-016-0267-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/07/2016] [Indexed: 01/04/2023]
Abstract
Primary antibody deficiencies (PADs), the most prevalent inherited primary immunodeficiencies (PIDs), are associated with a wide range of genetic alterations (both monogenic or polygenic) in B cell-specific genes. However, correlations between the genotype and clinical manifestations are not evident in all cases indicating that genetic interactions, environmental and epigenetic factors may have a role in PAD pathogenesis. The recent identification of key defects in DNA methylation in common variable immunodeficiency as well as the multiple evidences on the role of epigenetic control during B cell differentiation, activation and during antibody formation highlight the importance of investing research efforts in dissecting the participation of epigenetic defects in this group of diseases. This review focuses on the role of epigenetic control in B cell biology which can provide clues for the study of potential novel pathogenic defects involved in PADs.
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Affiliation(s)
- Virginia C Rodríguez-Cortez
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Lucia Del Pino-Molina
- Clinical Immunology Department, University Hospital La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
- Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Javier Rodríguez-Ubreva
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, University Hospital La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
- Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Esteban Ballestar
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain.
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57
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Wiencke JK, Butler R, Hsuang G, Eliot M, Kim S, Sepulveda MA, Siegel D, Houseman EA, Kelsey KT. The DNA methylation profile of activated human natural killer cells. Epigenetics 2016; 11:363-80. [PMID: 26967308 DOI: 10.1080/15592294.2016.1163454] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Natural killer (NK) cells are now recognized to exhibit characteristics akin to cells of the adaptive immune system. The generation of adaptive memory is linked to epigenetic reprogramming including alterations in DNA methylation. The study herein found reproducible genome wide DNA methylation changes associated with human NK cell activation. Activation led predominately to CpG hypomethylation (81% of significant loci). Bioinformatics analysis confirmed that non-coding and gene-associated differentially methylated sites (DMS) are enriched for immune related functions (i.e., immune cell activation). Known DNA methylation-regulated immune loci were also identified in activated NK cells (e.g., TNFA, LTA, IL13, CSF2). Twenty-one loci were designated high priority and further investigated as potential markers of NK activation. BHLHE40 was identified as a viable candidate for which a droplet digital PCR assay for demethylation was developed. The assay revealed high demethylation in activated NK cells and low demethylation in naïve NK, T- and B-cells. We conclude the NK cell methylome is plastic with potential for remodeling. The differentially methylated region signature of activated NKs revealed similarities with T cell activation, but also provided unique biomarker candidates of NK activation, which could be useful in epigenome-wide association studies to interrogate the role of NK subtypes in global methylation changes associated with exposures and/or disease states.
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Affiliation(s)
- John K Wiencke
- a Department of Neurological Surgery , University of California San Francisco , San Francisco , CA
| | - Rondi Butler
- b Brown University , Department of Epidemiology , Providence , RI
| | - George Hsuang
- a Department of Neurological Surgery , University of California San Francisco , San Francisco , CA
| | - Melissa Eliot
- b Brown University , Department of Epidemiology , Providence , RI
| | - Stephanie Kim
- b Brown University , Department of Epidemiology , Providence , RI
| | - Manuel A Sepulveda
- d Janssen Oncology Therapeutic Area, Janssen Research and Development, LLC, Pharmaceutical Companies of Johnson & Johnson , 1400 Welsh and McKean Roads, Spring House , PA
| | - Derick Siegel
- d Janssen Oncology Therapeutic Area, Janssen Research and Development, LLC, Pharmaceutical Companies of Johnson & Johnson , 1400 Welsh and McKean Roads, Spring House , PA
| | - E Andres Houseman
- e University of Oregon, College of Public Health and Human Science , Corvallis , OR
| | - Karl T Kelsey
- b Brown University , Department of Epidemiology , Providence , RI.,c Department of Laboratory Medicine and Pathology , Providence , RI
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58
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Sharmin M, Bravo HC, Hannenhalli S. Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer. BMC Cancer 2016; 16:88. [PMID: 26868017 PMCID: PMC4750190 DOI: 10.1186/s12885-016-2128-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 02/04/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Large mega base-pair genomic regions show robust alterations in DNA methylation levels in multiple cancers. A vast majority of these regions are hypomethylated in cancers. These regions are generally enriched for CpG islands, Lamin Associated Domains and Large organized chromatin lysine modification domains, and are associated with stochastic variability in gene expression. Given the size and consistency of hypomethylated blocks (HMB) across cancer types, we hypothesized that the immediate causes of methylation instability are likely to be encoded in the genomic region near HMB boundaries, in terms of specific genomic or epigenomic signatures. However, a detailed characterization of the HMB boundaries has not been reported. METHOD Here, we focused on ~13 k HMBs, encompassing approximately half of the genome, identified in colon cancer. We modeled the genomic features of HMB boundaries by Random Forest to identify their salient features, in terms of transcription factor (TF) binding motifs. Additionally we analyzed various epigenomic marks, and chromatin structural features of HMB boundaries relative to the non-HMB genomic regions. RESULT We found that the classical promoter epigenomic mark--H3K4me3, is highly enriched at HMB boundaries, as are CTCF bound sites. HMB boundaries harbor distinct combinations of TF motifs. Our Random Forest model based on TF motifs can accurately distinguish boundaries not only from regions inside and outside HMBs, but surprisingly, from active promoters as well. Interestingly, the distinguishing TFs and their interacting proteins are involved in chromatin modification. Finally, HMB boundaries significantly coincide with the boundaries of Topologically Associating Domains of the chromatin. CONCLUSION Our analyses suggest that the overall architecture of HMBs is guided by pre-existing chromatin architecture, and are associated with aberrant activity of promoter-like sequences at the boundary.
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Affiliation(s)
- Mahfuza Sharmin
- Department of Computer Science, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Héctor Corrada Bravo
- Department of Computer Science, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA.
| | - Sridhar Hannenhalli
- Department of Cell and Molecular Biology, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA.
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Fernández-Santiago R, Carballo-Carbajal I, Castellano G, Torrent R, Richaud Y, Sánchez-Danés A, Vilarrasa-Blasi R, Sánchez-Pla A, Mosquera JL, Soriano J, López-Barneo J, Canals JM, Alberch J, Raya Á, Vila M, Consiglio A, Martín-Subero JI, Ezquerra M, Tolosa E. Aberrant epigenome in iPSC-derived dopaminergic neurons from Parkinson's disease patients. EMBO Mol Med 2015; 7:1529-46. [PMID: 26516212 PMCID: PMC4693505 DOI: 10.15252/emmm.201505439] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 09/24/2015] [Accepted: 09/28/2015] [Indexed: 12/13/2022] Open
Abstract
The epigenomic landscape of Parkinson's disease (PD) remains unknown. We performed a genomewide DNA methylation and a transcriptome studies in induced pluripotent stem cell (iPSC)-derived dopaminergic neurons (DAn) generated by cell reprogramming of somatic skin cells from patients with monogenic LRRK2-associated PD (L2PD) or sporadic PD (sPD), and healthy subjects. We observed extensive DNA methylation changes in PD DAn, and of RNA expression, which were common in L2PD and sPD. No significant methylation differences were present in parental skin cells, undifferentiated iPSCs nor iPSC-derived neural cultures not-enriched-in-DAn. These findings suggest the presence of molecular defects in PD somatic cells which manifest only upon differentiation into the DAn cells targeted in PD. The methylation profile from PD DAn, but not from controls, resembled that of neural cultures not-enriched-in-DAn indicating a failure to fully acquire the epigenetic identity own to healthy DAn in PD. The PD-associated hypermethylation was prominent in gene regulatory regions such as enhancers and was related to the RNA and/or protein downregulation of a network of transcription factors relevant to PD (FOXA1, NR3C1, HNF4A, and FOSL2). Using a patient-specific iPSC-based DAn model, our study provides the first evidence that epigenetic deregulation is associated with monogenic and sporadic PD.
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Affiliation(s)
- Rubén Fernández-Santiago
- Laboratory of Neurodegenerative Disorders, Department of Neurology, Hospital Clínic of Barcelona Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) University of Barcelona (UB), Barcelona, Spain Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain Cell Therapy Program, Faculty of Medicine, University of Barcelona (UB), Barcelona, Spain
| | - Iria Carballo-Carbajal
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain Neurodegenerative Diseases Research Laboratory, Hospital Vall d'Hebron Vall d'Hebron Research Institute (VHIR) Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Giancarlo Castellano
- Department of Pathological Anatomy, Pharmacology and Microbiology, University of Barcelona (UB) Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Roger Torrent
- Institute for Biomedicine (IBUB) University of Barcelona (UB), Barcelona, Spain
| | - Yvonne Richaud
- Control of Stem Cell Potency Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain Centre for Networked Biomedical Research on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN), Zaragoza, Spain
| | | | - Roser Vilarrasa-Blasi
- Department of Pathological Anatomy, Pharmacology and Microbiology, University of Barcelona (UB) Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Alex Sánchez-Pla
- Department of Statistics, University of Barcelona (UB), Barcelona, Spain Department of Statistics, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - José Luis Mosquera
- Department of Statistics, University of Barcelona (UB), Barcelona, Spain
| | - Jordi Soriano
- Departament d'Estructura i Constituents de la Matèria (ECM), Facultat de Física, University of Barcelona (UB), Barcelona, Spain
| | - José López-Barneo
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain Institute of Biomedicine of Seville (IBiS) Hospital Universitario Virgen del Rocío Consejo Superior de Investigaciones Científicas (CSIC) University of Seville, Seville, Spain
| | - Josep M Canals
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain Cell Therapy Program, Faculty of Medicine, University of Barcelona (UB), Barcelona, Spain Department of Cell Biology, Immunology and Neuroscience, Faculty of Medicine, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) University of Barcelona (UB), Barcelona, Spain
| | - Jordi Alberch
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain Cell Therapy Program, Faculty of Medicine, University of Barcelona (UB), Barcelona, Spain Department of Cell Biology, Immunology and Neuroscience, Faculty of Medicine, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) University of Barcelona (UB), Barcelona, Spain
| | - Ángel Raya
- Control of Stem Cell Potency Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain Centre for Networked Biomedical Research on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN), Zaragoza, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Miquel Vila
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain Neurodegenerative Diseases Research Laboratory, Hospital Vall d'Hebron Vall d'Hebron Research Institute (VHIR) Universitat Autònoma de Barcelona (UAB), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Antonella Consiglio
- Institute for Biomedicine (IBUB) University of Barcelona (UB), Barcelona, Spain Department of Molecular and Translational Medicine, University of Brescia and National Institute of Neuroscience, Brescia, Italy
| | - José I Martín-Subero
- Department of Pathological Anatomy, Pharmacology and Microbiology, University of Barcelona (UB) Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mario Ezquerra
- Laboratory of Neurodegenerative Disorders, Department of Neurology, Hospital Clínic of Barcelona Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) University of Barcelona (UB), Barcelona, Spain Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain Cell Therapy Program, Faculty of Medicine, University of Barcelona (UB), Barcelona, Spain
| | - Eduardo Tolosa
- Laboratory of Neurodegenerative Disorders, Department of Neurology, Hospital Clínic of Barcelona Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) University of Barcelona (UB), Barcelona, Spain Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain Cell Therapy Program, Faculty of Medicine, University of Barcelona (UB), Barcelona, Spain Movement Disorders Unit, Department of Neurology, Hospital Clínic of Barcelona Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) University of Barcelona (UB), Barcelona, Spain
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Cell-Cycle-Dependent Reconfiguration of the DNA Methylome during Terminal Differentiation of Human B Cells into Plasma Cells. Cell Rep 2015; 13:1059-71. [DOI: 10.1016/j.celrep.2015.09.051] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 07/06/2015] [Accepted: 09/17/2015] [Indexed: 01/22/2023] Open
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Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, Kolarova J, Lu Q, Otto C, Wagener R, Arnolds J, Burkhardt B, Claviez A, Drexler HG, Eberth S, Eils R, Flicek P, Haas S, Humme M, Karsch D, Kerstens HH, Klapper W, Kreuz M, Lawerenz C, Lenzek D, Loeffler M, López C, MacLeod RA, Martens JH, Kulis M, Martín-Subero JI, Möller P, Nage I, Picelli S, Vater I, Rohde M, Rosenstiel P, Rosolowski M, Russell RB, Schilhabel M, Schlesner M, Stadler PF, Szczepanowski M, Trümper L, Stunnenberg HG, Küppers R, Ammerpohl O, Lichter P, Siebert R, Hoffmann S, Radlwimmer B. DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nat Genet 2015; 47:1316-1325. [PMID: 26437030 PMCID: PMC5444523 DOI: 10.1038/ng.3413] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 09/08/2015] [Indexed: 12/14/2022]
Abstract
Although Burkitt lymphomas and follicular lymphomas both have features of germinal center B cells, they are biologically and clinically quite distinct. Here we performed whole-genome bisulfite, genome and transcriptome sequencing in 13 IG-MYC translocation-positive Burkitt lymphoma, nine BCL2 translocation-positive follicular lymphoma and four normal germinal center B cell samples. Comparison of Burkitt and follicular lymphoma samples showed differential methylation of intragenic regions that strongly correlated with expression of associated genes, for example, genes active in germinal center dark-zone and light-zone B cells. Integrative pathway analyses of regions differentially methylated in Burkitt and follicular lymphomas implicated DNA methylation as cooperating with somatic mutation of sphingosine phosphate signaling, as well as the TCF3-ID3 and SWI/SNF complexes, in a large fraction of Burkitt lymphomas. Taken together, our results demonstrate a tight connection between somatic mutation, DNA methylation and transcriptional control in key B cell pathways deregulated differentially in Burkitt lymphoma and other germinal center B cell lymphomas.
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Affiliation(s)
- Helene Kretzmer
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
| | - Stephan H. Bernhart
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
| | - Wei Wang
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Andrea Haake
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Marc A. Weniger
- German ICGC MMML-Seq-project
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
| | - Anke K. Bergmann
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
- BLUEPRINT project
| | - Matthew J. Betts
- Cell Networks, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Enrique Carrillo-de-Santa-Pau
- BLUEPRINT project
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Gero Doose
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
| | - Jana Gutwein
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Julia Richter
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Volker Hovestadt
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Bingding Huang
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
| | - Daniel Rico
- BLUEPRINT project
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Frank Jühling
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Julia Kolarova
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Qianhao Lu
- Cell Networks, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Christian Otto
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Rabea Wagener
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Judith Arnolds
- Department of Otorhinolaryngology, University of Duisburg-Essen, Essen, Germany
| | - Birgit Burkhardt
- German ICGC MMML-Seq-project
- University Hospital Muenster - Pediatric Hematology and Oncology, Münster Germany
| | - Alexander Claviez
- German ICGC MMML-Seq-project
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Hans G. Drexler
- Leibniz-Institut DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sonja Eberth
- German ICGC MMML-Seq-project
- Leibniz-Institut DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Department of Hematology and Oncology, Georg-Augusts-University of Göttingen, Göttingen, Germany
| | - Roland Eils
- German ICGC MMML-Seq-project
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
- Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Paul Flicek
- BLUEPRINT project
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Siegfried Haas
- German ICGC MMML-Seq-project
- Friedrich-Ebert Hospital Neumuenster, Clinics for Haematology, Oncology and Nephrology, Neumünster, Germany
| | - Michael Humme
- German ICGC MMML-Seq-project
- Institute of Pathology, Charité – University Medicine Berlin, Berlin, Germany
| | - Dennis Karsch
- German ICGC MMML-Seq-project
- Department of Internal Medicine II: Hematology and Oncology, University Medical Centre, Campus Kiel, Kiel, Germany
| | - Hinrik H.D. Kerstens
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - Wolfram Klapper
- German ICGC MMML-Seq-project
- Hematopathology Section, Christian-Albrechts-University, Kiel, Germany
| | - Markus Kreuz
- German ICGC MMML-Seq-project
- BLUEPRINT project
- Institute for Medical Informatics Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Chris Lawerenz
- German ICGC MMML-Seq-project
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
| | - Dido Lenzek
- German ICGC MMML-Seq-project
- Institute of Pathology, Charité – University Medicine Berlin, Berlin, Germany
| | - Markus Loeffler
- German ICGC MMML-Seq-project
- BLUEPRINT project
- Institute for Medical Informatics Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Cristina López
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Roderick A.F. MacLeod
- Leibniz-Institut DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Joost H.A. Martens
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - Marta Kulis
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - José Ignacio Martín-Subero
- BLUEPRINT project
- Departamento de Anatomía Patológica, Farmacología y Microbiología, Universitat de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Peter Möller
- German ICGC MMML-Seq-project
- Institute of Pathology, Medical Faculty of the Ulm University, Ulm, Germany
| | - Inga Nage
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Simone Picelli
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Inga Vater
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Marius Rohde
- German ICGC MMML-Seq-project
- University Hospital Giessen, Pediatric Hematology and Oncology, Giessen, Germany
| | - Philip Rosenstiel
- German ICGC MMML-Seq-project
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Maciej Rosolowski
- German ICGC MMML-Seq-project
- Institute for Medical Informatics Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Robert B. Russell
- Cell Networks, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Markus Schilhabel
- German ICGC MMML-Seq-project
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Matthias Schlesner
- German ICGC MMML-Seq-project
- Deutsches Krebsforschungszentrum Heidelberg (DKFZ), Division Theoretical Bioinformatics, Heidelberg, Germany
| | - Peter F. Stadler
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
- RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany
| | | | - Lorenz Trümper
- German ICGC MMML-Seq-project
- Department of Hematology and Oncology, Georg-Augusts-University of Göttingen, Göttingen, Germany
| | - Hendrik G. Stunnenberg
- BLUEPRINT project
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen, Netherlands
| | - Ralf Küppers
- German ICGC MMML-Seq-project
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
- BLUEPRINT project
| | - Ole Ammerpohl
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Peter Lichter
- German ICGC MMML-Seq-project
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
| | - Reiner Siebert
- German ICGC MMML-Seq-project
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
- BLUEPRINT project
| | - Steve Hoffmann
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
- German ICGC MMML-Seq-project
- BLUEPRINT project
| | - Bernhard Radlwimmer
- German ICGC MMML-Seq-project
- German Cancer Research Center (DKFZ), Division Molecular Genetics, Heidelberg, Germany
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Lee ST, Wiemels JL. Genome-wide CpG island methylation and intergenic demethylation propensities vary among different tumor sites. Nucleic Acids Res 2015; 44:1105-17. [PMID: 26464434 PMCID: PMC4756811 DOI: 10.1093/nar/gkv1038] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 09/30/2015] [Indexed: 12/20/2022] Open
Abstract
The epigenetic landscape of cancer includes both focal hypermethylation and broader hypomethylation in a genome-wide manner. By means of a comprehensive genomic analysis on 6637 tissues of 21 tumor types, we here show that the degrees of overall methylation in CpG island (CGI) and demethylation in intergenic regions, defined as ‘backbone’, largely vary among different tumors. Depending on tumor type, both CGI methylation and backbone demethylation are often associated with clinical, epidemiological and biological features such as age, sex, smoking history, anatomic location, histological type and grade, stage, molecular subtype and biological pathways. We found connections between CGI methylation and hypermutability, microsatellite instability, IDH1 mutation, 19p gain and polycomb features, and backbone demethylation with chromosomal instability, NSD1 and TP53 mutations, 5q and 19p loss and long repressive domains. These broad epigenetic patterns add a new dimension to our understanding of tumor biology and its clinical implications.
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Affiliation(s)
- Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, 120752, Republic of Korea
| | - Joseph L Wiemels
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, CA 94158, USA
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63
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Rodriguez RM, Lopez-Larrea C, Suarez-Alvarez B. Epigenetic dynamics during CD4+ T cells lineage commitment. Int J Biochem Cell Biol 2015; 67:75-85. [DOI: 10.1016/j.biocel.2015.04.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 04/27/2015] [Accepted: 04/29/2015] [Indexed: 02/06/2023]
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64
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Mallik S, Maulik U. MiRNA-TF-gene network analysis through ranking of biomolecules for multi-informative uterine leiomyoma dataset. J Biomed Inform 2015; 57:308-19. [PMID: 26297985 DOI: 10.1016/j.jbi.2015.08.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 06/26/2015] [Accepted: 08/11/2015] [Indexed: 12/12/2022]
Abstract
Gene ranking is an important problem in bioinformatics. Here, we propose a new framework for ranking biomolecules (viz., miRNAs, transcription-factors/TFs and genes) in a multi-informative uterine leiomyoma dataset having both gene expression and methylation data using (statistical) eigenvector centrality based approach. At first, genes that are both differentially expressed and methylated, are identified using Limma statistical test. A network, comprising these genes, corresponding TFs from TRANSFAC and ITFP databases, and targeter miRNAs from miRWalk database, is then built. The biomolecules are then ranked based on eigenvector centrality. Our proposed method provides better average accuracy in hub gene and non-hub gene classifications than other methods. Furthermore, pre-ranked Gene set enrichment analysis is applied on the pathway database as well as GO-term databases of Molecular Signatures Database with providing a pre-ranked gene-list based on different centrality values for comparing among the ranking methods. Finally, top novel potential gene-markers for the uterine leiomyoma are provided.
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Affiliation(s)
- Saurav Mallik
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata 700108, India.
| | - Ujjwal Maulik
- Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India.
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65
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Almamun M, Levinson BT, Gater ST, Schnabel RD, Arthur GL, Davis JW, Taylor KH. Genome-wide DNA methylation analysis in precursor B-cells. Epigenetics 2015; 9:1588-95. [PMID: 25484143 PMCID: PMC4622941 DOI: 10.4161/15592294.2014.983379] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is responsible for regulating gene expression and cellular differentiation and for maintaining genomic stability during normal human development. Furthermore, it plays a significant role in the regulation of hematopoiesis. In order to elucidate the influence of DNA methylation during B-cell development, genome-wide DNA methylation status of pro-B, pre-BI, pre-BII, and naïve-B-cells isolated from human umbilical cord blood was determined using the methylated CpG island recovery assay followed by next generation sequencing. On average, 182–200 million sequences were generated for each precursor B-cell subset in 10 biological replicates. An overall decrease in methylation was observed during the transition from pro-B to pre-BI, whereas no differential methylation was observed in the pre-BI to pre-BII transition or in the pre-BII to naïve B-cell transition. Most of the methylated regions were located within intergenic and intronic regions not present in a CpG island context. Putative novel enhancers were identified in these regions that were differentially methylated between pro-B and pre-BI cells. The genome-wide methylation profiles are publically available and may be used to gain a better understanding of the involvement of atypical DNA methylation in the pathogenesis of malignancies associated with precursor B-cells.
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Key Words
- CG dinucleotide
- CLP, common lymphoid progenitor cells
- CpGI, CpG island
- DMRs, differentially methylated regions
- DNA methylation
- FDR, false discovery rate.
- H3K27ac, histone H3 lysine 27 acetylation
- H3K4me1, histone H3 lysine 4 monomethylation
- HCB, human umbilical cord blood
- HSCs, haematopoietic stem cells
- MBDs, methyl CpG binding domains
- MIRA-seq, methylated CpG island recovery assay (MIRA) followed by next generation sequencing
- MeCP2, methyl CpG binding protein 2
- Pre-B, precursor B-cell; CD
- Pro-B, progenitor B-cell
- ROIs, regions of interest
- TFs, transcription factors
- acute lymphoblastic leukemia; CpG
- cluster of differentiation; ALL
- enhancer
- next-generation sequencing
- precursor B-cell
- umbilical cord blood
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Affiliation(s)
- Md Almamun
- a Department of Pathology and Anatomical Sciences ; University of Missouri-Columbia ; Columbia , MO USA
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66
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Monozygotic twins discordant for common variable immunodeficiency reveal impaired DNA demethylation during naïve-to-memory B-cell transition. Nat Commun 2015; 6:7335. [PMID: 26081581 PMCID: PMC4557293 DOI: 10.1038/ncomms8335] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 04/28/2015] [Indexed: 02/06/2023] Open
Abstract
Common variable immunodeficiency (CVID), the most frequent primary immunodeficiency characterized by loss of B-cell function, depends partly on genetic defects, and epigenetic changes are thought to contribute to its aetiology. Here we perform a high-throughput DNA methylation analysis of this disorder using a pair of CVID-discordant MZ twins and show predominant gain of DNA methylation in CVID B cells with respect to those from the healthy sibling in critical B lymphocyte genes, such as PIK3CD, BCL2L1, RPS6KB2, TCF3 and KCNN4. Individual analysis confirms hypermethylation of these genes. Analysis in naive, unswitched and switched memory B cells in a CVID patient cohort shows impaired ability to demethylate and upregulate these genes in transitioning from naive to memory cells in CVID. Our results not only indicate a role for epigenetic alterations in CVID but also identify relevant DNA methylation changes in B cells that could explain the clinical manifestations of CVID individuals.
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67
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Whole-genome fingerprint of the DNA methylome during human B cell differentiation. Nat Genet 2015; 47:746-56. [PMID: 26053498 DOI: 10.1038/ng.3291] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/03/2015] [Indexed: 02/06/2023]
Abstract
We analyzed the DNA methylome of ten subpopulations spanning the entire B cell differentiation program by whole-genome bisulfite sequencing and high-density microarrays. We observed that non-CpG methylation disappeared upon B cell commitment, whereas CpG methylation changed extensively during B cell maturation, showing an accumulative pattern and affecting around 30% of all measured CpG sites. Early differentiation stages mainly displayed enhancer demethylation, which was associated with upregulation of key B cell transcription factors and affected multiple genes involved in B cell biology. Late differentiation stages, in contrast, showed extensive demethylation of heterochromatin and methylation gain at Polycomb-repressed areas, and genes with apparent functional impact in B cells were not affected. This signature, which has previously been linked to aging and cancer, was particularly widespread in mature cells with an extended lifespan. Comparing B cell neoplasms with their normal counterparts, we determined that they frequently acquire methylation changes in regions already undergoing dynamic methylation during normal B cell differentiation.
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68
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Tallmadge RL, Shen L, Tseng CT, Miller SC, Barry J, Felippe MJB. Bone marrow transcriptome and epigenome profiles of equine common variable immunodeficiency patients unveil block of B lymphocyte differentiation. Clin Immunol 2015; 160:261-76. [PMID: 25988861 DOI: 10.1016/j.clim.2015.05.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 05/06/2015] [Accepted: 05/08/2015] [Indexed: 12/30/2022]
Abstract
Common variable immunodeficiency (CVID) is a late-onset humoral deficiency characterized by B lymphocyte dysfunction or loss, decreased immunoglobulin production, and recurrent bacterial infections. CVID is the most frequent human primary immunodeficiency but still presents challenges in the understanding of its etiology and treatment. CVID in equine patients manifests with a natural impairment of B lymphocyte differentiation, and is a unique model to identify genetic and epigenetic mechanisms of disease. Bone marrow transcriptome analyses revealed decreased expression of genes indicative of the pro-B cell differentiation stage, importantly PAX5 (p≤0.023). We hypothesized that aberrant epigenetic regulation caused PAX5 gene silencing, resulting in the late-onset and non-familial manifestation of CVID. A significant increase in PAX5 enhancer region methylation was identified in equine CVID patients by genome-wide reduced-representation bisulfite sequencing and bisulfite PCR sequencing (p=0.000). Thus, we demonstrate that integrating transcriptomics and epigenetics in CVID enlightens potential mechanisms of dysfunctional B lymphopoiesis or function.
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Affiliation(s)
- Rebecca L Tallmadge
- Equine Immunology Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Lishuang Shen
- Cornell Mammalian Cell Reprogramming Core, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Chia T Tseng
- Equine Immunology Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Steven C Miller
- Equine Immunology Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Jay Barry
- Cornell Statistical Consulting Unit, Cornell University, Ithaca, NY 14853, USA
| | - M Julia B Felippe
- Equine Immunology Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
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Yang X, Shao X, Gao L, Zhang S. Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin. Hum Mol Genet 2015; 24:4374-84. [DOI: 10.1093/hmg/ddv172] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/05/2015] [Indexed: 12/23/2022] Open
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70
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Lee ST, Muench MO, Fomin ME, Xiao J, Zhou M, de Smith A, Martín-Subero JI, Heath S, Houseman EA, Roy R, Wrensch M, Wiencke J, Metayer C, Wiemels JL. Epigenetic remodeling in B-cell acute lymphoblastic leukemia occurs in two tracks and employs embryonic stem cell-like signatures. Nucleic Acids Res 2015; 43:2590-602. [PMID: 25690899 PMCID: PMC4357708 DOI: 10.1093/nar/gkv103] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We investigated DNA methylomes of pediatric B-cell acute lymphoblastic leukemias (B-ALLs) using whole-genome bisulfite sequencing and high-definition microarrays, along with RNA expression profiles. Epigenetic alteration of B-ALLs occurred in two tracks: de novo methylation of small functional compartments and demethylation of large inter-compartmental backbones. The deviations were exaggerated in lamina-associated domains, with differences corresponding to methylation clusters and/or cytogenetic groups. Our data also suggested a pivotal role of polycomb and CTBP2 in de novo methylation, which may be traced back to bivalency status of embryonic stem cells. Driven by these potent epigenetic modulations, suppression of polycomb target genes was observed along with disruption of developmental fate and cell cycle and mismatch repair pathways and altered activities of key upstream regulators.
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Affiliation(s)
- Seung-Tae Lee
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 120752, Republic of Korea
| | - Marcus O Muench
- Blood Systems Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA Liver Center and Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Marina E Fomin
- Blood Systems Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Jianqiao Xiao
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Mi Zhou
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Adam de Smith
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - José I Martín-Subero
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Simon Heath
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08036, Spain
| | - E Andres Houseman
- Department of Public Health, Oregon State University, Corvallis, OR, 97331 USA
| | - Ritu Roy
- Cancer Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California at San Francisco, San Francisco, CA 94158, USA
| | - John Wiencke
- Department of Neurological Surgery, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Catherine Metayer
- Division of Epidemiology, School of Public Health, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Joseph L Wiemels
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA Department of Neurological Surgery, University of California at San Francisco, San Francisco, CA 94158, USA
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Agirre X, Castellano G, Pascual M, Heath S, Kulis M, Segura V, Bergmann A, Esteve A, Merkel A, Raineri E, Agueda L, Blanc J, Richardson D, Clarke L, Datta A, Russiñol N, Queirós AC, Beekman R, Rodríguez-Madoz JR, San José-Enériz E, Fang F, Gutiérrez NC, García-Verdugo JM, Robson MI, Schirmer EC, Guruceaga E, Martens JHA, Gut M, Calasanz MJ, Flicek P, Siebert R, Campo E, Miguel JFS, Melnick A, Stunnenberg HG, Gut IG, Prosper F, Martín-Subero JI. Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers. Genome Res 2015; 25:478-87. [PMID: 25644835 PMCID: PMC4381520 DOI: 10.1101/gr.180240.114] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 01/22/2015] [Indexed: 12/20/2022]
Abstract
While analyzing the DNA methylome of multiple myeloma (MM), a plasma cell neoplasm, by whole-genome bisulfite sequencing and high-density arrays, we observed a highly heterogeneous pattern globally characterized by regional DNA hypermethylation embedded in extensive hypomethylation. In contrast to the widely reported DNA hypermethylation of promoter-associated CpG islands (CGIs) in cancer, hypermethylated sites in MM, as opposed to normal plasma cells, were located outside CpG islands and were unexpectedly associated with intronic enhancer regions defined in normal B cells and plasma cells. Both RNA-seq and in vitro reporter assays indicated that enhancer hypermethylation is globally associated with down-regulation of its host genes. ChIP-seq and DNase-seq further revealed that DNA hypermethylation in these regions is related to enhancer decommissioning. Hypermethylated enhancer regions overlapped with binding sites of B cell-specific transcription factors (TFs) and the degree of enhancer methylation inversely correlated with expression levels of these TFs in MM. Furthermore, hypermethylated regions in MM were methylated in stem cells and gradually became demethylated during normal B-cell differentiation, suggesting that MM cells either reacquire epigenetic features of undifferentiated cells or maintain an epigenetic signature of a putative myeloma stem cell progenitor. Overall, we have identified DNA hypermethylation of developmentally regulated enhancers as a new type of epigenetic modification associated with the pathogenesis of MM.
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Affiliation(s)
- Xabier Agirre
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, 31008 Pamplona, Spain;
| | - Giancarlo Castellano
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Marien Pascual
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, 31008 Pamplona, Spain
| | - Simon Heath
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Marta Kulis
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Victor Segura
- Unidad de Bioinformática, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, 31008 Pamplona, Spain
| | - Anke Bergmann
- Institute of Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Anna Esteve
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Angelika Merkel
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Emanuele Raineri
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Lidia Agueda
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Julie Blanc
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - David Richardson
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge, CB10 1SD, United Kingdom
| | - Laura Clarke
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge, CB10 1SD, United Kingdom
| | - Avik Datta
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge, CB10 1SD, United Kingdom
| | - Nuria Russiñol
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Ana C Queirós
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Renée Beekman
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Juan R Rodríguez-Madoz
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, 31008 Pamplona, Spain
| | - Edurne San José-Enériz
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, 31008 Pamplona, Spain
| | - Fang Fang
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | | | - José M García-Verdugo
- Department of Cellular Morphology, University of Valencia, Unidad Mixta CIPF-UVEG, CIBERNED, 46100 Valencia, Spain
| | - Michael I Robson
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Eric C Schirmer
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Elisabeth Guruceaga
- Unidad de Bioinformática, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, 31008 Pamplona, Spain
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6500 HB Nijmegen, The Netherlands
| | - Marta Gut
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Maria J Calasanz
- Departamento de Genética, Universidad de Navarra, 31008 Pamplona, Spain
| | - Paul Flicek
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge, CB10 1SD, United Kingdom
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Elías Campo
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Jesús F San Miguel
- Clínica Universidad de Navarra, Universidad de Navarra, 31008 Pamplona, Spain
| | - Ari Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6500 HB Nijmegen, The Netherlands
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Felipe Prosper
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, 31008 Pamplona, Spain; Clínica Universidad de Navarra, Universidad de Navarra, 31008 Pamplona, Spain
| | - José I Martín-Subero
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain;
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72
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Rodriguez RM, Suarez-Alvarez B, Mosén-Ansorena D, García-Peydró M, Fuentes P, García-León MJ, Gonzalez-Lahera A, Macias-Camara N, Toribio ML, Aransay AM, Lopez-Larrea C. Regulation of the transcriptional program by DNA methylation during human αβ T-cell development. Nucleic Acids Res 2014; 43:760-74. [PMID: 25539926 PMCID: PMC4333391 DOI: 10.1093/nar/gku1340] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Thymocyte differentiation is a complex process involving well-defined sequential developmental stages that ultimately result in the generation of mature T-cells. In this study, we analyzed DNA methylation and gene expression profiles at successive human thymus developmental stages. Gain and loss of methylation occurred during thymocyte differentiation, but DNA demethylation was much more frequent than de novo methylation and more strongly correlated with gene expression. These changes took place in CpG-poor regions and were closely associated with T-cell differentiation and TCR function. Up to 88 genes that encode transcriptional regulators, some of whose functions in T-cell development are as yet unknown, were differentially methylated during differentiation. Interestingly, no reversion of accumulated DNA methylation changes was observed as differentiation progressed, except in a very small subset of key genes (RAG1, RAG2, CD8A, PTCRA, etc.), indicating that methylation changes are mostly unique and irreversible events. Our study explores the contribution of DNA methylation to T-cell lymphopoiesis and provides a fine-scale map of differentially methylated regions associated with gene expression changes. These can lay the molecular foundations for a better interpretation of the regulatory networks driving human thymopoiesis.
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Affiliation(s)
- Ramon M Rodriguez
- Department of Immunology, Hospital Universitario Central de Asturias, 33006 Oviedo, Spain
| | - Beatriz Suarez-Alvarez
- Cellular Biology in Renal Diseases Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - David Mosén-Ansorena
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Technological Park of Bizkaia - Building 801A, 48160 Derio, Spain
| | - Marina García-Peydró
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Patricia Fuentes
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - María J García-León
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Aintzane Gonzalez-Lahera
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Technological Park of Bizkaia - Building 801A, 48160 Derio, Spain
| | - Nuria Macias-Camara
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Technological Park of Bizkaia - Building 801A, 48160 Derio, Spain
| | - María L Toribio
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Ana M Aransay
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Technological Park of Bizkaia - Building 801A, 48160 Derio, Spain
| | - Carlos Lopez-Larrea
- Department of Immunology, Hospital Universitario Central de Asturias, 33006 Oviedo, Spain Fundación Renal 'Íñigo Álvarez de Toledo', 28003 Madrid, Spain
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73
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Yang Q, Wu X, Sun J, Cui J, Li L. Epigenetic Features Induced by Ischemia-Hypoxia in Cultured Rat Astrocytes. Mol Neurobiol 2014; 53:436-445. [DOI: 10.1007/s12035-014-9027-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/21/2014] [Indexed: 11/25/2022]
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74
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Qu Y, Lennartsson A, Gaidzik VI, Deneberg S, Karimi M, Bengtzén S, Höglund M, Bullinger L, Döhner K, Lehmann S. Differential methylation in CN-AML preferentially targets non-CGI regions and is dictated by DNMT3A mutational status and associated with predominant hypomethylation of HOX genes. Epigenetics 2014; 9:1108-19. [PMID: 24866170 DOI: 10.4161/epi.29315] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The extent and role of aberrant DNA methylation in promoter CpG islands (CGIs) have been extensively studied in leukemia and other malignancies. Still, CGIs represent only a small fraction of the methylome. We aimed to characterize genome-wide differential methylation of cytogenetically normal AML (CN-AML) cells compared with normal CD34(+) bone marrow cells using the Illumina 450K methylation array. Differential methylation in CN-AML was most prominent in genomic areas far from CGIs, in so called open sea regions. Furthermore, differential methylation was specifically found in genes encoding transcription factors (TFs), with WT1 being the most differentially methylated TF. Among genetic mutations in AML, DNMT3A mutations showed the most prominent association with the DNA methylation pattern, characterized by hypomethylation of CGIs (as compared with DNMT3A wild type cases). The differential methylation in DNMT3A mutant cells vs. wild type cells was predominantly found in HOX genes, which were hypomethylated. These results were confirmed and validated in an independent CN-AML cohort. In conclusion, we show that, in CN-AML, the most pronounced changes in DNA methylation occur in non-CGI regions and that DNMT3A mutations confer a pattern of global hypomethylation that specifically targets HOX genes.
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Affiliation(s)
- Ying Qu
- Center for Hematology and Regenerative Medicine (HERM); Department of Medicine Huddinge; Karolinska Institute; Stockholm, Sweden
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition; NOVUM; Karolinska Institutet; Stockholm, Sweden
| | - Verena I Gaidzik
- Department of Internal Medicine III; University Hospital of Ulm; Ulm, Germany
| | - Stefan Deneberg
- Center for Hematology and Regenerative Medicine (HERM); Department of Medicine Huddinge; Karolinska Institute; Stockholm, Sweden; Hematology Centre, M54; Karolinska University Hospital and Karolinska Institute; Stockholm, Sweden
| | - Mohsen Karimi
- Center for Hematology and Regenerative Medicine (HERM); Department of Medicine Huddinge; Karolinska Institute; Stockholm, Sweden
| | - Sofia Bengtzén
- Center for Hematology and Regenerative Medicine (HERM); Department of Medicine Huddinge; Karolinska Institute; Stockholm, Sweden
| | - Martin Höglund
- Department of Hematology; Uppsala University Hospital; Uppsala, Sweden
| | - Lars Bullinger
- Department of Internal Medicine III; University Hospital of Ulm; Ulm, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III; University Hospital of Ulm; Ulm, Germany
| | - Sören Lehmann
- Center for Hematology and Regenerative Medicine (HERM); Department of Medicine Huddinge; Karolinska Institute; Stockholm, Sweden; Hematology Centre, M54; Karolinska University Hospital and Karolinska Institute; Stockholm, Sweden
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75
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Zhao L, Sun MA, Li Z, Bai X, Yu M, Wang M, Liang L, Shao X, Arnovitz S, Wang Q, He C, Lu X, Chen J, Xie H. The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation. Genome Res 2014; 24:1296-307. [PMID: 24835587 PMCID: PMC4120083 DOI: 10.1101/gr.163147.113] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The faithful transmission of DNA methylation patterns through cell divisions is essential for the daughter cells to retain a proper cell identity. To achieve a comprehensive assessment of methylation fidelity, we implemented a genome-scale hairpin bisulfite sequencing approach to generate methylation data for DNA double strands simultaneously. We show here that methylation fidelity increases globally during differentiation of mouse embryonic stem cells (mESCs), and is particularly high in the promoter regions of actively expressed genes and positively correlated with active histone modification marks and binding of transcription factors. The majority of intermediately (40%–60%) methylated CpG dinucleotides are hemi-methylated and have low methylation fidelity, particularly in the differentiating mESCs. While 5-hmC and 5-mC tend to coexist, there is no significant correlation between 5-hmC levels and methylation fidelity. Our findings may shed new light on our understanding of the origins of methylation variations and the mechanisms underlying DNA methylation transmission.
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Affiliation(s)
- Lei Zhao
- Laboratory of Genome Variation and Precision Biomedicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming-An Sun
- Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24060, USA
| | - Zejuan Li
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois 60637, USA
| | - Xue Bai
- Laboratory of Genome Variation and Precision Biomedicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Miao Yu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Min Wang
- Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24060, USA
| | - Liji Liang
- Laboratory of Genome Variation and Precision Biomedicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojian Shao
- Laboratory of Genome Variation and Precision Biomedicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Stephen Arnovitz
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois 60637, USA
| | - Qianfei Wang
- Laboratory of Genome Variation and Precision Biomedicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Xuemei Lu
- Laboratory of Genome Variation and Precision Biomedicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianjun Chen
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois 60637, USA
| | - Hehuang Xie
- Laboratory of Genome Variation and Precision Biomedicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24060, USA; Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24060, USA
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76
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Langevin SM, Houseman EA, Accomando WP, Koestler DC, Christensen BC, Nelson HH, Karagas MR, Marsit CJ, Wiencke JK, Kelsey KT. Leukocyte-adjusted epigenome-wide association studies of blood from solid tumor patients. Epigenetics 2014; 9:884-95. [PMID: 24671036 DOI: 10.4161/epi.28575] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Epigenome-wide studies of DNA methylation using blood-derived DNA from cancer patients are complicated by the heterogeneity of cell types within blood and the associated cell lineage specification of DNA methylation signatures. Here, we applied a novel set of analytic approaches to assess the association between cancer case-status and DNA methylation adjusted for leukocyte variation using blood specimens from three case-control cancer studies (bladder: 223 cases, 205 controls; head and neck: 92 cases, 92 controls; and ovarian: 131 cases, 274 controls). Using previously published data on leukocyte-specific CpG loci and a recently described approach to deconvolute subject-specific blood composition, we performed an epigenome-wide analysis to examine the association between blood-based DNA methylation patterns and each of the three aforementioned solid tumor types adjusted for cellular heterogeneity in blood. After adjusting for leukocyte profile in our epigenome-wide analysis, the omnibus association between case-status and methylation was significant for all three studies (bladder cancer: P = 0.047; HNSCC: P = 0.013; ovarian cancer: P = 0.0002). Subsequent analyses revealed that CpG sites associated with cancer were enriched for transcription factor binding motifs involved with cancer-associated pathways. These results support the existence of cancer-associated DNA methylation profiles in the blood of solid tumor patients that are independent of alterations in normal leukocyte distributions. Adoption of the methods developed here will make it feasible to rigorously assess the influence of variability of normal leukocyte profiles when investigating cancer related changes in blood-based epigenome-wide association studies.
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Affiliation(s)
- Scott M Langevin
- Department of Environmental Health; University of Cincinnati College of Medicine; Cincinnati, OH USA; Department of Epidemiology; Brown University; Providence, RI USA
| | - E Andres Houseman
- Department of Biostatistics; Oregon State University College of Public Health and Human Sciences; Corvallis, OR USA
| | - William P Accomando
- Department of Pathology & Laboratory Medicine; Brown University; Providence, RI USA
| | - Devin C Koestler
- Department of Community and Family Medicine; Section of Biostatistics and Epidemiology; Dartmouth Medical School; Lebanon, NH USA
| | - Brock C Christensen
- Department of Community and Family Medicine; Section of Biostatistics and Epidemiology; Dartmouth Medical School; Lebanon, NH USA; Department of Pharmacology and Toxicology; Dartmouth Medical School; Lebanon, NH USA
| | - Heather H Nelson
- Division of Epidemiology and Community Health; University of Minnesota Masonic Cancer Center; Minneapolis, MN USA
| | - Margaret R Karagas
- Department of Community and Family Medicine; Section of Biostatistics and Epidemiology; Dartmouth Medical School; Lebanon, NH USA
| | - Carmen J Marsit
- Department of Community and Family Medicine; Section of Biostatistics and Epidemiology; Dartmouth Medical School; Lebanon, NH USA; Department of Pharmacology and Toxicology; Dartmouth Medical School; Lebanon, NH USA
| | - John K Wiencke
- Department of Neurological Surgery; University of California San Francisco; San Francisco, CA USA
| | - Karl T Kelsey
- Department of Epidemiology; Brown University; Providence, RI USA; Department of Pathology & Laboratory Medicine; Brown University; Providence, RI USA
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77
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Varela-Rey M, Iruarrizaga-Lejarreta M, Lozano JJ, Aransay AM, Fernandez AF, Lavin JL, Mósen-Ansorena D, Berdasco M, Turmaine M, Luka Z, Wagner C, Lu SC, Esteller M, Mirsky R, Jessen KR, Fraga MF, Martínez-Chantar ML, Mato JM, Woodhoo A. S-adenosylmethionine levels regulate the schwann cell DNA methylome. Neuron 2014; 81:1024-1039. [PMID: 24607226 PMCID: PMC3960855 DOI: 10.1016/j.neuron.2014.01.037] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2014] [Indexed: 10/25/2022]
Abstract
Axonal myelination is essential for rapid saltatory impulse conduction in the nervous system, and malformation or destruction of myelin sheaths leads to motor and sensory disabilities. DNA methylation is an essential epigenetic modification during mammalian development, yet its role in myelination remains obscure. Here, using high-resolution methylome maps, we show that DNA methylation could play a key gene regulatory role in peripheral nerve myelination and that S-adenosylmethionine (SAMe), the principal methyl donor in cytosine methylation, regulates the methylome dynamics during this process. Our studies also point to a possible role of SAMe in establishing the aberrant DNA methylation patterns in a mouse model of diabetic neuropathy, implicating SAMe in the pathogenesis of this disease. These critical observations establish a link between SAMe and DNA methylation status in a defined biological system, providing a mechanism that could direct methylation changes during cellular differentiation and in diverse pathological situations.
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Affiliation(s)
- Marta Varela-Rey
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain
| | - Marta Iruarrizaga-Lejarreta
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain
| | - Juan José Lozano
- Bioinformatic Platform, CIBERehd, Centre Esther Koplovitz (CEK), C/Rosselló 153 Subsuelo, 08036 Barcelona, Spain
| | - Ana María Aransay
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain
| | - Agustín F Fernandez
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - José Luis Lavin
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain
| | - David Mósen-Ansorena
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain
| | - María Berdasco
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 09908 Catalonia, Spain
| | - Marc Turmaine
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Zigmund Luka
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-0146, USA
| | - Conrad Wagner
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-0146, USA
| | - Shelly C Lu
- Division of Gastrointestinal and Liver Diseases, USC Research Center for Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 09908 Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010 Catalonia, Spain
| | - Rhona Mirsky
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Kristján R Jessen
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Mario F Fraga
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33006 Oviedo, Spain; Department of Immunology and Oncology, National Center for Biotechnology, CNB-CSIC, Cantoblanco, E-28049Madrid, Spain
| | - María L Martínez-Chantar
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain; Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, E-48080 Bilbao, Spain
| | - José M Mato
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain
| | - Ashwin Woodhoo
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia Technology Park, Derio, 48160 Bizkaia, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
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78
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Xiao J, Lee ST, Xiao Y, Ma X, Houseman EA, Hsu LI, Roy R, Wrensch M, de Smith AJ, Chokkalingam A, Buffler P, Wiencke JK, Wiemels JL. PTPRG inhibition by DNA methylation and cooperation with RAS gene activation in childhood acute lymphoblastic leukemia. Int J Cancer 2014; 135:1101-9. [PMID: 24496747 DOI: 10.1002/ijc.28759] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 01/24/2014] [Indexed: 01/12/2023]
Abstract
While the cytogenetic and genetic characteristics of childhood acute lymphoblastic leukemias (ALL) are well studied, less clearly understood are the contributing epigenetic mechanisms that influence the leukemia phenotype. Our previous studies and others identified gene mutation (RAS) and DNA methylation (FHIT) to be associated with the most common cytogenetic subgroup of childhood ALL, high hyperdiploidy (having five more chromosomes). We screened DNA methylation profiles, using a genome-wide high-dimension platform of 166 childhood ALLs and 6 normal pre-B cell samples and observed a strong association of DNA methylation status at the PTPRG locus in human samples with levels of PTPRG gene expression as well as with RAS gene mutation status. In the 293 cell line, we found that PTPRG expression induces dephosphorylation of ERK, a downstream RAS target that may be critical for mutant RAS-induced cell growth. In addition, PTPRG expression is upregulated by RAS activation under DNA hypomethylating conditions. An element within the PTPRG promoter is bound by the RAS-responsive transcription factor RREB1, also under hypomethylating conditions. In conclusion, we provide evidence that DNA methylation of the PTPRG gene is a complementary event in oncogenesis induced by RAS mutations. Evidence for additional roles for PTPR family member genes is also suggested. This provides a potential therapeutic target for RAS-related leukemias as well as insight into childhood ALL etiology and pathophysiology.
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Affiliation(s)
- Jianqiao Xiao
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA
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79
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Kile ML, Houseman EA, Baccarelli AA, Quamruzzaman Q, Rahman M, Mostofa G, Cardenas A, Wright RO, Christiani DC. Effect of prenatal arsenic exposure on DNA methylation and leukocyte subpopulations in cord blood. Epigenetics 2014; 9:774-82. [PMID: 24525453 DOI: 10.4161/epi.28153] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Prenatal arsenic exposure is associated with increased risk of disease in adulthood. This has led to considerable interest in arsenic's ability to disrupt fetal programming. Many studies report that arsenic exposure alters DNA methylation in whole blood but these studies did not adjust for cell mixture. In this study, we examined the relationship between arsenic in maternal drinking water collected ≤ 16 weeks gestational age and DNA methylation in cord blood (n = 44) adjusting for leukocyte-tagged differentially methylated regions. DNA methylation was quantified using the Infinium HumanMethylation 450 BeadChip array. Recursively partitioned mixture modeling examined the relationship between arsenic and methylation at 473,844 CpG sites. Median arsenic concentration in water was 12 µg/L (range<1- 510 µg/L). Log 10 arsenic was associated with altered DNA methylation across the epigenome (P = 0.002); however, adjusting for leukocyte distributions attenuated this association (P = 0.013). We also observed that arsenic had a strong effect on the distribution of leukocytes in cord blood. In adjusted models, every log 10 increase in maternal drinking water arsenic exposure was estimated to increase CD8+ T cells by 7.4% (P = 0.0004) and decrease in CD4+ T cells by 9.2% (P = 0.0002). These results show that prenatal exposure to arsenic had an exposure-dependent effect on specific T cell subpopulations in cord blood and altered DNA methylation in cord blood. Future research is needed to determine if these small changes in DNA methylation alter gene expression or are associated with adverse health effects.
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Affiliation(s)
- Molly L Kile
- Oregon State University; College of Public Health and Human Sciences; Corvallis, OR USA
| | - E Andres Houseman
- Oregon State University; College of Public Health and Human Sciences; Corvallis, OR USA
| | | | | | | | | | - Andres Cardenas
- Oregon State University; College of Public Health and Human Sciences; Corvallis, OR USA
| | - Robert O Wright
- Preventative Medicine and Pediatrics; Mt Sinai School of Medicine; New York, NY USA
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80
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Sibbons CM, Brenna JT, Lawrence P, Hoile SP, Clarke-Harris R, Lillycrop KA, Burdge GC. Effect of sex hormones on n-3 polyunsaturated fatty acid biosynthesis in HepG2 cells and in human primary hepatocytes. Prostaglandins Leukot Essent Fatty Acids 2014; 90:47-54. [PMID: 24411721 PMCID: PMC4046896 DOI: 10.1016/j.plefa.2013.12.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 01/25/2023]
Abstract
Female humans and rodents have been shown to have higher 22:6n-3 status and synthesis than males. It is unclear which sex hormone is involved. We investigated the specificity of the effects of physiological concentrations of sex hormones in vitro on the mRNA expression of genes involved in polyunsaturated fatty acid (PUFA) biosynthesis and on the conversion of [d5]-18:3n-3 to longer chain fatty acids. Progesterone, but not 17α-ethynylestradiol or testosterone, increased FADS2, FADS1, ELOVl 5 and ELOVl 2 mRNA expression in HepG2 cells, but only FADS2 in primary human hepatocytes. In HepG2 cells, these changes were accompanied by hypomethylation of specific CpG loci in the FADS2 promoter. Progesterone, not 17α-ethynylestradiol or testosterone, increased conversion of [d5]-18:3n-3 to 20:5n-3, 22:5n-3 and 22:6n-3. These findings show that progesterone increases n-3 PUFA biosynthesis by up-regulating the mRNA expression of genes involved in this pathway, possibly via changes in the epigenetic regulation of FADS2.
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Affiliation(s)
- Charlene M Sibbons
- Academic Unit of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - J Thomas Brenna
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States
| | - Peter Lawrence
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States
| | - Samuel P Hoile
- Academic Unit of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Rebecca Clarke-Harris
- Academic Unit of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Karen A Lillycrop
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK
| | - Graham C Burdge
- Academic Unit of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.
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81
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Xu L, Chen YC, Nakajima S, Chong J, Wang L, Lan L, Zhang C, Wang D. A Chemical Probe Targets DNA 5-Formylcytosine Sites and Inhibits TDG Excision, Polymerases Bypass, and Gene Expression. Chem Sci 2014; 5:567-574. [PMID: 24883182 DOI: 10.1039/c3sc51849c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Dynamic regulation and faithful maintenance of proper DNA methylation patterns are essential for many cellular functions. 5-Formylcytosine (5fC), a newly discovered oxidized form of methylcytosine (mC) is involved in active DNA demethylation process. The latest progresses suggest exciting novel functional roles of this residue. Chemical tools are desired to further elucidate the functional roles of 5fC and to modulate dynamics of DNA demethylation and downstream biological processes. Here we designed and constructed a chemical probe, consisting of an aldehyde targeting group and an intercalation group. This molecule can selectively react with 5fC and subsequently inhibit base excision by thymine DNA glycosylase (TDG) and cause significant pausing for both DNA and RNA polymerase elongation. Further investigation using a GFP reporter system in living cells revealed that the ligand modification in 5fC sites at 5'-UTR of the GFP gene greatly inhibited the GFP expression level. These results altogether confirmed our successful design and established a new approach for generating functional ligands that target the formylcytosine sites and modulate 5fC-related biological processes.
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Affiliation(s)
- Liang Xu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, 92093, United States
| | - Ying-Chu Chen
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Satoshi Nakajima
- Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania 15213, United States ; University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Jenny Chong
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, 92093, United States
| | - Lanfeng Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, 92093, United States
| | - Li Lan
- Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania 15213, United States ; University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Chao Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Dong Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, 92093, United States
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82
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Zheng Q, Zeng TT, Chen J, Liu H, Zhang H, Su J. Association between DNA methyltransferases 3B gene polymorphisms and the susceptibility to acute myeloid leukemia in Chinese Han population. PLoS One 2013; 8:e74626. [PMID: 24069326 PMCID: PMC3775800 DOI: 10.1371/journal.pone.0074626] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/06/2013] [Indexed: 02/05/2023] Open
Abstract
DNMT3B plays a crucial role in the generation of aberrant methylation during carcinogenesis. Polymorphisms in the DNMT3B gene may influence the DNA methylation enzymatic activity of DNMT3B, thereby modulating the susceptibility to AML. Thus, we investigated the association between SNPs in the DNMT3Bgene and their haplotypes with the risk of AML in the Chinese Han population. The DNMT3B genotype was determined by HRM in 317 de novo AML patients and 406 healthy control subjects matched for age and gender. Among the 5 SNPs investigated in this study, rs2424913 demonstrated no polymorphisms in the Chinese Han populations, rs1569686 and rs2424908 were significantly associated with AML risk. The GG genotype of rs1569686 was associated with increased AML risk (OR: 5.76; 95%CI: 2.60-12.73; P<0.01) compared with the TT genotype, and individuals with a G allele had a significantly increased risk (OR: 1.89; 95%CI: 1.41-2.52; P<0.01) for AML compared with those harboring a C allele, this polymorphism can predict the risk of AML in a minority of patients. While the CC genotype of rs2424908 appeared to reduce the AML risk (OR: 0.57; 95%CI: 0.36-0.91; P=0.01) compared with the TT genotype, individuals with a C allele were associated with a lower risk (OR: 0.79, 95%CI: 0.64-0.97, P=0.03) for developing AML compared with those harboring a T allele. The other 2 SNPs, rs6087990 and rs6119954, had no significant association with AML risk in the study population. The CGGT, CTAT, TGAT, and CGAT haplotypes of rs6087990, rs1569686, rs6119954, and rs2424908 appeared to significantly increase the AML risk, and the TTGC haplotype appeared to significantly reduce the risk. These results suggest that DNMT3B polymorphisms may contribute to the genetic susceptibility to AML; in particular, the G allele of rs1569686 serves as a risk factor for AML, whereas the C allele of rs2424908 represents a potential protective factor.
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Affiliation(s)
- Qin Zheng
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Ting-ting Zeng
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Jiao Chen
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Hua Liu
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - He Zhang
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Jun Su
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
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83
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Intragenic DNA methylation in transcriptional regulation, normal differentiation and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1161-74. [PMID: 23938249 DOI: 10.1016/j.bbagrm.2013.08.001] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 02/06/2023]
Abstract
Ever since the discovery of DNA methylation at cytosine residues, the role of this so called fifth base has been extensively studied and debated. Until recently, the majority of DNA methylation studies focused on the analysis of CpG islands associated to promoter regions. However, with the upcoming possibilities to study DNA methylation in a genome-wide context, this epigenetic mark can now be studied in an unbiased manner. As a result, recent studies have shown that not only promoters but also intragenic and intergenic regions are widely modulated during physiological processes and disease. In particular, it is becoming increasingly clear that DNA methylation in the gene body is not just a passive witness of gene transcription but it seems to be actively involved in multiple gene regulation processes. In this review we discuss the potential role of intragenic DNA methylation in alternative promoter usage, regulation of short and long non-coding RNAs, alternative RNA processing, as well as enhancer activity. Furthermore, we summarize how the intragenic DNA methylome is modified both during normal cell differentiation and neoplastic transformation.
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84
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Liu Y, Ding J, Reynolds LM, Lohman K, Register TC, De La Fuente A, Howard TD, Hawkins GA, Cui W, Morris J, Smith SG, Barr RG, Kaufman JD, Burke GL, Post W, Shea S, McCall CE, Siscovick D, Jacobs DR, Tracy RP, Herrington DM, Hoeschele I. Methylomics of gene expression in human monocytes. Hum Mol Genet 2013; 22:5065-74. [PMID: 23900078 DOI: 10.1093/hmg/ddt356] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is one of several epigenetic mechanisms that contribute to the regulation of gene expression; however, the extent to which methylation of CpG dinucleotides correlates with gene expression at the genome-wide level is still largely unknown. Using purified primary monocytes from subjects in a large community-based cohort (n = 1264), we characterized methylation (>485 000 CpG sites) and mRNA expression (>48K transcripts) and carried out genome-wide association analyses of 8370 expression phenotypes. We identified 11 203 potential cis-acting CpG loci whose degree of methylation was associated with gene expression (eMS) at a false discovery rate threshold of 0.001. Most of the associations were consistent in effect size and direction of effect across sex and three ethnicities. Contrary to expectation, these eMS were not predominately enriched in promoter regions, or CpG islands, but rather in the 3' UTR, gene bodies, CpG shores or 'offshore' sites, and both positive and negative correlations between methylation and expression were observed across all locations. eMS were enriched for regions predicted to be regulatory by ENCODE (Encyclopedia of DNA Elements) data in multiple cell types, particularly enhancers. One of the strongest association signals detected (P < 2.2 × 10(-308)) was a methylation probe (cg17005068) in the promoter/enhancer region of the glutathione S-transferase theta 1 gene (GSTT1, encoding the detoxification enzyme) with GSTT1 mRNA expression. Our study provides a detailed description of the epigenetic architecture in human monocytes and its relationship to gene expression. These data may help prioritize interrogation of biologically relevant methylation loci and provide new insights into the epigenetic basis of human health and diseases.
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Affiliation(s)
- Yongmei Liu
- Wake Forest School of Medicine, Winston-Salem, NC, USA
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85
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Suárez-Álvarez B, Baragaño Raneros A, Ortega F, López-Larrea C. Epigenetic modulation of the immune function: a potential target for tolerance. Epigenetics 2013; 8:694-702. [PMID: 23803720 PMCID: PMC3781188 DOI: 10.4161/epi.25201] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Great efforts in the field of solid organ transplantation are being devoted to identifying biomarkers that allow a transplanted patient's immune status to be established. Recently, it has been well documented that epigenetic mechanisms like DNA methylation and histone modifications regulate the expression of immune system-related genes, modifying the development of the innate and adaptive immune responses. An in-depth knowledge of these epigenetic mechanisms could modulate the immune response after transplantation and to develop new therapeutic strategies. Epigenetic modifiers, such as histone deacetylase (HDAC) inhibitors have considerable potential as anti-inflammatory and immunosuppressive agents, but their effect on transplantation has not hitherto been known. Moreover, the detection of epigenetic marks in key immune genes could be useful as biomarkers of rejection and progression among transplanted patients. Here, we describe recent discoveries concerning the epigenetic regulation of the immune system, and how this knowledge could be translated to the field of transplantation.
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86
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Kitagawa Y, Ohkura N, Sakaguchi S. Molecular determinants of regulatory T cell development: the essential roles of epigenetic changes. Front Immunol 2013; 4:106. [PMID: 23675373 PMCID: PMC3650462 DOI: 10.3389/fimmu.2013.00106] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 04/25/2013] [Indexed: 01/16/2023] Open
Abstract
Regulatory T (Treg) cells constitute a distinct T cell subset, which plays a key role in immune tolerance and homeostasis. The transcription factor Foxp3 controls a substantial part of Treg cell development and function. Yet its expression alone is insufficient for conferring developmental and functional characteristics of Treg cells. There is accumulating evidence that concurrent induction of Treg-specific epigenetic changes and Foxp3 expression is crucial for lineage specification and functional stability of Treg cells. This review discusses recent progress in our understanding of molecular features of Treg cells, in particular, the molecular basis of how a population of developing T cells is driven to the Treg cell lineage and how its function is stably maintained.
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Affiliation(s)
- Yohko Kitagawa
- Department of Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University Suita, Japan
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87
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Warden CD, Lee H, Tompkins JD, Li X, Wang C, Riggs AD, Yu H, Jove R, Yuan YC. COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis. Nucleic Acids Res 2013; 41:e117. [PMID: 23598999 PMCID: PMC3675470 DOI: 10.1093/nar/gkt242] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution DNA methylation data produced by either an Illumina methylation array or targeted bisulfite sequencing. The goal of the COHCAP algorithm is to identify CpG islands that show a consistent pattern of methylation among CpG sites. COHCAP is currently the only DNA methylation package that provides integration with gene expression data to identify a subset of CpG islands that are most likely to regulate downstream gene expression, and it can generate lists of differentially methylated CpG islands with ∼50% concordance with gene expression from both cell line data and heterogeneous patient data. For example, this article describes known breast cancer biomarkers (such as estrogen receptor) with a negative correlation between DNA methylation and gene expression. COHCAP also provides visualization for quality control metrics, regions of differential methylation and correlation between methylation and gene expression. This software is freely available at https://sourceforge.net/projects/cohcap/.
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Affiliation(s)
- Charles D Warden
- Bioinformatics Core, City of Hope National Medical Center, Duarte, CA 91010, USA.
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