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Kumar K, Kumar S, Datta K, Fornace AJ, Suman S. High-LET-Radiation-Induced Persistent DNA Damage Response Signaling and Gastrointestinal Cancer Development. Curr Oncol 2023; 30:5497-5514. [PMID: 37366899 DOI: 10.3390/curroncol30060416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/28/2023] Open
Abstract
Ionizing radiation (IR) dose, dose rate, and linear energy transfer (LET) determine cellular DNA damage quality and quantity. High-LET heavy ions are prevalent in the deep space environment and can deposit a much greater fraction of total energy in a shorter distance within a cell, causing extensive DNA damage relative to the same dose of low-LET photon radiation. Based on the DNA damage tolerance of a cell, cellular responses are initiated for recovery, cell death, senescence, or proliferation, which are determined through a concerted action of signaling networks classified as DNA damage response (DDR) signaling. The IR-induced DDR initiates cell cycle arrest to repair damaged DNA. When DNA damage is beyond the cellular repair capacity, the DDR for cell death is initiated. An alternative DDR-associated anti-proliferative pathway is the onset of cellular senescence with persistent cell cycle arrest, which is primarily a defense mechanism against oncogenesis. Ongoing DNA damage accumulation below the cell death threshold but above the senescence threshold, along with persistent SASP signaling after chronic exposure to space radiation, pose an increased risk of tumorigenesis in the proliferative gastrointestinal (GI) epithelium, where a subset of IR-induced senescent cells can acquire a senescence-associated secretory phenotype (SASP) and potentially drive oncogenic signaling in nearby bystander cells. Moreover, DDR alterations could result in both somatic gene mutations as well as activation of the pro-inflammatory, pro-oncogenic SASP signaling known to accelerate adenoma-to-carcinoma progression during radiation-induced GI cancer development. In this review, we describe the complex interplay between persistent DNA damage, DDR, cellular senescence, and SASP-associated pro-inflammatory oncogenic signaling in the context of GI carcinogenesis.
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Affiliation(s)
- Kamendra Kumar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Santosh Kumar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Kamal Datta
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
- Department of Biochemistry and Molecular & Cellular Biology and Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Albert J Fornace
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
- Department of Biochemistry and Molecular & Cellular Biology and Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Shubhankar Suman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
- Department of Biochemistry and Molecular & Cellular Biology and Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA
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2
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Tricarico R, Madzo J, Scher G, Cohen M, Jelinek J, Maegawa S, Nagarathinam R, Scher C, Chang WC, Nicolas E, Slifker M, Zhou Y, Devarajan K, Cai KQ, Kwok T, Nakajima P, Xu J, Mancuso P, Doneddu V, Bagella L, Williams R, Balachandran S, Maskalenko N, Campbell K, Ma X, Cañadas I, Viana-Errasti J, Moreno V, Valle L, Grivennikov S, Peshkova I, Kurilenko N, Mazitova A, Koltsova E, Lee H, Walsh M, Duttweiler R, Whetstine JR, Yen TJ, Issa JP, Bellacosa A. TET1 and TDG Suppress Inflammatory Response in Intestinal Tumorigenesis: Implications for Colorectal Tumors With the CpG Island Methylator Phenotype. Gastroenterology 2023; 164:921-936.e1. [PMID: 36764492 PMCID: PMC10586516 DOI: 10.1053/j.gastro.2023.01.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 12/28/2022] [Accepted: 01/14/2023] [Indexed: 02/12/2023]
Abstract
BACKGROUND & AIMS Aberrant DNA methylation is frequent in colorectal cancer (CRC), but underlying mechanisms and pathologic consequences are poorly understood. METHODS We disrupted active DNA demethylation genes Tet1 and/or Tdg from ApcMin mice and characterized the methylome and transcriptome of colonic adenomas. Data were compared to human colonic adenocarcinomas (COAD) in The Cancer Genome Atlas. RESULTS There were increased numbers of small intestinal adenomas in ApcMin mice expressing the TdgN151A allele, whereas Tet1-deficient and Tet1/TdgN151A-double heterozygous ApcMin colonic adenomas were larger with features of erosion and invasion. We detected reduction in global DNA hypomethylation in colonic adenomas from Tet1- and Tdg-mutant ApcMin mice and hypermethylation of CpG islands in Tet1-mutant ApcMin adenomas. Up-regulation of inflammatory, immune, and interferon response genes was present in Tet1- and Tdg-mutant colonic adenomas compared to control ApcMin adenomas. This up-regulation was also seen in murine colonic organoids and human CRC lines infected with lentiviruses expressing TET1 or TDG short hairpin RNA. A 127-gene inflammatory signature separated colonic adenocarcinomas into 4 groups, closely aligned with their microsatellite or chromosomal instability and characterized by different levels of DNA methylation and DNMT1 expression that anticorrelated with TET1 expression. Tumors with the CpG island methylator phenotype (CIMP) had concerted high DNMT1/low TET1 expression. TET1 or TDG knockdown in CRC lines enhanced killing by natural killer cells. CONCLUSIONS Our findings reveal a novel epigenetic regulation, linked to the type of genomic instability, by which TET1/TDG-mediated DNA demethylation decreases methylation levels and inflammatory/interferon/immune responses. CIMP in CRC is triggered by an imbalance of methylating activities over demethylating activities. These mice represent a model of CIMP CRC.
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Affiliation(s)
- Rossella Tricarico
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jozef Madzo
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Gabrielle Scher
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Maya Cohen
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | - Shinji Maegawa
- University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Carly Scher
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Wen-Chi Chang
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Emmanuelle Nicolas
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Michael Slifker
- Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Yan Zhou
- Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Karthik Devarajan
- Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Kathy Q Cai
- Experimental Histopathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Tim Kwok
- Cell Culture Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Pamela Nakajima
- Cell Culture Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jinfei Xu
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Pietro Mancuso
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Valentina Doneddu
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania
| | - Riley Williams
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Siddharth Balachandran
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Nicholas Maskalenko
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Kerry Campbell
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Xueying Ma
- Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Israel Cañadas
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Julen Viana-Errasti
- Hereditary Cancer Program Catalan Institute of Oncology, Oncobell Program, Investigación Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology, Oncobell Program, Investigación Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Laura Valle
- Hereditary Cancer Program Catalan Institute of Oncology, Oncobell Program, Investigación Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Sergei Grivennikov
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Iuliia Peshkova
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Natalia Kurilenko
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Aleksandra Mazitova
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Ekaterina Koltsova
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Hayan Lee
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Martin Walsh
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Reuben Duttweiler
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Timothy J Yen
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | - Alfonso Bellacosa
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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Zhang Y, Zhu F, Teng J, Zheng B, Lou Z, Feng H, Xue L, Qian Y. Effects of salinity stress on methylation of the liver genome and complement gene in large yellow croaker (Larimichthys crocea). FISH & SHELLFISH IMMUNOLOGY 2022; 129:207-220. [PMID: 36058436 DOI: 10.1016/j.fsi.2022.08.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/06/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
Salinity is an important environmental factor that affects the yield and quality of large yellow croaker (Larimichthys crocea) during aquaculture. Here, whole-genome bisulfite sequencing (WGBS), RNA-seq, bisulfite sequencing PCR (BSP), quantitative real-time PCR (qPCR), and dual luciferase reporter gene detection technologies were used to analyze the DNA methylation characteristics and patterns of the liver genome, the expression and methylation levels of important immune genes in large yellow croaker in response to salinity stress. The results of WGBS showed that the cytosine methylation of CG type was dominant, CpGIsland and repeat regions were important regions where DNA methylation occurred, and the DNA methylation in upstream 2k (2000bp upstream of the promoter) and repeat regions had different changes in the liver tissue of large yellow croaker in the response to the 12‰, 24‰, 36‰ salinity stress of 4 w (weeks). In the combined analysis of WGBS and transcriptome, the complement and coagulation cascade pathways were significantly enriched, in which the complement-related genes C7, C3, C5, C4, C1R, MASP1, and CD59 were mainly changed in response to salinity stress. In the studied area of MASP1 gene promoter, the methylation levels of many CpG sites as well as total cytosine were strongly negatively correlated with mRNA expression level. Methylation function analysis of MASP1 promoter further proved that DNA methylation could inhibit the activity of MASP1 promoter, indicating that salinity may affect the expressions of complement-related genes by DNA methylation of gene promoter region.
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Affiliation(s)
- Yu Zhang
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China; Fisheries College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Fei Zhu
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China; Jiangsu Marine Fisheries Research Institute, Nantong, Jiangsu, 226007, China
| | - Jian Teng
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China
| | - Baoxiao Zheng
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China
| | - Zhengjia Lou
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China
| | - Huijie Feng
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China
| | - Liangyi Xue
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China.
| | - Yunxia Qian
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China
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Yan Y, Zhang H, Gao S, Zhang H, Zhang X, Chen W, Lin W, Xie Q. Differential DNA Methylation and Gene Expression Between ALV-J-Positive and ALV-J-Negative Chickens. Front Vet Sci 2021; 8:659840. [PMID: 34136553 PMCID: PMC8203102 DOI: 10.3389/fvets.2021.659840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/28/2021] [Indexed: 01/24/2023] Open
Abstract
Background: Avian leukosis virus subgroup J (ALV-J) is an oncogenic virus that causes serious economic losses in the poultry industry; unfortunately, there is no effective vaccine against ALV-J. DNA methylation plays a crucial role in several biological processes, and an increasing number of diseases have been proven to be related to alterations in DNA methylation. In this study, we screened ALV-J-positive and -negative chickens. Subsequently, we generated and provided the genome-wide gene expression and DNA methylation profiles by MeDIP-seq and RNA-seq of ALV-J-positive and -negative chicken samples; 8,304 differentially methylated regions (DMRs) were identified by MeDIP-seq analysis (p ≤ 0.005) and 515 differentially expressed genes were identified by RNA-seq analysis (p ≤ 0.05). As a result of an integration analysis, we screened six candidate genes to identify ALV-J-negative chickens that possessed differential methylation in the promoter region. Furthermore, TGFB2 played an important role in tumorigenesis and cancer progression, which suggested TGFB2 may be an indicator for identifying ALV-J infections.
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Affiliation(s)
- Yiming Yan
- Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Huihua Zhang
- College of Life Science and Engineering, Foshan University, Foshan, China
| | - Shuang Gao
- Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Huanmin Zhang
- United States Department of Agriculture (USDA), Agriculture Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, United States
| | - Xinheng Zhang
- Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Weiguo Chen
- Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Wencheng Lin
- Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Qingmei Xie
- Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
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5
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Casalino L, Verde P. Multifaceted Roles of DNA Methylation in Neoplastic Transformation, from Tumor Suppressors to EMT and Metastasis. Genes (Basel) 2020; 11:E922. [PMID: 32806509 PMCID: PMC7463745 DOI: 10.3390/genes11080922] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/30/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Among the major mechanisms involved in tumorigenesis, DNA methylation is an important epigenetic modification impacting both genomic stability and gene expression. Methylation of promoter-proximal CpG islands (CGIs) and transcriptional silencing of tumor suppressors represent the best characterized epigenetic changes in neoplastic cells. The global cancer-associated effects of DNA hypomethylation influence chromatin architecture and reactivation of repetitive elements. Moreover, recent analyses of cancer cell methylomes highlight the role of the DNA hypomethylation of super-enhancer regions critically controlling the expression of key oncogenic players. We will first summarize some basic aspects of DNA methylation in tumorigenesis, along with the role of dysregulated DNA methyltransferases and TET (Ten-Eleven Translocation)-family methylcytosine dioxygenases. We will then examine the potential contribution of epimutations to causality and heritability of cancer. By reviewing some representative genes subjected to hypermethylation-mediated silencing, we will survey their oncosuppressor functions and roles as biomarkers in various types of cancer. Epithelial-to-mesenchymal transition (EMT) and the gain of stem-like properties are critically involved in cancer cell dissemination, metastasis, and therapeutic resistance. However, the driver vs passenger roles of epigenetic changes, such as DNA methylation in EMT, are still poorly understood. Therefore, we will focus our attention on several aspects of DNA methylation in control of EMT and metastasis suppressors, including both protein-coding and noncoding genes.
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Affiliation(s)
- Laura Casalino
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, CNR, 80100 Naples, Italy
| | - Pasquale Verde
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, CNR, 80100 Naples, Italy
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6
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The Epigenetic Progenitor Origin of Cancer Reassessed: DNA Methylation Brings Balance to the Stem Force. EPIGENOMES 2020; 4:epigenomes4020008. [PMID: 34968242 PMCID: PMC8594692 DOI: 10.3390/epigenomes4020008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 12/17/2022] Open
Abstract
Cancer initiation and progression toward malignant stages occur as the results of accumulating genetic alterations and epigenetic dysregulation. During the last decade, the development of next generation sequencing (NGS) technologies and the increasing pan-genomic knowledge have revolutionized how we consider the evolving epigenetic landscapes during homeostasis and tumor progression. DNA methylation represents the best studied mark and is considered as a common mechanism of epigenetic regulation in normal homeostasis and cancer. A remarkable amount of work has recently started clarifying the central role played by DNA methylation dynamics on the maintenance of cell identity and on cell fate decisions during the different steps of normal development and tumor evolution. Importantly, a growing number of studies show that DNA methylation is key in the maintenance of adult stemness and in orchestrating commitment in multiple ways. Perturbations of the normal DNA methylation patterns impair the homeostatic balance and can lead to tumor initiation. Therefore, DNA methylation represents an interesting therapeutic target to recover homeostasis in tumor stem cells.
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7
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Bruschi M, Garnier L, Cleroux E, Giordano A, Dumas M, Bardet AF, Kergrohen T, Quesada S, Cesses P, Weber M, Gerbe F, Jay P. Loss of Apc Rapidly Impairs DNA Methylation Programs and Cell Fate Decisions in Lgr5 + Intestinal Stem Cells. Cancer Res 2020; 80:2101-2113. [PMID: 32213541 DOI: 10.1158/0008-5472.can-19-2104] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/13/2020] [Accepted: 03/19/2020] [Indexed: 12/24/2022]
Abstract
Colorectal cancer initiation and progression result from the accumulation of genetic and epigenetic alterations. Although aberrant gene expression and DNA methylation profiles are considered hallmarks of colorectal cancer development, the precise timing at which these are produced during tumor establishment remains elusive. Here we investigated the early transcriptional and epigenetic changes induced by adenomatous polyposis coli (Apc) inactivation in intestinal crypts. Hyperactivation of the Wnt pathway via Apc inactivation in crypt base columnar intestinal stem cells (ISC) led to their rapid accumulation driven by an impaired molecular commitment to differentiation, which was associated with discrete alterations in DNA methylation. Importantly, inhibiting the enzymes responsible for de novo DNA methylation restored the responsiveness of Apc-deficient intestinal organoids to stimuli regulating the proliferation-to-differentiation transition in ISC. This work reveals that early DNA methylation changes play critical roles in the establishment of the impaired fate decision program consecutive to Apc loss of function. SIGNIFICANCE: This study demonstrates the functional impact of changes in DNA methylation to determine the colorectal cancer cell phenotype following loss of Apc function.
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Affiliation(s)
- Marco Bruschi
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Laure Garnier
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Elouan Cleroux
- UMR 7242 Biotechnology and Cell Signaling, CNRS, University of Strasbourg, Illkirch, France
| | - Alicia Giordano
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Michael Dumas
- UMR 7242 Biotechnology and Cell Signaling, CNRS, University of Strasbourg, Illkirch, France
| | - Anaïs F Bardet
- UMR 7242 Biotechnology and Cell Signaling, CNRS, University of Strasbourg, Illkirch, France
| | - Thomas Kergrohen
- Département de Cancérologie de l'Enfant et de l'Adolescent, Institut de Cancérologie Gustave Roussy, Université Paris-Sud, Université Paris-Saclay, Villejuif Cedex, France
| | - Stanislas Quesada
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Pierre Cesses
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Michael Weber
- UMR 7242 Biotechnology and Cell Signaling, CNRS, University of Strasbourg, Illkirch, France
| | - François Gerbe
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France.
| | - Philippe Jay
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France.
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8
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Wu R, Wang L, Yin R, Hudlikar R, Li S, Kuo HCD, Peter R, Sargsyan D, Guo Y, Liu X, Kong AN. Epigenetics/epigenomics and prevention by curcumin of early stages of inflammatory-driven colon cancer. Mol Carcinog 2020; 59:227-236. [PMID: 31820492 PMCID: PMC6946865 DOI: 10.1002/mc.23146] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/25/2019] [Accepted: 11/30/2019] [Indexed: 12/14/2022]
Abstract
Colorectal cancer (CRC) is associated with significant morbidity and mortality in the US and worldwide. CRC is the second most common cancer-related death in both men and women globally. Chronic inflammation has been identified as one of the major risk factors of CRC. It may drive genetic and epigenetic/epigenomic alterations, such as DNA methylation, histone modification, and non-coding RNA regulation. Current prevention modalities for CRC are limited and some treatment regimens such as use the nonsteroidal anti-inflammatory drug aspirin may have severe side effects, namely gastrointestinal ulceration and bleeding. Therefore, there is an urgent need of developing alternative strategies. Recently, increasing evidence suggests that several dietary cancer chemopreventive phytochemicals possess anti-inflammation and antioxidative stress activities, and may prevent cancers including CRC. Curcumin (CUR) is the yellow pigment that is found in the rhizomes of turmeric (Curcuma longa). Many studies have demonstrated that CUR exhibit strong anticancer, antioxidative stress, and anti-inflammatory activities by regulating signaling pathways, such as nuclear factor erythroid-2-related factor 2, nuclear factor-κB, and epigenetics/epigenomics pathways of histones modifications, and DNA methylation. In this review, we will discuss the latest evidence in epigenetics/epigenomics alterations by CUR in CRC and their potential contribution in the prevention of CRC.
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Affiliation(s)
- Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Lujing Wang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
- Graduate Program in Pharmaceutical Science, Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Ran Yin
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Rasika Hudlikar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Shanyi Li
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Hsiao-Chen D Kuo
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
- Graduate Program in Pharmaceutical Science, Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Rebecca Peter
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
- Graduate Program in Pharmaceutical Science, Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Davit Sargsyan
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
- Graduate Program in Pharmaceutical Science, Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Yue Guo
- Janssen Research & Development, Spring House, Pennsylvania
| | - Xia Liu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
- Department of Pharmacology, School of Basic Medical Science, Lanzhou University, Lanzhou, China
| | - A N Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
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9
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Uribe-Lewis S, Carroll T, Menon S, Nicholson A, Manasterski PJ, Winton DJ, Buczacki SJA, Murrell A. 5-hydroxymethylcytosine and gene activity in mouse intestinal differentiation. Sci Rep 2020; 10:546. [PMID: 31953501 PMCID: PMC6969059 DOI: 10.1038/s41598-019-57214-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/19/2019] [Indexed: 12/17/2022] Open
Abstract
Cytosine hydroxymethylation (5hmC) in mammalian DNA is the product of oxidation of methylated cytosines (5mC) by Ten-Eleven-Translocation (TET) enzymes. While it has been shown that the TETs influence 5mC metabolism, pluripotency and differentiation during early embryonic development, the functional relationship between gene expression and 5hmC in adult (somatic) stem cell differentiation is still unknown. Here we report that 5hmC levels undergo highly dynamic changes during adult stem cell differentiation from intestinal progenitors to differentiated intestinal epithelium. We profiled 5hmC and gene activity in purified mouse intestinal progenitors and differentiated progeny to identify 43425 differentially hydroxymethylated regions and 5325 differentially expressed genes. These differentially marked regions showed both losses and gains of 5hmC after differentiation, despite lower global levels of 5hmC in progenitor cells. In progenitors, 5hmC did not correlate with gene transcript levels, however, upon differentiation the global increase in 5hmC content showed an overall positive correlation with gene expression level as well as prominent associations with histone modifications that typify active genes and enhancer elements. Our data support a gene regulatory role for 5hmC that is predominant over its role in controlling DNA methylation states.
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Affiliation(s)
- Santiago Uribe-Lewis
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University New York, New York, NY, 10065, USA
| | - Suraj Menon
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Anna Nicholson
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Piotr J Manasterski
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Douglas J Winton
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Simon J A Buczacki
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Addenbrookes Biomedical Campus, Cambridge, CB2 0AF, UK
| | - Adele Murrell
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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10
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Zhu Y, Cao Z, Lu C. Microfluidic MeDIP-seq for low-input methylomic analysis of mammary tumorigenesis in mice. Analyst 2019; 144:1904-1915. [PMID: 30631869 DOI: 10.1039/c8an02271b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Studies of dynamic epigenomic changes during tumorigenesis using mice often require profiling epigenomes using a tiny quantity of tissue samples. Conventional epigenomic tests do not support such analysis due to the large amount of materials required by these assays. In this study, we developed an ultrasensitive microfluidics-based methylated DNA immunoprecipitation followed by next-generation sequencing (MeDIP-seq) technology for profiling methylomes using as little as 0.5 ng DNA (or ∼100 cells) with 1.5 h on-chip process for immunoprecipitation. This technology enabled us to examine genome-wide DNA methylation in a C3(1)/SV40 T-antigen transgenic mouse model during different stages of mammary cancer development. Using our data, we identified differentially methylated regions and their associated genes in different periods of cancer development. Our results showed that unique methylomic features were presented in various tumor developmental stages.
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Affiliation(s)
- Yan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA.
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11
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Guo Y, Wu R, Gaspar JM, Sargsyan D, Su ZY, Zhang C, Gao L, Cheng D, Li W, Wang C, Yin R, Fang M, Verzi MP, Hart RP, Kong AN. DNA methylome and transcriptome alterations and cancer prevention by curcumin in colitis-accelerated colon cancer in mice. Carcinogenesis 2019; 39:669-680. [PMID: 29547900 DOI: 10.1093/carcin/bgy043] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 03/12/2018] [Indexed: 12/17/2022] Open
Abstract
Inflammation is highly associated with colon carcinogenesis. Epigenetic mechanisms could play an important role in the initiation and progression of colon cancer. Curcumin, a dietary phytochemical, shows promising effects in suppressing colitis-associated colon cancer in azoxymethane-dextran sulfate sodium (AOM-DSS) mice. However, the potential epigenetic mechanisms of curcumin in colon cancer remain unknown. In this study, the anticancer effect of curcumin in suppressing colon cancer in an 18-week AOM-DSS colon cancer mouse model was confirmed. We identified lists of differentially expressed and differentially methylated genes in pairwise comparisons and several pathways involved in the potential anticancer effect of curcumin. These pathways include LPS/IL-1-mediated inhibition of RXR function, Nrf2-mediated oxidative stress response, production of NO and ROS in macrophages and IL-6 signaling. Among these genes, Tnf stood out with decreased DNA CpG methylation of Tnf in the AOM-DSS group and reversal of the AOM-DSS induced Tnf demethylation by curcumin. These observations in Tnf methylation correlated with increased and decreased Tnf expression in RNA-seq. The functional role of DNA methylation of Tnf was further confirmed by in vitro luciferase transcriptional activity assay. In addition, the DNA methylation level in a group of inflammatory genes was decreased in the AOM+DSS group but restored by curcumin and was validated by pyrosequencing. This study shows for the first time epigenomic changes in DNA CpG methylation in the inflammatory response from colitis-associated colon cancer and the reversal of their CpG methylation changes by curcumin. Future clinical epigenetic studies with curcumin in inflammation-associated colon cancer would be warranted.
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Affiliation(s)
- Yue Guo
- Graduate Program in Pharmaceutical Science, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - John M Gaspar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Davit Sargsyan
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Zheng-Yuan Su
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan City, Taiwan
| | - Chengyue Zhang
- Graduate Program in Pharmaceutical Science, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Linbo Gao
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - David Cheng
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Wenji Li
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Chao Wang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Ran Yin
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Mingzhu Fang
- Environmental and Occupational Health Sciences Institute, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Michael P Verzi
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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12
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Assessment of concordance between fresh-frozen and formalin-fixed paraffin embedded tumor DNA methylation using a targeted sequencing approach. Oncotarget 2018; 8:48126-48137. [PMID: 28611295 PMCID: PMC5564631 DOI: 10.18632/oncotarget.18296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 04/03/2017] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is altered in many types of disease, including metastatic colorectal cancer. However, the methylome has not yet been fully described in archival formalin-fixed paraffin embedded (FFPE) samples in the context of matched fresh-frozen (FF) tumor material at base-pair resolution using a targeted approach. Using next-generation sequencing, we investigated three pairs of matched FFPE and FF samples to determine the extent of their similarity. We identified a ‘bowing’ pattern specific to FFPE samples categorized by a lower CG proportion at the start of sequence reads. We have found no evidence that this affected methylation calling, nor concordance of results. We also found no significant increase in deamination, measured by C>T transitions, previously considered a result of crosslinking DNA by formalin fixation and a barrier to the use of FFPE in methylation studies. The methods used in this study have shown sensitivity of between 60-70% based on positions also methylated in colorectal cancer cell lines. We demonstrate that FFPE material is a useful source of tumor material for methylation studies using targeted sequencing.
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13
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Data on novel DNA methylation changes induced by valproic acid in human hepatocytes. Data Brief 2017; 16:161-171. [PMID: 29201983 PMCID: PMC5702865 DOI: 10.1016/j.dib.2017.11.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/03/2017] [Accepted: 11/08/2017] [Indexed: 12/12/2022] Open
Abstract
Valproic acid (VPA) is a widely prescribed antiepileptic drug in the world. Despite its pharmacological importance, it may cause liver toxicity and steatosis. However the exact mechanism of the steatosis formation is unknown. The data presented in this DIB publication is used to further investigate the VPA-induced mechanisms of steatosis by analyzing changes in patterns of methylation. Therefore, primary human hepatocytes (PHHs) were exposed to VPA at a concentration which was shown to cause steatosis without inducing overt cytotoxicity. VPA was administered for 5 days daily to PHHs. Furthermore, after 5 days VPA-treatment parts of the PHHs were followed for a 3 days washout. Differentially methylated DNA regions (DMRs) were identified by using the ‘Methylated DNA Immuno-Precipitation - sequencing’ (MeDIP-seq) method. The data presented in this DIB demonstrate induced steatosis pathways by all DMRs during VPA-treatment, covering interesting drug-induced steatosis genes (persistent DMRs upon terminating VPA treatment and the EP300 network). This was illustrated in our associated article (Wolters et al., 2017) [1]. MeDIP-seq raw data are available on ArrayExpress (accession number: E-MTAB-4437).
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14
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Wolters JEJ, van Breda SGJ, Caiment F, Claessen SM, de Kok TMCM, Kleinjans JCS. Nuclear and Mitochondrial DNA Methylation Patterns Induced by Valproic Acid in Human Hepatocytes. Chem Res Toxicol 2017; 30:1847-1854. [PMID: 28853863 PMCID: PMC5645762 DOI: 10.1021/acs.chemrestox.7b00171] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Valproic
acid (VPA) is one of the most widely prescribed antiepileptic
drugs in the world. Despite its pharmacological importance, it may
cause liver toxicity and steatosis through mitochondrial dysfunction.
The aim of this study is to further investigate VPA-induced mechanisms
of steatosis by analyzing changes in patterns of methylation in nuclear
DNA (nDNA) and mitochondrial DNA (mtDNA). Therefore, primary human
hepatocytes (PHHs) were exposed to an incubation concentration of
VPA that was shown to cause steatosis without inducing overt cytotoxicity.
VPA was administered daily for 5 days, and this was followed by a
3 day washout (WO). Methylated DNA regions (DMRs) were identified
by using the methylated DNA immunoprecipitation–sequencing
(MeDIP-seq) method. The nDNA DMRs after VPA treatment could indeed
be classified into oxidative stress- and steatosis-related pathways.
In particular, networks of the steatosis-related gene EP300 provided novel insight into the mechanisms of toxicity induced by
VPA treatment. Furthermore, we suggest that VPA induces a crosstalk
between nDNA hypermethylation and mtDNA hypomethylation that plays
a role in oxidative stress and steatosis development. Although most
VPA-induced methylation patterns appeared reversible upon terminating
VPA treatment, 31 nDNA DMRs (including 5 zinc finger protein genes)
remained persistent after the WO period. Overall, we have shown that
MeDIP-seq analysis is highly informative in disclosing novel mechanisms
of VPA-induced toxicity in PHHs. Our results thus provide a prototype
for the novel generation of interesting methylation biomarkers for
repeated dose liver toxicity in vitro.
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Affiliation(s)
- Jarno E J Wolters
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Simone G J van Breda
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Sandra M Claessen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Theo M C M de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Jos C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
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15
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Genome-wide DNA methylation and transcriptome analyses reveal genes involved in immune responses of pig peripheral blood mononuclear cells to poly I:C. Sci Rep 2017; 7:9709. [PMID: 28852164 PMCID: PMC5575306 DOI: 10.1038/s41598-017-10648-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/10/2017] [Indexed: 12/14/2022] Open
Abstract
DNA methylation changes play essential roles in regulating the activities of genes involved in immune responses. Understanding of variable DNA methylation linked to immune responses may contribute to identifying biologically promising epigenetic markers for pathogenesis of diseases. Here, we generated genome-wide DNA methylation and transcriptomic profiles of six pairs of polyinosinic-polycytidylic acid-treated pig peripheral blood mononuclear cell (PBMC) samples and corresponding controls using methylated DNA immunoprecipitation sequencing and RNA sequencing. Comparative methylome analyses identified 5,827 differentially methylated regions and 615 genes showing differential expression between the two groups. Integrative analyses revealed inverse associations between DNA methylation around transcriptional start site and gene expression levels. Furthermore, 70 differentially methylated and expressed genes were identified such as TNFRSF9, IDO1 and EBI3. Functional annotation revealed the enriched categories including positive regulation of immune system process and regulation of leukocyte activation. These findings demonstrated DNA methylation changes occurring in immune responses of PBMCs to poly I:C stimulation and a subset of genes potentially regulated by DNA methylation in the immune responses. The PBMC DNA methylome provides an epigenetic overview of this physiological system in response to viral infection, and we expect it to constitute a valuable resource for future epigenetic epidemiology studies in pigs.
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16
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Yuan H, Li N, Fu D, Ren J, Hui J, Peng J, Liu Y, Qiu T, Jiang M, Pan Q, Han Y, Wang X, Li Q, Qin J. Histone methyltransferase SETD2 modulates alternative splicing to inhibit intestinal tumorigenesis. J Clin Invest 2017; 127:3375-3391. [PMID: 28825595 DOI: 10.1172/jci94292] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/23/2017] [Indexed: 12/27/2022] Open
Abstract
The histone H3K36 methyltransferase SETD2 is frequently mutated or deleted in a variety of human tumors. Nevertheless, the role of SETD2 loss in oncogenesis remains largely undefined. Here, we found that SETD2 counteracts Wnt signaling and its inactivation promotes intestinal tumorigenesis in mouse models of colorectal cancer (CRC). SETD2 was not required for intestinal homeostasis under steady state; however, upon irradiation, genetic inactivation of Setd2 in mouse intestinal epithelium facilitated the self-renewal of intestinal stem/progenitor cells as well as tissue regeneration. Furthermore, depletion of SETD2 enhanced the susceptibility to tumorigenesis in the context of dysregulated Wnt signaling. Mechanistic characterizations indicated that SETD2 downregulation affects the alternative splicing of a subset of genes implicated in tumorigenesis. Importantly, we uncovered that SETD2 ablation reduces intron retention of dishevelled segment polarity protein 2 (DVL2) pre-mRNA, which would otherwise be degraded by nonsense-mediated decay, thereby augmenting Wnt signaling. The signaling cascades mediated by SETD2 were further substantiated by a CRC patient cohort analysis. Together, our studies highlight SETD2 as an integral regulator of Wnt signaling through epigenetic regulation of RNA processing during tissue regeneration and tumorigenesis.
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Affiliation(s)
- Huairui Yuan
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
| | - Ni Li
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
| | - Da Fu
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiale Ren
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Junjie Peng
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yongfeng Liu
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
| | - Tong Qiu
- Department of Obstetrics, Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Min Jiang
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
| | - Qiang Pan
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
| | - Ying Han
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiaoming Wang
- Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Qintong Li
- Department of Obstetrics, Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jun Qin
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
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17
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Lienhard M, Grasse S, Rolff J, Frese S, Schirmer U, Becker M, Börno S, Timmermann B, Chavez L, Sültmann H, Leschber G, Fichtner I, Schweiger MR, Herwig R. QSEA-modelling of genome-wide DNA methylation from sequencing enrichment experiments. Nucleic Acids Res 2017; 45:e44. [PMID: 27913729 PMCID: PMC5389680 DOI: 10.1093/nar/gkw1193] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/17/2016] [Indexed: 12/22/2022] Open
Abstract
Genome-wide enrichment of methylated DNA followed by sequencing (MeDIP-seq) offers a reasonable compromise between experimental costs and genomic coverage. However, the computational analysis of these experiments is complex, and quantification of the enrichment signals in terms of absolute levels of methylation requires specific transformation. In this work, we present QSEA, Quantitative Sequence Enrichment Analysis, a comprehensive workflow for the modelling and subsequent quantification of MeDIP-seq data. As the central part of the workflow we have developed a Bayesian statistical model that transforms the enrichment read counts to absolute levels of methylation and, thus, enhances interpretability and facilitates comparison with other methylation assays. We suggest several calibration strategies for the critical parameters of the model, either using additional data or fairly general assumptions. By comparing the results with bisulfite sequencing (BS) validation data, we show the improvement of QSEA over existing methods. Additionally, we generated a clinically relevant benchmark data set consisting of methylation enrichment experiments (MeDIP-seq), BS-based validation experiments (Methyl-seq) as well as gene expression experiments (RNA-seq) derived from non-small cell lung cancer patients, and show that the workflow retrieves well-known lung tumour methylation markers that are causative for gene expression changes, demonstrating the applicability of QSEA for clinical studies. QSEA is implemented in R and available from the Bioconductor repository 3.4 (www.bioconductor.org/packages/qsea).
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Affiliation(s)
- Matthias Lienhard
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany
| | - Sabrina Grasse
- Functional Epigenomics, University Hospital Cologne, Cologne 50937, Germany
| | - Jana Rolff
- Experimental Pharmacology & Oncology Berlin-Buch GmbH, Berlin 13125, Germany
| | - Steffen Frese
- Department of Thoracic Surgery, ELK Berlin Chest Hospital, Berlin 13125, Germany
| | - Uwe Schirmer
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany
| | - Michael Becker
- Experimental Pharmacology & Oncology Berlin-Buch GmbH, Berlin 13125, Germany
| | - Stefan Börno
- Sequencing Core Facility, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany
| | - Lukas Chavez
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Holger Sültmann
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany
| | - Gunda Leschber
- Department of Thoracic Surgery, ELK Berlin Chest Hospital, Berlin 13125, Germany
| | - Iduna Fichtner
- Experimental Pharmacology & Oncology Berlin-Buch GmbH, Berlin 13125, Germany
| | - Michal R Schweiger
- Functional Epigenomics, University Hospital Cologne, Cologne 50937, Germany.,Department of Vertebrate Genomics, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany
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18
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ADAM Metalloprotease-Released Cancer Biomarkers. Trends Cancer 2017; 3:482-490. [DOI: 10.1016/j.trecan.2017.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/28/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022]
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19
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Rezasoltani S, Asadzadeh-Aghdaei H, Nazemalhosseini-Mojarad E, Dabiri H, Ghanbari R, Zali MR. Gut microbiota, epigenetic modification and colorectal cancer. IRANIAN JOURNAL OF MICROBIOLOGY 2017; 9:55-63. [PMID: 29213996 PMCID: PMC5715278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Micro-organisms contain 90% of cells in human body and trillions foreign genes versus less than 30 thousand of their own. The human colon host various species of microorganisms, appraised at more than 1014 microbiota and contained of over a thousand species. Although each one's profile is separable, the relative abundance and distribution of bacterial species is the same between healthy ones, causing conservation of each person's overall health. Germline DNA mutations have been attributed to the less than 5% of CRC occurrence while more than 90% is associated with the epigenetic regulation. The most ubiquitous environmental factor in epigenetic modification is gut microbiota. Disruptive changes in the gut microbiome strongly contributed to the improvement of colorectal cancer. Gut microbiota may play critical role in progression of CRC via their metabolite or their structural component interacting with host intestinal epithelial cell (IEC). Herein we discuss the mechanism of epigenetic modification and its implication in CRC development, progression even metastasis by gut microbiota induction.
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Affiliation(s)
- Sama Rezasoltani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh-Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Corresponding author: Ehsan Nazemalhosseini-Mojarad, PhD, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran. Tel: +98-21-22432516
| | - Hossein Dabiri
- Department of Medical Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Ghanbari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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20
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Sheaffer KL, Elliott EN, Kaestner KH. DNA Hypomethylation Contributes to Genomic Instability and Intestinal Cancer Initiation. Cancer Prev Res (Phila) 2016; 9:534-46. [PMID: 26883721 DOI: 10.1158/1940-6207.capr-15-0349] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/08/2016] [Indexed: 12/12/2022]
Abstract
Intestinal cancer is a heterogeneous disease driven by genetic mutations and epigenetic changes. Approximately 80% of sporadic colorectal cancers are initiated by mutation and inactivation of the adenomatous polyposis coli (APC) gene, which results in unrestrained intestinal epithelial growth and formation of adenomas. Aberrant DNA methylation promotes cancer progression by the inactivation of tumor suppressor genes via promoter methylation. In addition, global DNA hypomethylation is often seen before the formation of adenomas, suggesting that it contributes to neoplastic transformation. Previous studies employed mice with a hypomorphic mutation in DNA methyltransferase 1 (Dnmt1), which exhibited constitutive global DNA hypomethylation and decreased tumorigenesis in the Apc(Min/+) mouse model of intestinal cancer. However, the consequences of intestinal epithelial-specific acute hypomethylation during Apc(Min/+) tumor initiation have not been reported. Using temporally controlled intestinal epithelial-specific gene ablation, we show that total loss of Dnmt1 in the Apc(Min/+) mouse model of intestinal cancer causes accelerated adenoma initiation. Deletion of Dnmt1 precipitates an acute response characterized by hypomethylation of repetitive elements and genomic instability, which surprisingly is followed by remethylation with time. Two months post-Dnmt1 ablation, mice display increased macroadenoma load, consistent with a role for Dnmt1 and DNA methylation in maintaining genomic stability. These data suggest that DNA hypomethylation plays a previously unappreciated role in intestinal adenoma initiation. Cancer Prev Res; 9(7); 534-46. ©2016 AACRSee related article by Lee and Laird, p. 509.
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Affiliation(s)
- Karyn L Sheaffer
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ellen N Elliott
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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21
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Selmin OI, Fang C, Lyon AM, Doetschman TC, Thompson PA, Martinez JD, Smith JW, Lance PM, Romagnolo DF. Inactivation of Adenomatous Polyposis Coli Reduces Bile Acid/Farnesoid X Receptor Expression through Fxr gene CpG Methylation in Mouse Colon Tumors and Human Colon Cancer Cells. J Nutr 2016; 146:236-42. [PMID: 26609171 PMCID: PMC6636391 DOI: 10.3945/jn.115.216580] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 11/03/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The farnesoid X receptor (FXR) regulates bile acid (BA) metabolism and possesses tumor suppressor functions. FXR expression is reduced in colorectal tumors of subjects carrying inactivated adenomatous polyposis coli (APC). Identifying the mechanisms responsible for this reduction may offer new molecular targets for colon cancer prevention. OBJECTIVE We investigated how APC inactivation influences the regulation of FXR expression in colonic mucosal cells. We hypothesized that APC inactivation would epigenetically repress nuclear receptor subfamily 1, group H, member 4 (FXR gene name) expression through increased CpG methylation. METHODS Normal proximal colonic mucosa and normal-appearing adjacent colonic mucosa and colon tumors were collected from wild-type C57BL/6J and Apc-deficient (Apc(Min) (/+)) male mice, respectively. The expression of Fxr, ileal bile acid-binding protein (Ibabp), small heterodimer partner (Shp), and cyclooxygenase-2 (Cox-2) were determined by real-time polymerase chain reaction. In both normal and adjacent colonic mucosa and colon tumors, we measured CpG methylation of Fxr in bisulfonated genomic DNA. In vitro, we measured the impact of APC inactivation and deoxycholic acid (DCA) treatment on FXR expression in human colon cancer HCT-116 cells transfected with silencing RNA for APC and HT-29 cells carrying inactivated APC. RESULTS In Apc(Min) (/+) mice, constitutive CpG methylation of the Fxrα3/4 promoter was linked to reduced (60-90%) baseline Fxr, Ibabp, and Shp and increased Cox-2 expression in apparently normal adjacent mucosa and colon tumors. Apc knockdown in HCT-116 cells increased cellular myelocytomatosis (c-MYC) and lowered (∼50%) FXR expression, which was further reduced (∼80%) by DCA. In human HCT-116 but not HT-29 colon cancer cells, DCA induced FXR expression and lowered CpG methylation of FXR. CONCLUSIONS We conclude that the loss of APC function favors the silencing of FXR expression through CpG hypermethylation in mouse colonic mucosa and human colon cells, leading to reduced expression of downstream targets (SHP, IBABP) involved in BA homeostasis while increasing the expression of factors (COX-2, c-MYC) that contribute to inflammation and colon cancer.
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Affiliation(s)
- Ornella I Selmin
- Department of Nutritional Sciences, University of Arizona, Tucson, AZ,University of Arizona Cancer Center, University of Arizona, Tucson, AZ
| | - Changming Fang
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ
| | - Adam M Lyon
- Department of Nutritional Sciences, University of Arizona, Tucson, AZ
| | - Tom C Doetschman
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ
| | | | - Jesse D Martinez
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ
| | - Jeffrey W Smith
- Sanford/Burnham Medical Research Institute, Cancer Center Division, La
Jolla, CA
| | - Peter M Lance
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ
| | - Donato F Romagnolo
- Department of Nutritional Sciences and University of Arizona Cancer Center, University of Arizona, Tucson, AZ; and
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22
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Cao Z, Lu C. A Microfluidic Device with Integrated Sonication and Immunoprecipitation for Sensitive Epigenetic Assays. Anal Chem 2016; 88:1965-72. [PMID: 26745449 PMCID: PMC4741277 DOI: 10.1021/acs.analchem.5b04707] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Epigenetic
studies increasingly require analysis of a small number
of cells that are of one specific type and derived from patients or
animals. In this report, we demonstrate a simple microfluidic device
that integrates sonication and immunoprecipitation (IP) for epigenetic
assays, such as chromatin immunoprecipitation (ChIP) and methylated
DNA immunoprecipitation (MeDIP). By incorporating an ultrasonic transducer
with a microfluidic chamber, we implemented microscale sonication
for both shearing chromatin/DNA and mixing/washing of IP beads. Such
integration allowed highly sensitive tests starting with 100 cross-linked
cells for ChIP or 500 pg of genomic DNA for MeDIP (compared to 106–107 cells for ChIP and 1–10 μg
of DNA for MeDIP in conventional assays). The entire on-chip process
of sonication and IP took only 1 h. Our tool will be useful for highly
sensitive epigenetic studies based on a small quantity of sample.
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Affiliation(s)
- Zhenning Cao
- Department of Biomedical Engineering and Mechanics, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech , Blacksburg, Virginia 24061, United States
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23
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Epigenetic changes and alternate promoter usage by human colon cancers for expressing DCLK1-isoforms: Clinical Implications. Sci Rep 2015; 5:14983. [PMID: 26447334 PMCID: PMC4597220 DOI: 10.1038/srep14983] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 09/15/2015] [Indexed: 12/15/2022] Open
Abstract
DCLK1 specifically marks colon/pancreatic cancers in mice, and is expressed by human colon adenocarcinomas (hCRCs). Down-regulation of DCLK1 results in loss of cancer-stem-cells (CSCs), and inhibits spheroidal/xenograft growths from hCRC-cells. The 5'-promoter of DCLK1-gene is reportedly hypermethylated in hCRCs, resulting in loss of expression of DCLK1-transcripts, originating from 5'(α)-promoter (termed DCLK1-L, in here). However, in mouse colon-tumors, 5'-promoter of DCLK1-gene remains unchanged, and DCLK1-L, originating from 5'(α)-promoter, is expressed. We hypothesized that elevated levels of DCLK1-protein in hCRC-cells, may be transcribed/translated from an alternate-promoter. Several in silico and molecular biology approaches were used to test our hypothesis. We report for the first time that majority of hCRCs express short-transcripts of DCLK1 (termed DCLK1-S, in here) from an alternate β-promoter in IntronV of the gene, while normal-colons mainly express DCLK1-L from 5'(α)-promoter. We additionally report an important role of β-catenin and TCF4/LEF binding-sites for activating (α)-promoter, while activated NF-κBp65 (bound to NF-κB-cis-element), activates (β)-promoter in cancer-cells. DCLK1-S expression was examined in a cohort of 92 CRC patients; high-expressors had significantly worse overall-survival compared to low-expressors. Our novel findings' regarding usage of alternate (β)-promoter by hCRCs, suggests that DCLK1-S may represent an important target for preventing/inhibiting colon-cancers, and for eliminating colon-CSCs.
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24
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McIntyre RE, Buczacki SJ, Arends MJ, Adams DJ. Mouse models of colorectal cancer as preclinical models. Bioessays 2015; 37:909-20. [PMID: 26115037 PMCID: PMC4755199 DOI: 10.1002/bies.201500032] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 12/15/2022]
Abstract
In this review, we discuss the application of mouse models to the identification and pre-clinical validation of novel therapeutic targets in colorectal cancer, and to the search for early disease biomarkers. Large-scale genomic, transcriptomic and epigenomic profiling of colorectal carcinomas has led to the identification of many candidate genes whose direct contribution to tumourigenesis is yet to be defined; we discuss the utility of cross-species comparative 'omics-based approaches to this problem. We highlight recent progress in modelling late-stage disease using mice, and discuss ways in which mouse models could better recapitulate the complexity of human cancers to tackle the problem of therapeutic resistance and recurrence after surgical resection.
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Affiliation(s)
- Rebecca E. McIntyre
- Experimental Cancer GeneticsWellcome Trust Sanger InstituteHinxtonCambridgeUK
| | | | - Mark J. Arends
- Edinburgh Cancer Research UK CentreUniversity of EdinburghEdinburghUK
| | - David J. Adams
- Experimental Cancer GeneticsWellcome Trust Sanger InstituteHinxtonCambridgeUK
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25
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Gao S, Zou D, Mao L, Zhou Q, Jia W, Huang Y, Zhao S, Chen G, Wu S, Li D, Xia F, Chen H, Chen M, Ørntoft TF, Bolund L, Sørensen KD. SMAP: a streamlined methylation analysis pipeline for bisulfite sequencing. Gigascience 2015; 4:29. [PMID: 26140213 PMCID: PMC4488126 DOI: 10.1186/s13742-015-0070-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 06/17/2015] [Indexed: 11/10/2022] Open
Abstract
Background DNA methylation has important roles in the regulation of gene expression and cellular specification. Reduced representation bisulfite sequencing (RRBS) has prevailed in methylation studies due to its cost-effectiveness and single-base resolution. The rapid accumulation of RRBS data demands well designed analytical tools. Findings To streamline the data processing of DNA methylation from multiple RRBS samples, we present a flexible pipeline named SMAP, whose features include: (i) handling of single—and/or paired-end diverse bisulfite sequencing data with reduced false-positive rates in differentially methylated regions; (ii) detection of allele-specific methylation events with improved algorithms; (iii) a built-in pipeline for detection of novel single nucleotide polymorphisms (SNPs); (iv) support of multiple user-defined restriction enzymes; (v) conduction of all methylation analyses in a single-step operation when well configured. Conclusions Simulation and experimental data validated the high accuracy of SMAP for SNP detection and methylation identification. Most analyses required in methylation studies (such as estimation of methylation levels, differentially methylated cytosine groups, and allele-specific methylation regions) can be executed readily with SMAP. All raw data from diverse samples could be processed in parallel and ‘packetized’ streams. A simple user guide to the methylation applications is also provided. Electronic supplementary material The online version of this article (doi:10.1186/s13742-015-0070-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shengjie Gao
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark ; BGI Co Ltd, Shenzhen, 518083 China ; Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Dan Zou
- BGI Co Ltd, Shenzhen, 518083 China ; School of Computer Science, National University of Defense Technology, Changsha, 410073 China
| | - Likai Mao
- BGI Co Ltd, Shenzhen, 518083 China ; Genomic Biology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Wenlong Jia
- BGI Co Ltd, Shenzhen, 518083 China ; Department of Computer Science, City University of Hong Kong, Hong Kong, 999077 China
| | - Yi Huang
- Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | | | | | - Song Wu
- Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | | | - Fei Xia
- Electronic Engineering College, Naval Engineering University, Jiefang Avenue #717, Wuhan, 430033 China
| | | | | | - Torben F Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Bolund
- BGI Co Ltd, Shenzhen, 518083 China ; Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Karina D Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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26
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Kaspi A, Ziemann M, Keating ST, Khurana I, Connor T, Spolding B, Cooper A, Lazarus R, Walder K, Zimmet P, El-Osta A. Non-referenced genome assembly from epigenomic short-read data. Epigenetics 2015; 9:1329-38. [PMID: 25437048 DOI: 10.4161/15592294.2014.969610] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Current computational methods used to analyze changes in DNA methylation and chromatin modification rely on sequenced genomes. Here we describe a pipeline for the detection of these changes from short-read sequence data that does not require a reference genome. Open source software packages were used for sequence assembly, alignment, and measurement of differential enrichment. The method was evaluated by comparing results with reference-based results showing a strong correlation between chromatin modification and gene expression. We then used our de novo sequence assembly to build the DNA methylation profile for the non-referenced Psammomys obesus genome. The pipeline described uses open source software for fast annotation and visualization of unreferenced genomic regions from short-read data.
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Affiliation(s)
- Antony Kaspi
- a Epigenetics in Human Health and Disease Laboratory ; Baker IDI Heart and Diabetes Institute ; The Alfred Medical Research and Education Precinct ; Melbourne , Victoria , Australia
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27
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Guo Y, Lee JH, Shu L, Huang Y, Li W, Zhang C, Yang AY, Boyanapalli SS, Perekatt A, Hart RP, Verzi M, Kong ANT. Association of aberrant DNA methylation in Apc(min/+) mice with the epithelial-mesenchymal transition and Wnt/β-catenin pathways: genome-wide analysis using MeDIP-seq. Cell Biosci 2015; 5:24. [PMID: 26101583 PMCID: PMC4476183 DOI: 10.1186/s13578-015-0013-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/11/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Aberrant DNA methylation at the 5-carbon on cytosine residues (5mC) in CpG dinucleotides is probably the most extensively characterized epigenetic modification in colon cancer. It has been suggested that the loss of adenomatous polyposis coli (APC) function initiates tumorigenesis and that additional genetic and epigenetic events are involved in colon cancer progression. We aimed to study the genome-wide DNA methylation profiles of intestinal tumorigenesis in Apc(min/+) mice. RESULTS Methylated DNA immunoprecipitation (MeDIP) followed by next-generation sequencing was used to determine the global profile of DNA methylation changes in Apc(min/+) mice. DNA was extracted from adenomatous polyps from Apc(min/+) mice and from normal intestinal tissue from age-matched Apc(+/+) littermates, and the MeDIP-seq assay was performed. Ingenuity Pathway Analysis (IPA) software was used to analyze the data for gene interactions. A total of 17,265 differentially methylated regions (DMRs) displayed a ≥ 2-fold change (log2) in methylation in Apc(min/+) mice; among these DMRs, 9,078 (52.6 %) and 8,187 (47.4 %) exhibited increased and decreased methylation, respectively. Genes with altered methylation patterns were mainly mapped to networks and biological functions associated with cancer and gastrointestinal diseases. Among these networks, several canonical pathways, such as the epithelial-mesenchymal transition (EMT) and Wnt/β-catenin pathways, were significantly associated with genome-wide methylation changes in polyps from Apc(min/+) mice. The identification of certain differentially methylated molecules in the EMT and Wnt/β-catenin pathways, such as APC2 (adenomatosis polyposis coli 2), SFRP2 (secreted frizzled-related protein 2), and DKK3 (dickkopf-related protein 3), was consistent with previous publications. CONCLUSIONS Our findings indicated that Apc(min/+) mice exhibited extensive aberrant DNA methylation that affected certain signaling pathways, such as the EMT and Wnt/β-catenin pathways. The genome-wide DNA methylation profile of Apc(min/+) mice is informative for future studies investigating epigenetic gene regulation in colon tumorigenesis and the prevention of colon cancer.
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Affiliation(s)
- Yue Guo
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Jong Hun Lee
- Department of Food Science and Biotechnology, College of Life Science, CHA University, Gyeonggi-do, 463-400 South Korea
| | - Limin Shu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Ying Huang
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Wenji Li
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Chengyue Zhang
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Anne Yuqing Yang
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Sarandeep Ss Boyanapalli
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA.,Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Ansu Perekatt
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Michael Verzi
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Ah-Ng Tony Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
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28
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Forn M, Díez-Villanueva A, Merlos-Suárez A, Muñoz M, Lois S, Carriò E, Jordà M, Bigas A, Batlle E, Peinado MA. Overlapping DNA methylation dynamics in mouse intestinal cell differentiation and early stages of malignant progression. PLoS One 2015; 10:e0123263. [PMID: 25933092 PMCID: PMC4416816 DOI: 10.1371/journal.pone.0123263] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/17/2015] [Indexed: 12/20/2022] Open
Abstract
Mouse models of intestinal crypt cell differentiation and tumorigenesis have been used to characterize the molecular mechanisms underlying both processes. DNA methylation is a key epigenetic mark and plays an important role in cell identity and differentiation programs and cancer. To get insights into the dynamics of cell differentiation and malignant transformation we have compared the DNA methylation profiles along the mouse small intestine crypt and early stages of tumorigenesis. Genome-scale analysis of DNA methylation together with microarray gene expression have been applied to compare intestinal crypt stem cells (EphB2high), differentiated cells (EphB2negative), ApcMin/+ adenomas and the corresponding non-tumor adjacent tissue, together with small and large intestine samples and the colon cancer cell line CT26. Compared with late stages, small intestine crypt differentiation and early stages of tumorigenesis display few and relatively small changes in DNA methylation. Hypermethylated loci are largely shared by the two processes and affect the proximities of promoter and enhancer regions, with enrichment in genes associated with the intestinal stem cell signature and the PRC2 complex. The hypermethylation is progressive, with minute levels in differentiated cells, as compared with intestinal stem cells, and reaching full methylation in advanced stages. Hypomethylation shows different signatures in differentiation and cancer and is already present in the non-tumor tissue adjacent to the adenomas in ApcMin/+ mice, but at lower levels than advanced cancers. This study provides a reference framework to decipher the mechanisms driving mouse intestinal tumorigenesis and also the human counterpart.
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Affiliation(s)
- Marta Forn
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Díez-Villanueva
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Merlos-Suárez
- Institute for Research in Biomedicine (IRB Barcelona) 08028 Barcelona, Spain
| | - Mar Muñoz
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Sergi Lois
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Elvira Carriò
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Mireia Jordà
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Bigas
- Institut Hospital del Mar d’Investigació Mèdica (IMIM) 08003 Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona) 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Miguel A. Peinado
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
- * E-mail:
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29
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Epididymal Region-Specific miRNA Expression and DNA Methylation and Their Roles in Controlling Gene Expression in Rats. PLoS One 2015; 10:e0124450. [PMID: 25901964 PMCID: PMC4406618 DOI: 10.1371/journal.pone.0124450] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 03/13/2015] [Indexed: 02/02/2023] Open
Abstract
Region-specific gene expression is an intriguing feature of the mammalian epididymis. This unique property is essential for sperm maturation and storage, and it also implicates stringent and multi-level regulations of gene expression. Over the past decade, the androgen-driven activation of epididymal gene transcription has been extensively studied. However, it still remains largely unexplored whether and how other regulatory mechanisms, such as miRNAs and DNA methylation, are involved in controlling regional gene expression in the epididymis. Using microarray-based approaches, we studied the regional miRNA expression and DNA methylation profiles in 4 distinct epididymal regions (initial segment, caput, corpus and cauda) of rats. We found that the miR-200 family members were more expressed in caput, compared with cauda. By GSEA analysis, the differential expression of miR-200 family between caput and cauda was shown to be negatively correlated with their predicted target genes, among which 4 bona fide targets were verified by luciferase reporter assay. Predicted target genes of miR-200 family have enriched functions in anti-apoptosis, cell transportation and development, implying the regional diversity in epididymal functions. On the other hand, we revealed epididymal DNA methylation of 2002 CpG islands and 2771 gene promoters (-3.88-0.97 kb), among which 1350 (67.43%) CpG islands and 2095 (75.60%) promoters contained region-specific DNA methylation. We observed significant and distinct functional enrichment in genes with specifically methylated promoters in each epididymal regions, but these DNA methylations did not show significant correlation with repressed gene transcription in the mature epididymis. Conclusively, we investigated the regional miRNA expression and DNA methylation in the rat epididymis and revealed a potential role of miR-200 family in gene expression regulation between caput and cauda. This may contribute to the distinct physiological function in sperm maturation / storage of caput / cauda epididymis.
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30
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Abu-Remaileh M, Bender S, Raddatz G, Ansari I, Cohen D, Gutekunst J, Musch T, Linhart H, Breiling A, Pikarsky E, Bergman Y, Lyko F. Chronic inflammation induces a novel epigenetic program that is conserved in intestinal adenomas and in colorectal cancer. Cancer Res 2015; 75:2120-30. [PMID: 25808873 DOI: 10.1158/0008-5472.can-14-3295] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/12/2015] [Indexed: 12/13/2022]
Abstract
Chronic inflammation represents a major risk factor for tumor formation, but the underlying mechanisms have remained largely unknown. Epigenetic mechanisms can record the effects of environmental challenges on the genome level and could therefore play an important role in the pathogenesis of inflammation-associated tumors. Using single-base methylation maps and transcriptome analyses of a colitis-induced mouse colon cancer model, we identified a novel epigenetic program that is characterized by hypermethylation of DNA methylation valleys that are characterized by low CpG density and active chromatin marks. This program is conserved and functional in mouse intestinal adenomas and results in silencing of active intestinal genes that are involved in gastrointestinal homeostasis and injury response. Further analyses reveal that the program represents a prominent feature of human colorectal cancer and can be used to correctly classify colorectal cancer samples with high accuracy. Together, our results show that inflammatory signals establish a novel epigenetic program that silences a specific set of genes that contribute to inflammation-induced cellular transformation.
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Affiliation(s)
- Monther Abu-Remaileh
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Sebastian Bender
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Günter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Ihab Ansari
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Daphne Cohen
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Tanja Musch
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Heinz Linhart
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany. Salem Medical Center, University of Heidelberg, Heidelberg, Germany. Department of Hematology/Oncology, University of Heidelberg Medical Center, Heidelberg, Germany
| | - Achim Breiling
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Eli Pikarsky
- The Lautenberg Center for Immunology, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel.
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany.
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31
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Cheng RYS, Shang Y, Limjunyawong N, Dao T, Das S, Rabold R, Sham JSK, Mitzner W, Tang WY. Alterations of the lung methylome in allergic airway hyper-responsiveness. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:244-255. [PMID: 24446183 PMCID: PMC4125208 DOI: 10.1002/em.21851] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/20/2013] [Accepted: 12/28/2013] [Indexed: 05/29/2023]
Abstract
Asthma is a chronic airway disorder characterized by recurrent attacks of breathlessness and wheezing, affecting 300 million people around the world (available at: www.who.int). To date, genetic factors associated with asthma susceptibility have been unable to explain the full etiology of asthma. Recent studies have demonstrated that the epigenetic disruption of gene expression plays an equally important role in the development of asthma through interaction with our environment. We sensitized 6-week-old C57BL/6J mice with house-dust-mite (HDM) extracts intraperitoneally followed by 5 weeks of exposure to HDM challenges (three times a week) intratracheally. HDM-exposed mice showed an increase in airway hyper-responsiveness (AHR) and inflammation together with structural remodeling of the airways. We applied methylated DNA immunoprecipitation-next generation sequencing (MeDIP-seq) for profiling of DNA methylation changes in the lungs in response to HDM. We observed about 20 million reads by a single-run of massive parallel sequencing. We performed bioinformatics and pathway analysis on the raw sequencing data to identify differentially methylated candidate genes in HDM-exposed mice. Specifically, we have revealed that the transforming growth factor beta signaling pathway is epigenetically modulated by chronic exposure to HDM. Here, we demonstrated that a specific allergen may play a role in AHR through an epigenetic mechanism by disrupting the expression of genes in lungs that might be involved in airway inflammation and remodeling. Our findings provide new insights into the potential mechanisms by which environmental allergens induce allergic asthma and such insights may assist in the development of novel preventive and therapeutic options for this debilitative disease.
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Affiliation(s)
- Robert YS Cheng
- Radiation Biology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Yan Shang
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
- Department of Respiratory Diseases, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Nathachit Limjunyawong
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Tyna Dao
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Sandhya Das
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Richard Rabold
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - James SK Sham
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Wayne Mitzner
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Wan-Yee Tang
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
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32
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Brglez V, Pucer A, Pungerčar J, Lambeau G, Petan T. Secreted phospholipases A₂are differentially expressed and epigenetically silenced in human breast cancer cells. Biochem Biophys Res Commun 2014; 445:230-5. [PMID: 24508801 DOI: 10.1016/j.bbrc.2014.01.182] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 01/29/2014] [Indexed: 02/06/2023]
Abstract
Secreted phospholipases A2 (sPLA2s) have recently been associated with several cancers, but their role in breast cancer is unknown. Here we demonstrate that mRNA expression of group IIA, III and X sPLA2s differs both in vivo in tumour biopsies and in breast cancer cells in vitro. Their expression is differentially regulated by DNA methylation and histone acetylation and, significantly, all three genes are silenced in aggressive triple negative cells due to both mechanisms. The transcription start site promoter region and the upstream CpG islands, exclusive to the group X sPLA2 gene, have variable roles in the regulation of sPLA2 expression. Our results suggest that the differential expression of hGIIA, hGIII and hGX sPLA2s in breast cancer cells is a consequence of various degrees of epigenetic silencing due to DNA hypermethylation and histone deacetylation.
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Affiliation(s)
- Vesna Brglez
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Anja Pucer
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Jože Pungerčar
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Gérard Lambeau
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS et Université de Nice Sophia Antipolis, UMR 6097, Sophia Antipolis, Valbonne, France
| | - Toni Petan
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia.
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33
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Tanabe S. Role of mesenchymal stem cells in cell life and their signaling. World J Stem Cells 2014; 6:24-32. [PMID: 24567785 PMCID: PMC3927011 DOI: 10.4252/wjsc.v6.i1.24] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 11/18/2013] [Accepted: 12/13/2013] [Indexed: 02/06/2023] Open
Abstract
Mesenchymal stem cells (MSCs) have various roles in the body and cellular environment, and the cellular phenotypes of MSCs changes in different conditions. MSCs support the maintenance of other cells, and the capacity of MSCs to differentiate into several cell types makes the cells unique and full of possibilities. The involvement of MSCs in the epithelial-mesenchymal transition is an important property of these cells. In this review, the role of MSCs in cell life, including their application in therapy, is first described, and the signaling mechanism of MSCs is investigated for a further understanding of these cells.
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34
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Lienhard M, Grimm C, Morkel M, Herwig R, Chavez L. MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. ACTA ACUST UNITED AC 2013; 30:284-6. [PMID: 24227674 PMCID: PMC3892689 DOI: 10.1093/bioinformatics/btt650] [Citation(s) in RCA: 234] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Motivation: DNA enrichment followed by sequencing is a versatile tool in molecular biology, with a wide variety of applications including genome-wide analysis of epigenetic marks and mechanisms. A common requirement of these diverse applications is a comparison of read coverage between experimental conditions. The amount of samples generated for such comparisons ranges from few replicates to hundreds of samples per condition for epigenome-wide association studies. Consequently, there is an urgent need for software that allows for fast and simple processing and comparison of sequencing data derived from enriched DNA. Results: Here, we present a major update of the R/Bioconductor package MEDIPS, which allows for an arbitrary number of replicates per group and integrates sophisticated statistical methods for the detection of differential coverage between experimental conditions. Our approach can be applied to a diversity of quantitative sequencing data. In addition, our update adds novel functionality to MEDIPS, including correlation analysis between samples, and takes advantage of Bioconductor’s annotation databases to facilitate annotation of specific genomic regions. Availability and implementation: The latest version of MEDIPS is available as version 1.12.0 and part of Bioconductor 2.13. The package comes with a manual containing detailed description of its functionality and is available at http://www.bioconductor.org. Contact:lienhard@molgen.mpg.de Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthias Lienhard
- Departments of Vertebrate Genomics and Developmental Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany, Department of Rheumatology and Clinical Immunology, Institute of Pathology, Laboratory of Molecular Tumour Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany and Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
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35
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Yang T, Owen JL, Lightfoot YL, Kladde MP, Mohamadzadeh M. Microbiota impact on the epigenetic regulation of colorectal cancer. Trends Mol Med 2013; 19:714-25. [PMID: 24051204 DOI: 10.1016/j.molmed.2013.08.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 08/02/2013] [Accepted: 08/22/2013] [Indexed: 12/12/2022]
Abstract
Mechanisms of colorectal cancer (CRC) development can be generally divided into three categories: genetic, epigenetic, and aberrant immunologic signaling pathways, all of which may be triggered by an imbalanced intestinal microbiota. Aberrant gut microbial composition, termed 'dysbiosis', has been reported in inflammatory bowel disease patients who are at increased risk for CRC development. Recent studies indicate that it is feasible to rescue experimental models of colonic cancer by oral treatment with genetically engineered beneficial bacteria and/or their immune-regulating gene products. Here, we review the mechanisms of epigenetic modulation implicated in the development and progression of CRC, which may be the result of dysbiosis, and therefore may be amenable to therapeutic intervention.
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Affiliation(s)
- Tao Yang
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, FL 32608 USA; Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Florida, Gainesville, FL 32610 USA
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36
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Forn M, Muñoz M, Tauriello DVF, Merlos-Suárez A, Rodilla V, Bigas A, Batlle E, Jordà M, Peinado MA. Long range epigenetic silencing is a trans-species mechanism that results in cancer specific deregulation by overriding the chromatin domains of normal cells. Mol Oncol 2013; 7:1129-41. [PMID: 24035705 DOI: 10.1016/j.molonc.2013.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 01/08/2023] Open
Abstract
DNA methylation and chromatin remodeling are frequently implicated in the silencing of genes involved in carcinogenesis. Long Range Epigenetic Silencing (LRES) is a mechanism of gene inactivation that affects multiple contiguous CpG islands and has been described in different human cancer types. However, it is unknown whether there is a coordinated regulation of the genes embedded in these regions in normal cells and in early stages of tumor progression. To better characterize the molecular events associated with the regulation and remodeling of these regions we analyzed two regions undergoing LRES in human colon cancer in the mouse model. We demonstrate that LRES also occurs in murine cancer in vivo and mimics the molecular features of the human phenomenon, namely, downregulation of gene expression, acquisition of inactive histone marks, and DNA hypermethylation of specific CpG islands. The genes embedded in these regions showed a dynamic and autonomous regulation during mouse intestinal cell differentiation, indicating that, in the framework considered here, the coordinated regulation in LRES is restricted to cancer. Unexpectedly, benign adenomas in Apc(Min/+) mice showed overexpression of most of the genes affected by LRES in cancer, which suggests that the repressive remodeling of the region is a late event. Chromatin immunoprecipitation analysis of the transcriptional insulator CTCF in mouse colon cancer cells revealed disrupted chromatin domain boundaries as compared with normal cells. Malignant regression of cancer cells by in vitro differentiation resulted in partial reversion of LRES and gain of CTCF binding. We conclude that genes in LRES regions are plastically regulated in cell differentiation and hyperproliferation, but are constrained to a coordinated repression by abolishing boundaries and the autonomous regulation of chromatin domains in cancer cells.
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Affiliation(s)
- Marta Forn
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain
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