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Li M, Shi M, Xu Y, Qiu J, Lv Q. Histone Methyltransferase KMT2D Regulates H3K4 Methylation and is Involved in the Pathogenesis of Ovarian Cancer. Cell Transplant 2021; 30:9636897211027521. [PMID: 34705580 PMCID: PMC8554562 DOI: 10.1177/09636897211027521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
To investigate the function of histone-lysine N-methyltransferase 2D (KMT2D) on the methylation of H3 lysine 4 (H3K4) in the progression of Ovarian cancer (OV). KMT2D, ESR1 and H3K4me expressions in surgical resected tumors and tumor adjacent tissues of OV from 198 patients were determined using immunohistochemistry (IHC). Human OV cell lines including SKOV3, HO-8910 cells and normal ovarian epithelial cell line IOSE80 were employed for in vitro experiment, and BALB/C female nude mice were used for in vivo study. qRT-PCR and Western blotting were implemented for measuring the KMT2D, ESR1, PTGS2, STAT3, VEGFR2, H3K4me and ELF3 levels. Chromatin immunoprecipitation (ChIP) analysis was used for studying the binding between ESR1 and H3K4me. Edu staining assay was executed to determine cell viability, and colony formation and cell invasion assay. The immunofluorescence method was utilized for the visualization of protein expression and distribution in cells. In this study, KMT2D, ESR1 and H3K4me were found upregulated in OV progression. Mutated H3K4me could inhibit the proliferation, colony formation and invasion ability of OV cells. Mutated H3K4me could also hinder the ESR1 in SKOV3 expressions and HO-8910 cells, which would further mediate PTGS2/STAT3/VEGF pathway. In vivo studies also demonstrated that mutated H3K4me inhibited OV progression via targeting ESR1. All the ChIP-PCR analysis indicated the moderator effect of H3K4me on ESR1. Our findings indicated that ESR1 played an important role in the OV progression. Besides, H3K4me could promote cell proliferation and inhibit apoptosis of OV cells. Meanwhile, it could also targets the ESR1 production to enhance the migration and invasion of OV cells, which was through the activation of ESR1-ELF3-PTGS2-STAT3-VEGF cascade signaling pathway.
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Affiliation(s)
- Ming Li
- Department of Pathology, the Affiliated Suzhou Municipal Hospital of Nanjing Medical University, Suzhou, China
- Co-first author
| | - Mengdie Shi
- Department of obstetrics and gynecology, the Affiliated Suzhou Municipal Hospital of Nanjing Medical University, Suzhou, China
- Co-first author
| | - Ying Xu
- Department of obstetrics and gynecology, the Affiliated Suzhou Municipal Hospital of Nanjing Medical University, Suzhou, China
| | - Jianping Qiu
- Department of obstetrics and gynecology, the Affiliated Suzhou Municipal Hospital of Nanjing Medical University, Suzhou, China
- Jianping Qiu, Department of obstetrics and gynecology, the Affiliated Suzhou Municipal Hospital of Nanjing Medical University, No.242 Guangji Road, Suzhou, 215008, China.
| | - Qing Lv
- Department of Breast Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China
- Qing Lv, Department of Breast Surgery, Affiliated Hospital of Jiangnan University, No.1000 Hefeng Road, Wuxi, 214000, China.
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52
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Helmprobst F, Kneitz S, Klotz B, Naville M, Dechaud C, Volff JN, Schartl M. Differential expression of transposable elements in the medaka melanoma model. PLoS One 2021; 16:e0251713. [PMID: 34705830 PMCID: PMC8550402 DOI: 10.1371/journal.pone.0251713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/30/2021] [Indexed: 12/16/2022] Open
Abstract
Malignant melanoma incidence is rising worldwide. Its treatment in an advanced state is difficult, and the prognosis of this severe disease is still very poor. One major source of these difficulties is the high rate of metastasis and increased genomic instability leading to a high mutation rate and the development of resistance against therapeutic approaches. Here we investigate as one source of genomic instability the contribution of activation of transposable elements (TEs) within the tumor. We used the well-established medaka melanoma model and RNA-sequencing to investigate the differential expression of TEs in wildtype and transgenic fish carrying melanoma. We constructed a medaka-specific TE sequence library and identified TE sequences that were specifically upregulated in tumors. Validation by qRT- PCR confirmed a specific upregulation of a LINE and an LTR element in malignant melanomas of transgenic fish.
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Affiliation(s)
- Frederik Helmprobst
- Physiological Chemistry, Biocenter, University of Würzburg, Würzburg, Germany
- Department of Neuropathology, Philipps-University Marburg, Marburg, Germany
- * E-mail: (FH); (MS)
| | - Susanne Kneitz
- Physiological Chemistry, Biocenter, University of Würzburg, Würzburg, Germany
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Barbara Klotz
- Physiological Chemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, United States of America
- Developmental Biochemistry, University of Würzburg, Würzburg, Germany
- * E-mail: (FH); (MS)
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The Role of Emerin in Cancer Progression and Metastasis. Int J Mol Sci 2021; 22:ijms222011289. [PMID: 34681951 PMCID: PMC8537873 DOI: 10.3390/ijms222011289] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/27/2022] Open
Abstract
It is commonly recognized in the field that cancer cells exhibit changes in the size and shape of their nuclei. These features often serve as important biomarkers in the diagnosis and prognosis of cancer patients. Nuclear size can significantly impact cell migration due to its incredibly large size. Nuclear structural changes are predicted to regulate cancer cell migration. Nuclear abnormalities are common across a vast spectrum of cancer types, regardless of tissue source, mutational spectrum, and signaling dependencies. The pervasiveness of nuclear alterations suggests that changes in nuclear structure may be crucially linked to the transformation process. The factors driving these nuclear abnormalities, and the functional consequences, are not completely understood. Nuclear envelope proteins play an important role in regulating nuclear size and structure in cancer. Altered expression of nuclear lamina proteins, including emerin, is found in many cancers and this expression is correlated with better clinical outcomes. A model is emerging whereby emerin, as well as other nuclear lamina proteins, binding to the nucleoskeleton regulates the nuclear structure to impact metastasis. In this model, emerin and lamins play a central role in metastatic transformation, since decreased emerin expression during transformation causes the nuclear structural defects required for increased cell migration, intravasation, and extravasation. Herein, we discuss the cellular functions of nuclear lamina proteins, with a particular focus on emerin, and how these functions impact cancer progression and metastasis.
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54
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Neinavaie F, Ibrahim-Hashim A, Kramer AM, Brown JS, Richards CL. The Genomic Processes of Biological Invasions: From Invasive Species to Cancer Metastases and Back Again. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.681100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The concept of invasion is useful across a broad range of contexts, spanning from the fine scale landscape of cancer tumors up to the broader landscape of ecosystems. Invasion biology provides extraordinary opportunities for studying the mechanistic basis of contemporary evolution at the molecular level. Although the field of invasion genetics was established in ecology and evolution more than 50 years ago, there is still a limited understanding of how genomic level processes translate into invasive phenotypes across different taxa in response to complex environmental conditions. This is largely because the study of most invasive species is limited by information about complex genome level processes. We lack good reference genomes for most species. Rigorous studies to examine genomic processes are generally too costly. On the contrary, cancer studies are fortified with extensive resources for studying genome level dynamics and the interactions among genetic and non-genetic mechanisms. Extensive analysis of primary tumors and metastatic samples have revealed the importance of several genomic mechanisms including higher mutation rates, specific types of mutations, aneuploidy or whole genome doubling and non-genetic effects. Metastatic sites can be directly compared to primary tumor cell counterparts. At the same time, clonal dynamics shape the genomics and evolution of metastatic cancers. Clonal diversity varies by cancer type, and the tumors’ donor and recipient tissues. Still, the cancer research community has been unable to identify any common events that provide a universal predictor of “metastatic potential” which parallels findings in evolutionary ecology. Instead, invasion in cancer studies depends strongly on context, including order of events and clonal composition. The detailed studies of the behavior of a variety of human cancers promises to inform our understanding of genome level dynamics in the diversity of invasive species and provide novel insights for management.
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55
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Genetics of Chronic Lymphocytic Leukemia. ACTA ACUST UNITED AC 2021; 27:259-265. [PMID: 34398552 DOI: 10.1097/ppo.0000000000000538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
ABSTRACT During the past 10 years, relevant advances have been made in the understanding of the pathogenesis of chronic lymphocytic leukemia via the integrated analysis of its genome and related epigenome, and transcriptome. These analyses also had an impact on our understanding of the initiation, as well as of the evolution of chronic lymphocytic leukemia, including resistance to chemotherapy and sensitivity and resistance to novel targeted therapies. This chapter will review the current state of the art in this field, with emphasis on the genetic heterogeneity of the disease and the biological pathways that are altered by the genetic lesions.
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56
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Pressley M, Salvioli M, Lewis DB, Richards CL, Brown JS, Staňková K. Evolutionary Dynamics of Treatment-Induced Resistance in Cancer Informs Understanding of Rapid Evolution in Natural Systems. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.681121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Rapid evolution is ubiquitous in nature. We briefly review some of this quite broadly, particularly in the context of response to anthropogenic disturbances. Nowhere is this more evident, replicated and accessible to study than in cancer. Curiously cancer has been late - relative to fisheries, antibiotic resistance, pest management and evolution in human dominated landscapes - in recognizing the need for evolutionarily informed management strategies. The speed of evolution matters. Here, we employ game-theoretic modeling to compare time to progression with continuous maximum tolerable dose to that of adaptive therapy where treatment is discontinued when the population of cancer cells gets below half of its initial size and re-administered when the cancer cells recover, forming cycles with and without treatment. We show that the success of adaptive therapy relative to continuous maximum tolerable dose therapy is much higher if the population of cancer cells is defined by two cell types (sensitive vs. resistant in a polymorphic population). Additionally, the relative increase in time to progression increases with the speed of evolution. These results hold with and without a cost of resistance in cancer cells. On the other hand, treatment-induced resistance can be modeled as a quantitative trait in a monomorphic population of cancer cells. In that case, when evolution is rapid, there is no advantage to adaptive therapy. Initial responses to therapy are blunted by the cancer cells evolving too quickly. Our study emphasizes how cancer provides a unique system for studying rapid evolutionary changes within tumor ecosystems in response to human interventions; and allows us to contrast and compare this system to other human managed or dominated systems in nature.
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57
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Nuclear Organization during Hepatogenesis in Zebrafish Requires Uhrf1. Genes (Basel) 2021; 12:genes12071081. [PMID: 34356097 PMCID: PMC8304062 DOI: 10.3390/genes12071081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 01/07/2023] Open
Abstract
Acquisition of cellular fate during development is initiated and maintained by well-coordinated patterns of gene expression that are dictated by the epigenetic landscape and genome organization in the nucleus. While the epigenetic marks that mediate developmental gene expression patterns during organogenesis have been well studied, less is known about how epigenetic marks influence nuclear organization during development. This study examines the relationship between nuclear structure, chromatin accessibility, DNA methylation, and gene expression during hepatic outgrowth in zebrafish larvae. We investigate the relationship between these features using mutants that lack DNA methylation. Hepatocyte nuclear morphology was established coincident with hepatocyte differentiation at 80 h post-fertilization (hpf), and nuclear shape and size continued to change until the conclusion of outgrowth and morphogenesis at 120 hpf. Integrating ATAC-Seq analysis with DNA methylation profiling of zebrafish livers at 120 hpf showed that closed and highly methylated chromatin occupies most transposable elements and that open chromatin correlated with gene expression. DNA hypomethylation, due to mutation of genes encoding ubiquitin-like, containing PHD and RING Finger Domains 1 (uhrf1) and DNA methyltransferase (dnmt1), did not block hepatocyte differentiation, but had dramatic effects on nuclear organization. Hepatocytes in uhrf1 mutants have large, deformed nuclei with multiple nucleoli, downregulation of nucleolar genes, and a complete lack of the nuclear lamina. Loss of lamin B2 staining was phenocopied by dnmt1 mutation. Together, these data show that hepatocyte nuclear morphogenesis coincides with organ morphogenesis and outgrowth, and that DNA methylation directs chromatin organization, and, in turn, hepatocyte nuclear shape and size during liver development.
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58
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Das AB, Seddon AR, O'Connor KM, Hampton MB. Regulation of the epigenetic landscape by immune cell oxidants. Free Radic Biol Med 2021; 170:131-149. [PMID: 33444713 DOI: 10.1016/j.freeradbiomed.2020.12.453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/21/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022]
Abstract
Excessive production of microbicidal oxidants by neutrophils can damage host tissue. The short-term response of cells to oxidative stress is well understood, but the mechanisms behind long-term consequences require further clarification. Epigenetic pathways mediate cellular adaptation, and are therefore a potential target of oxidative stress. Indeed, there is evidence that many proteins and metabolites involved in epigenetic pathways are redox sensitive. In this review we provide an overview of the epigenetic landscape and discuss the potential for redox regulation. Using this information, we highlight specific examples where neutrophil oxidants react with epigenetic pathway components. We also use published data from redox proteomics to map out known intersections between oxidative stress and epigenetics that may signpost helpful directions for future investigation. Finally, we discuss the role neutrophils play in adaptive pathologies with a focus on tumour initiation and progression. We hope this information will stimulate further discourse on the emerging field of redox epigenomics.
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Affiliation(s)
- Andrew B Das
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Annika R Seddon
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Karina M O'Connor
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
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59
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Wang S, Alpsoy A, Sood S, Ordonez-Rubiano SC, Dhiman A, Sun Y, Jiao G, Krusemark CJ, Dykhuizen EC. A Potent, Selective CBX2 Chromodomain Ligand and Its Cellular Activity During Prostate Cancer Neuroendocrine Differentiation. Chembiochem 2021; 22:2335-2344. [PMID: 33950564 PMCID: PMC8358665 DOI: 10.1002/cbic.202100118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/04/2021] [Indexed: 12/16/2022]
Abstract
Polycomb group (PcG) proteins are epigenetic regulators that facilitate both embryonic development and cancer progression. PcG proteins form Polycomb repressive complexes 1 and 2 (PRC1 and PRC2). PRC2 trimethylates histone H3 lysine 27 (H3K27me3), a histone mark recognized by the N-terminal chromodomain (ChD) of the CBX subunit of canonical PRC1. There are five PcG CBX paralogs in humans. CBX2 in particular is upregulated in a variety of cancers, particularly in advanced prostate cancers. Using CBX2 inhibitors to understand and target CBX2 in prostate cancer is highly desirable; however, high structural similarity among the CBX ChDs has been challenging for developing selective CBX ChD inhibitors. Here, we utilize selections of focused DNA encoded libraries (DELs) for the discovery of a selective CBX2 chromodomain probe, SW2_152F. SW2_152F binds to CBX2 ChD with a Kd of 80 nM and displays 24-1000-fold selectivity for CBX2 ChD over other CBX paralogs in vitro. SW2_152F is cell permeable, selectively inhibits CBX2 chromatin binding in cells, and blocks neuroendocrine differentiation of prostate cancer cell lines in response to androgen deprivation.
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Affiliation(s)
- Sijie Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Aktan Alpsoy
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
- Purdue Life Science Interdisciplinary Graduate Program, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Surbhi Sood
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
- Purdue Life Science Interdisciplinary Graduate Program, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Sandra Carolina Ordonez-Rubiano
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Yixing Sun
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Guanming Jiao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Casey J. Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
- Purdue Center for Cancer Research, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Emily C. Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
- Purdue Center for Cancer Research, 201 S. University St. West Lafayette, IN, 47907 USA
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60
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Kepp O, Bezu L, Yamazaki T, Di Virgilio F, Smyth MJ, Kroemer G, Galluzzi L. ATP and cancer immunosurveillance. EMBO J 2021; 40:e108130. [PMID: 34121201 DOI: 10.15252/embj.2021108130] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/24/2021] [Accepted: 04/05/2021] [Indexed: 12/14/2022] Open
Abstract
While intracellular adenosine triphosphate (ATP) occupies a key position in the bioenergetic metabolism of all the cellular compartments that form the tumor microenvironment (TME), extracellular ATP operates as a potent signal transducer. The net effects of purinergic signaling on the biology of the TME depend not only on the specific receptors and cell types involved, but also on the activation status of cis- and trans-regulatory circuitries. As an additional layer of complexity, extracellular ATP is rapidly catabolized by ectonucleotidases, culminating in the accumulation of metabolites that mediate distinct biological effects. Here, we discuss the molecular and cellular mechanisms through which ATP and its degradation products influence cancer immunosurveillance, with a focus on therapeutically targetable circuitries.
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Affiliation(s)
- Oliver Kepp
- Equipe labellisée par la Ligue contre le cancer, Centre de Recherche des Cordeliers, INSERM U1138, Sorbonne Université, Université de Paris, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
| | - Lucillia Bezu
- Equipe labellisée par la Ligue contre le cancer, Centre de Recherche des Cordeliers, INSERM U1138, Sorbonne Université, Université de Paris, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
| | - Takahiro Yamazaki
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | | | - Mark J Smyth
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Qld, Australia
| | - Guido Kroemer
- Equipe labellisée par la Ligue contre le cancer, Centre de Recherche des Cordeliers, INSERM U1138, Sorbonne Université, Université de Paris, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.,Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China.,Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA.,Sandra and Edward Meyer Cancer Center, New York, NY, USA.,Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA.,Department of Dermatology, Yale School of Medicine, New Haven, CT, USA.,Université de Paris, Paris, France
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61
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Butera A, Melino G, Amelio I. Epigenetic "Drivers" of Cancer. J Mol Biol 2021; 433:167094. [PMID: 34119490 DOI: 10.1016/j.jmb.2021.167094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/21/2021] [Accepted: 06/02/2021] [Indexed: 12/13/2022]
Abstract
Genetics is at the basis of cancer initiation and evolution, but emerging evidence indicates that mutations are not sufficient to produce cancer, indicating a role for epigenetic contributions to the different stages of tumorigenesis. While the genetic tracks of cancer have been widely investigated, the epigenetic "drivers" remain a vague definition. Gene-environment interactions can produce gene-regulatory programs that dictate pathogenesis; this implies a reciprocal relationship where environmental factors contribute to genetic mechanisms of tumorigenesis (i.e. mutagenesis) and genetic factors influence the cellular response to extrinsic stress. In this review article, we attempt to summarise the most remarkable findings demonstrating a contribution of epigenetic factors as proper "drivers" of tumorigenesis. We also try to pose attention on the relevance of epigenetic mechanisms as downstream consequences of genes versus environment interaction.
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Affiliation(s)
- Alessio Butera
- TOR Centre of Excellence, University of Rome Tor Vergata, Italy
| | - Gerry Melino
- TOR Centre of Excellence, University of Rome Tor Vergata, Italy.
| | - Ivano Amelio
- TOR Centre of Excellence, University of Rome Tor Vergata, Italy; School of Life Sciences, University of Nottingham, UK.
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62
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Mounger J, Ainouche ML, Bossdorf O, Cavé-Radet A, Li B, Parepa M, Salmon A, Yang J, Richards CL. Epigenetics and the success of invasive plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200117. [PMID: 33866809 PMCID: PMC8059582 DOI: 10.1098/rstb.2020.0117] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
Biological invasions impose ecological and economic problems on a global scale, but also provide extraordinary opportunities for studying contemporary evolution. It is critical to understand the evolutionary processes that underly invasion success in order to successfully manage existing invaders, and to prevent future invasions. As successful invasive species sometimes are suspected to rapidly adjust to their new environments in spite of very low genetic diversity, we are obliged to re-evaluate genomic-level processes that translate into phenotypic diversity. In this paper, we review work that supports the idea that trait variation, within and among invasive populations, can be created through epigenetic or other non-genetic processes, particularly in clonal invaders where somatic changes can persist indefinitely. We consider several processes that have been implicated as adaptive in invasion success, focusing on various forms of 'genomic shock' resulting from exposure to environmental stress, hybridization and whole-genome duplication (polyploidy), and leading to various patterns of gene expression re-programming and epigenetic changes that contribute to phenotypic variation or even novelty. These mechanisms can contribute to transgressive phenotypes, including hybrid vigour and novel traits, and may thus help to understand the huge successes of some plant invaders, especially those that are genetically impoverished. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Jeannie Mounger
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Avenue, Tampa, FL 33617, USA
| | - Malika L. Ainouche
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Armand Cavé-Radet
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Bo Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Madalin Parepa
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Armel Salmon
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
| | - Ji Yang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Christina L. Richards
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Avenue, Tampa, FL 33617, USA
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
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63
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Fayyaz S, Attar R, Xu B, Sabitaliyevich UY, Adylova A, Fares M, Qureshi MZ, Yaylim I, Alaaeddine N. Realizing the Potential of Blueberry as Natural Inhibitor of Metastasis and Powerful Apoptosis Inducer: Tapping the Treasure Trove for Effective Regulation of Cell Signaling Pathways. Anticancer Agents Med Chem 2021; 20:1780-1786. [PMID: 32160854 DOI: 10.2174/1871520620666200311103206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/20/2019] [Accepted: 11/04/2019] [Indexed: 12/20/2022]
Abstract
Blueberries belong to the genus Vaccinium of the family Ericaceae. Rapidly accumulating experimentally verified data is uncovering the tremendous pharmacological properties of biologically active constituents of blueberries against different diseases. Our rapidly evolving knowledge about the multifaceted nature of cancer has opened new horizons to search for different strategies to target multiple effectors of oncogenic networks to effectively inhibit cancer onset and progression. Excitingly, whole blueberry powder and various bioactive constituents (pterostilbene, malvidin-3-galactoside) of blueberries have been shown to efficiently inhibit metastasis in animal models. These results are encouraging and future studies must focus on the identification of cell signaling pathways effectively modulated by blueberries in different cancers. It seems exciting to note that researchers are focusing on metastasis inhibitory effects of blueberry; however, to reap full benefits, it is necessary to take a step back and critically re-interpret the mechanisms used by active components of blueberry to inhibit or prevent metastasis. JAK/STAT, TGF/SMAD, Notch, SHH/GLI, and Wnt/ β-Catenin have been shown to be directly involved in the regulation of metastasis. However, because of limited studies, it is difficult to critically assess the true potential of blueberry. Loss of apoptosis, metastasis and deregulation of signaling pathways are branching trajectories of molecular oncology. Accordingly, we have to emphasize on these essential facets to realistically claim blueberry as "Superfood". Different clinical trials have been conducted to gather clinical evidence about the chemopreventive role of blueberry or its bioactive components in cancer patients. But it seems clear that because of the lack of sufficient proof-of-concept studies, we cannot extract significant information about the transition of blueberry into the next phases of clinical trials. Overview of the existing scientific evidence revealed visible knowledge gaps and a better understanding of the targets of blueberry will be helpful in efficient and meaningful translation of laboratory findings to clinically effective therapeutics.
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Affiliation(s)
- Sundas Fayyaz
- Department of Biochemistry, Rashid Latif Medical College (RLMC), Lahore, Pakistan
| | - Rukset Attar
- Department of Obstetrics and Gynecology, Yeditepe University, Istanbul, Turkey
| | - Baojun Xu
- Food Science and Technology Program, Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai 519087, China
| | - Uteuliyev Y Sabitaliyevich
- Department of Postgraduate Education and Research, Kazakhstan Medical University KSPH, Almaty, Kazakhstan
| | - Aima Adylova
- Department of Postgraduate Education and Research, Kazakhstan Medical University KSPH, Almaty, Kazakhstan
| | | | - Muhammad Z Qureshi
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Al-Qassim, Saudi Arabia
| | - Ilhan Yaylim
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Nada Alaaeddine
- Faculty of Medical Sciences, Neuroscience Research Center, Lebanese University, Beirut, Lebanon
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64
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Park C, Jeong K, Park JH, Jung S, Bae JM, Kim K, Ock CY, Kim M, Keam B, Kim TM, Jeon YK, Lee SH, Lee JS, Kim DW, Kang GH, Chung DH, Heo DS. Pan-cancer methylation analysis reveals an inverse correlation of tumor immunogenicity with methylation aberrancy. Cancer Immunol Immunother 2021; 70:1605-1617. [PMID: 33230567 DOI: 10.1007/s00262-020-02796-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/07/2020] [Indexed: 12/21/2022]
Abstract
Tumor immunogenicity is driven by various genomic and transcriptomic factors but the association with the overall status of methylation aberrancy is not well established. We analyzed The Cancer Genome Atlas pan-cancer database to investigate whether the overall methylation aberrancy links to the immune evasion of tumor. We created the definitions of hypermethylation burden, hypomethylation burden and methylation burden to establish the values that represent the degree of methylation aberrancy from human methylation 450 K array data. Both hypermethylation burden and hypomethylation burden significantly correlated with global methylation level as well as methylation subtypes defined in previous literatures. Then we evaluated whether methylation burden correlates with tumor immunogenicity and found that methylation burden showed a significant negative correlation with cytolytic activity score, which represent cytotoxic T cell activity, in pan-cancer (Spearman rho = - 0.37, p < 0.001) and 30 of 33 individual cancer types. Furthermore, this correlation was independent of mutation burden and chromosomal instability in multivariate regression analysis. We validated the findings in the external cohorts and outcomes of patients who were treated with immune checkpoint inhibitors, which showed that high methylation burden group had significantly poor progression-free survival (Hazard ratio 1.74, p = 0.038). Overall, the degree of methylation aberrancy negatively correlated with tumor immunogenicity. These findings emphasize the importance of methylation aberrancy for tumors to evade immune surveillance and warrant further development of methylation biomarker.
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Affiliation(s)
- Changhee Park
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Kyeonghun Jeong
- Division of Clinical Bioinformatics, Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Joon-Hyeong Park
- Division of Clinical Bioinformatics, Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Sohee Jung
- Division of Clinical Bioinformatics, Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Jeong Mo Bae
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kwangsoo Kim
- Transdisciplinary Department of Medicine & Advanced Technology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Chan-Young Ock
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
| | - Miso Kim
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Bhumsuk Keam
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Tae Min Kim
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Se-Hoon Lee
- Division of Hematology/Oncology, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ju-Seog Lee
- Department of Systems Biology, Division of Basic Sciences, MD Anderson Cancer Center, Houston, TX, USA
| | - Dong-Wan Kim
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Doo Hyun Chung
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Dae Seog Heo
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
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Schnell AP, Kohrt S, Thoma-Kress AK. Latency Reversing Agents: Kick and Kill of HTLV-1? Int J Mol Sci 2021; 22:ijms22115545. [PMID: 34073995 PMCID: PMC8197370 DOI: 10.3390/ijms22115545] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/14/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1), the cause of adult T-cell leukemia/lymphoma (ATLL), is a retrovirus, which integrates into the host genome and persistently infects CD4+ T-cells. Virus propagation is stimulated by (1) clonal expansion of infected cells and (2) de novo infection. Viral gene expression is induced by the transactivator protein Tax, which recruits host factors like positive transcription elongation factor b (P-TEFb) to the viral promoter. Since HTLV-1 gene expression is repressed in vivo by viral, cellular, and epigenetic mechanisms in late phases of infection, HTLV-1 avoids an efficient CD8+ cytotoxic T-cell (CTL) response directed against the immunodominant viral Tax antigen. Hence, therapeutic strategies using latency reversing agents (LRAs) sought to transiently activate viral gene expression and antigen presentation of Tax to enhance CTL responses towards HTLV-1, and thus, to expose the latent HTLV-1 reservoir to immune destruction. Here, we review strategies that aimed at enhancing Tax expression and Tax-specific CTL responses to interfere with HTLV-1 latency. Further, we provide an overview of LRAs including (1) histone deacetylase inhibitors (HDACi) and (2) activators of P-TEFb, that have mainly been studied in context of human immunodeficiency virus (HIV), but which may also be powerful in the context of HTLV-1.
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Moderate DNA hypomethylation suppresses intestinal tumorigenesis by promoting caspase-3 expression and apoptosis. Oncogenesis 2021; 10:38. [PMID: 33947834 PMCID: PMC8096944 DOI: 10.1038/s41389-021-00328-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/18/2021] [Accepted: 04/09/2021] [Indexed: 12/14/2022] Open
Abstract
Global DNA hypomethylation is a most common epigenetic alteration in human neoplasia. However, accumulative evidence shows that global DNA hypomethylation impacts tumorigenesis in a tissue-specific manner, promoting tumorigenesis in some but suppressing tumorigenesis in others including colorectal cancer. The underlying mechanisms, especially how DNA hypomethylation suppresses tumorigenesis, remain largely unknown. Here, we investigate how DNA hypomethylation affects intestinal tumorigenesis by using an Uhrf1 tandem tudor domain knockin mutant mouse model (Uhrf1ki/ki) that exhibits a moderate ~10% reduction of global DNA methylation. We found that both chemical-induced colorectal carcinogenesis and Apc loss of heterozygosity (LOH)-induced intestinal tumorigenesis are substantially suppressed in the Uhrf1 mutant mice. Furthermore, unlike Dnmt1 hypomorphic mice in which DNA hypomethylation suppresses the incidence of macroscopic intestinal tumors but promotes the formation of microadenoma in ApcMin/+ background, Uhrf1ki/ki/ApcMin/+ mice have markedly reduced incidence of both microadenoma and macroadenoma. DNA hypomethylation does not appear to affect Apc LOH, activation of the Wnt or Hippo pathway, or tumor cell proliferation, but acts cooperatively with activated Wnt pathway to enhance the caspase-3 gene expression, activation, and apoptosis. Furthermore, increased caspase-3 expression correlates with DNA hypomethylation within the caspase-3 enhancer regions. Taken together, we present a new mouse model for investigating the role of and the molecular mechanisms by which DNA hypomethylation suppresses intestinal tumorigenesis. Our finding that a moderate DNA hypomethylation is sufficient to suppress intestinal tumorigenesis by promoting caspase-3 expression and apoptosis sheds new light on DNA-methylation inhibitor-based colorectal cancer therapeutics.
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Dnmt3a deficiency in the skin causes focal, canonical DNA hypomethylation and a cellular proliferation phenotype. Proc Natl Acad Sci U S A 2021; 118:2022760118. [PMID: 33846253 PMCID: PMC8072215 DOI: 10.1073/pnas.2022760118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
DNA hypomethylation is a feature of epidermal cells from aged and sun-exposed skin, but the mechanisms responsible for this methylation loss are not known. Dnmt3a is the dominant de novo DNA methyltransferase in the skin; while epidermal Dnmt3a deficiency creates a premalignant state in which keratinocytes are more easily transformed by topical mutagens, the conditions responsible for this increased susceptibility to transformation are not well understood. Using whole genome bisulfite sequencing, we identified a focal, canonical DNA hypomethylation phenotype in the epidermal cells of Dnmt3a-deficient mice. Single-cell transcriptomic analysis revealed an increased proportion of cells with a proliferative gene expression signature, while other populations in the skin were relatively unchanged. Although total DNMT3A deficiency has not been described in human disease states, rare patients with an overgrowth syndrome associated with behavioral abnormalities and an increased risk of cancer often have heterozygous, germline mutations in DNMT3A that reduce its function (Tatton-Brown Rahman syndrome [TBRS]). We evaluated the DNA methylation phenotype of the skin from a TBRS patient with a germline DNMT3A R882H mutation, which encodes a dominant-negative protein that reduces its methyltransferase function by ∼80%. We detected a focal, canonical hypomethylation phenotype that revealed considerable overlap with hypomethylated regions found in Dnmt3a-deficient mouse skin. Together, these data suggest that DNMT3A loss creates a premalignant epigenetic state associated with a hyperproliferative phenotype in the skin and further suggest that DNMT3A acts as a tumor suppressor in the skin.
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Yu H, Zhang D, Lian M. Identification of an epigenetic prognostic signature for patients with lower-grade gliomas. CNS Neurosci Ther 2021; 27:470-483. [PMID: 33459509 PMCID: PMC7941239 DOI: 10.1111/cns.13587] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/25/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Glioma is the most common malignant primary brain tumor with survival outcome for patients with lower-grade gliomas (LGGs) being quite variable. Epigenetic modifications in LGGs appear tightly linked to patient clinical outcomes but are not commonly used as clinical tools. AIMS We aimed to derive an epigenetic enzyme gene signature for LGGs that would allow for improved clinical risk stratification. RESULTS The study employed transcriptomic data of 711 lower-grade gliomas from three publically available data sets. Based on least absolute shrinkage and selection operator (LASSO) Cox regression analysis, we discovered a 13-gene epigenetic signature that strongly predicts poor overall survival in LGGs. The robust prediction ability for survival was further verified in two independent validation cohorts. The signature was also significantly associated with malignant molecular signatures including wild-type IDH, unmethylated MGMT promoter, and non-codeletion of 1p19q together with linkage to multiple oncogenic pathways. Interestingly, our results showed that immune infiltration of MDSCs together with mRNA expression of immune inhibition biomarkers was also positively correlated with the epigenetic signature. Lastly, we confirmed the oncogenic role of SMYD2 in glioma tumor cells in functional assays. CONCLUSIONS We report a novel epigenetic gene signature that harbors robust survival prediction value for LGG patients that is tightly linked to activation of multiple oncogenic pathways.
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Affiliation(s)
- Hai Yu
- Department of NeurosurgeryThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
- Center of Brain ScienceThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Duanni Zhang
- Shaanxi Provincial People's HospitalXi'anShaanxiChina
| | - Minxue Lian
- Department of NeurosurgeryThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
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69
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Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains. Nat Commun 2021; 12:1419. [PMID: 33658503 PMCID: PMC7930052 DOI: 10.1038/s41467-021-21707-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetic mechanisms contribute to the initiation and development of cancer, and epigenetic variation promotes dynamic gene expression patterns that facilitate tumor evolution and adaptation. While the NCI-60 panel represents a diverse set of human cancer cell lines that has been used to screen chemical compounds, a comprehensive epigenomic atlas of these cells has been lacking. Here, we report an integrative analysis of 60 human cancer epigenomes, representing a catalog of activating and repressive histone modifications. We identify genome-wide maps of canonical sharp and broad H3K4me3 domains at promoter regions of tumor suppressors, H3K27ac-marked conventional enhancers and super enhancers, and widespread inter-cancer and intra-cancer specific variability in H3K9me3 and H4K20me3-marked heterochromatin domains. Furthermore, we identify features of chromatin states, including chromatin state switching along chromosomes, correlation of histone modification density with genetic mutations, DNA methylation, enrichment of DNA binding motifs in regulatory regions, and gene activity and inactivity. These findings underscore the importance of integrating epigenomic maps with gene expression and genetic variation data to understand the molecular basis of human cancer. Our findings provide a resource for mining epigenomic maps of human cancer cells and for identifying epigenetic therapeutic targets.
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70
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Tu Z, Chen X, Tian T, Chen G, Huang M. Prognostic significance of epigenetic regulatory gene expression in patients with non-small-cell lung cancer. Aging (Albany NY) 2021; 13:7397-7415. [PMID: 33658396 PMCID: PMC7993691 DOI: 10.18632/aging.202600] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/08/2020] [Indexed: 02/05/2023]
Abstract
In this study, we used public databases to investigate the prognostic significance of epigenetic regulatory gene expression in patients with non small-cell lung cancer (NSCLC). Oncomine database analysis showed that the mRNA levels of seven epigenetic regulatory genes, UHRF1, EZH2, TTF2, SUV39H2, PCNA, WHSC1 and RAD54L, genes were significantly upregulated in NSCLC patients as compared to normal lung tissues. Functional enrichment analysis of these seven genes showed that the most enriched GO terms were DNA repair and rhythmic process, whereas, the most enriched KEGG pathway was lysine degradation pathway. The mRNA and protein expression levels of UHRF1, EZH2, TTF2, WHSC1 and RAD54L significantly correlated with tumor stage in NSCLC patients. Moreover, NSCLC patients exhibiting higher UHRF1, EZH2, WHSC1 and RAD54L mRNA and protein expression levels had poorer progression-free survival and overall survival. These findings demonstrate that UHRF1, EZH2, WHSC1 and RAD54L are potential prognostic biomarkers to distinguish high-risk from low-risk NSCLC patients.
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Affiliation(s)
- Zegui Tu
- Department of Thoracic Oncology, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, P.R. China.,West China Medical School, Sichuan University, Chengdu 610041, P.R. China
| | - Xiancheng Chen
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, P.R. China
| | - Tian Tian
- Department of Thoracic Oncology, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, P.R. China.,West China Medical School, Sichuan University, Chengdu 610041, P.R. China
| | - Guo Chen
- Global Infotech Software Limited Corporation, Chengdu 610041, Sichuan, P.R. China
| | - Meijuan Huang
- Department of Thoracic Oncology, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, P.R. China.,West China Medical School, Sichuan University, Chengdu 610041, P.R. China.,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, P.R. China
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71
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Martella A, Fisher DI. Regulation of Gene Expression and the Elucidative Role of CRISPR-Based Epigenetic Modifiers and CRISPR-Induced Chromosome Conformational Changes. CRISPR J 2021; 4:43-57. [PMID: 33616442 DOI: 10.1089/crispr.2020.0108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In complex multicellular systems, gene expression is regulated at multiple stages through interconnected complex molecular pathways and regulatory networks. Transcription is the first step in gene expression and is subject to multiple layers of regulation in which epigenetic mechanisms such as DNA methylation, histone tail modifications, and chromosomal conformation play an essential role. In recent years, CRISPR-Cas9 systems have been employed to unearth this complexity and provide new insights on the contribution of chromatin dysregulation in the development of genetic diseases, as well as new tools to prevent or reverse this dysregulation. In this review, we outline the recent development of a variety of CRISPR-based epigenetic editors for targeted DNA methylation/demethylation, histone modification, and three-dimensional DNA conformational change, highlighting their relative performance and impact on gene regulation. Finally, we provide insights on the future developments aimed to accelerate our understanding of the causal relationship between epigenetic marks, genome organization, and gene regulation.
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Affiliation(s)
- Andrea Martella
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - David I Fisher
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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Zhang J, Burnaevskiy N, Annis J, Han W, Hou D, Ladd P, Lee L, Mendenhall AR, Oshima J, Martin GM. Cell-to-Cell Variation in Gene Expression for Cultured Human Cells Is Controlled in Trans by Diverse Genes: Implications for the Pathobiology of Aging. J Gerontol A Biol Sci Med Sci 2021; 75:2295-2298. [PMID: 31957802 DOI: 10.1093/gerona/glaa027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Indexed: 11/13/2022] Open
Abstract
Cell-to-cell variation in gene expression increases among homologous cells within multiple tissues during aging. We call this phenomenon variegated gene expression (VGE). Long, healthy life requires robust and coordinated gene expression. We posit that nature may have evolved VGE as a bet-hedging mechanism to protect reproductively active populations. The price we may pay is accelerated aging. That hypothesis will require the demonstration that genetic loci are capable of modulating degrees of VGE. While loci controlling VGE in yeast and genes controlling interindividual variation in gene expression in Caenorhabditis elegans have been identified, there has been no compelling evidence for the role of specific genetic loci in modulations of VGE of specific targets in humans. With the assistance of a core facility, we used a customized library of siRNA constructs to screen 1,195 human genes to identify loci contributing to the control of VGE of a gene with relevance to the biology of aging. We identified approximately 50 loci controlling VGE of the prolongevity gene, SIRT1. Because of its partial homology to FOXO3A, a variant of which is enriched in centenarians, our laboratory independently confirmed that the knockdown of FOXF2 greatly diminished VGE of SIRT1 but had little impact upon the VGE of WRN. While the role of these VGE-altering genes on aging in vivo remains to be determined, we hypothesize that some of these genes can be targeted to increase functionality during aging.
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Affiliation(s)
- Jiaming Zhang
- Department of Pathology, University of Washington, Seattle
| | | | - James Annis
- Quellos High-throughput Screening Core, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle
| | - Wenyan Han
- Department of Pathology, University of Washington, Seattle
| | - Deyin Hou
- Department of Pathology, University of Washington, Seattle
| | - Paula Ladd
- Department of Pathology, University of Washington, Seattle
| | - Lin Lee
- Department of Pathology, University of Washington, Seattle
| | | | - Junko Oshima
- Department of Pathology, University of Washington, Seattle
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Reclassification of Kidney Clear Cell Carcinoma Based on Immune Cell Gene-Related DNA CpG Pairs. Biomedicines 2021; 9:biomedicines9020215. [PMID: 33672457 PMCID: PMC7923436 DOI: 10.3390/biomedicines9020215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 12/18/2022] Open
Abstract
Background: A new method was developed based on the relative ranking of gene expression level, overcoming the flaw of the batch effect, and having reliable results in various studies. In the current study, we defined the two methylation sites as a pair. The methylation level in a specific sample was subject to pairwise comparison to calculate a score for each CpGs-pair. The score was defined as a CpGs-pair score. If the first immune-related CpG value was higher than the second one in a specific CpGs-pair, the output score of this immune-related CpGs-pair was 1; otherwise, the output score was 0. This study aimed to construct a new classification of Kidney Clear Cell Carcinoma (KIRC) based on DNA CpGs (methylation sites) pairs. Methods: In this study, the biomarkers of 28 kinds of immune infiltration cells and corresponding methylation sites were acquired. The methylation data were compared between KIRC and normal tissue samples, and differentially methylated sites (DMSs) were obtained. Then, DNA CpGs-pairs were obtained according to the pairs of DMSs. In total, 441 DNA CpGs-pairs were utilized to construct a classification using unsupervised clustering analysis. We also analyzed the potential mechanism and therapy of different subtypes, and validated them in a testing set. Results: The classification of KIRC contained three subgroups. The clinicopathological features were different across three subgroups. The distribution of immune cells, immune checkpoints and immune-related mechanisms were significantly different across the three clusters. The mutation and copy number variation (CNV) were also different. The clinicopathological features and potential mechanism in the testing dataset were consistent with those in the training set. Conclusions: Our findings provide a new accurate and stable classification for developing personalized treatments for the new specific subtypes.
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74
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Takeshima H, Niwa T, Yamashita S, Takamura-Enya T, Iida N, Wakabayashi M, Nanjo S, Abe M, Sugiyama T, Kim YJ, Ushijima T. TET repression and increased DNMT activity synergistically induce aberrant DNA methylation. J Clin Invest 2021; 130:5370-5379. [PMID: 32663196 DOI: 10.1172/jci124070] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 07/07/2020] [Indexed: 01/15/2023] Open
Abstract
Chronic inflammation is deeply involved in various human disorders, such as cancer, neurodegenerative disorders, and metabolic disorders. Induction of epigenetic alterations, especially aberrant DNA methylation, is one of the major mechanisms, but how it is induced is still unclear. Here, we found that expression of TET genes, methylation erasers, was downregulated in inflamed mouse and human tissues, and that this was caused by upregulation of TET-targeting miRNAs such as MIR20A, MIR26B, and MIR29C, likely due to activation of NF-κB signaling downstream of IL-1β and TNF-α. However, TET knockdown induced only mild aberrant methylation. Nitric oxide (NO), produced by NOS2, enhanced enzymatic activity of DNA methyltransferases (DNMTs), methylation writers, and NO exposure induced minimal aberrant methylation. In contrast, a combination of TET knockdown and NO exposure synergistically induced aberrant methylation, involving genomic regions not methylated by either alone. The results showed that a vicious combination of TET repression, due to NF-κB activation, and DNMT activation, due to NO production, is responsible for aberrant methylation induction in human tissues.
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Affiliation(s)
- Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tohru Niwa
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Takeji Takamura-Enya
- Department of Applied Chemistry, Kanagawa Institute of Technology, Kanagawa, Japan
| | - Naoko Iida
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Mika Wakabayashi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Sohachi Nanjo
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Masanobu Abe
- Department of Oral and Maxillofacial Surgery, University of Tokyo Hospital, Tokyo, Japan.,Division for Health Service Promotion, University of Tokyo, Tokyo, Japan
| | - Toshiro Sugiyama
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Young-Joon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
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75
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Sharma A, Liu H, Herwig-Carl MC, Chand Dakal T, Schmidt-Wolf IGH. Epigenetic Regulatory Enzymes: mutation Prevalence and Coexistence in Cancers. Cancer Invest 2021; 39:257-273. [PMID: 33411587 DOI: 10.1080/07357907.2021.1872593] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Epigenetic regulation is an important layer of transcriptional control with the particularity to affect the broad spectrum of genome. Over the years, largely due to the substantial number of recurrent mutations, there have been hundreds of novel driver genes characterized in various cancers. Additionally, the relative contribution of two dysregulated epigenomic entities (DNA methylation and histone modifications) that gradually drive the cancer phenotype remains in the research focus. However, a complex scenario arises when the disease phenotype does not harbor any relevant mutation or an abnormal transcription level. Although the cancer landscape involves the contribution of multiple genetic and non-genetic factors, herein, we discuss specifically the mutation spectrum of epigenetically-related enzymes in cancer. In addition, we address the coexistence of these two epigenetic entities in malignant human diseases, especially cancer. We suggest that the study of epigenetically-related somatic mutations in the early cellular differentiation stage of embryonic development might help to understand their later-staged footprints in the cancer genome. Furthermore, understanding the co-occurrence and/or inverse association of different disease types and redefining the general definition of "healthy" controls could provide insights into the genome reorganization.
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Affiliation(s)
- Amit Sharma
- Department of Integrated Oncology, CIO Bonn, University Hospital Bonn, Bonn, Germany.,Department of Neurology, University Hospital Bonn, Bonn, Germany
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | | | - Tikam Chand Dakal
- Department of Biotechnology, Mohanlal Sukhadia University, Rajasthan, India
| | - Ingo G H Schmidt-Wolf
- Department of Integrated Oncology, CIO Bonn, University Hospital Bonn, Bonn, Germany
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76
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Kung PP, Fan C, Gukasyan HJ, Huang B, Kephart S, Kraus M, Lee JH, Sutton SC, Yamazaki S, Zehnder L. Design and Characterization of a Pyridone-Containing EZH2 Inhibitor Phosphate Prodrug. J Med Chem 2021; 64:1725-1732. [PMID: 33529029 DOI: 10.1021/acs.jmedchem.0c02112] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A pyridone-derived phosphate prodrug of an enhancer of zeste homolog 2 (EZH2) inhibitor was designed and synthesized to improve the inhibitor's aqueous solubility. This prodrug (compound 5) was profiled in pharmacokinetic experiments to assess its ability to deliver the corresponding parent compound (compound 2) to animals in vivo following oral administration. Results from these studies showed that the prodrug was efficiently converted to its parent compound in vivo. In separate experiments, the prodrug demonstrated impressive in vivo tumor growth inhibition in a diffuse large B-cell lymphoma Karpas-422 cell line-derived xenograft model. The described prodrug strategy is expected to be generally applicable to poorly soluble pyridone-containing EZH2 inhibitors and provides a new option to enable such compounds to achieve sufficiently high exposures in vivo.
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77
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Mendenhall AR, Martin GM, Kaeberlein M, Anderson RM. Cell-to-cell variation in gene expression and the aging process. GeroScience 2021; 43:181-196. [PMID: 33595768 PMCID: PMC8050212 DOI: 10.1007/s11357-021-00339-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
There is tremendous variation in biological traits, and much of it is not accounted for by variation in DNA sequence, including human diseases and lifespan. Emerging evidence points to differences in the execution of the genetic program as a key source of variation, be it stochastic variation or programmed variation. Here we discuss variation in gene expression as an intrinsic property and how it could contribute to variation in traits, including the rate of aging. The review is divided into sections describing the historical context and evidence to date for nongenetic variation, the different approaches that may be used to detect nongenetic variation, and recent findings showing that the amount of variation in gene expression can be both genetically programmed and epigenetically controlled. Finally, we present evidence that changes in cell-to-cell variation in gene expression emerge as part of the aging process and may be linked to disease vulnerability as a function of age. These emerging concepts are likely to be important across the spectrum of biomedical research and may well underpin what we understand as biological aging.
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Affiliation(s)
- Alexander R Mendenhall
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA.
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA.
| | - George M Martin
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA
| | - Rozalyn M Anderson
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin and Geriatric Research Education and Clinical Center, William S Middleton Memorial Veterans Hospital, Madison, WI, USA.
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78
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Pernar CH, Parmigiani G, Giovannucci EL, Rimm EB, Tyekucheva S, Loda M, Finn SP, Heiden MGV, Fiorentino M, Ebot EM, Mucci LA. Gene Expression Pathways in Prostate Tissue Associated with Vigorous Physical Activity in Prostate Cancer. Cancer Epidemiol Biomarkers Prev 2021; 30:751-756. [PMID: 33500320 DOI: 10.1158/1055-9965.epi-20-1461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/10/2020] [Accepted: 01/08/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Men engaged in high physical activity have lower risks of advanced and fatal prostate cancer. Mechanisms underlying this association are not well understood but may include systemic and tumor-specific effects. We investigated potential mechanisms linking physical activity and gene expression in prostate tissue from men with prostate cancer. METHODS We included a subset of 118 men in the Health Professionals Follow-up Study diagnosed with prostate cancer between 1986 and 2005 with whole-transcriptome gene expression profiling on tumor and adjacent normal prostate tissue and physical activity data. Long-term vigorous physical activity was self-reported as the average time spent engaged in various forms of recreational physical activity at baseline and biennially until prostate cancer diagnosis. Gene set enrichment analysis was performed among KEGG and Hallmark gene sets to identify pathways with differential expression based on vigorous physical activity. RESULTS In adjacent normal tissue, we identified 25 KEGG gene sets enriched (downregulated) in the highest compared with lowest quintile of vigorous physical activity at an FDR <0.10, including a number of cancer- and immune-related pathways. Although no gene sets reached statistical significance in tumor tissue, top gene sets differentially expressed included TGF beta, apoptosis, and p53 signaling pathways. CONCLUSIONS These findings suggest that physical activity may influence the tumor microenvironment. Future studies are needed to confirm these findings and further investigate potential mechanisms linking physical activity to lethal prostate cancer. IMPACT Identification of gene expression alterations in the prostate associated with physical activity can improve our understanding of prostate cancer etiology.
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Affiliation(s)
- Claire H Pernar
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.
| | - Giovanni Parmigiani
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Eric B Rimm
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Svitlana Tyekucheva
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York Presbyterian Hospital, New York, New York
| | - Stephen P Finn
- Department of Histopathology, Trinity College, Dublin, Ireland.,Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew G Vander Heiden
- Koch Institute for Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michelangelo Fiorentino
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Pathology Unit, Addarii Institute, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Ericka M Ebot
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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79
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Vasantharajan SS, Eccles MR, Rodger EJ, Pattison S, McCall JL, Gray ES, Calapre L, Chatterjee A. The Epigenetic landscape of Circulating tumour cells. Biochim Biophys Acta Rev Cancer 2021; 1875:188514. [PMID: 33497709 DOI: 10.1016/j.bbcan.2021.188514] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 12/31/2022]
Abstract
Cancer metastasis is the main reason for the high mortality in patients, contributing to 90% of cancer-related deaths. Biomarkers for early detection and therapeutic monitoring are essential to improve cancer outcomes. Circulating tumour cells (CTCs) arise from solid tumours and are capable of metastatic dissemination via the bloodstream or lymphatic system. Thus, CTCs can potentially be developed as a minimally invasive biomarker for early detection and therapeutic monitoring. Despite its clinical potential, research on CTCs remains limited, and this is likely due to their low numbers, short half-life, and the lack of robust methods for their isolation. There is also a need for molecular characterisation of CTCs to identify tumour-specific features, such as epigenetic signatures of metastasis. This review provides an overview of the epigenetic landscape of CTCs. We discuss the role of epigenetic modifications in CTC dissemination,metastatic tumour formation and progression and highlight its clinical implications.
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Affiliation(s)
| | - Michael R Eccles
- Department of Pathology, Otago Medical School-Dunedin Campus, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand.
| | - Euan J Rodger
- Department of Pathology, Otago Medical School-Dunedin Campus, New Zealand.
| | - Sharon Pattison
- Department of Medicine, Otago Medical School-Dunedin Campus, New Zealand.
| | - John L McCall
- Department of Surgical Sciences, Otago Medical School-Dunedin Campus, New Zealand.
| | - Elin S Gray
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia.
| | - Leslie Calapre
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia.
| | - Aniruddha Chatterjee
- Department of Pathology, Otago Medical School-Dunedin Campus, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand.
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80
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Han Q, Kono TJY, Knutson CG, Parry NM, Seiler CL, Fox JG, Tannenbaum SR, Tretyakova NY. Multi-Omics Characterization of Inflammatory Bowel Disease-Induced Hyperplasia/Dysplasia in the Rag2-/-/ Il10-/- Mouse Model. Int J Mol Sci 2020; 22:ijms22010364. [PMID: 33396408 PMCID: PMC7795000 DOI: 10.3390/ijms22010364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/26/2022] Open
Abstract
Epigenetic dysregulation is hypothesized to play a role in the observed association between inflammatory bowel disease (IBD) and colon tumor development. In the present work, DNA methylome, hydroxymethylome, and transcriptome analyses were conducted in proximal colon tissues harvested from the Helicobacter hepaticus (H. hepaticus)-infected murine model of IBD. Reduced representation bisulfite sequencing (RRBS) and oxidative RRBS (oxRRBS) analyses identified 1606 differentially methylated regions (DMR) and 3011 differentially hydroxymethylated regions (DhMR). These DMR/DhMR overlapped with genes that are associated with gastrointestinal disease, inflammatory disease, and cancer. RNA-seq revealed pronounced expression changes of a number of genes associated with inflammation and cancer. Several genes including Duox2, Tgm2, Cdhr5, and Hk2 exhibited changes in both DNA methylation/hydroxymethylation and gene expression levels. Overall, our results suggest that chronic inflammation triggers changes in methylation and hydroxymethylation patterns in the genome, altering the expression of key tumorigenesis genes and potentially contributing to the initiation of colorectal cancer.
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Affiliation(s)
- Qiyuan Han
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Thomas J. Y. Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Charles G. Knutson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Nicola M. Parry
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
| | - Christopher L. Seiler
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
| | - James G. Fox
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Steven R. Tannenbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
- Correspondence: ; Tel.: +1-612-626-3432
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81
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Saha N, Muntean AG. Insight into the multi-faceted role of the SUV family of H3K9 methyltransferases in carcinogenesis and cancer progression. Biochim Biophys Acta Rev Cancer 2020; 1875:188498. [PMID: 33373647 DOI: 10.1016/j.bbcan.2020.188498] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022]
Abstract
Growing evidence implicates histone H3 lysine 9 methylation in tumorigenesis. The SUV family of H3K9 methyltransferases, which include G9a, GLP, SETDB1, SETDB2, SUV39H1 and SUV39H2 deposit H3K9me1/2/3 marks at euchromatic and heterochromatic regions, catalyzed by their conserved SET domain. In cancer, this family of enzymes can be deregulated by genomic alterations and transcriptional mis-expression leading to alteration of transcriptional programs. In solid and hematological malignancies, studies have uncovered pro-oncogenic roles for several H3K9 methyltransferases and accordingly, small molecule inhibitors are being tested as potential therapies. However, emerging evidence demonstrate onco-suppressive roles for these enzymes in cancer development as well. Here, we review the role H3K9 methyltransferases play in tumorigenesis focusing on gene targets and biological pathways affected due to misregulation of these enzymes. We also discuss molecular mechanisms regulating H3K9 methyltransferases and their influence on cancer. Finally, we describe the impact of H3K9 methylation on therapy induced resistance in carcinoma. Converging evidence point to multi-faceted roles for H3K9 methyltransferases in development and cancer that encourages a deeper understanding of these enzymes to inform novel therapy.
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Affiliation(s)
- Nirmalya Saha
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America
| | - Andrew G Muntean
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America.
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82
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Haase S, Nuñez FM, Gauss JC, Thompson S, Brumley E, Lowenstein P, Castro MG. Hemispherical Pediatric High-Grade Glioma: Molecular Basis and Therapeutic Opportunities. Int J Mol Sci 2020; 21:ijms21249654. [PMID: 33348922 PMCID: PMC7766684 DOI: 10.3390/ijms21249654] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
In this review, we discuss the molecular characteristics, development, evolution, and therapeutic perspectives for pediatric high-grade glioma (pHGG) arising in cerebral hemispheres. Recently, the understanding of biology of pHGG experienced a revolution with discoveries arising from genomic and epigenomic high-throughput profiling techniques. These findings led to identification of prevalent molecular alterations in pHGG and revealed a strong connection between epigenetic dysregulation and pHGG development. Although we are only beginning to unravel the molecular biology underlying pHGG, there is a desperate need to develop therapies that would improve the outcome of pHGG patients, as current therapies do not elicit significant improvement in median survival for this patient population. We explore the molecular and cell biology and clinical state-of-the-art of pediatric high-grade gliomas (pHGGs) arising in cerebral hemispheres. We discuss the role of driving mutations, with a special consideration of the role of epigenetic-disrupting mutations. We will also discuss the possibilities of targeting unique molecular vulnerabilities of hemispherical pHGG to design innovative tailored therapies.
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Affiliation(s)
- Santiago Haase
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Fernando M. Nuñez
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jessica C. Gauss
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sarah Thompson
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Emily Brumley
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Pedro Lowenstein
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria G. Castro
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (F.M.N.); (J.C.G.); (S.T.); (E.B.); (P.L.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Correspondence:
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83
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Mukherjee S, Adhikary S, Gadad SS, Mondal P, Sen S, Choudhari R, Singh V, Adhikari S, Mandal P, Chaudhuri S, Sengupta A, Lakshmanaswamy R, Chakrabarti P, Roy S, Das C. Suppression of poised oncogenes by ZMYND8 promotes chemo-sensitization. Cell Death Dis 2020; 11:1073. [PMID: 33323928 PMCID: PMC7738522 DOI: 10.1038/s41419-020-03129-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/06/2023]
Abstract
The major challenge in chemotherapy lies in the gain of therapeutic resistance properties of cancer cells. The relatively small fraction of chemo-resistant cancer cells outgrows and are responsible for tumor relapse, with acquired invasiveness and stemness. We demonstrate that zinc-finger MYND type-8 (ZMYND8), a putative chromatin reader, suppresses stemness, drug resistance, and tumor-promoting genes, which are hallmarks of cancer. Reinstating ZMYND8 suppresses chemotherapeutic drug doxorubicin-induced tumorigenic potential (at a sublethal dose) and drug resistance, thereby resetting the transcriptional program of cells to the epithelial state. The ability of ZMYND8 to chemo-sensitize doxorubicin-treated metastatic breast cancer cells by downregulating tumor-associated genes was further confirmed by transcriptome analysis. Interestingly, we observed that ZMYND8 overexpression in doxorubicin-treated cells stimulated those involved in a good prognosis in breast cancer. Consistently, sensitizing the cancer cells with ZMYND8 followed by doxorubicin treatment led to tumor regression in vivo and revert back the phenotypes associated with drug resistance and stemness. Intriguingly, ZMYND8 modulates the bivalent or poised oncogenes through its association with KDM5C and EZH2, thereby chemo-sensitizing the cells to chemotherapy for better disease-free survival. Collectively, our findings indicate that poised chromatin is instrumental for the acquisition of chemo-resistance by cancer cells and propose ZMYND8 as a suitable epigenetic tool that can re-sensitize the chemo-refractory breast carcinoma.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Carcinogenesis/drug effects
- Carcinogenesis/genetics
- Carcinogenesis/pathology
- Cell Line, Tumor
- Cell Movement/drug effects
- Cell Movement/genetics
- Down-Regulation/drug effects
- Down-Regulation/genetics
- Doxorubicin/pharmacology
- Doxorubicin/therapeutic use
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Enhancer of Zeste Homolog 2 Protein/metabolism
- Epigenesis, Genetic/drug effects
- Epithelial-Mesenchymal Transition/drug effects
- Epithelial-Mesenchymal Transition/genetics
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Genome, Human
- Histone Demethylases/metabolism
- Humans
- Mice, Inbred BALB C
- Mice, Nude
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Oncogenes
- Phenotype
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Treatment Outcome
- Triple Negative Breast Neoplasms/drug therapy
- Triple Negative Breast Neoplasms/genetics
- Triple Negative Breast Neoplasms/pathology
- Tumor Suppressor Proteins/metabolism
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Affiliation(s)
- Shravanti Mukherjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Santanu Adhikary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Shrikanth S Gadad
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
- Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynaecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhaba National Institute, Mumbai, India
| | - Sabyasachi Sen
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Ramesh Choudhari
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
- Shri B. M. Patil Medical College, Hospital and Research Centre, BLDE (Deemed to be University), Vijayapura, Karnataka, 586103, India
| | - Vipin Singh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhaba National Institute, Mumbai, India
| | - Swagata Adhikari
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhaba National Institute, Mumbai, India
| | - Pratiti Mandal
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Soumi Chaudhuri
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Amrita Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Rajkumar Lakshmanaswamy
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
- Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
| | - Partha Chakrabarti
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India.
- Homi Bhaba National Institute, Mumbai, India.
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84
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Nutini A, Sohail A. Deep learning of the role of interleukin IL-17 and its action in promoting cancer. BIO-ALGORITHMS AND MED-SYSTEMS 2020; 16. [DOI: 10.1515/bams-2020-0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Abstract
In breast cancer patients, metastasis remains a major cause of death. The metastasis formation process is given by an interaction between the cancer cells and the microenvironment that surrounds them. In this article, we develop a mathematical model that analyzes the role of interleukin IL-17 and its action in promoting cancer and in facilitating tissue metastasis in breast cancer, using a dynamic analysis based on a stochastic process that accounts for the local and global action of this molecule. The model uses the Ornstein–Uhlembeck and Markov process in continuous time. It focuses on the oncological expansion and the interaction between the interleukin IL-17 and cell populations This analysis tends to clarify the processes underlying the metastasis expansion mechanism both for a better understanding of the pathological event and for a possible better control of therapeutic strategies.
IL-17 is a proinflammatory interleukin that acts when there is tissue damage or when there is a pathological situation caused by an external pathogen or by a pathological condition such as cancer.
This research is focused on the role of interleukin IL-17 which, especially in the case of breast cancer, turns out to be a dominant “communication pin” since it interconnects with the activity of different cell populations affected by the oncological phenomenon. Stochastic modeling strategies, specially the Ornstein-Uhlenbeck process, with the aid of numerical algorithms are elaborated in this review.
The role of IL-17 is discussed in this manuscript at all the stages of cancer. It is discussed that IL-17 also acts as “metastasis promoter” as a result of its proinflammatory nature. The stochastic nature of IL-17 is discussed based on the evidence provided by recent literature.
The resulting dynamical analysis can help to select the most appropriate therapeutic strategy.
Cancer cells, in the case of breast cancer, have high level of IL-17 receptors (IL-17R); therefore the interleukin itself has direct effects on these cells. Immunotherapy research, focused on this cytokine and interlinked with the stochastic modeling, seems to be a promising avenue.
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Affiliation(s)
- Alessandro Nutini
- Center for Study in Motor Science , Biomechanics dept , Lucca , Italy
| | - Ayesha Sohail
- Department of Mathematics , Comsats University Islamabad , Lahore 54000 , Pakistan
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85
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Bakhshi TJ, Georgel PT. Genetic and epigenetic determinants of diffuse large B-cell lymphoma. Blood Cancer J 2020; 10:123. [PMID: 33277464 PMCID: PMC7718920 DOI: 10.1038/s41408-020-00389-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/25/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common type of lymphoma and is notorious for its heterogeneity, aggressive nature, and the frequent development of resistance and/or relapse after treatment with standard chemotherapy. To address these problems, a strong emphasis has been placed on researching the molecular origins and mechanisms of DLBCL to develop effective treatments. One of the major insights produced by such research is that DLBCL almost always stems from genetic damage that occurs during the germinal center (GC) reaction, which is required for the production of high-affinity antibodies. Indeed, there is significant overlap between the mechanisms that govern the GC reaction and those that drive the progression of DLBCL. A second important insight is that some of the most frequent genetic mutations that occur in DLBCL are those related to chromatin and epigenetics, especially those related to proteins that “write” histone post-translational modifications (PTMs). Mutation or deletion of these epigenetic writers often renders cells unable to epigenetically “switch on” critical gene sets that are required to exit the GC reaction, differentiate, repair DNA, and other essential cellular functions. Failure to activate these genes locks cells into a genotoxic state that is conducive to oncogenesis and/or relapse.
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Affiliation(s)
- Tanner J Bakhshi
- Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, 25755, USA
| | - Philippe T Georgel
- Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, 25755, USA. .,Department of Biological Sciences, Cell Differentiation and Development Center, Byrd Biotechnology Science Center, Marshall University, Huntington, WV, 25755, USA.
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86
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Heng J, Heng HH. Genome chaos: Creating new genomic information essential for cancer macroevolution. Semin Cancer Biol 2020; 81:160-175. [PMID: 33189848 DOI: 10.1016/j.semcancer.2020.11.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/26/2020] [Accepted: 11/04/2020] [Indexed: 12/15/2022]
Abstract
Cancer research has traditionally focused on the characterization of individual molecular mechanisms that can contribute to cancer. Due to the multiple levels of genomic and non-genomic heterogeneity, however, overwhelming molecular mechanisms have been identified, most with low clinical predictability. It is thus necessary to search for new concepts to unify these diverse mechanisms and develop better strategies to understand and treat cancer. In recent years, two-phased cancer evolution (comprised of the genome reorganization-mediated punctuated phase and gene mutation-mediated stepwise phase), initially described by tracing karyotype evolution, was confirmed by the Cancer Genome Project. In particular, genome chaos, the process of rapid and massive genome reorganization, has been commonly detected in various cancers-especially during key phase transitions, including cellular transformation, metastasis, and drug resistance-suggesting the importance of genome-level changes in cancer evolution. In this Perspective, genome chaos is used as a discussion point to illustrate new genome-mediated somatic evolutionary frameworks. By rephrasing cancer as a new system emergent from normal tissue, we present the multiple levels (or scales) of genomic and non-genomic information. Of these levels, evolutionary studies at the chromosomal level are determined to be of ultimate importance, since altered genomes change the karyotype coding and karyotype change is the key event for punctuated cellular macroevolution. Using this lens, we differentiate and analyze developmental processes and cancer evolution, as well as compare the informational relationship between genome chaos and its various subtypes in the context of macroevolution under crisis. Furthermore, the process of deterministic genome chaos is discussed to interpret apparently random events (including stressors, chromosomal variation subtypes, surviving cells with new karyotypes, and emergent stable cellular populations) as nonrandom patterns, which supports the new cancer evolutionary model that unifies genome and gene contributions during different phases of cancer evolution. Finally, the new perspective of using cancer as a model for organismal evolution is briefly addressed, emphasizing the Genome Theory as a new and necessary conceptual framework for future research and its practical implications, not only in cancer but evolutionary biology as a whole.
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Affiliation(s)
- Julie Heng
- Harvard College, 86 Brattle Street Cambridge, MA, 02138, USA
| | - Henry H Heng
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Department of Pathology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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87
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García-Santisteban I, Romero-Garmendia I, Cilleros-Portet A, Bilbao JR, Fernandez-Jimenez N. Celiac disease susceptibility: The genome and beyond. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 358:1-45. [PMID: 33707051 DOI: 10.1016/bs.ircmb.2020.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Celiac Disease (CeD) is an immune-mediated complex disease that is triggered by the ingestion of gluten and develops in genetically susceptible individuals. It has been known for a long time that the Human Leucocyte Antigen (HLA) molecules DQ2 and DQ8 are necessary, although not sufficient, for the disease development, and therefore other susceptibility genes and (epi)genetic events must participate in CeD pathogenesis. The advances in Genomics during the last 15 years have made CeD one of the immune-related disorders with the best-characterized genetic component. In the present work, we will first review the main Genome-Wide Association Studies (GWAS) carried out in the disorder, and emphasize post-GWAS discoveries, including diverse integrative strategies, SNP prioritization approaches, and insights into the Microbiome through the host Genomics. Second, we will explore CeD-related Epigenetics and Epigenomics, mostly focusing on the emerging knowledge of the celiac methylome, and the vast but yet under-explored non-coding RNA (ncRNA) landscape. We conclude that much has been done in the field although there are still completely unvisited areas in the post-Genomics of CeD. Chromatin conformation and accessibility, and Epitranscriptomics are promising domains that need to be unveiled to complete the big picture of the celiac Genome.
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Affiliation(s)
- Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain; Spanish Biomedical Research Center in Diabetes and associated Metabolic Disorders, CIBERDEM, Madrid, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain.
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88
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Kedhari Sundaram M, Haque S, Somvanshi P, Bhardwaj T, Hussain A. Epigallocatechin gallate inhibits HeLa cells by modulation of epigenetics and signaling pathways. 3 Biotech 2020; 10:484. [PMID: 33117625 PMCID: PMC7584697 DOI: 10.1007/s13205-020-02473-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022] Open
Abstract
This study examines the effect of epigallocatechin gallate (EGCG) on signaling pathways, epigenetic modulators and tumour suppressor genes in cervical cancer cells, HeLa. qRT-PCR, ELISA-based enzymatic assays and in silico studies were used to catalogue the modulation of these genes by EGCG treatment. qRT-PCR showed transcriptional modulation of several epigenetic modifiers including DNA methyltransferases and histone modifiers (DNMT1, DNMT3B, DNMT3A, AURKA, AURKC, AURKB, KDM4A, KDM5C, PRMT7, PRMT6, UBE2B, HDAC5, HDAC6, HDAC7 and HDAC11. Furthermore, ELISA-based assays showed that EGCG lowered the activity of DNA methyltransferases, histone deacetylases and histone methyltransferases (H3K9). Molecular docking results suggests that EGCG may competitively inhibit some epigenetic enzymes (DNMT1, DNMT3A, HDAC2, HDAC3, HDAC4, HDAC7 and EZH2). A functional outcome of these epigenetic alterations could be inferred from the reversal of promoter hypermethylation of tumour suppressor genes by quantitative methylation array and transcriptional re-expression of tumour suppressor genes including TP73, PTEN, SOCS1, CDH1, RARβ, and DAPK1 by qRT-PCR. Downregulation of key signaling moieties of PI3K, Wnt and MAPK pathways, cell cycle regulators, metastasis regulators and pro-inflammatory moieties including TERT, CCNB1, CCNB2, MMP2, MMP7. PIK3C2B, PIK3CA, MAPK8 and IL6 was also observed. In silico protein-protein interaction network analysis followed by KEGG analysis discerned the active participation of gene sets towards cancer pathways. This study comprehensively explains EGCG's anti-cancer mechanism via the synchronized transcriptional alteration of several molecular targets across different signaling pathways and reversal of tumour suppressor gene silencing through modulation of epigenetic enzymes.
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Affiliation(s)
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, 45142 Saudi Arabia
| | - Pallavi Somvanshi
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070 India
| | - Tulika Bhardwaj
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070 India
| | - Arif Hussain
- School of Life Sciences, Manipal Academy of Higher Education, PO Box 345050, Dubai, United Arab Emirates
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89
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A Methylation-Based Reclassification of Bladder Cancer Based on Immune Cell Genes. Cancers (Basel) 2020; 12:cancers12103054. [PMID: 33092083 PMCID: PMC7593922 DOI: 10.3390/cancers12103054] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Bladder cancer (BC) development is highly related to immune cell infiltration. In this study, we aimed to construct a new classification of bladder cancer molecular subtypes based on immune-cell-associated CpG(Methylation) sites. The classification was accurate and stable. BC patients were successfully divided into three subtypes based on the immune-cell-associated CpG sites. The clinicopathologic features, distribution of immune cells, level of expression of checkpoints, stromal score, immune score, ESTIMATEScore, tumor purity, APC co_inhibition, APC co_stimulation, HLA, MHC class_I, Type I IFN_respons, Type II IFN response, and DNA stemness score (DNAss) presented significant differences among the three subgroups. The specific genomic alteration was also different across subgroups. High-level immune infiltration showed a correlation with high-level methylation. A lower RNA stemness score (RNAss) was associated with higher immune infiltration. Cluster 2 demonstrated a better response to chemotherapy. The anti-cancer targeted drug therapy results are different among the three subgroups. Abstract Background: Bladder cancer is highly related to immune cell infiltration. This study aimed to develop a new classification of BC molecular subtypes based on immune-cell-associated CpG sites. Methods: The genes of 28 types of immune cells were obtained from previous studies. Then, methylation sites corresponding to immune-cell-associated genes were acquired. Differentially methylated sites (DMSs) were identified between normal samples and bladder cancer samples. Unsupervised clustering analysis of differentially methylated sites was performed to divide the sites into several subtypes. Then, the potential mechanism of different subtypes was explored. Results: Bladder cancer patients were divided into three groups. The cluster 3 subtype had the best prognosis. Cluster 1 had the poorest prognosis. The distribution of immune cells, level of expression of checkpoints, stromal score, immune score, ESTIMATEScore, tumor purity, APC co_inhibition, APC co_stimulation, HLA, MHC class_I, Type I IFN Response, Type II IFN Response, and DNAss presented significant differences among the three subgroups. The distribution of genomic alterations was also different. Conclusions: The proposed classification was accurate and stable. BC patients could be divided into three subtypes based on the immune-cell-associated CpG sites. Specific biological signaling pathways, immune mechanisms, and genomic alterations were varied among the three subgroups. High-level immune infiltration was correlated with high-level methylation. The lower RNAss was associated with higher immune infiltration. The study of the intratumoral immune microenvironment may provide a new perspective for BC therapy.
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90
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Miller BF, Pisanic Ii TR, Margolin G, Petrykowska HM, Athamanolap P, Goncearenco A, Osei-Tutu A, Annunziata CM, Wang TH, Elnitski L. Leveraging locus-specific epigenetic heterogeneity to improve the performance of blood-based DNA methylation biomarkers. Clin Epigenetics 2020; 12:154. [PMID: 33081832 PMCID: PMC7574234 DOI: 10.1186/s13148-020-00939-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 09/21/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Variation in intercellular methylation patterns can complicate the use of methylation biomarkers for clinical diagnostic applications such as blood-based cancer testing. Here, we describe development and validation of a methylation density binary classification method called EpiClass (available for download at https://github.com/Elnitskilab/EpiClass ) that can be used to predict and optimize the performance of methylation biomarkers, particularly in challenging, heterogeneous samples such as liquid biopsies. This approach is based upon leveraging statistical differences in single-molecule sample methylation density distributions to identify ideal thresholds for sample classification. RESULTS We developed and tested the classifier using reduced representation bisulfite sequencing (RRBS) data derived from ovarian carcinoma tissue DNA and controls. We used these data to perform in silico simulations using methylation density profiles from individual epiallelic copies of ZNF154, a genomic locus known to be recurrently methylated in numerous cancer types. From these profiles, we predicted the performance of the classifier in liquid biopsies for the detection of epithelial ovarian carcinomas (EOC). In silico analysis indicated that EpiClass could be leveraged to better identify cancer-positive liquid biopsy samples by implementing precise thresholds with respect to methylation density profiles derived from circulating cell-free DNA (cfDNA) analysis. These predictions were confirmed experimentally using DREAMing to perform digital methylation density analysis on a cohort of low volume (1-ml) plasma samples obtained from 26 EOC-positive and 41 cancer-free women. EpiClass performance was then validated in an independent cohort of 24 plasma specimens, derived from a longitudinal study of 8 EOC-positive women, and 12 plasma specimens derived from 12 healthy women, respectively, attaining a sensitivity/specificity of 91.7%/100.0%. Direct comparison of CA-125 measurements with EpiClass demonstrated that EpiClass was able to better identify EOC-positive women than standard CA-125 assessment. Finally, we used independent whole genome bisulfite sequencing (WGBS) datasets to demonstrate that EpiClass can also identify other cancer types as well or better than alternative methylation-based classifiers. CONCLUSIONS Our results indicate that assessment of intramolecular methylation density distributions calculated from cfDNA facilitates the use of methylation biomarkers for diagnostic applications. Furthermore, we demonstrated that EpiClass analysis of ZNF154 methylation was able to outperform CA-125 in the detection of etiologically diverse ovarian carcinomas, indicating broad utility of ZNF154 for use as a biomarker of ovarian cancer.
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Affiliation(s)
- Brendan F Miller
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Thomas R Pisanic Ii
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Gennady Margolin
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hanna M Petrykowska
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pornpat Athamanolap
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Alexander Goncearenco
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Akosua Osei-Tutu
- Women's Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christina M Annunziata
- Women's Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tza-Huei Wang
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Laura Elnitski
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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91
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Halaburkova A, Cahais V, Novoloaca A, Araujo MGDS, Khoueiry R, Ghantous A, Herceg Z. Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes. Genome Res 2020; 30:1517-1532. [PMID: 32963031 PMCID: PMC7605261 DOI: 10.1101/gr.268292.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/26/2020] [Indexed: 12/24/2022]
Abstract
The recent identification of recurrently mutated epigenetic regulator genes (ERGs) supports their critical role in tumorigenesis. We conducted a pan-cancer analysis integrating (epi)genome, transcriptome, and DNA methylome alterations in a curated list of 426 ERGs across 33 cancer types, comprising 10,845 tumor and 730 normal tissues. We found that, in addition to mutations, copy number alterations in ERGs were more frequent than previously anticipated and tightly linked to expression aberrations. Novel bioinformatics approaches, integrating the strengths of various driver prediction and multi-omics algorithms, and an orthogonal in vitro screen (CRISPR-Cas9) targeting all ERGs revealed genes with driver roles within and across malignancies and shared driver mechanisms operating across multiple cancer types and hallmarks. This is the largest and most comprehensive analysis thus far; it is also the first experimental effort to specifically identify ERG drivers (epidrivers) and characterize their deregulation and functional impact in oncogenic processes.
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Affiliation(s)
- Andrea Halaburkova
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Alexei Novoloaca
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | | | - Rita Khoueiry
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
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92
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Eich ML, Athar M, Ferguson JE, Varambally S. EZH2-Targeted Therapies in Cancer: Hype or a Reality. Cancer Res 2020; 80:5449-5458. [PMID: 32978169 DOI: 10.1158/0008-5472.can-20-2147] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/24/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022]
Abstract
Next-generation genomic sequencing has identified multiple novel molecular alterations in cancer. Since the identification of DNA methylation and histone modification, it has become evident that genes encoding epigenetic modifiers that locally and globally regulate gene expression play a crucial role in normal development and cancer progression. The histone methyltransferase enhancer of zeste homolog 2 (EZH2) is the enzymatic catalytic subunit of the polycomb-repressive complex 2 (PRC2) that can alter gene expression by trimethylating lysine 27 on histone 3 (H3K27). EZH2 is involved in global transcriptional repression, mainly targeting tumor-suppressor genes. EZH2 is commonly overexpressed in cancer and shows activating mutations in subtypes of lymphoma. Extensive studies have uncovered an important role for EZH2 in cancer progression and have suggested that it may be a useful therapeutic target. In addition, tumors harboring mutations in other epigenetic genes such as ARID1A, KDM6, and BAP1 are highly sensitive to EZH2 inhibition, thus increasing its potential as a therapeutic target. Recent studies also suggest that inhibition of EZH2 enhances the response to tumor immunotherapy. Many small-molecule inhibitors have been developed to target EZH2 or the PRC2 complex, with some of these inhibitors now in early clinical trials reporting clinical responses with acceptable tolerability. In this review, we highlight the recent advances in targeting EZH2, its successes, and potential limitations, and we discuss the future directions of this therapeutic subclass.
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Affiliation(s)
- Marie-Lisa Eich
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Mohammad Athar
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - James E Ferguson
- Department of Urology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Sooryanarayana Varambally
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
- Informatics Institute, University of Alabama at Birmingham, Birmingham, Alabama
- Michigan Center for Translational Pathology, Department of Pathology, The University of Michigan, Ann Arbor, Michigan
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93
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Zhao Y, Feng F, Guo QH, Wang YP, Zhao R. Role of succinate dehydrogenase deficiency and oncometabolites in gastrointestinal stromal tumors. World J Gastroenterol 2020; 26:5074-5089. [PMID: 32982110 PMCID: PMC7495036 DOI: 10.3748/wjg.v26.i34.5074] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/14/2020] [Accepted: 08/21/2020] [Indexed: 02/06/2023] Open
Abstract
Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. At the molecular level, GISTs can be categorized into two groups based on the causative oncogenic mutations. Approximately 85% of GISTs are caused by gain-of-function mutations in the tyrosine kinase receptor KIT or platelet-derived growth factor receptor alpha (PDGFRA). The remaining GISTs, referred to as wild-type (WT) GISTs, are often deficient in succinate dehydrogenase complex (SDH), a key metabolic enzyme complex in the tricarboxylic acid (TCA) cycle and electron transport chain. SDH deficiency leads to the accumulation of succinate, a metabolite produced by the TCA cycle. Succinate inhibits α-ketoglutarate-dependent dioxygenase family enzymes, which comprise approximately 60 members and regulate key aspects of tumorigenesis such as DNA and histone demethylation, hypoxia responses, and m6A mRNA modification. For this reason, succinate and metabolites with similar structures, such as D-2-hydroxyglutarate and fumarate, are considered oncometabolites. In this article, we review recent advances in the understanding of how metabolic enzyme mutations and oncometabolites drive human cancer with an emphasis on SDH mutations and succinate in WT GISTs.
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Affiliation(s)
- Yue Zhao
- Department of Gastroenterology, the First Hospital of Lanzhou University, Key Laboratory for Gastrointestinal Disease of Gansu Province, Lanzhou 730000, Gansu Province, China
| | - Fei Feng
- Department of Ultrasound, the First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Qing-Hong Guo
- Department of Gastroenterology, the First Hospital of Lanzhou University, Key Laboratory for Gastrointestinal Disease of Gansu Province, Lanzhou 730000, Gansu Province, China
| | - Yu-Ping Wang
- Department of Gastroenterology, the First Hospital of Lanzhou University, Key Laboratory for Gastrointestinal Disease of Gansu Province, Lanzhou 730000, Gansu Province, China
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, School of Medicine, the University of Alabama at Birmingham, Birmingham, AL 35294, United States
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94
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A versatile reporter system for multiplexed screening of effective epigenome editors. Nat Protoc 2020; 15:3410-3440. [PMID: 32887975 DOI: 10.1038/s41596-020-0380-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 06/25/2020] [Indexed: 12/25/2022]
Abstract
The formation and function of highly specialized cells and tissues in a multicellular organism from a single genome are enabled through differential spatiotemporal access to the information contained in the genomic DNA. The epigenome plays an essential role in how DNA information can be accessed, and in the last decade the link between epigenetic aberrations and pathologies has become increasingly clear. Methods to precisely modify the epigenome are hence attracting interest as potential novel therapeutics. We recently described a platform, designer epigenome modifier (DEM), capable of precisely editing the epigenome of a cell to control the expression of selected genes. Here, we provide a detailed protocol to streamline the process of identifying DEMs that efficiently and selectively bind to their intended target site and inactivate expression of the target gene. Further, we describe the procedure to simultaneously regulate the expression of up to three genes in a multiplexed fashion. The protocol is divided into four stages that guide the user through the generation of the multicolor reporter cell line and its use for selecting functional DEMs. The duration of the whole procedure described varies from ~6 weeks when using a single reporter up to 13 weeks for fine-tuning the multiplex epigenome editing abilities of selected DEMs using three reporters. Given the great interest in epigenome editing in various fields of biomedical research, this protocol will help scientists to explore these novel technologies for their research.
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95
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Lee D, Park Y, Kim S. Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches. Brief Bioinform 2020; 22:5896573. [PMID: 34020548 DOI: 10.1093/bib/bbaa188] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/29/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022] Open
Abstract
The multi-omics molecular characterization of cancer opened a new horizon for our understanding of cancer biology and therapeutic strategies. However, a tumor biopsy comprises diverse types of cells limited not only to cancerous cells but also to tumor microenvironmental cells and adjacent normal cells. This heterogeneity is a major confounding factor that hampers a robust and reproducible bioinformatic analysis for biomarker identification using multi-omics profiles. Besides, the heterogeneity itself has been recognized over the years for its significant prognostic values in some cancer types, thus offering another promising avenue for therapeutic intervention. A number of computational approaches to unravel such heterogeneity from high-throughput molecular profiles of a tumor sample have been proposed, but most of them rely on the data from an individual omics layer. Since the heterogeneity of cells is widely distributed across multi-omics layers, methods based on an individual layer can only partially characterize the heterogeneous admixture of cells. To help facilitate further development of the methodologies that synchronously account for several multi-omics profiles, we wrote a comprehensive review of diverse approaches to characterize tumor heterogeneity based on three different omics layers: genome, epigenome and transcriptome. As a result, this review can be useful for the analysis of multi-omics profiles produced by many large-scale consortia. Contact:sunkim.bioinfo@snu.ac.kr.
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Affiliation(s)
- Dohoon Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
| | - Youngjune Park
- Department of Computer Science and Engineering, Institute of Engineering Research, Seoul National University, Seoul 08826, Korea
| | - Sun Kim
- Bioinformatics Institute, Seoul National University, Seoul 08826, Korea
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Ionizing Radiation-Induced Epigenetic Modifications and Their Relevance to Radiation Protection. Int J Mol Sci 2020; 21:ijms21175993. [PMID: 32825382 PMCID: PMC7503247 DOI: 10.3390/ijms21175993] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
The present system of radiation protection assumes that exposure at low doses and/or low dose-rates leads to health risks linearly related to the dose. They are evaluated by a combination of epidemiological data and radiobiological models. The latter imply that radiation induces deleterious effects via genetic mutation caused by DNA damage with a linear dose-dependence. This picture is challenged by the observation of radiation-induced epigenetic effects (changes in gene expression without altering the DNA sequence) and of non-linear responses, such as non-targeted and adaptive responses, that in turn can be controlled by gene expression networks. Here, we review important aspects of the biological response to ionizing radiation in which epigenetic mechanisms are, or could be, involved, focusing on the possible implications to the low dose issue in radiation protection. We examine in particular radiation-induced cancer, non-cancer diseases and transgenerational (hereditary) effects. We conclude that more realistic models of radiation-induced cancer should include epigenetic contribution, particularly in the initiation and progression phases, while the impact on hereditary risk evaluation is expected to be low. Epigenetic effects are also relevant in the dispute about possible "beneficial" effects at low dose and/or low dose-rate exposures, including those given by the natural background radiation.
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97
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Madhu B, Uribe-Lewis S, Bachman M, Murrell A, Griffiths JR. Apc Min/+ tumours and normal mouse small intestines show linear metabolite concentration and DNA cytosine hydroxymethylation gradients from pylorus to colon. Sci Rep 2020; 10:13616. [PMID: 32788746 PMCID: PMC7423954 DOI: 10.1038/s41598-020-70579-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022] Open
Abstract
Topographical variations of metabolite concentrations have been reported in the duodenum, jejunum and ileum of the small intestine, and in human intestinal tumours from those regions, but there are no published metabolite concentrations measurements correlated with linear position in the mouse small intestine or intestinal tumours. Since DNA methylation dynamics are influenced by metabolite concentrations, they too could show linear anatomical variation. We measured metabolites by HR-MAS 1H NMR spectroscopy and DNA cytosine modifications by LC/MS, in normal small intestines of C57BL/6J wild-type mice, and in normal and tumour samples from ApcMin/+ mice. Wild-type mouse intestines showed approximately linear, negative concentration gradations from the pylorus (i.e. the junction with the stomach) of alanine, choline compounds, creatine, leucine and valine. ApcMin/+ mouse tumours showed negative choline and valine gradients, but a positive glycine gradient. 5-Hydroxymethylcytosine showed a positive gradient in the tumours. The linear gradients we found along the length of the mouse small intestine and in tumours contrast with previous reports of discrete concentration changes in the duodenum, jejunum and ileum. To our knowledge, this is also the first report of a systematic measurement of global levels of DNA cytosine modification in wild-type and ApcMin/+ mouse small intestine.
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Affiliation(s)
- Basetti Madhu
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
| | - Santiago Uribe-Lewis
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Martin Bachman
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.,Discovery Science and Technology, Medicines Discovery Catapult, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Adele Murrell
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.,Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - John R Griffiths
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
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98
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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: 38] [Impact Index Per Article: 9.5] [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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99
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Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, Ung M, Ma L, Yu S, Cao Q, Harmanci A, Yan KK, Sethi A, Gürsoy G, Schoenberg MR, Rozowsky J, Warrell J, Emani P, Yang YT, Galeev T, Kong X, Liu S, Li X, Krishnan J, Feng Y, Rivera-Mulia JC, Adrian J, Broach JR, Bolt M, Moran J, Fitzgerald D, Dileep V, Liu T, Mei S, Sasaki T, Trevilla-Garcia C, Wang S, Wang Y, Zang C, Wang D, Klein RJ, Snyder M, Gilbert DM, Yip K, Cheng C, Yue F, Liu XS, White KP, Gerstein M. An integrative ENCODE resource for cancer genomics. Nat Commun 2020; 11:3696. [PMID: 32728046 PMCID: PMC7391744 DOI: 10.1038/s41467-020-14743-w] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal annotation for genome interpretation. However, for particular applications, it may be advantageous to use a customized annotation. Here, we develop such a custom annotation by leveraging advanced assays, such as eCLIP, Hi-C, and whole-genome STARR-seq on a number of data-rich ENCODE cell types. A key aspect of this annotation is comprehensive and experimentally derived networks of both transcription factors and RNA-binding proteins (TFs and RBPs). Cancer, a disease of system-wide dysregulation, is an ideal application for such a network-based annotation. Specifically, for cancer-associated cell types, we put regulators into hierarchies and measure their network change (rewiring) during oncogenesis. We also extensively survey TF-RBP crosstalk, highlighting how SUB1, a previously uncharacterized RBP, drives aberrant tumor expression and amplifies the effect of MYC, a well-known oncogenic TF. Furthermore, we show how our annotation allows us to place oncogenic transformations in the context of a broad cell space; here, many normal-to-tumor transitions move towards a stem-like state, while oncogene knockdowns show an opposing trend. Finally, we organize the resource into a coherent workflow to prioritize key elements and variants, in addition to regulators. We showcase the application of this prioritization to somatic burdening, cancer differential expression and GWAS. Targeted validations of the prioritized regulators, elements and variants using siRNA knockdowns, CRISPR-based editing, and luciferase assays demonstrate the value of the ENCODE resource.
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Affiliation(s)
- Jing Zhang
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Donghoon Lee
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Vineet Dhiman
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Peng Jiang
- Department of Data Science, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jie Xu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, 17033, USA
| | - Patrick McGillivray
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
| | - Jason Liu
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - William Meyerson
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Declan Clarke
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Mengting Gu
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Shantao Li
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Shaoke Lou
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jinrui Xu
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Lucas Lochovsky
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Matthew Ung
- Department of Biomedical Data Science, Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03765, USA
| | - Lijia Ma
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
| | - Shan Yu
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Qin Cao
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Arif Harmanci
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Koon-Kiu Yan
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Anurag Sethi
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Gamze Gürsoy
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Michael Rutenberg Schoenberg
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Joel Rozowsky
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jonathan Warrell
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Prashant Emani
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Yucheng T Yang
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Timur Galeev
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Xiangmeng Kong
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Shuang Liu
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Xiaotong Li
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jayanth Krishnan
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Yanlin Feng
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Juan Carlos Rivera-Mulia
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Jessica Adrian
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - James R Broach
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, 17033, USA
| | - Michael Bolt
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Jennifer Moran
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Dominic Fitzgerald
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Tingting Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
| | - Shenglin Mei
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Takayo Sasaki
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Claudia Trevilla-Garcia
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Su Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Yanli Wang
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, 17033, USA
| | - Chongzhi Zang
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53726, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Kevin Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Chao Cheng
- Department of Biomedical Data Science, Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03765, USA
- Department of Medicine, Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA.
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, 17033, USA.
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
| | - Kevin P White
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.
- Tempus Labs, Chicago, IL, 60654, USA.
| | - Mark Gerstein
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06520, USA.
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA.
- Department of Computer Science, Yale University, New Haven, CT, 06520, USA.
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA.
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100
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Cao W, Lee H, Wu W, Zaman A, McCorkle S, Yan M, Chen J, Xing Q, Sinnott-Armstrong N, Xu H, Sailani MR, Tang W, Cui Y, Liu J, Guan H, Lv P, Sun X, Sun L, Han P, Lou Y, Chang J, Wang J, Gao Y, Guo J, Schenk G, Shain AH, Biddle FG, Collisson E, Snyder M, Bivona TG. Multi-faceted epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma. Nat Commun 2020; 11:3675. [PMID: 32699215 PMCID: PMC7376194 DOI: 10.1038/s41467-020-17227-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/17/2020] [Indexed: 12/20/2022] Open
Abstract
Epigenetic landscapes can shape physiologic and disease phenotypes. We used integrative, high resolution multi-omics methods to delineate the methylome landscape and characterize the oncogenic drivers of esophageal squamous cell carcinoma (ESCC). We found 98% of CpGs are hypomethylated across the ESCC genome. Hypo-methylated regions are enriched in areas with heterochromatin binding markers (H3K9me3, H3K27me3), while hyper-methylated regions are enriched in polycomb repressive complex (EZH2/SUZ12) recognizing regions. Altered methylation in promoters, enhancers, and gene bodies, as well as in polycomb repressive complex occupancy and CTCF binding sites are associated with cancer-specific gene dysregulation. Epigenetic-mediated activation of non-canonical WNT/β-catenin/MMP signaling and a YY1/lncRNA ESCCAL-1/ribosomal protein network are uncovered and validated as potential novel ESCC driver alterations. This study advances our understanding of how epigenetic landscapes shape cancer pathogenesis and provides a resource for biomarker and target discovery.
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Grants
- U01 CA217882 NCI NIH HHS
- R01 CA239604 NCI NIH HHS
- K22 CA217997 NCI NIH HHS
- R01 CA227807 NCI NIH HHS
- U54 CA224081 NCI NIH HHS
- R01 CA211052 NCI NIH HHS
- S10 OD020141 NIH HHS
- U24 CA210974 NCI NIH HHS
- R01 CA222862 NCI NIH HHS
- R01 CA230263 NCI NIH HHS
- R01 CA169338 NCI NIH HHS
- R01 CA204302 NCI NIH HHS
- R01 CA178015 NCI NIH HHS
- the National Natural Science Foundation of China (Grants 81171992, 31570899), the Natural Science Foundation of Henan (Grants 182102310328, 162300410279, 182300410374, 192102310096); the Education Department of Henan Province(18B310022,19A320037).
- National Natural Science Foundation of China (National Science Foundation of China)
- the Natural Science Foundation of Henan (Grants 182102310328, 162300410279, 182300410374, 192102310096); the Education Department of Henan Province(18B310022,19A320037). This work used the Genome Sequencing Service Center by Stanford Center for Genomics and Personalized Medicine Sequencing Center, supported by the grant award NIH S10OD020141. E.A.C acknowledge funding support from NCI Grants R01 [CA178015, CA222862, CA227807, CA239604, CA230263] and U24 [CA210974]. T.G.B acknowledges funding support from NIH / NCI U01CA217882, NIH / NCI U54CA224081, NIH / NCI R01CA204302, NIH / NCI R01CA211052, NIH / NCI R01CA169338, and the Pew-Stewart Foundations.
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Affiliation(s)
- Wei Cao
- Translational Medical Center, Zhengzhou Central Hospital Affiliated Zhengzhou University, Zhengzhou, China.
| | - Hayan Lee
- Department of Genetics, School of Medicine, Stanford University, CA, USA
| | - Wei Wu
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
| | - Aubhishek Zaman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Sean McCorkle
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, USA
| | - Ming Yan
- Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Justin Chen
- Department of Genetics, School of Medicine, Stanford University, CA, USA
| | - Qinghe Xing
- Institutes of Biomedical Sciences and Children's Hospital, Fudan University, Shanghai, China
| | | | - Hongen Xu
- Precision Medicine Center, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - M Reza Sailani
- Department of Genetics, School of Medicine, Stanford University, CA, USA
| | - Wenxue Tang
- Precision Medicine Center, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuanbo Cui
- Translational Medical Center, Zhengzhou Central Hospital Affiliated Zhengzhou University, Zhengzhou, China
| | - Jia Liu
- Translational Medical Center, Zhengzhou Central Hospital Affiliated Zhengzhou University, Zhengzhou, China
| | - Hongyan Guan
- Translational Medical Center, Zhengzhou Central Hospital Affiliated Zhengzhou University, Zhengzhou, China
| | - Pengju Lv
- Translational Medical Center, Zhengzhou Central Hospital Affiliated Zhengzhou University, Zhengzhou, China
| | - Xiaoyan Sun
- Translational Medical Center, Zhengzhou Central Hospital Affiliated Zhengzhou University, Zhengzhou, China
| | - Lei Sun
- Translational Medical Center, Zhengzhou Central Hospital Affiliated Zhengzhou University, Zhengzhou, China
| | - Pengli Han
- Translational Medical Center, Zhengzhou Central Hospital Affiliated Zhengzhou University, Zhengzhou, China
| | - Yanan Lou
- Translational Medical Center, Zhengzhou Central Hospital Affiliated Zhengzhou University, Zhengzhou, China
| | - Jing Chang
- Jiangsu Mai Jian Biotechnology Development Company, Wuxi, China
| | - Jinwu Wang
- Department of Pathology, Linzhou Cancer Hospital, Linzhou, China
| | - Yuchi Gao
- Annoroad Gene Company, Beijing, China
| | - Jiancheng Guo
- Precision Medicine Center, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Gundolf Schenk
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Alan Hunter Shain
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Fred G Biddle
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Eric Collisson
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, CA, USA.
| | - Trever G Bivona
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
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