1
|
Zhang Z, Wang P, Chen S, Xiang D, Chen J, Huang W, Liu X, Yi T, Wang D, Pu Y, He L, Zhang H. NXPH4 can be used as a biomarker for pan-cancer and promotes colon cancer progression. Aging (Albany NY) 2024; 16:5866-5886. [PMID: 38613793 PMCID: PMC11042927 DOI: 10.18632/aging.205648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/17/2024] [Indexed: 04/15/2024]
Abstract
NXPH4 promotes cancer proliferation and invasion. However, its specific role and mechanism in cancer remain unclear. Transcriptome and clinical data for pan-cancer were derived from the TCGA database. K-M survival curve and univariate Cox were used for prognostic analysis. CIBERSORT and TIMER algorithms were employed to calculate immune cell infiltration. Gene set enrichment analysis (GSEA) was employed for investigating the function of NXPH4. Western blot verified differential expression of NXPH4 in colon cancer. Functional assays (CCK-8, plate clonogenicity assay, wound healing assay, and Transwell assay) confirmed the impact of NXPH4 on proliferation, invasion, and migration of colon cancer cells. Dysregulation of NXPH4 in pan-cancer suggests its potential as a diagnostic and prognostic marker for certain cancers, including colon and liver cancer. High expression of NXPH4 in pan-cancer might be associated with the increase in copy number and hypomethylation. NXPH4 expression in pan-cancer is substantially linked to immune cell infiltration in the immune microenvironment. NXPH4 expression is associated with the susceptibility to immunotherapy and chemotherapy. Western blot further confirmed the higher expression of NXPH4 in colon cancer. Knockdown of NXPH4 significantly suppresses proliferation, invasion, and migration of colon cancer cell lines HT-29 and HCT116, as validated by functional assays.
Collapse
Affiliation(s)
- Zhipeng Zhang
- Department of Anorectal Surgery, The Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, China
| | - Pengfei Wang
- Department of Gastrointestinal Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Siwen Chen
- The Sixth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dezhi Xiang
- Department of Anorectal Surgery, The Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, China
| | - Jinzhen Chen
- Department of Anorectal Surgery, The Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, China
| | - Wanchang Huang
- Department of Anorectal Surgery, The Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, China
| | - Xiao Liu
- Department of Anorectal Surgery, The Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, China
| | - Tongwen Yi
- Department of Anorectal Surgery, The Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, China
| | - Dawei Wang
- Key Laboratory of Hepatosplenic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yunfei Pu
- Key Laboratory of Hepatosplenic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Longfu He
- Department of Anorectal Surgery, The Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, China
| | - Hao Zhang
- Department of Physiology, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
| |
Collapse
|
2
|
Seem K, Kaur S, Kumar S, Mohapatra T. Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression. Crit Rev Biochem Mol Biol 2024:1-30. [PMID: 38440883 DOI: 10.1080/10409238.2024.2320659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024]
Abstract
Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the contemporary era of epigenetics. The changes in DNA methylation, histone modification, non-coding RNA biogenesis, and chromatin remodeling play crucial roles in genomic functions and regulation of gene expression. More importantly, some of these changes are inherited to the next generations as a part of epigenetic memory and play significant roles in gene expression. The sum total of all changes in DNA bases, histone proteins, and ncRNA biogenesis constitutes the epigenome. Continuous progress in deciphering epigenetic regulations and the existence of heritable epigenetic/epiallelic variations associated with trait of interest enables to deploy epigenome editing tools to modulate gene expression. DNA methylation marks can be utilized in epigenome editing for the manipulation of gene expression. Initially, genome/epigenome editing technologies relied on zinc-finger protein or transcriptional activator-like effector protein. However, the discovery of clustered regulatory interspaced short palindromic repeats CRISPR)/deadCRISPR-associated protein 9 (dCas9) enabled epigenome editing to be more specific/efficient for targeted DNA (de)methylation. One of the major concerns has been the off-target effects, wherein epigenome editing may unintentionally modify gene/regulatory element which may cause unintended change/harmful effects. Moreover, epigenome editing of germline cell raises several ethical/safety issues. This review focuses on the recent developments in epigenome editing tools/techniques, technological limitations, and future perspectives of this emerging technology in therapeutics for human diseases as well as plant improvement to achieve sustainable developmental goals.
Collapse
Affiliation(s)
- Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
| |
Collapse
|
3
|
Koijam AS, Singh KD, Nameirakpam BS, Haobam R, Rajashekar Y. Drug addiction and treatment: An epigenetic perspective. Biomed Pharmacother 2024; 170:115951. [PMID: 38043446 DOI: 10.1016/j.biopha.2023.115951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023] Open
Abstract
Drug addiction is a complex disease affected by numerous genetic and environmental factors. Brain regions in reward pathway, neuronal adaptations, genetic and epigenetic interactions causing transcriptional enhancement or repression of multiple genes induce different addiction phenotypes for varying duration. Addictive drug use causes epigenetic alterations and similarly epigenetic changes induced by environment can promote addiction. Epigenetic mechanisms include DNA methylation and post-translational modifications like methylation, acetylation, phosphorylation, ubiquitylation, sumoylation, dopaminylation and crotonylation of histones, and ADP-ribosylation. Non-coding RNAs also induce epigenetic changes. This review discusses these above areas and stresses the need for exploring epidrugs as a treatment alternative and adjunct, considering the limited success of current addiction treatment strategies. Epigenome editing complexes have lately been effective in eukaryotic systems. Targeted DNA cleavage techniques such as CRISPR-Cas9 system, CRISPR-dCas9 complexes, transcription activator-like effector nucleases (TALENs) and zinc-finger nucleases (ZFNs) have been exploited as targeted DNA recognition or anchoring platforms, fused with epigenetic writer or eraser proteins and delivered by transfection or transduction methods. Efficacy of epidrugs is seen in various neuropsychiatric conditions and initial results in addiction treatment involving model organisms are remarkable. Epidrugs present a promising alternative treatment for addiction.
Collapse
Affiliation(s)
- Arunkumar Singh Koijam
- Insect Bioresources Laboratory, Animal Bioresources Programme, Institute of Bioresources & Sustainable Development, Department of Biotechnology, Govt. of India, Takyelpat, Imphal 795001, Manipur, India
| | - Kabrambam Dasanta Singh
- Insect Bioresources Laboratory, Animal Bioresources Programme, Institute of Bioresources & Sustainable Development, Department of Biotechnology, Govt. of India, Takyelpat, Imphal 795001, Manipur, India
| | - Bunindro Singh Nameirakpam
- Insect Bioresources Laboratory, Animal Bioresources Programme, Institute of Bioresources & Sustainable Development, Department of Biotechnology, Govt. of India, Takyelpat, Imphal 795001, Manipur, India
| | - Reena Haobam
- Department of Biotechnology, Manipur University, Canchipur, Imphal 795003, Manipur, India
| | - Yallappa Rajashekar
- Insect Bioresources Laboratory, Animal Bioresources Programme, Institute of Bioresources & Sustainable Development, Department of Biotechnology, Govt. of India, Takyelpat, Imphal 795001, Manipur, India.
| |
Collapse
|
4
|
An Y, Talwar CS, Park KH, Ahn WC, Lee SJ, Go SR, Cho JH, Kim DY, Kim YS, Cho S, Kim JH, Kim TJ, Woo EJ. Design of hypoxia responsive CRISPR-Cas9 for target gene regulation. Sci Rep 2023; 13:16763. [PMID: 37798384 PMCID: PMC10556097 DOI: 10.1038/s41598-023-43711-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023] Open
Abstract
The CRISPR-Cas9 system is a widely used gene-editing tool, offering unprecedented opportunities for treating various diseases. Controlling Cas9/dCas9 activity at specific location and time to avoid undesirable effects is very important. Here, we report a conditionally active CRISPR-Cas9 system that regulates target gene expression upon sensing cellular environmental change. We conjugated the oxygen-sensing transcription activation domain (TAD) of hypoxia-inducing factor (HIF-1α) with the Cas9/dCas9 protein. The Cas9-TAD conjugate significantly increased endogenous target gene cleavage under hypoxic conditions compared with that under normoxic conditions, whereas the dCas9-TAD conjugate upregulated endogenous gene transcription. Furthermore, the conjugate system effectively downregulated the expression of SNAIL, an essential gene in cancer metastasis, and upregulated the expression of the tumour-related genes HNF4 and NEUROD1 under hypoxic conditions. Since hypoxia is closely associated with cancer, the hypoxia-dependent Cas9/dCas9 system is a novel addition to the molecular tool kit that functions in response to cellular signals and has potential application for gene therapeutics.
Collapse
Affiliation(s)
- Yan An
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
- Division of Animal, Horticultural and Food Sciences, Graduate School of Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Chandana S Talwar
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon, 305-333, Republic of Korea
| | - Kwang-Hyun Park
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
| | - Woo-Chan Ahn
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
| | - Su-Jin Lee
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon, 305-333, Republic of Korea
| | - Seong-Ryeong Go
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon, 305-333, Republic of Korea
| | - Jin Hwa Cho
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
| | - Do Yon Kim
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon, 305-333, Republic of Korea
| | - Yong-Sam Kim
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon, 305-333, Republic of Korea
| | - Sayeon Cho
- Laboratory of Molecular and Pharmacological Cell Biology, College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jeong-Hoon Kim
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon, 305-333, Republic of Korea
| | - Tae-Jip Kim
- Division of Animal, Horticultural and Food Sciences, Graduate School of Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Eui-Jeon Woo
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea.
- Department of Bioscience, University of Science and Technology, Daejeon, 305-333, Republic of Korea.
| |
Collapse
|
5
|
Sapozhnikov DM, Szyf M. Increasing Specificity of Targeted DNA Methylation Editing by Non-Enzymatic CRISPR/dCas9-Based Steric Hindrance. Biomedicines 2023; 11:biomedicines11051238. [PMID: 37238909 DOI: 10.3390/biomedicines11051238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
As advances in genome engineering inch the technology towards wider clinical use-slowed by technical and ethical hurdles-a newer offshoot, termed "epigenome engineering", offers the ability to correct disease-causing changes in the DNA without changing its sequence and, thus, without some of the unfavorable correlates of doing so. In this review, we note some of the shortcomings of epigenetic editing technology-specifically the risks involved in the introduction of epigenetic enzymes-and highlight an alternative epigenetic editing strategy using physical occlusion to modify epigenetic marks at target sites without a requirement for any epigenetic enzyme. This may prove to be a safer alternative for more specific epigenetic editing.
Collapse
Affiliation(s)
- Daniel M Sapozhnikov
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3G 1Y6, Canada
| |
Collapse
|
6
|
Wei A, Wu H. Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers. Development 2022; 149:dev182683. [PMID: 36519514 PMCID: PMC10108609 DOI: 10.1242/dev.182683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA methylation is a highly conserved epigenetic modification that plays essential roles in mammalian gene regulation, genome stability and development. Despite being primarily considered a stable and heritable epigenetic silencing mechanism at heterochromatic and repetitive regions, whole genome methylome analysis reveals that DNA methylation can be highly cell-type specific and dynamic within proximal and distal gene regulatory elements during early embryonic development, stem cell differentiation and reprogramming, and tissue maturation. In this Review, we focus on the mechanisms and functions of regulated DNA methylation and demethylation, highlighting how these dynamics, together with crosstalk between DNA methylation and histone modifications at distinct regulatory regions, contribute to mammalian development and tissue maturation. We also discuss how recent technological advances in single-cell and long-read methylome sequencing, along with targeted epigenome-editing, are enabling unprecedented high-resolution and mechanistic dissection of DNA methylome dynamics.
Collapse
Affiliation(s)
- Alex Wei
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
7
|
Gudmunds E, Wheat CW, Khila A, Husby A. Functional genomic tools for emerging model species. Trends Ecol Evol 2022; 37:1104-15. [PMID: 35914975 DOI: 10.1016/j.tree.2022.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 01/12/2023]
Abstract
Most studies in the field of ecology and evolution aiming to connect genotype to phenotype rarely validate identified loci using functional tools. Recent developments in RNA interference (RNAi) and clustered regularly interspaced palindromic repeats (CRISPR)-Cas genome editing have dramatically increased the feasibility of functional validation. However, these methods come with specific challenges when applied to emerging model organisms, including limited spatial control of gene silencing, low knock-in efficiencies, and low throughput of functional validation. Moreover, many functional studies to date do not recapitulate ecologically relevant variation, and this limits their scope for deeper insights into evolutionary processes. We therefore argue that increased use of gene editing by allelic replacement through homology-directed repair (HDR) would greatly benefit the field of ecology and evolution.
Collapse
|
8
|
Luo B, Zhang Y, An P, Lan F, Wu Y. Covalent organic framework nanosheet anchored with highly dispersed Au nanoparticles as a novel nanoprobe for DNA methylation detection. J Colloid Interface Sci 2022; 626:241-250. [DOI: 10.1016/j.jcis.2022.06.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/08/2022] [Accepted: 06/28/2022] [Indexed: 10/31/2022]
|
9
|
de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, Farnham PJ, Blancafort P, Lister R. Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. Genome Biol 2022; 23:163. [PMID: 35883107 PMCID: PMC9316731 DOI: 10.1186/s13059-022-02728-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 07/06/2022] [Indexed: 12/22/2022] Open
Abstract
Background Cytosine DNA methylation is widely described as a transcriptional repressive mark with the capacity to silence promoters. Epigenome engineering techniques enable direct testing of the effect of induced DNA methylation on endogenous promoters; however, the downstream effects have not yet been comprehensively assessed. Results Here, we simultaneously induce methylation at thousands of promoters in human cells using an engineered zinc finger-DNMT3A fusion protein, enabling us to test the effect of forced DNA methylation upon transcription, chromatin accessibility, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that transcriptional responses to DNA methylation are highly context-specific, including lack of repression, as well as cases of increased gene expression, which appears to be driven by the eviction of methyl-sensitive transcriptional repressors. Furthermore, we find that some regulatory networks can override DNA methylation and that promoter methylation can cause alternative promoter usage. DNA methylation deposited at promoter and distal regulatory regions is rapidly erased after removal of the zinc finger-DNMT3A fusion protein, in a process combining passive and TET-mediated demethylation. Finally, we demonstrate that induced DNA methylation can exist simultaneously on promoter nucleosomes that possess the active histone modification H3K4me3, or DNA bound by the initiated form of RNA polymerase II. Conclusions These findings have important implications for epigenome engineering and demonstrate that the response of promoters to DNA methylation is more complex than previously appreciated. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02728-5.
Collapse
Affiliation(s)
- Alex de Mendoza
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia. .,School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Trung Viet Nguyen
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Daniel Poppe
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Sam Buckberry
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jahnvi Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Matthew R Grimmer
- Department of Biochemistry and Molecular Medicine, University of Southern California, 1450 Biggy St, Los Angeles, CA, 90089, USA.,Integrated Genetics and Genomics, University of California, Davis, 451 Health Sciences Dr, Davis, CA, 95616, USA.,Department of Neurological Surgery, University of California, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Sabine Stolzenburg
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Ozren Bogdanovic
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Alicia Oshlack
- The Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia.,School of BioScience, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine, University of Southern California, 1450 Biggy St, Los Angeles, CA, 90089, USA
| | - Pilar Blancafort
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.,School of Anatomy, Physiology and Human Biology, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia.,The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.
| |
Collapse
|
10
|
Cheng B, Rong A, Li W, Bi X, Qiu X, Subramanian VS. DNMT3a-Mediated Enterocyte Barrier Dysfunction Contributes to Ulcerative Colitis via Facilitating the Interaction of Enterocytes and B Cells. Mediators Inflamm 2022; 2022:1-15. [PMID: 35574272 PMCID: PMC9106515 DOI: 10.1155/2022/4862763] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 03/04/2022] [Accepted: 04/01/2022] [Indexed: 12/13/2022] Open
Abstract
Objective Dysfunction of the enterocyte barrier is associated with the development of ulcerative colitis (UC). This study was aimed at exploring the effect of DNMT3a on enterocyte barrier function in the progression of UC and the underlying mechanism. Method Mice were given 3.5% dextran sodium sulphate (DSS) in drinking water to induce colitis. The primary intestinal epithelial cells (IECs) were isolated and treated with lipopolysaccharide (LPS) to establish an in vitro inflammatory model. We detected mouse clinical symptoms, histopathological damage, enterocyte barrier function, B cell differentiation, DNA methylation level, and cytokine production. Subsequently, the effect of DNMT3a from IECs on B cell differentiation was explored by a cocultural experiment. Result DSS treatment significantly reduced the body weight and colonic length, increased disease activity index (DAI), and aggravated histopathological damage. In addition, DSS treatment induced downregulation of tight junction (TJ) protein, anti-inflammatory cytokines (IL-10 and TGF-β), and the number of anti-inflammatory B cells (CD1d+) in intestinal epithelial tissues, while upregulated proinflammatory cytokines (IL-6 and TNF-α), proinflammatory B cells (CD138+), and DNA methylation level. Further in vitro results revealed that DNMT3a silencing or TNFSF13 overexpression in IECs partly abolished the result of LPS-induced epithelial barrier dysfunction, as well as abrogated the effect of IEC-regulated B cell differentiation, while si-TACI transfection reversed these effects. Moreover, DNMT3a silencing decreased TNFSF13 methylation level and induced CD1d+ B cell differentiation, and the si-TNFSF13 transfection reversed the trend of B cell differentiation but did not affect TNFSF13 methylation level. Conclusion Our study suggests that DNMT3a induces enterocyte barrier dysfunction to aggravate UC progression via TNFSF13-mediated interaction of enterocyte and B cells.
Collapse
|
11
|
de Pontual L, Tomé S. Overview of the Complex Relationship between Epigenetics Markers, CTG Repeat Instability and Symptoms in Myotonic Dystrophy Type 1. Int J Mol Sci 2022; 23:ijms23073477. [PMID: 35408837 PMCID: PMC8998570 DOI: 10.3390/ijms23073477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 02/05/2023] Open
Abstract
Among the trinucleotide repeat disorders, myotonic dystrophy type 1 (DM1) is one of the most complex neuromuscular diseases caused by an unstable CTG repeat expansion in the DMPK gene. DM1 patients exhibit high variability in the dynamics of CTG repeat instability and in the manifestations and progression of the disease. The largest expanded alleles are generally associated with the earliest and most severe clinical form. However, CTG repeat length alone is not sufficient to predict disease severity and progression, suggesting the involvement of other factors. Several data support the role of epigenetic alterations in clinical and genetic variability. By highlighting epigenetic alterations in DM1, this review provides a new avenue on how these changes can serve as biomarkers to predict clinical features and the mutation behavior.
Collapse
Affiliation(s)
| | - Stéphanie Tomé
- Correspondence: ; Tel.: +33-1-42-16-57-16; Fax: +33-1-42-16-57-00
| |
Collapse
|
12
|
Luviano N, Duval D, Ittiprasert W, Allienne JF, Tavernier G, Chaparro C, Cosseau C, Grunau C. Hit-and-Run Epigenetic Editing for Vectors of Snail-Borne Parasitic Diseases. Front Cell Dev Biol 2022; 10:794650. [PMID: 35295851 PMCID: PMC8920497 DOI: 10.3389/fcell.2022.794650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/03/2022] [Indexed: 11/25/2022] Open
Abstract
Snail-borne parasitic diseases represent an important challenge to human and animal health. Control strategies that target the intermediate snail host has proved very effective. Epigenetic mechanisms are involved in developmental processes and therefore play a fundamental role in developmental variation. DNA methylation is an important epigenetic information carrier in eukaryotes that plays a major role in the control of chromatin structure. Epigenome editing tools have been instrumental to demonstrate functional importance of this mark for gene expression in vertebrates. In invertebrates, such tools are missing, and the role of DNA methylation remains unknown. Here we demonstrate that methylome engineering can be used to modify in vivo the CpG methylation level of a target gene in the freshwater snail Biomphalaria glabrata, intermediate host of the human parasite Schistosoma mansoni. We used a dCas9-SunTag-DNMT3A complex and synthetic sgRNA to transfect B. glabrata embryos and observed an increase of CpG methylation at the target site in 50% of the hatching snails.
Collapse
Affiliation(s)
- Nelia Luviano
- IHPE, Univ Perpignan Via Domitia, CNRS, Ifremer, Univ Montpellier, Perpignan, France
| | - David Duval
- IHPE, Univ Perpignan Via Domitia, CNRS, Ifremer, Univ Montpellier, Perpignan, France
| | - Wannaporn Ittiprasert
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States.,Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
| | | | - Geneviève Tavernier
- Transgenesis Core Facility of UMS006/Inserm/Paul Sabatier University/National Medical Veterinary School, Toulouse, France.,Inserm UMR 1048, Paul Sabatier University, Toulouse, France
| | - Cristian Chaparro
- IHPE, Univ Perpignan Via Domitia, CNRS, Ifremer, Univ Montpellier, Perpignan, France
| | - Celine Cosseau
- IHPE, Univ Perpignan Via Domitia, CNRS, Ifremer, Univ Montpellier, Perpignan, France
| | - Christoph Grunau
- IHPE, Univ Perpignan Via Domitia, CNRS, Ifremer, Univ Montpellier, Perpignan, France
| |
Collapse
|
13
|
Boye TL, Steenholdt C, Jensen KB, Nielsen OH. Molecular manipulations and intestinal stem cell-derived organoids in inflammatory bowel disease. Stem Cells 2022; 40:447-457. [DOI: 10.1093/stmcls/sxac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022]
Abstract
Abstract
The pathogenesis of inflammatory bowel diseases (IBD) involves genetic predisposition, environmental factors, and a broadly dysregulated intestinal immune response to the commensal intestinal microflora. The interface between genetic predisposition and environmental factors is reflected in the epigenetic regulation at the transcriptional level. Treatment targets now involve mucosal and histological healing, but the future might additionally include normalization of intestinal cellular functions also at the molecular level, for example comprising complete restoration of phenotypic, genotypic, and epigenetic states. Recent developments in patient-derived epithelial intestinal stem cell (ISC) organoid technologies have opened exciting new therapeutic opportunities to potentially attain molecular healing by combining stem cell therapy with molecular manipulations using (epi)drugs and/or CRISPR/Cas9 genome editing. Here, we are the first to discuss the possibility for phenotypic, genotypic, and epigenetic restoration via molecular manipulations and stem cell therapy in IBD from a clinical perspective.
Collapse
Affiliation(s)
- Theresa Louise Boye
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, DK-2730 Herlev, Denmark
| | - Casper Steenholdt
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, DK-2730 Herlev, Denmark
| | - Kim Bak Jensen
- Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Ole Haagen Nielsen
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, DK-2730 Herlev, Denmark
| |
Collapse
|
14
|
Marx N, Eisenhut P, Weinguny M, Klanert G, Borth N. How to train your cell - Towards controlling phenotypes by harnessing the epigenome of Chinese hamster ovary production cell lines. Biotechnol Adv 2022; 56:107924. [PMID: 35149147 DOI: 10.1016/j.biotechadv.2022.107924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 11/24/2022]
Abstract
Recent advances in omics technologies and the broad availability of big datasets have revolutionized our understanding of Chinese hamster ovary cells in their role as the most prevalent host for production of complex biopharmaceuticals. In consequence, our perception of this "workhorse of the biopharmaceutical industry" has successively shifted from that of a nicely working, but unknown recombinant protein producing black box to a biological system governed by multiple complex regulatory layers that might possibly be harnessed and manipulated at will. Despite the tremendous progress that has been made to characterize CHO cells on various omics levels, our understanding is still far from complete. The well-known inherent genetic plasticity of any immortalized and rapidly dividing cell line also characterizes CHO cells and can lead to problematic instability of recombinant protein production. While the high mutational frequency has been a focus of CHO cell research for decades, the impact of epigenetics and its role in differential gene expression has only recently been addressed. In this review we provide an overview about the current understanding of epigenetic regulation in CHO cells and discuss its significance for shaping the cell's phenotype. We also look into current state-of-the-art technology that can be applied to harness and manipulate the epigenetic network so as to nudge CHO cells towards a specific phenotype. Here, we revise current strategies on site-directed integration and random as well as targeted epigenome modifications. Finally, we address open questions that need to be investigated to exploit the full repertoire of fine-tuned control of multiplexed gene expression using epigenetic and systems biology tools.
Collapse
Affiliation(s)
- Nicolas Marx
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Eisenhut
- Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria
| | - Marcus Weinguny
- University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria
| | - Gerald Klanert
- Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria
| | - Nicole Borth
- University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria.
| |
Collapse
|
15
|
Singh M, Thakur M, Mishra M, Yadav M, Vibhuti R, Menon AM, Nagda G, Dwivedi VP, Dakal TC, Yadav V. Gene regulation of intracellular adhesion molecule-1 (ICAM-1): A molecule with multiple functions. Immunol Lett 2021; 240:123-136. [PMID: 34715236 DOI: 10.1016/j.imlet.2021.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 01/04/2023]
Abstract
Intracellular adhesion molecule 1 (ICAM-1) is one of the most extensively studied inducible cell adhesion molecules which is responsible for several immune functions like T cell activation, extravasation, inflammation, etc. The molecule is constitutively expressed over the cell surface and is regulated up / down in response to inflammatory mediators like cellular stress, proinflammatory cytokines, viral infection. These stimuli modulate the expression of ICAM-1 primarily through regulating the ICAM-1 gene transcription. On account of the presence of various binding sites for NF-κB, AP-1, SP-1, and many other transcription factors, the architecture of the ICAM-1 promoter become complex. Transcription factors in union with other transcription factors, coactivators, and suppressors promote their assembly in a stereospecific manner on ICAM-1 promoter which mediates ICAM-1 regulation in response to different stimuli. Along with transcriptional regulation, epigenetic modifications also play a pivotal role in controlling ICAM-1 expression on different cell types. In this review, we summarize the regulation of ICAM-1 expression both at the transcriptional as well as post-transcriptional level with an emphasis on transcription factors and signaling pathways involved.
Collapse
Affiliation(s)
- Mona Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi-110067 India
| | - Mony Thakur
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana-123031 India
| | - Manish Mishra
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research- Institute of Microbial Technology, Chandigarh-160036 India
| | - Manisha Yadav
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research- Institute of Microbial Technology, Chandigarh-160036 India
| | - Rajkamal Vibhuti
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana-123031 India
| | - Athira M Menon
- Genome and computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan 313001 India
| | - Girima Nagda
- Department of Zoology, Mohanlal Sukhadia University, Udaipur, Rajasthan-313001 India
| | - Ved Prakash Dwivedi
- International Centre for Genetic Engineering and Biotechnology, ICGEB Campus, Aruna Asaf Ali Marg, New Delhi-110067 India
| | - Tikam Chand Dakal
- Genome and computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan 313001 India
| | - Vinod Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana-123031 India
| |
Collapse
|
16
|
Abstract
BACKGROUND The impact of abusive alcohol consumption on human health is remarkable. According to the World Health Organization (WHO), approximately 3.3 million people die annually because of harmful alcohol consumption (the figure represents around 5.9% of global deaths). Alcohol Use Disorder (AUD) is a chronic disease where individuals exhibit compulsive alcohol drinking and present negative emotional states when they do not drink. In the most severe manifestations of AUD, the individuals lose control over intake despite a decided will to stop drinking. Given the multiple faces and the specific forms of this disease, the term AUD often appears in the plural (AUDs). Since only a few approved pharmacological treatments are available to treat AUD and they do not apply to all individuals or AUD forms, the search for compounds that may help to eliminate the burden of the disease and complement other therapeutical approaches is necessary. METHODS This work reviews recent research focused on the involvement of epigenetic mechanisms in the pathophysiology of AUD. Excessive drinking leads to chronic and compulsive consumption that eventually damages the organism. The central nervous system is a key target and is the focus of this study. The search for the genetic and epigenetic mechanisms behind the intricated dysregulation induced by ethanol will aid researchers in establishing new therapy approaches. CONCLUSION Recent findings in the field of epigenetics are essential and offer new windows for observation and research. The study of small molecules that inhibit key epienzymes involved in nucleosome architecture dynamics is necessary in order to prove their action and specificity in the laboratory and to test their effectivity and safety in clinical trials with selected patients bearing defined alterations caused by ethanol.
Collapse
Affiliation(s)
- F. David Rodriguez
- Department of Biochemistry and Molecular Biology, Faculty of Chemistry, University of Salamanca and Group GIR BMD (Bases Moleculares del Desarrollo), University of Salamanca, Salamanca, Spain
| |
Collapse
|
17
|
Murthy M, Cheng YY, Holton JL, Bettencourt C. Neurodegenerative movement disorders: An epigenetics perspective and promise for the future. Neuropathol Appl Neurobiol 2021; 47:897-909. [PMID: 34318515 PMCID: PMC9291277 DOI: 10.1111/nan.12757] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/12/2021] [Indexed: 02/02/2023]
Abstract
Neurodegenerative movement disorders (NMDs) are age‐dependent disorders that are characterised by the degeneration and loss of neurons, typically accompanied by pathological accumulation of different protein aggregates in the brain, which lead to motor symptoms. NMDs include Parkinson's disease, multiple system atrophy, progressive supranuclear palsy, and Huntington's disease, among others. Epigenetic modifications are responsible for functional gene regulation during development, adult life and ageing and have progressively been implicated in complex diseases such as cancer and more recently in neurodegenerative diseases, such as NMDs. DNA methylation is by far the most widely studied epigenetic modification and consists of the reversible addition of a methyl group to the DNA without changing the DNA sequence. Although this research field is still in its infancy in relation to NMDs, an increasing number of studies point towards a role for DNA methylation in disease processes. This review addresses recent advances in epigenetic and epigenomic research in NMDs, with a focus on human brain DNA methylation studies. We discuss the current understanding of the DNA methylation changes underlying these disorders, the potential for use of these DNA modifications in peripheral tissues as biomarkers in early disease detection, classification and progression as well as a promising role in future disease management and therapy.
Collapse
Affiliation(s)
- Megha Murthy
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Yun Yung Cheng
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Janice L Holton
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Conceição Bettencourt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| |
Collapse
|
18
|
Ślaska-Kiss K, Zsibrita N, Koncz M, Albert P, Csábrádi Á, Szentes S, Kiss A. Lowering DNA binding affinity of SssI DNA methyltransferase does not enhance the specificity of targeted DNA methylation in E. coli. Sci Rep 2021; 11:15226. [PMID: 34315949 DOI: 10.1038/s41598-021-94528-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022] Open
Abstract
Targeted DNA methylation is a technique that aims to methylate cytosines in selected genomic loci. In the most widely used approach a CG-specific DNA methyltransferase (MTase) is fused to a sequence specific DNA binding protein, which binds in the vicinity of the targeted CG site(s). Although the technique has high potential for studying the role of DNA methylation in higher eukaryotes, its usefulness is hampered by insufficient methylation specificity. One of the approaches proposed to suppress methylation at unwanted sites is to use MTase variants with reduced DNA binding affinity. In this work we investigated how methylation specificity of chimeric MTases containing variants of the CG-specific prokaryotic MTase M.SssI fused to zinc finger or dCas9 targeting domains is influenced by mutations affecting catalytic activity and/or DNA binding affinity of the MTase domain. Specificity of targeted DNA methylation was assayed in E. coli harboring a plasmid with the target site. Digestions of the isolated plasmids with methylation sensitive restriction enzymes revealed that specificity of targeted DNA methylation was dependent on the activity but not on the DNA binding affinity of the MTase. These results have implications for the design of strategies of targeted DNA methylation.
Collapse
|
19
|
Pan H, Renaud L, Chaligne R, Bloehdorn J, Tausch E, Mertens D, Fink AM, Fischer K, Zhang C, Betel D, Gnirke A, Imielinski M, Moreaux J, Hallek M, Meissner A, Stilgenbauer S, Wu CJ, Elemento O, Landau DA. Discovery of Candidate DNA Methylation Cancer Driver Genes. Cancer Discov 2021; 11:2266-2281. [PMID: 33972312 DOI: 10.1158/2159-8290.cd-20-1334] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/25/2021] [Accepted: 04/15/2021] [Indexed: 02/07/2023]
Abstract
Epigenetic alterations, such as promoter hypermethylation, may drive cancer through tumor suppressor gene inactivation. However, we have limited ability to differentiate driver DNA methylation (DNAme) changes from passenger events. We developed DNAme driver inference-MethSig-accounting for the varying stochastic hypermethylation rate across the genome and between samples. We applied MethSig to bisulfite sequencing data of chronic lymphocytic leukemia (CLL), multiple myeloma, ductal carcinoma in situ, glioblastoma, and to methylation array data across 18 tumor types in TCGA. MethSig resulted in well-calibrated quantile-quantile plots and reproducible inference of likely DNAme drivers with increased sensitivity/specificity compared with benchmarked methods. CRISPR/Cas9 knockout of selected candidate CLL DNAme drivers provided a fitness advantage with and without therapeutic intervention. Notably, DNAme driver risk score was closely associated with adverse outcome in independent CLL cohorts. Collectively, MethSig represents a novel inference framework for DNAme driver discovery to chart the role of aberrant DNAme in cancer. SIGNIFICANCE: MethSig provides a novel statistical framework for the analysis of DNA methylation changes in cancer, to specifically identify candidate DNA methylation driver genes of cancer progression and relapse, empowering the discovery of epigenetic mechanisms that enhance cancer cell fitness.This article is highlighted in the In This Issue feature, p. 2113.
Collapse
Affiliation(s)
- Heng Pan
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Loïc Renaud
- New York Genome Center, New York, New York.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York.,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York.,Inserm, UMR-S 1172, Lille, France
| | - Ronan Chaligne
- New York Genome Center, New York, New York.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York.,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | | | - Eugen Tausch
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Daniel Mertens
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna Maria Fink
- German CLL Study Group, and Department I of Internal Medicine, and Center of Integrated Oncology ABCD, University of Cologne, Cologne, Germany
| | - Kirsten Fischer
- German CLL Study Group, and Department I of Internal Medicine, and Center of Integrated Oncology ABCD, University of Cologne, Cologne, Germany
| | - Chao Zhang
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York.,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Doron Betel
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York.,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Marcin Imielinski
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York.,New York Genome Center, New York, New York.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Jérôme Moreaux
- IGH, CNRS, Univ Montpellier, France.,CHU Montpellier, Department of Biological Hematology, Montpellier, France.,UFR de Médecine, Univ Montpellier, Montpellier, France.,Institut Universitaire de France (IUF), France
| | - Michael Hallek
- German CLL Study Group, and Department I of Internal Medicine, and Center of Integrated Oncology ABCD, University of Cologne, Cologne, Germany
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Dan A Landau
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York. .,New York Genome Center, New York, New York.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York.,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| |
Collapse
|
20
|
Abstract
DNA methylation is an epigenetic modification that contributes to essential biological processes such as retrotransposon silencing, cell differentiation, genomic imprinting and X-chromosome inactivation. DNA methylation generates a stable epigenetic mark associated with silencing of gene expression. Aberrant DNA methylation is associated with the development of different tumor types. Reversing DNA methylation is a rational strategy to restore gene re-expression and induce cell differentiation in cancer. DNA hypomethylating agents is a class of drugs that demonstrated efficacy in different tumors. In this chapter, the classification of DNA hypomethylating agents, their pharmacodynamics and their potential drawbacks will be discussed.
Collapse
Affiliation(s)
- Md Gias Uddin
- Department of Pharmaceutical & Administrative Sciences, School of Pharmacy, University of Charleston, Charleston, WV, United States
| | - Tamer E Fandy
- Department of Pharmaceutical & Administrative Sciences, School of Pharmacy, University of Charleston, Charleston, WV, United States.
| |
Collapse
|
21
|
Li Y, Xu Y, Liu T, Chang H, Yang X. The regulation mechanisms and the Lamarckian inheritance property of DNA methylation in animals. Mamm Genome 2021; 32:135-52. [PMID: 33860357 DOI: 10.1007/s00335-021-09870-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/05/2021] [Indexed: 12/19/2022]
Abstract
DNA methylation is a stable and heritable epigenetic mechanism, of which the main functions are stabilizing the transcription of genes and promoting genetic conservation. In animals, the direct molecular inducers of DNA methylation mainly include histone covalent modification and non-coding RNA, whereas the fundamental regulators of DNA methylation are genetic and environmental factors. As is well known, competition is present everywhere in life systems, and will finally strike a balance that is optimal for the animal's survival and reproduction. The same goes for the regulation of DNA methylation. Genetic and environmental factors, respectively, are responsible for the programmed and plasticity changes of DNA methylation, and keen competition exists between genetically influenced procedural remodeling and environmentally influenced plastic alteration. In this process, genetic and environmental factors collaboratively decide the methylation patterns of corresponding loci. DNA methylation alterations induced by environmental factors can be transgenerationally inherited, and exhibit the characteristic of Lamarckian inheritance. Further research on regulatory mechanisms and the environmental plasticity of DNA methylation will provide strong support for understanding the biological function and evolutionary effects of DNA methylation.
Collapse
|
22
|
Fal K, Tomkova D, Vachon G, Chabouté ME, Berr A, Carles CC. Chromatin Manipulation and Editing: Challenges, New Technologies and Their Use in Plants. Int J Mol Sci 2021; 22:E512. [PMID: 33419220 PMCID: PMC7825600 DOI: 10.3390/ijms22020512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/25/2022] Open
Abstract
An ongoing challenge in functional epigenomics is to develop tools for precise manipulation of epigenetic marks. These tools would allow moving from correlation-based to causal-based findings, a necessary step to reach conclusions on mechanistic principles. In this review, we describe and discuss the advantages and limits of tools and technologies developed to impact epigenetic marks, and which could be employed to study their direct effect on nuclear and chromatin structure, on transcription, and their further genuine role in plant cell fate and development. On one hand, epigenome-wide approaches include drug inhibitors for chromatin modifiers or readers, nanobodies against histone marks or lines expressing modified histones or mutant chromatin effectors. On the other hand, locus-specific approaches consist in targeting precise regions on the chromatin, with engineered proteins able to modify epigenetic marks. Early systems use effectors in fusion with protein domains that recognize a specific DNA sequence (Zinc Finger or TALEs), while the more recent dCas9 approach operates through RNA-DNA interaction, thereby providing more flexibility and modularity for tool designs. Current developments of "second generation", chimeric dCas9 systems, aiming at better targeting efficiency and modifier capacity have recently been tested in plants and provided promising results. Finally, recent proof-of-concept studies forecast even finer tools, such as inducible/switchable systems, that will allow temporal analyses of the molecular events that follow a change in a specific chromatin mark.
Collapse
Affiliation(s)
- Kateryna Fal
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France; (K.F.); (G.V.)
| | - Denisa Tomkova
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg CEDEX, France; (D.T.); (M.-E.C.)
| | - Gilles Vachon
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France; (K.F.); (G.V.)
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg CEDEX, France; (D.T.); (M.-E.C.)
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg CEDEX, France; (D.T.); (M.-E.C.)
| | - Cristel C. Carles
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France; (K.F.); (G.V.)
| |
Collapse
|
23
|
Abstract
Methylation of DNA at cytosine bases is an important DNA modification underlying normal development and disease states. Despite decades of research into the biological function of DNA methylation, most of the observations so far have relied primarily on associative data between observed changes in DNA methylation states and local changes in transcriptional activity or chromatin state processes. This is primarily due to the lack of molecular tools to precisely modify DNA methylation in the genome. Recent advances in genome editing technologies have allowed repurposing the CRISPR-Cas9 system for epigenome editing by fusing the catalytically dead Cas9 (dCas9) to epigenome modifying enzymes. Moreover, methods of recruiting multiple protein domains, including the SunTag system, have increased the efficacy of epigenome editing at target sites. Here, we describe an end-to-end protocol for efficient targeted removal of DNA methylation by recruiting multiple catalytic domain of TET1 enzymes to the target sites with the dCas9-SunTag system, including sgRNA design, molecular cloning, delivery of plasmid into mammalian cells, and targeted DNA methylation analysis.
Collapse
Affiliation(s)
- Trung Viet Nguyen
- ARC Center of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
- The Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Ryan Lister
- ARC Center of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.
- The Harry Perkins Institute of Medical Research, Perth, WA, Australia.
| |
Collapse
|
24
|
Abstract
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) is one of the hallmark of biological tools, contemplated as a valid and hopeful alternatives to genome editing. Advancements in CRISPR-based technologies have empowered scientists with an editing kit that allows them to employ their knowledge for deleting, replacing and lately “Gene Surgery”, and provides unique control over genes in broad range of species, and presumably in humans. These fast-growing technologies have high strength and flexibility and are becoming an adaptable tool with implementations that are altering organism’s genome and easily used for chromatin manipulation. In addition to the popularity of CRISPR in genome engineering and modern biology, this major tool authorizes breakthrough discoveries and methodological advancements in science. As scientists are developing new types of experiments, some of the applications are raising questions about what CRISPR can enable. The results of evidence-based research strongly suggest that CRISPR is becoming a practical tool for genome-engineering and to create genetically modified eukaryotes, which is needed to establish guidelines on new regulatory concerns for scientific communities.
Collapse
Affiliation(s)
- Zhabiz Golkar
- Division of Academic Affairs, Voorhees College, Denmark, SC, USA.
| |
Collapse
|
25
|
Kiely M, Tse LA, Koka H, Wang D, Lee P, Wang F, Wu C, Tsang KH, Chan WC, Law SH, Zhang H, Karlins E, Zhu B, Hutchinson A, Hicks B, Zhu B, Yang XR. Age-related DNA methylation in paired normal and tumour breast tissue in Chinese breast cancer patients. Epigenetics 2020; 16:677-691. [PMID: 32970968 PMCID: PMC8143246 DOI: 10.1080/15592294.2020.1819661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Age-related DNA methylation is a potential mechanism contributing to breast cancer development. Studies of primarily Caucasian women have identified many CpG sites of age-related methylation in non-diseased breast tissue possibly driving cancer development over time. There is a paucity of studies involving Asian women whose ages at breast cancer onset are usually younger than Caucasians. We identified the 181 most consistent age-related methylation events in non-diseased breast tissue across published studies. Age-related methylation events were measured in adjacent normal and breast tumour tissue in an exclusively Asian population at the previously identified age-related methylation sites. Age-related methylation was found in 118 probes in adjacent normal breast tissue. Methylation of 99% of these sites was increased with age and predominantly located on CpG islands in promoter regions. To ascertain biological relevance to breast cancer, we focused on the 37 sites with overall higher methylation in tumour compared to adjacent normal samples. Some sites positively related to age, including AQP5 and CORO6, inversely correlated with gene expression. Several others have known involvement in suppression of carcinogenesis including GPC5 and SST, suggesting that perturbation of epigenetic regulation at these sites due to ageing may contribute to the progression of carcinogenesis. This study highlights an age-related methylation landscape in non-tumour tissue, consistent not just across studies, but also across different populations. We present candidate age-related methylation sites warranting further investigation as potential epigenetic drivers of breast cancer. They may serve as potential targets of site-specific demethylation intervention strategies for the prevention of age-related breast cancer.
Collapse
Affiliation(s)
- Maeve Kiely
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Lap Ah Tse
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Hela Koka
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Priscilla Lee
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Feng Wang
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Cherry Wu
- North District Hospital, Hong Kong, China
| | | | | | | | - Han Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| |
Collapse
|
26
|
Lee JH, Saito Y, Park SJ, Nakai K. Existence and possible roles of independent non-CpG methylation in the mammalian brain. DNA Res 2020; 27:dsaa020. [PMID: 32970817 PMCID: PMC7750974 DOI: 10.1093/dnares/dsaa020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022] Open
Abstract
Methylated non-CpGs (mCpHs) in mammalian cells yield weak enrichment signals and colocalize with methylated CpGs (mCpGs), thus have been considered byproducts of hyperactive methyltransferases. However, mCpHs are cell type-specific and associated with epigenetic regulation, although their dependency on mCpGs remains to be elucidated. In this study, we demonstrated that mCpHs colocalize with mCpGs in pluripotent stem cells, but not in brain cells. In addition, profiling genome-wide methylation patterns using a hidden Markov model revealed abundant genomic regions in which CpGs and CpHs are differentially methylated in brain. These regions were frequently located in putative enhancers, and mCpHs within the enhancers increased in correlation with brain age. The enhancers with hypermethylated CpHs were associated with genes functionally enriched in immune responses, and some of the genes were related to neuroinflammation and degeneration. This study provides insight into the roles of non-CpG methylation as an epigenetic code in the mammalian brain genome.
Collapse
Affiliation(s)
- Jong-Hun Lee
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yutaka Saito
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Sung-Joon Park
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| |
Collapse
|
27
|
Yamaguchi T, Uchida E, Okada T, Ozawa K, Onodera M, Kume A, Shimada T, Takahashi S, Tani K, Nasu Y, Mashimo T, Mizuguchi H, Mitani K, Maki K. Aspects of Gene Therapy Products Using Current Genome-Editing Technology in Japan. Hum Gene Ther 2020; 31:1043-1053. [PMID: 32731837 PMCID: PMC7585607 DOI: 10.1089/hum.2020.156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The development of genome-editing technology could lead to breakthrough gene therapy. Genome editing has made it possible to easily knock out or modify a target gene, while current gene therapy using a virus vector or plasmid hampering modification with respect to gene replacement therapies. Clinical development using these genome-editing tools is progressing rapidly. However, it is also becoming clear that there is a possibility of unintended gene sequence modification or deletion, or the insertion of undesired genes, or the selection of cells with abnormalities in the cancer suppressor gene p53; these unwanted actions are not possible with current gene therapy. The Science Board of the Pharmaceuticals and Medical Devices Agency of Japan has compiled a report on the expected aspects of such genome-editing technology and the risks associated with it. This article summarizes the history of that discussion and compares the key concepts with information provided by other regulatory authorities.
Collapse
Affiliation(s)
- Teruhide Yamaguchi
- Kanazawa Institute of Technology, Ishikawa, Japan.,Nihon Pharmaceutical University
| | | | | | | | | | | | | | | | | | - Yasutomo Nasu
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | | | | | | | | |
Collapse
|
28
|
Zhang J, Yang C, Wu C, Cui W, Wang L. DNA Methyltransferases in Cancer: Biology, Paradox, Aberrations, and Targeted Therapy. Cancers (Basel) 2020; 12:cancers12082123. [PMID: 32751889 PMCID: PMC7465608 DOI: 10.3390/cancers12082123] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/14/2020] [Accepted: 07/20/2020] [Indexed: 02/07/2023] Open
Abstract
DNA methyltransferases are an essential class of modifiers in epigenetics. In mammals, DNMT1, DNMT3A and DNMT3B participate in DNA methylation to regulate normal biological functions, such as embryo development, cell differentiation and gene transcription. Aberrant functions of DNMTs are frequently associated with tumorigenesis. DNMT aberrations usually affect tumor-related factors, such as hypermethylated suppressor genes and genomic instability, which increase the malignancy of tumors, worsen the prognosis for patients, and greatly increase the difficulty of cancer therapy. However, the impact of DNMTs on tumors is still controversial, and therapeutic approaches targeting DNMTs are still under exploration. Here, we summarize the biological functions and paradoxes associated with DNMTs and we discuss some emerging strategies for targeting DNMTs in tumors, which may provide novel ideas for cancer therapy.
Collapse
Affiliation(s)
- Jiayu Zhang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China; (J.Z.); (C.Y.); (C.W.)
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Cheng Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China; (J.Z.); (C.Y.); (C.W.)
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Chunfu Wu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China; (J.Z.); (C.Y.); (C.W.)
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Wei Cui
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China; (J.Z.); (C.Y.); (C.W.)
- Correspondence: (W.C.); (L.W.)
| | - Lihui Wang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China; (J.Z.); (C.Y.); (C.W.)
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
- Correspondence: (W.C.); (L.W.)
| |
Collapse
|
29
|
Matsushita J, Suzuki T, Okamura K, Ichihara G, Nohara K. Identification by TCGA database search of five genes that are aberrantly expressed and involved in hepatocellular carcinoma potentially via DNA methylation changes. Environ Health Prev Med 2020; 25:31. [PMID: 32703154 PMCID: PMC7376645 DOI: 10.1186/s12199-020-00871-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/05/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Various treatments for hepatocellular carcinoma (HCC) are utilized in clinical practice; however, the prognosis is still poor on account of high recurrence rates. DNA methylation levels of CpG islands around promoters (promoter CpGis) inversely regulate gene expression and closely involved in carcinogenesis. As a new strategy, several chemicals globally inhibiting DNA methylation have been developed aiming at reducing DNA methylation levels and maintaining the expression of tumor suppressor genes. On the other hand, since these drugs nonspecifically modify DNA methylation, they can cause serious adverse effects. In order to ameliorate the methods by targeting specific CpGs, information of cancer-related genes that are regulated by DNA methylation is required. METHODS We searched candidate genes whose expressions were regulated by DNA methylation of promoter CpGi and which are involved in HCC cases. To do so, we first identified genes whose expression were changed in HCC by comparing gene expressions of 371 HCC tissues and 41 non-tumor tissues using the Cancer Genome Atlas (TCGA) database. The genes were further selected for poor prognosis by log-rank test of Kaplan-Meier plot and for cancer relevance by Pubmed search. Expression profiles of upregulated genes in HCC tissues were assessed by Gene Ontology (GO) analysis. Finally, using DNA methylation data of TCGA database, we selected genes whose promoter DNA methylation levels were inversely correlated with gene expression. RESULTS We found 115 genes which were significantly up- or downregulated in HCC tissues and were associated with poor prognosis and cancer relevance. The upregulated genes were significantly enriched in cell division, cell cycle, and cell proliferation. Among the upregulated genes in HCC, we identified hypomethylation of CpGis around promoters of FANCB, KIF15, KIF4A, ERCC6L, and UBE2C. In addition, TCGA data showed that the tumor suppressor gene P16 is unexpectedly overexpressed in many types of cancers. CONCLUSIONS We identified five candidate genes whose expressions were regulated by DNA methylation of promoter CpGi and associate with cancer cases and poor prognosis in HCC. Modification of site-specific DNA methylation of these genes enables a different approach for HCC treatment with higher selectivity and lower adverse effects.
Collapse
Affiliation(s)
- Junya Matsushita
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan.,Graduate School of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Takehiro Suzuki
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan
| | - Kazuyuki Okamura
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan
| | - Gaku Ichihara
- Graduate School of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Keiko Nohara
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan.
| |
Collapse
|
30
|
Gallego-Bartolomé J. DNA methylation in plants: mechanisms and tools for targeted manipulation. New Phytol 2020; 227:38-44. [PMID: 32159848 DOI: 10.1111/nph.16529] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/19/2020] [Indexed: 05/23/2023]
Abstract
DNA methylation is an epigenetic mark that regulates multiple processes, such as gene expression and genome stability. Mutants and pharmacological treatments have been instrumental in the study of this mark in plants, although their genome-wide effect complicates the direct association between changes in methylation and a particular phenotype. A variety of tools that allow locus-specific manipulation of DNA methylation can be used to assess its direct role in specific processes, as well as to create novel epialleles. Recently, new tools that recruit the methylation machinery directly to target loci through programmable DNA-binding proteins have expanded the tool kit available to researchers. This review provides an overview of DNA methylation in plants and discusses the tools that have recently been developed for its manipulation.
Collapse
Affiliation(s)
- Javier Gallego-Bartolomé
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universidad Politécnica de Valencia, 46011, Valencia, Spain
| |
Collapse
|
31
|
Abstract
Epigenetic editing refers to the locus-specific targeting of epigenetic enzymes to rewrite the local epigenetic landscape of an endogenous genomic site, often with the aim of transcriptional reprogramming. Implementing clustered regularly interspaced short palindromic repeat-dCas9 greatly accelerated the advancement of epigenetic editing, yielding preclinical therapeutic successes using a variety of epigenetic enzymes. Here, we review the current applications of these epigenetic editing tools in mammals and shed light on biochemical improvements that facilitate versatile applications.
Collapse
Affiliation(s)
- Rutger A F Gjaltema
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| |
Collapse
|
32
|
Gjaltema RAF, Goubert D, Huisman C, del Pilar García Tobilla C, Koncz M, Jellema PG, Wu D, Brouwer U, Kiss A, Verschure PJ, Bank RA, Rots MG. KRAB-Induced Heterochromatin Effectively Silences PLOD2 Gene Expression in Somatic Cells and is Resilient to TGFβ1 Activation. Int J Mol Sci 2020; 21:ijms21103634. [PMID: 32455614 PMCID: PMC7279273 DOI: 10.3390/ijms21103634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022] Open
Abstract
Epigenetic editing, an emerging technique used for the modulation of gene expression in mammalian cells, is a promising strategy to correct disease-related gene expression. Although epigenetic reprogramming results in sustained transcriptional modulation in several in vivo models, further studies are needed to develop this approach into a straightforward technology for effective and specific interventions. Important goals of current research efforts are understanding the context-dependency of successful epigenetic editing and finding the most effective epigenetic effector(s) for specific tasks. Here we tested whether the fibrosis- and cancer-associated PLOD2 gene can be repressed by the DNA methyltransferase M.SssI, or by the non-catalytic Krüppel associated box (KRAB) repressor directed to the PLOD2 promoter via zinc finger- or CRISPR-dCas9-mediated targeting. M.SssI fusions induced de novo DNA methylation, changed histone modifications in a context-dependent manner, and led to 50%–70% reduction in PLOD2 expression in fibrotic fibroblasts and in MDA-MB-231 cancer cells. Targeting KRAB to PLOD2 resulted in the deposition of repressive histone modifications without DNA methylation and in almost complete PLOD2 silencing. Interestingly, both long-term TGFβ1-induced, as well as unstimulated PLOD2 expression, was completely repressed by KRAB, while M.SssI only prevented the TGFβ1-induced PLOD2 expression. Targeting transiently expressed dCas9-KRAB resulted in sustained PLOD2 repression in HEK293T and MCF-7 cells. Together, these findings point to KRAB outperforming DNA methylation as a small potent targeting epigenetic effector for silencing TGFβ1-induced and uninduced PLOD2 expression.
Collapse
Affiliation(s)
- Rutger A. F. Gjaltema
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
- MATRIX Research Group, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Désirée Goubert
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
| | - Christian Huisman
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
| | - Consuelo del Pilar García Tobilla
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
| | - Mihály Koncz
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (M.K.); (A.K.)
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Pytrick G. Jellema
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
- MATRIX Research Group, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Dandan Wu
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
| | - Uilke Brouwer
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
- MATRIX Research Group, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Antal Kiss
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (M.K.); (A.K.)
| | - Pernette J. Verschure
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands;
| | - Ruud A. Bank
- MATRIX Research Group, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Marianne G. Rots
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
- Correspondence: ; Tel.: +31-50-3610153
| |
Collapse
|
33
|
Beiter T, Nieß AM, Moser D. Transcriptional memory in skeletal muscle. Don't forget (to) exercise. J Cell Physiol 2020; 235:5476-5489. [PMID: 31967338 DOI: 10.1002/jcp.29535] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022]
Abstract
Transcriptional memory describes an ancient and highly conserved form of cellular learning that enables cells to benefit from recent experience by retaining a mitotically inheritable but reversible memory of the initial transcriptional response when encountering an environmental or physiological stimulus. Herein, we will review recent progress made in the understanding of how cells can make use of diverse constituents of the epigenetic toolbox to retain a transcriptional memory of past states and perturbations. Specifically, we will outline how these mechanisms will help to improve our understanding of skeletal muscle plasticity in health and disease. We describe the epigenetic road map that allows skeletal muscle fibers to navigate through training-induced adaptation processes, and how epigenetic memory marks can preserve an autobiographical history of lifestyle behavior changes, pathological challenges, and aging. We will further consider some key findings in the field of exercise epigenomics to emphasize major challenges when interpreting dynamic changes in the chromatin landscape in response to acute exercise and training.
Collapse
Affiliation(s)
- Thomas Beiter
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Andreas M Nieß
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Dirk Moser
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| |
Collapse
|
34
|
Hofacker D, Broche J, Laistner L, Adam S, Bashtrykov P, Jeltsch A. Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects. Int J Mol Sci 2020; 21:ijms21020502. [PMID: 31941101 PMCID: PMC7013458 DOI: 10.3390/ijms21020502] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/22/2022] Open
Abstract
Epigenome editing is a promising technology, potentially allowing the stable reprogramming of gene expression profiles without alteration of the DNA sequence. Targeted DNA methylation has been successfully documented by many groups for silencing selected genes, but recent publications have raised concerns regarding its specificity. In the current work, we developed new EpiEditors for programmable DNA methylation in cells with a high efficiency and improved specificity. First, we demonstrated that the catalytically deactivated Cas9 protein (dCas9)-SunTag scaffold, which has been used earlier for signal amplification, can be combined with the DNMT3A-DNMT3L single-chain effector domain, allowing for a strong methylation at the target genomic locus. We demonstrated that off-target activity of this system is mainly due to untargeted freely diffusing DNMT3A-DNMT3L subunits. Therefore, we generated several DNMT3A-DNMT3L variants containing mutations in the DNMT3A part, which reduced their endogenous DNA binding. We analyzed the genome-wide DNA methylation of selected variants and confirmed a striking reduction of untargeted methylation, most pronounced for the R887E mutant. For all potential applications of targeted DNA methylation, the efficiency and specificity of the treatment are the key factors. By developing highly active targeted methylation systems with strongly improved specificity, our work contributes to future applications of this approach.
Collapse
Affiliation(s)
| | | | | | | | - Pavel Bashtrykov
- Correspondence: or (P.B.); or (A.J.); Tel.: +49-711-685-64363 (P.B.); +49-711-685-64390 (A.J.); Fax: +49-711-685-64392 (P.B. & A.J.)
| | - Albert Jeltsch
- Correspondence: or (P.B.); or (A.J.); Tel.: +49-711-685-64363 (P.B.); +49-711-685-64390 (A.J.); Fax: +49-711-685-64392 (P.B. & A.J.)
| |
Collapse
|
35
|
Abstract
Gene therapy is currently considered as the optimal treatment for inborn errors of metabolism (IEMs), as it aims to permanently compensate for the primary genetic defect. However, emerging gene editing approaches such as CRISPR-Cas9, in which the DNA of the host organism is edited at a precise location, may have outperforming therapeutic potential. Gene editing strategies aim to correct the actual genetic mutation, while circumventing issues associated with conventional compensation gene therapy. Such strategies can also be repurposed to normalize gene expression changes that occur secondary to the genetic defect. Moreover, besides the genetic causes of IEMs, it is increasingly recognized that their clinical phenotypes are associated with epigenetic changes. Because epigenetic alterations are principally reversible, this may offer new opportunities for treatment of IEM patients. Here, we present an overview of the promises of epigenetics in eventually treating IEMs. We discuss the concepts of gene and epigenetic editing, and the advantages and disadvantages of current and upcoming gene-based therapies for treatment of IEMs.
Collapse
Affiliation(s)
- Martijn G. S. Rutten
- Department of PediatricsUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Marianne G. Rots
- Department of Pathology and Medical BiologyUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Maaike H. Oosterveer
- Department of PediatricsUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| |
Collapse
|
36
|
Sandoval JE, Reich NO. The R882H substitution in the human de novo DNA methyltransferase DNMT3A disrupts allosteric regulation by the tumor supressor p53. J Biol Chem 2019; 294:18207-18219. [PMID: 31640986 DOI: 10.1074/jbc.ra119.010827] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/18/2019] [Indexed: 12/14/2022] Open
Abstract
A myriad of protein partners modulate the activity of the human DNA methyltransferase 3A (DNMT3A), whose interactions with these other proteins are frequently altered during oncogenesis. We show here that the tumor suppressor p53 decreases DNMT3A activity by forming a heterotetramer complex with DNMT3A. Mutational and modeling experiments suggested that p53 interacts with the same region in DNMT3A as does the structurally characterized DNMT3L. We observed that the p53-mediated repression of DNMT3A activity is blocked by amino acid substitutions within this interface, but surprisingly, also by a distal DNMT3A residue, R882H. DNMT3A R882H occurs frequently in various cancers, including acute myeloid leukemia, and our results suggest that the effects of R882H and other DNMT3A mutations may go beyond changes in DNMT3A methylation activity. To further understand the dynamics of how protein-protein interactions modulate DNMT3A activity, we determined that p53 has a greater affinity for DNMT3A than for DNMT3L and that p53 readily displaces DNMT3L from the DNMT3A:DNMT3L heterotetramer. Interestingly, this occurred even when the preformed DNMT3A:DNMT3L complex was actively methylating DNA. The frequently identified p53 substitutions (R248W and R273H), whereas able to regulate DNMT3A function when forming the DNMT3A:p53 heterotetramer, no longer displaced DNMT3L from the DNMT3A:DNMT3L heterotetramer. The results of our work highlight the complex interplay between DNMT3A, p53, and DNMT3L and how these interactions are further modulated by clinically derived mutations in each of the interacting partners.
Collapse
Affiliation(s)
- Jonathan E Sandoval
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106-9510
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510.
| |
Collapse
|
37
|
Vignaux PA, Bregio C, Hathaway NA. Contribution of promoter DNA sequence to heterochromatin formation velocity and memory of gene repression in mouse embryo fibroblasts. PLoS One 2019; 14:e0217699. [PMID: 31269077 DOI: 10.1371/journal.pone.0217699] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 05/16/2019] [Indexed: 01/01/2023] Open
Abstract
Durable gene silencing through the formation of compact heterochromatin domains plays a critical role during mammalian development in establishing defined tissues capable of retaining cellular identity. Hallmarks of heterochromatin gene repression are the binding of heterochromatin protein 1 (HP1), trimethylation of lysine 9 on histone H3 (H3K9me3) and the methylation of cytosine residues of DNA. HP1 binds directly to the H3K9me3 histone modification, and while DNA methyltransferases have been found in complex with histone methyltransferases and HP1, there remains much to be known about the relationship between DNA sequence and HP1 in differentiated mammalian cells. To further explore this interplay in a controlled system, we designed a system to test the effect of promoter CpG content on the formation kinetics and memory of an HP1-mediated heterochromatin domain in mouse embryo fibroblasts (MEF)s. To do this, we have constructed a side-by-side comparison of wild-type (CpGFull) and CpG-depleted (CpGDep) promoter-driven reporter constructs in the context of the Chromatin in vivo Assay (CiA), which uses chemically-induced proximity (CIP) to tether the chromoshadow domain of HP1α (csHP1α) to a fluorescent reporter gene in a reversible, chemically-dependent manner. By comparing the response of CpGFull and CpGDep reporter constructs, we discovered that the heterochromatin formation by recruitment of csHP1α is unaffected by the underlying CpG dinucleotide content of the promoter, as measured by the velocity of gene silencing or enrichment of H3K9me3 at the silenced gene. However, recovery from long-term silencing is measurably faster in the CpG-depleted reporter lines. These data provide evidence that the stability of the HP1 heterochromatin domain is reliant on the underlying DNA sequence. Moreover, these cell lines represent a new modular system with which to study the effect of the underlying DNA sequences on the efficacy of epigenetic modifiers.
Collapse
|
38
|
Le Berre G, Hossard V, Riou JF, Guieysse-Peugeot AL. Repression of TERRA Expression by Subtelomeric DNA Methylation Is Dependent on NRF1 Binding. Int J Mol Sci 2019; 20:E2791. [PMID: 31181625 DOI: 10.3390/ijms20112791] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 05/29/2019] [Accepted: 06/04/2019] [Indexed: 12/25/2022] Open
Abstract
Chromosome ends are transcribed into long noncoding telomeric repeat-containing RNA (TERRA) from subtelomeric promoters. A class of TERRA promoters are associated with CpG islands embedded in repetitive DNA tracts. Cytosines in these subtelomeric CpG islands are frequently methylated in telomerase-positive cancer cells, and demethylation induced by depletion of DNA methyltransferases is associated with increased TERRA levels. However, the direct evidence and the underlying mechanism regulating TERRA expression through subtelomeric CpG islands methylation are still to establish. To analyze TERRA regulation by subtelomeric DNA methylation in human cell line (HeLa), we used an epigenetic engineering tool based on CRISPR-dCas9 (clustered regularly interspaced short palindromic repeats - dead CRISPR associated protein 9) associated with TET1 (ten-eleven 1 hydroxylase) to specifically demethylate subtelomeric CpG islands. This targeted demethylation caused an up-regulation of TERRA, and the enhanced TERRA production depended on the methyl-sensitive transcription factor NRF1 (nuclear respiratory factor 1). Since AMPK (AMP-activated protein kinase) is a well-known activator of NRF1, we treated cells with an AMPK inhibitor (compound C). Surprisingly, compound C treatment increased TERRA levels but did not inhibit AMPK activity in these experimental conditions. Altogether, our results provide new insight in the fine-tuning of TERRA at specific subtelomeric promoters and could allow identifying new regulators of TERRA.
Collapse
|
39
|
Sandoval JE, Huang YH, Muise A, Goodell MA, Reich NO. Mutations in the DNMT3A DNA methyltransferase in acute myeloid leukemia patients cause both loss and gain of function and differential regulation by protein partners. J Biol Chem 2019; 294:4898-4910. [PMID: 30705090 DOI: 10.1074/jbc.ra118.006795] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/24/2019] [Indexed: 01/08/2023] Open
Abstract
Eukaryotic DNA methylation prevents genomic instability by regulating the expression of oncogenes and tumor-suppressor genes. The negative effects of dysregulated DNA methylation are highlighted by a strong correlation between mutations in the de novo DNA methyltransferase gene DNA methyltransferase 3α (DNMT3A) and poor prognoses among acute myeloid leukemia (AML) patients. We show here that clinically observed DNMT3A mutations dramatically alter enzymatic activity, including mutations that lead to 6-fold hypermethylation and 3-fold hypomethylation of the human cyclin-dependent kinase inhibitor 2B (CDKN2B or p15) gene promoter. Our results provide insights into the clinically observed heterogeneity of p15 methylation in AML. Cytogenetically normal AML (CN-AML) constitutes 40-50% of all AML cases and is the most epigenetically diverse AML subtype with pronounced changes in non-CpG DNA methylation. We identified a subset of DNMT3A mutations that enhance the enzyme's ability to perform non-CpG methylation by 2-8-fold. Many of these mutations mapped to DNMT3A regions known to interact with proteins that themselves contribute to AML, such as thymine DNA glycosylase (TDG). Using functional mapping of TDG-DNMT3A interactions, we provide evidence that TDG and DNMT3-like (DNMT3L) bind distinct regions of DNMT3A. Furthermore, DNMT3A mutations caused diverse changes in the ability of TDG and DNMT3L to affect DNMT3A function. Cell-based studies of one of these DNMT3A mutations (S714C) replicated the enzymatic studies and revealed that it causes dramatic losses of genome-wide methylation. In summary, mutations in DNMT3A lead to diverse levels of activity, interactions with epigenetic machinery components and cellular changes.
Collapse
Affiliation(s)
- Jonathan E Sandoval
- From the Departments of Chemistry and Biochemistry and.,Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106-9510 and
| | - Yung-Hsin Huang
- the Program in Developmental Biology.,Stem Cells and Regenerative Medicine Center.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030
| | - Abigail Muise
- Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106-9510 and
| | - Margaret A Goodell
- the Program in Developmental Biology.,Stem Cells and Regenerative Medicine Center.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030
| | | |
Collapse
|
40
|
Yao Y. Genome editing: from tools to biological insights. Genome Biol 2018; 19:186. [PMID: 30400928 PMCID: PMC6219208 DOI: 10.1186/s13059-018-1570-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Yixin Yao
- Genome Biology, BMC, Shanghai, 200040, China.
| |
Collapse
|