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Shen D, Guo H, Yu P, Li A, Shan S, Chen X, Wu W, Tong X, Li H, Mei S. An ultra-sensitive CRISPR-Cas12a and aptamer-based biosensor utilizing Entropy-driven catalytic DNA networks for precise detection of DNA Methyltransferase 1. Talanta 2024; 276:126267. [PMID: 38762976 DOI: 10.1016/j.talanta.2024.126267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/03/2024] [Accepted: 05/14/2024] [Indexed: 05/21/2024]
Abstract
DNA Methyltransferase 1 (DNMT1) serves as a crucial biomarker associated with various diseases and is essential for evaluating DNA methylation levels, diagnosing diseases, and evaluating prognosis. As a result, a convenient, quantitative, and sensitive assay for detecting DNMT1 is in high demand. However, current techniques for DNMT1 detection struggle to balance accuracy, low cost, and high sensitivity, limiting their clinical usefulness. To address this challenge, we have developed a DNMT1 detection method (CAED), which combines aptamer-specific recognition with a highly programmable Entropy-driven catalysis DNA network and is further integrated with the CRISPR-Cas12a system. This innovative approach achieves a detection limit as low as 90.9 fmol/L. To demonstrate the clinical applicability and significance of our CAED method, we successfully measured DNMT1 levels in 10 plasma samples 10 cervical tissue samples. These results underscore the potential of our method as an accurate, affordable, and ultra-sensitive tool for evaluating DNMT1 levels. This innovative method offers a potent means for assessing DNMT1 levels and significantly advances disease diagnosis and health risk prediction. Plus, it establishes an innovative design framework for CRISPR-Cas12a-based biosensors, tailored explicitly for enzyme content quantification.
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Affiliation(s)
- Dongsheng Shen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China
| | - Hong Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China
| | - Ping Yu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China
| | - Ao Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China
| | - Shu Shan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China
| | - Xixi Chen
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Wenjun Wu
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Xiaowen Tong
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China
| | - Huaifang Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China.
| | - Shuaikang Mei
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China.
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Gonzalez-Avalos E, Onodera A, Samaniego-Castruita D, Rao A, Ay F. Predicting gene expression state and prioritizing putative enhancers using 5hmC signal. Genome Biol 2024; 25:142. [PMID: 38825692 PMCID: PMC11145787 DOI: 10.1186/s13059-024-03273-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/11/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND Like its parent base 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) is a direct epigenetic modification of cytosines in the context of CpG dinucleotides. 5hmC is the most abundant oxidized form of 5mC, generated through the action of TET dioxygenases at gene bodies of actively-transcribed genes and at active or lineage-specific enhancers. Although such enrichments are reported for 5hmC, to date, predictive models of gene expression state or putative regulatory regions for genes using 5hmC have not been developed. RESULTS Here, by using only 5hmC enrichment in genic regions and their vicinity, we develop neural network models that predict gene expression state across 49 cell types. We show that our deep neural network models distinguish high vs low expression state utilizing only 5hmC levels and these predictive models generalize to unseen cell types. Further, in order to leverage 5hmC signal in distal enhancers for expression prediction, we employ an Activity-by-Contact model and also develop a graph convolutional neural network model with both utilizing Hi-C data and 5hmC enrichment to prioritize enhancer-promoter links. These approaches identify known and novel putative enhancers for key genes in multiple immune cell subsets. CONCLUSIONS Our work highlights the importance of 5hmC in gene regulation through proximal and distal mechanisms and provides a framework to link it to genome function. With the recent advances in 6-letter DNA sequencing by short and long-read techniques, profiling of 5mC and 5hmC may be done routinely in the near future, hence, providing a broad range of applications for the methods developed here.
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Affiliation(s)
- Edahi Gonzalez-Avalos
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Atsushi Onodera
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Daniela Samaniego-Castruita
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Biological Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Anjana Rao
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Ferhat Ay
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
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Cheng JC, Swarup N, Morselli M, Huang WL, Aziz M, Caggiano C, Kordi M, Patel AA, Chia D, Kim Y, Li F, Wei F, Zaitlen N, Krysan K, Dubinett S, Pellegrini M, Wong DTW. Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA. Nucleic Acids Res 2024:gkae276. [PMID: 38797520 DOI: 10.1093/nar/gkae276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 05/29/2024] Open
Abstract
Whole-genome bisulfite sequencing (BS-Seq) measures cytosine methylation changes at single-base resolution and can be used to profile cell-free DNA (cfDNA). In plasma, ultrashort single-stranded cfDNA (uscfDNA, ∼50 nt) has been identified together with 167 bp double-stranded mononucleosomal cell-free DNA (mncfDNA). However, the methylation profile of uscfDNA has not been described. Conventional BS-Seq workflows may not be helpful because bisulfite conversion degrades larger DNA into smaller fragments, leading to erroneous categorization as uscfDNA. We describe the '5mCAdpBS-Seq' workflow in which pre-methylated 5mC (5-methylcytosine) single-stranded adapters are ligated to heat-denatured cfDNA before bisulfite conversion. This method retains only DNA fragments that are unaltered by bisulfite treatment, resulting in less biased uscfDNA methylation analysis. Using 5mCAdpBS-Seq, uscfDNA had lower levels of DNA methylation (∼15%) compared to mncfDNA and was enriched in promoters and CpG islands. Hypomethylated uscfDNA fragments were enriched in upstream transcription start sites (TSSs), and the intensity of enrichment was correlated with expressed genes of hemopoietic cells. Using tissue-of-origin deconvolution, we inferred that uscfDNA is derived primarily from eosinophils, neutrophils, and monocytes. As proof-of-principle, we show that characteristics of the methylation profile of uscfDNA can distinguish non-small cell lung carcinoma from non-cancer samples. The 5mCAdpBS-Seq workflow is recommended for any cfDNA methylation-based investigations.
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Affiliation(s)
- Jordan C Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marco Morselli
- Department of Molecular, Cell, and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Wei-Lun Huang
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan, Taiwan
| | - Mohammad Aziz
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christa Caggiano
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Misagh Kordi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - David Chia
- Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yong Kim
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Feng Li
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fang Wei
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Noah Zaitlen
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Kostyantyn Krysan
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Steve Dubinett
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David T W Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
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4
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Pinello N, Song R, Lee Q, Calonne E, Duan KL, Wong E, Tieng J, Mehravar M, Rong B, Lan F, Roediger B, Ma CJ, Yuan BF, Rasko JEJ, Larance M, Ye D, Fuks F, Wong JJL. Dynamic changes in RNA m 6A and 5 hmC influence gene expression programs during macrophage differentiation and polarisation. Cell Mol Life Sci 2024; 81:229. [PMID: 38780787 PMCID: PMC11116364 DOI: 10.1007/s00018-024-05261-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/27/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024]
Abstract
RNA modifications are essential for the establishment of cellular identity. Although increasing evidence indicates that RNA modifications regulate the innate immune response, their role in monocyte-to-macrophage differentiation and polarisation is unclear. While m6A has been widely studied, other RNA modifications, including 5 hmC, remain poorly characterised. We profiled m6A and 5 hmC epitranscriptomes, transcriptomes, translatomes and proteomes of monocytes and macrophages at rest and pro- and anti-inflammatory states. Transcriptome-wide mapping of m6A and 5 hmC reveals enrichment of m6A and/or 5 hmC on specific categories of transcripts essential for macrophage differentiation. Our analyses indicate that m6A and 5 hmC modifications are present in transcripts with critical functions in pro- and anti-inflammatory macrophages. Notably, we also discover the co-occurrence of m6A and 5 hmC on alternatively-spliced isoforms and/or opposing ends of the untranslated regions (UTR) of mRNAs with key roles in macrophage biology. In specific examples, RNA 5 hmC controls the decay of transcripts independently of m6A. This study provides (i) a comprehensive dataset to interrogate the role of RNA modifications in a plastic system (ii) a resource for exploring different layers of gene expression regulation in the context of human monocyte-to-macrophage differentiation and polarisation, (iii) new insights into RNA modifications as central regulators of effector cells in innate immunity.
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Affiliation(s)
- Natalia Pinello
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, 11400, Montevideo, Uruguay
| | - Renhua Song
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Quintin Lee
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Kun-Long Duan
- The Molecular and Cell Biology Lab, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Emilie Wong
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Jessica Tieng
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Majid Mehravar
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Bowen Rong
- Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Fei Lan
- Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Ben Roediger
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Skin Inflammation Group, Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Autoimmunity, Transplantation and Inflammation (ATI) Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Cheng-Jie Ma
- School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Bi-Feng Yuan
- School of Public Health, Wuhan University, Wuhan, 430071, China
| | - John E J Rasko
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Gene and Stem Cell Therapy Program, Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, NSW, Australia
| | - Mark Larance
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Charles Perkins Centre, School of Medical Sciences, University of Sydney, Sydney, 2006, Australia
| | - Dan Ye
- The Molecular and Cell Biology Lab, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Justin J-L Wong
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.
- Charles Perkins Centre, School of Medical Sciences, University of Sydney, Sydney, 2006, Australia.
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5
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Dachani S, Kaleem M, Mujtaba MA, Mahajan N, Ali SA, Almutairy AF, Mahmood D, Anwer MK, Ali MD, Kumar S. A Comprehensive Review of Various Therapeutic Strategies for the Management of Skin Cancer. ACS OMEGA 2024; 9:10030-10048. [PMID: 38463249 PMCID: PMC10918819 DOI: 10.1021/acsomega.3c09780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 03/12/2024]
Abstract
Skin cancer (SC) poses a global threat to the healthcare system and is expected to increase significantly over the next two decades if not diagnosed at an early stage. Early diagnosis is crucial for successful treatment, as the disease becomes more challenging to cure as it progresses. However, identifying new drugs, achieving clinical success, and overcoming drug resistance remain significant challenges. To overcome these obstacles and provide effective treatment, it is crucial to understand the causes of skin cancer, how cells grow and divide, factors that affect cell growth, and how drug resistance occurs. In this review, we have explained various therapeutic approaches for SC treatment via ligands, targeted photosensitizers, natural and synthetic drugs for the treatment of SC, an epigenetic approach for management of melanoma, photodynamic therapy, and targeted therapy for BRAF-mutated melanoma. This article also provides a detailed summary of the various natural drugs that are effective in managing melanoma and reducing the occurrence of skin cancer at early stages and focuses on the current status and future prospects of various therapies available for the management of skin cancer.
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Affiliation(s)
- Sudharshan
Reddy Dachani
- Department
of Pharmacy Practice, College of Pharmacy, Shaqra University, Al-Dawadmi Campus, Al-Dawadmi 11961, Saudi Arabia
| | - Mohammed Kaleem
- Department
of Pharmacology, Babasaheb Balpande College of Pharmacy, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440037, Maharashtra, India
| | - Md. Ali Mujtaba
- Department
of Pharmaceutics, Faculty of Pharmacy, Northern
Border University, Arar 91911, Saudi Arabia
| | - Nilesh Mahajan
- Department
of Pharmaceutics, Dabasaheb Balpande College of Pharmacy, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440037, Maharashtra, India
| | - Sayyed A. Ali
- Department
of Pharmaceutics, Dabasaheb Balpande College of Pharmacy, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440037, Maharashtra, India
| | - Ali F Almutairy
- Department
of Pharmacology and Toxicology, College of Pharmacy, Qassim University, Buraydah 51452, Saudi Arabia
| | - Danish Mahmood
- Department
of Pharmacology and Toxicology, College of Pharmacy, Qassim University, Buraydah 51452, Saudi Arabia
| | - Md. Khalid Anwer
- Department
of Pharmaceutics, College of Pharmacy, Prince
Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Mohammad Daud Ali
- Department
of Pharmacy, Mohammed Al-Mana College for
Medical Sciences, Abdulrazaq Bin Hammam Street, Al Safa 34222, Dammam, Saudi Arabia
| | - Sanjay Kumar
- Department
of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Uttar Pradesh 201306, India
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6
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Tigu AB, Bancos A. The Role of Epigenetic Modifier Mutations in Peripheral T-Cell Lymphomas. Curr Issues Mol Biol 2023; 45:8974-8988. [PMID: 37998740 PMCID: PMC10670124 DOI: 10.3390/cimb45110563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
Peripheral T-cell lymphomas (PTCLs) are a group of diseases with a low incidence, high degree of heterogeneity, and a dismal prognosis in most cases. Because of the low incidence of these diseases, there have been few therapeutic novelties developed over time. Nevertheless, this fact is changing presently as epigenetic modifiers have been shown to be recurrently mutated in some types of PTCLs, especially in the cases of PTCLs not otherwise specified (PTCL-NOS), T follicular helper (TFH), and angioimmunoblastic T-cell lymphoma (AITL). These have brought about more insight into PTCL biology, especially in the case of PTCLs arising from TFH lymphocytes. From a biological perspective, it has been observed that ten-eleven translocators (TET2) mutated T lymphocytes tend to polarize to TFH, while Tregs lose their inhibitory properties. IDH2 R172 was shown to have inhibitory effects on TET2, mimicking the effects of TET2 mutations, as well as having effects on histone methylation. DNA methyltransferase 3A (DNMT3A) loss-of-function, although it was shown to have opposite effects to TET2 from an inflammatory perspective, was also shown to increase the number of T lymphocyte progenitors. Aside from bringing about more knowledge of PTCL biology, these mutations were shown to increase the sensitivity of PTCLs to certain epigenetic therapies, like hypomethylating agents (HMAs) and histone deacetylase inhibitors (HDACis). Thus, to answer the question from the title of this review: We found the Achilles heel, but only for one of the Achilles.
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Affiliation(s)
- Adrian-Bogdan Tigu
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania;
- Academy of Romanian Scientists, Ilfov 3, 050044 Bucharest, Romania
| | - Anamaria Bancos
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania;
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
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Taghian Dinani H, Naderi N, Tavalaee M, Rabiee F, Nasr-Esfahani MH. Aberrant Expression of TET2 Accounts for DNA Hypomethylation in Varicocele. CELL JOURNAL 2023; 25:706-716. [PMID: 37865879 PMCID: PMC10591265 DOI: 10.22074/cellj.2023.2000170.1284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 10/23/2023]
Abstract
OBJECTIVE Epigenetic modifications such as DNA methylation play a key role in male infertility etiology. This study aimed to explore the global DNA methylation status in testicular spermatogenic cells of varicocele-induced rats and consider their semen quality, with a focus on key epigenetic marks, namely 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC), as well as the mRNA and proteins of ten-eleven translocation (TET) methylcytosine dioxygenases 1-3. MATERIALS AND METHODS In this experimental study, 24 mature male Wistar rats (8 in each group) were assigned amongst the control, sham, and varicocele groups. Sperm quality was assessed, and DNA methylation patterns of testicular spermatogenic cells were investigated using reverse transcription-polymerase chain reaction (RT-PCR), western blot, and immunofluorescence techniques. RESULTS Sperm parameters, chromatin and DNA integrity were significantly lower, and sperm lipid peroxidation significantly increased in varicocele-induced rats in comparison with control rats. During spermatogenesis in rat testis, 5-mC and 5-hmC epigenetic marks, and TET1-3 mRNA and proteins were expressed. In contrast to the 5-mC fluorescent signal which was presented in all testicular cells, the 5-hmC fluorescent signal was presented exclusively in spermatogonia and a few spermatids. In varicocele-induced rats, the 5-mC signal decreased in all cells within the tubules, whereas a strong signal of 5-hmC was detected in seminiferous tubules compared to the control group. As well, the levels of TET2 mRNA and protein expression were significantly upregulated in varicocele-induced rats in comparison with the control group. Also, our results showed that the varicocele-induced animals exhibited strong fluorescent signals of TET1-3 in testicular cells, whereas weak fluorescent signals were identified in the seminiferous tubules of the control animals. CONCLUSION Consequently, we showed TET2 upregulation and the 5-hmC gain at testicular levels are associated with varicocele and sperm quality decline, and therefore they can be exploited as potential biomarkers of spermatogenesis.
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Affiliation(s)
- Hengameh Taghian Dinani
- ACECR Institute of Higher Education, Isfahan Branch, Isfahan, Iran
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Nushin Naderi
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Marziyeh Tavalaee
- ACECR Institute of Higher Education, Isfahan Branch, Isfahan, Iran
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Farzaneh Rabiee
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- ACECR Institute of Higher Education, Isfahan Branch, Isfahan, Iran
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
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8
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Zhao M, Zou G, Tang J, Guo J, Wang F, Chen Z. Probe-labeled electrochemical approach for highly selective detection of 5-carboxycytosine in DNA. Anal Chim Acta 2023; 1273:341521. [PMID: 37423653 DOI: 10.1016/j.aca.2023.341521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023]
Abstract
5-carboxycytosine (5caC) plays a critical role as an intermediate form in DNA methylation and demethylation processes. Its distribution and quantity significantly influence the dynamic equilibrium of these processes, thereby impacting the normal physiological activities of organisms. However, the analysis of 5caC presents a significant challenge due to its low abundance in the genome, making it almost undetectable in most tissues. In response to this challenge, we propose a selective method for 5caC detection using differential pulse voltammetry (DPV) at glassy carbon electrode (GCE), hinging on probe labeling. The probe molecule Biotin LC-Hydrazide was introduced into the target base and the labeled DNA was immobilized onto the electrode surface with the help of T4 polynucleotide kinase (T4 PNK). Leveraging the precise and efficient recognition of streptavidin and biotin, streptavidin-horseradish peroxidase (SA-HRP) on the surface of the electrode catalyzed a redox reaction involving hydroquinone and hydrogen peroxide, resulting in an amplified current signal. This procedure allowed us to quantitatively detect 5caC based on variations in current signals. This method demonstrated good linearity ranging from 0.01 to 100 nM with a detection limit as low as 7.9 pM. We have successfully applied it to evaluate the 5caC levels in complex biological samples. The probe labeling contributes to a high selectivity for 5caC detection, while the sulfhydryl modification via T4 PNK efficiently circumvents the limitation of specific sequences. Encouragingly, no reports have been made about electrochemical methods for detecting 5caC in DNA, suggesting that our method offers a promising alternative for 5caC detection in clinical samples.
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Affiliation(s)
- Mei Zhao
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Guangrong Zou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Jing Tang
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Jingyi Guo
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Fang Wang
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China.
| | - Zilin Chen
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China.
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9
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Chen X, Xu H, Shu X, Song CX. Mapping epigenetic modifications by sequencing technologies. Cell Death Differ 2023:10.1038/s41418-023-01213-1. [PMID: 37658169 DOI: 10.1038/s41418-023-01213-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/03/2023] Open
Abstract
The "epigenetics" concept was first described in 1942. Thus far, chemical modifications on histones, DNA, and RNA have emerged as three important building blocks of epigenetic modifications. Many epigenetic modifications have been intensively studied and found to be involved in most essential biological processes as well as human diseases, including cancer. Precisely and quantitatively mapping over 100 [1], 17 [2], and 160 [3] different known types of epigenetic modifications in histone, DNA, and RNA is the key to understanding the role of epigenetic modifications in gene regulation in diverse biological processes. With the rapid development of sequencing technologies, scientists are able to detect specific epigenetic modifications with various quantitative, high-resolution, whole-genome/transcriptome approaches. Here, we summarize recent advances in epigenetic modification sequencing technologies, focusing on major histone, DNA, and RNA modifications in mammalian cells.
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Affiliation(s)
- Xiufei Chen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Haiqi Xu
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Xiao Shu
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
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10
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Wang T, Fowler JM, Liu L, Loo CE, Luo M, Schutsky EK, Berríos KN, DeNizio JE, Dvorak A, Downey N, Montermoso S, Pingul BY, Nasrallah M, Gosal WS, Wu H, Kohli RM. Direct enzymatic sequencing of 5-methylcytosine at single-base resolution. Nat Chem Biol 2023; 19:1004-1012. [PMID: 37322153 PMCID: PMC10763687 DOI: 10.1038/s41589-023-01318-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 03/17/2023] [Indexed: 06/17/2023]
Abstract
5-methylcytosine (5mC) is the most important DNA modification in mammalian genomes. The ideal method for 5mC localization would be both nondestructive of DNA and direct, without requiring inference based on detection of unmodified cytosines. Here we present direct methylation sequencing (DM-Seq), a bisulfite-free method for profiling 5mC at single-base resolution using nanogram quantities of DNA. DM-Seq employs two key DNA-modifying enzymes: a neomorphic DNA methyltransferase and a DNA deaminase capable of precise discrimination between cytosine modification states. Coupling these activities with deaminase-resistant adapters enables accurate detection of only 5mC via a C-to-T transition in sequencing. By comparison, we uncover a PCR-related underdetection bias with the hybrid enzymatic-chemical TET-assisted pyridine borane sequencing approach. Importantly, we show that DM-Seq, unlike bisulfite sequencing, unmasks prognostically important CpGs in a clinical tumor sample by not confounding 5mC with 5-hydroxymethylcytosine. DM-Seq thus offers an all-enzymatic, nondestructive, faithful and direct method for the reading of 5mC alone.
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Affiliation(s)
- Tong Wang
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Johanna M Fowler
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christian E Loo
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Meiqi Luo
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily K Schutsky
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Kiara N Berríos
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jamie E DeNizio
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ashley Dvorak
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Nick Downey
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Saira Montermoso
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Bianca Y Pingul
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - MacLean Nasrallah
- Department of Pathology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
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11
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Zhao L, Xu H, Liu X, Cheng Y, Xie J. The role of TET2-mediated ROBO4 hypomethylation in the development of diabetic retinopathy. J Transl Med 2023; 21:455. [PMID: 37430272 DOI: 10.1186/s12967-023-04310-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND In diabetic retinopathy, increasing evidence points to a link between the pathogenesis of retinal microangiopathy and the endothelial cell-specific factor roundabout4 (ROBO4). According to earlier research, specificity protein 1 (SP1) enhances the binding to the ROBO4 promoter, increasing Robo4 expression and hastening the progression of diabetic retinopathy. To determine if this is related to aberrant epigenetic modifications of ROBO4, we examined the methylation level of the ROBO4 promoter and the corresponding regulatory mechanism during the course of diabetic retinopathy and explored the effect of this mechanism on retinal vascular leakage and neovascularization. METHODS The methylation level of CpG sites in the ROBO4 promoter was detected in human retinal endothelial cells (HRECs) cultured under hyperglycemic conditions and retinas from streptozotocin-induced diabetic mice. The effects of hyperglycemia on DNA methyltransferase 1, Tet methylcytosine dioxygenase 2 (TET2), 5-methylcytosine, 5-hydroxymethylcytosine, and the binding of TET2 and SP1 to the ROBO4 promoter, as well as the expression of ROBO4, zonula occludens 1 (ZO-1) and occludin were examined. Short hairpin RNA was used to suppress the expression of TET2 or ROBO4 and the structural and functional changes in the retinal microvascular system were assessed. RESULTS In HRECs cultured under hyperglycemic conditions, the ROBO4 promoter methylation level decreased. Hyperglycemia-induced TET2 overexpression caused active demethylation of ROBO4 by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine, which enhanced the binding of SP1 to ROBO4, increased the expression of ROBO4, and decreased the expression of ZO-1 and occludin, leading to the abnormalities in monolayer permeability, migratory ability and angiogenesis of HRECs. The above pathway was also demonstrated in the retinas of diabetic mice, which caused leakage from retinal capillaries and neovascularization. Inhibition of TET2 or ROBO4 expression significantly ameliorated the dysfunction of HRECs and retinal vascular abnormalities. CONCLUSIONS In diabetes, TET2 can regulate the expression of ROBO4 and its downstream proteins by mediating active demethylation of the ROBO4 promoter, which accelerates the development of retinal vasculopathy. These findings suggest that TET2-induced ROBO4 hypomethylation is a potential therapeutic target, and anti- TET2/ROBO4 therapy is anticipated to emerge as a novel strategy for early intervention and delayed progression of diabetic retinopathy.
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Affiliation(s)
- Liangliang Zhao
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Haitao Xu
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Xin Liu
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Yan Cheng
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Jia'nan Xie
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, China.
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12
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Wang H, Liu B, Chen H, Xu P, Xue H, Yuan J. Dynamic changes of DNA methylation induced by benzo(a)pyrene in cancer. Genes Environ 2023; 45:21. [PMID: 37391844 DOI: 10.1186/s41021-023-00278-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/07/2023] [Indexed: 07/02/2023] Open
Abstract
Benzo(a)pyrene (BaP), the earliest and most significant carcinogen among polycyclic aromatic hydrocarbons (PAHs), has been found in foods, tobacco smoke, and automobiles exhaust, etc. Exposure to BaP induced DNA damage directly, or oxidative stress-related damage, resulting in cell apoptosis and carcinogenesis in human respiratory system, digestive system, reproductive system, etc. Moreover, BaP triggered genome-wide epigenetic alterations by methylation, which might cause disturbances in regulation of gene expression, and thereby induced cancer. It has been proved that BaP reduced genome-wide DNA methylation, and activated proto-oncogene by hypomethylation in the promoter region, but silenced tumor suppressor genes by promoter hypermethylation, resulting in cancer initiation and progression. Here we summarized the changes in DNA methylation in BaP exposure, and revealed the methylation of DNA plays a role in cancer development.
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Affiliation(s)
- Huizeng Wang
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, China
| | - Bingchun Liu
- Stem Cell Research Center, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, China
| | - Hong Chen
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, China
| | - Peixin Xu
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, China
| | - Huiting Xue
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, 010010, China.
| | - Jianlong Yuan
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, China.
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13
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Si TE, Li Z, Zhang J, Su S, Liu Y, Chen S, Peng GH, Cao J, Zang W. Epigenetic mechanisms of Müller glial reprogramming mediating retinal regeneration. Front Cell Dev Biol 2023; 11:1157893. [PMID: 37397254 PMCID: PMC10309042 DOI: 10.3389/fcell.2023.1157893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/08/2023] [Indexed: 07/04/2023] Open
Abstract
Retinal degenerative diseases, characterized by retinal neuronal death and severe vision loss, affect millions of people worldwide. One of the most promising treatment methods for retinal degenerative diseases is to reprogram non-neuronal cells into stem or progenitor cells, which then have the potential to re-differentiate to replace the dead neurons, thereby promoting retinal regeneration. Müller glia are the major glial cell type and play an important regulatory role in retinal metabolism and retinal cell regeneration. Müller glia can serve as a source of neurogenic progenitor cells in organisms with the ability to regenerate the nervous system. Current evidence points toward the reprogramming process of Müller glia, involving changes in the expression of pluripotent factors and other key signaling molecules that may be regulated by epigenetic mechanisms. This review summarizes recent knowledge of epigenetic modifications involved in the reprogramming process of Müller glia and the subsequent changes to gene expression and the outcomes. In living organisms, epigenetic mechanisms mainly include DNA methylation, histone modification, and microRNA-mediated miRNA degradation, all of which play a crucial role in the reprogramming process of Müller glia. The information presented in this review will improve the understanding of the mechanisms underlying the Müller glial reprogramming process and provide a research basis for the development of Müller glial reprogramming therapy for retinal degenerative diseases.
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Affiliation(s)
- Tian-En Si
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Zhixiao Li
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Jingjing Zhang
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Songxue Su
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Yupeng Liu
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Shiyue Chen
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Guang-Hua Peng
- Department of Pathophysiology, Basic Medical College, Zhengzhou University, Zhengzhou, China
- Laboratory of Visual Cell Differentiation and Regulation, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Jing Cao
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Weidong Zang
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
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14
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Sergeeva A, Davydova K, Perenkov A, Vedunova M. Mechanisms of human DNA methylation, alteration of methylation patterns in physiological processes and oncology. Gene 2023:147487. [PMID: 37211289 DOI: 10.1016/j.gene.2023.147487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
DNA methylation is one of the epigenetic modifications of the genome, the essence of which is the attachment of a methyl group to nitrogenous bases. In the eukaryote genome, cytosine is methylated in the vast majority of cases. About 98% of cytosines are methylated as part of CpG dinucleotides. They, in turn, form CpG islands, which are clusters of these dinucleotides. Islands located in the regulatory elements of genes are in particular interest. They are assumed to play an important role in the regulation of gene expression in humans. Besides that, cytosine methylation serves the functions of genomic imprinting, transposon suppression, epigenetic memory maintenance, X- chromosome inactivation, and embryonic development. Of particular interest are the enzymatic processes of methylation and demethylation. The methylation process always depends on the work of enzymatic complexes and is very precisely regulated. The methylation process largely depends on the functioning of three groups of enzymes: writers, readers and erasers. Writers include proteins of the DNMT family, readers are proteins containing the MBD, BTB/POZ or SET- and RING-associated domains and erasers are proteins of the TET family. Whereas demethylation can be performed not only by enzymatic complexes, but also passively during DNA replication. Hence, the maintenance of DNA methylation is important. Changes in methylation patterns are observed during embryonic development, aging, and cancers. In both aging and cancer, massive hypomethylation of the genome with local hypermethylation is observed. In this review, we will review the current understanding of the mechanisms of DNA methylation and demethylation in humans, the structure and distribution of CpG islands, the role of methylation in the regulation of gene expression, embryogenesis, aging, and cancer development.
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Affiliation(s)
- A Sergeeva
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - K Davydova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - A Perenkov
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - M Vedunova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
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15
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Onodera A, Kokubo K, Okano M, Onoue M, Kiuchi M, Iwamura C, Iinuma T, Kimura MY, Ebihara N, Hanazawa T, Nakayama T, Hirahara K. Pathogenic helper T cells as the novel therapeutic targets for immune-mediated intractable diseases. Pharmacol Ther 2023; 247:108445. [PMID: 37201737 DOI: 10.1016/j.pharmthera.2023.108445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/20/2023]
Abstract
Allergic diseases arise from a complex interplay between immune system and environmental factors. A link between the pathogenesis of allergic diseases and type 2 immune responses has become evident, with conventional and pathogenic type 2 helper T (Th2) cells involved in both. Recently, there has been a significant development in therapeutic agents for allergic diseases: IL-5 and IL-5 receptor antagonists, Janus kinase (JAK) inhibitors, and sublingual immunotherapy (SLIT). Mepolizumab, an IL-5, and Benralizumab, an IL-5 receptor antagonist, modulate eosinophilic inflammation mediated by IL-5-producing Th2 cells. Delgocitinib shows that JAK-associated signaling is essential for the inflammatory reaction in atopic dermatitis, one of the common allergic diseases. SLIT has a significant effect on allergic rhinitis by reducing pathogenic Th2 cell numbers. More recently, novel molecules that are involved in pathogenic Th2 cell-mediated allergic diseases have been identified. These include calcitonin gene-related peptide (CGRP), reactive oxygen species (ROS) scavenging machinery regulated by the Txnip-Nrf2-Blvrb axis, and myosin light chain 9 (Myl9), which interacts with CD69. This review provides an updated view of the recent research on treatment of allergic diseases and their cause: conventional and pathogenic Th2 cells.
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Affiliation(s)
- Atsushi Onodera
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Institute for Advanced Academic Research, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Kota Kokubo
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Mikiko Okano
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Miki Onoue
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Masahiro Kiuchi
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Chiaki Iwamura
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Tomohisa Iinuma
- Department of Experimental Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Motoko Y Kimura
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Chiba University "Synergy Institute for Futuristic Mucosal Vaccine Research and Development (cSIMVa), Japan Initiative for World-leading Vaccine Research and Development Centers, Japan Agency for Medical Research and Development (AMED), Chiba, Japan
| | - Nobuyuki Ebihara
- Department of Ophthalmology, Juntendo University Urayasu Hospital, Chiba 279-0021, Japan
| | - Toyoyuki Hanazawa
- Department of Experimental Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; AMED-CREST, AMED, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan.
| | - Kiyoshi Hirahara
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Chiba University "Synergy Institute for Futuristic Mucosal Vaccine Research and Development (cSIMVa), Japan Initiative for World-leading Vaccine Research and Development Centers, Japan Agency for Medical Research and Development (AMED), Chiba, Japan.
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16
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Yano N, Fedulov AV. Targeted DNA Demethylation: Vectors, Effectors and Perspectives. Biomedicines 2023; 11:biomedicines11051334. [PMID: 37239005 DOI: 10.3390/biomedicines11051334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Aberrant DNA hypermethylation at regulatory cis-elements of particular genes is seen in a plethora of pathological conditions including cardiovascular, neurological, immunological, gastrointestinal and renal diseases, as well as in cancer, diabetes and others. Thus, approaches for experimental and therapeutic DNA demethylation have a great potential to demonstrate mechanistic importance, and even causality of epigenetic alterations, and may open novel avenues to epigenetic cures. However, existing methods based on DNA methyltransferase inhibitors that elicit genome-wide demethylation are not suitable for treatment of diseases with specific epimutations and provide a limited experimental value. Therefore, gene-specific epigenetic editing is a critical approach for epigenetic re-activation of silenced genes. Site-specific demethylation can be achieved by utilizing sequence-dependent DNA-binding molecules such as zinc finger protein array (ZFA), transcription activator-like effector (TALE) and clustered regularly interspaced short palindromic repeat-associated dead Cas9 (CRISPR/dCas9). Synthetic proteins, where these DNA-binding domains are fused with the DNA demethylases such as ten-eleven translocation (Tet) and thymine DNA glycosylase (TDG) enzymes, successfully induced or enhanced transcriptional responsiveness at targeted loci. However, a number of challenges, including the dependence on transgenesis for delivery of the fusion constructs, remain issues to be solved. In this review, we detail current and potential approaches to gene-specific DNA demethylation as a novel epigenetic editing-based therapeutic strategy.
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Affiliation(s)
- Naohiro Yano
- Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, 593 Eddy Street, Providence, RI 02903, USA
| | - Alexey V Fedulov
- Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, 593 Eddy Street, Providence, RI 02903, USA
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17
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Effendi WI, Nagano T. Epigenetics Approaches toward Precision Medicine for Idiopathic Pulmonary Fibrosis: Focus on DNA Methylation. Biomedicines 2023; 11:biomedicines11041047. [PMID: 37189665 DOI: 10.3390/biomedicines11041047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Genetic information is not transmitted solely by DNA but by the epigenetics process. Epigenetics describes molecular missing link pathways that could bridge the gap between the genetic background and environmental risk factors that contribute to the pathogenesis of pulmonary fibrosis. Specific epigenetic patterns, especially DNA methylation, histone modifications, long non-coding, and microRNA (miRNAs), affect the endophenotypes underlying the development of idiopathic pulmonary fibrosis (IPF). Among all the epigenetic marks, DNA methylation modifications have been the most widely studied in IPF. This review summarizes the current knowledge concerning DNA methylation changes in pulmonary fibrosis and demonstrates a promising novel epigenetics-based precision medicine.
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18
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Castro-Muñoz LJ, Vázquez Ulloa E, Sahlgren C, Lizano M, De La Cruz-Hernández E, Contreras-Paredes A. Modulating epigenetic modifications for cancer therapy (Review). Oncol Rep 2023; 49:59. [PMID: 36799181 PMCID: PMC9942256 DOI: 10.3892/or.2023.8496] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/08/2022] [Indexed: 02/12/2023] Open
Abstract
Cancer is a global public health concern. Alterations in epigenetic processes are among the earliest genomic aberrations occurring during cancer development and are closely related to progression. Unlike genetic mutations, aberrations in epigenetic processes are reversible, which opens the possibility for novel pharmacological treatments. Non‑coding RNAs (ncRNAs) represent an essential epigenetic mechanism, and emerging evidence links ncRNAs to carcinogenesis. Epigenetic drugs (epidrugs) are a group of promising target therapies for cancer treatment acting as coadjuvants to reverse drug resistance in cancer. The present review describes central epigenetic aberrations during malignant transformation and explains how epidrugs target DNA methylation, histone modifications and ncRNAs. Furthermore, clinical trials focused on evaluating the effect of these epidrugs alone or in combination with other anticancer therapies and other ncRNA‑based therapies are discussed. The use of epidrugs promises to be an effective tool for reversing drug resistance in some patients with cancer.
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Affiliation(s)
| | - Elenaé Vázquez Ulloa
- Faculty of Science and Engineering/Cell Biology, University of Turku and Åbo Akademi University, Turku 20500, Finland,Turku Bioscience, University of Turku and Åbo Akademi University, Turku 20500, Finland
| | - Cecilia Sahlgren
- Faculty of Science and Engineering/Cell Biology, University of Turku and Åbo Akademi University, Turku 20500, Finland,Turku Bioscience, University of Turku and Åbo Akademi University, Turku 20500, Finland,Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Marcela Lizano
- Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Ciudad de Mexico 14080, Mexico,Departamento de Medicina Genomica y Toxicologia Ambiental, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Mexico 04510, Mexico
| | - Erick De La Cruz-Hernández
- Laboratory of Research in Metabolic and Infectious Diseases, Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco, Tabasco 86650, Mexico
| | - Adriana Contreras-Paredes
- Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Ciudad de Mexico 14080, Mexico,Correspondence to: Professor Adriana Contreras-Paredes, Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Avenue San Fernando, Col. Sección XVI, Tlalpan, Ciudad de Mexico 14080, Mexico, E-mail:
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19
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Pan-Cancer Landscape of NEIL3 in Tumor Microenvironment: A Promising Predictor for Chemotherapy and Immunotherapy. Cancers (Basel) 2022; 15:cancers15010109. [PMID: 36612106 PMCID: PMC9817722 DOI: 10.3390/cancers15010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
With the aim of enhancing the understanding of NEIL3 in prognosis prediction and therapy administration, we conducted a pan-cancer landscape analysis on NEIL3. The mutation characteristics, survival patterns, and immune features of NEIL3 across cancers were analyzed. Western blotting, qPCR, and immunohistochemistry were conducted to validate the bioinformatics results. The correlation between NEIL3 and chemotherapeutic drugs, as well as immunotherapies, was estimated. NEIL3 was identified as an oncogene with prognostic value in predicting clinical outcomes in multiple cancers. Combined with the neoantigen, tumor mutational burden (TMB), and microsatellite instability (MSI) results, a strong relationship between NEIL3 and the TME was observed. NEIL3 was demonstrated to be closely associated with multiple immune parameters, including infiltrating immunocytes and pro-inflammatory chemokines, which was verified by experiments. More importantly, patients with a higher expression of NEIL3 were revealed to be more sensitive to chemotherapeutic regimens and immune checkpoint inhibitors in selected cancers, implying that NEIL3 may be an indicator for therapeutic administration. Our study indicated NEIL3 has a strong association with the immune microenvironment and phenotypic changes in certain types of cancers, which facilitated the improved understanding of NEIL3 across cancers and highlighted the potential for clinical application of NEIL3 in precision medical stratification.
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20
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Myostatin Mutation Enhances Bovine Myogenic Differentiation through PI3K/AKT/mTOR Signalling via Removing DNA Methylation of RACK1. Cells 2022; 12:cells12010059. [PMID: 36611855 PMCID: PMC9818849 DOI: 10.3390/cells12010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/26/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Myostatin (MSTN) is a negative regulator of skeletal muscle development and plays an important role in muscle development. Fluctuations in gene expression influenced by DNA methylation are critical for homeostatic responses in muscle. However, little is known about the mechanisms underlying this fluctuation regulation and myogenic differentiation of skeletal muscle. Here we report a genome-wide analysis of DNA methylation dynamics in bovine skeletal muscle myogenesis after myostatin editing. We show that, after myostatin editing, an increase in TETs (DNA demethylases) and a concomitant increase in the receptor for activated C kinase 1 (RACK1) control the myogenic development of skeletal muscle. Interestingly, enhancement of PI3K/AKT/mTOR signaling by RACK1 appears to be an essential driver of myogenic differentiation, as it was associated with an increase in myogenic differentiation marker factors (MyHC and MyoG) during muscle differentiation. Overall, our results suggest that loss of myostatin promotes the myogenic differentiation response in skeletal muscle by decreasing DNA methylation of RACK1.
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21
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Wang D, Wu W, Callen E, Pavani R, Zolnerowich N, Kodali S, Zong D, Wong N, Noriega S, Nathan WJ, Matos-Rodrigues G, Chari R, Kruhlak MJ, Livak F, Ward M, Caldecott K, Di Stefano B, Nussenzweig A. Active DNA demethylation promotes cell fate specification and the DNA damage response. Science 2022; 378:983-989. [PMID: 36454826 PMCID: PMC10196940 DOI: 10.1126/science.add9838] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Neurons harbor high levels of single-strand DNA breaks (SSBs) that are targeted to neuronal enhancers, but the source of this endogenous damage remains unclear. Using two systems of postmitotic lineage specification-induced pluripotent stem cell-derived neurons and transdifferentiated macrophages-we show that thymidine DNA glycosylase (TDG)-driven excision of methylcytosines oxidized with ten-eleven translocation enzymes (TET) is a source of SSBs. Although macrophage differentiation favors short-patch base excision repair to fill in single-nucleotide gaps, neurons also frequently use the long-patch subpathway. Disrupting this gap-filling process using anti-neoplastic cytosine analogs triggers a DNA damage response and neuronal cell death, which is dependent on TDG. Thus, TET-mediated active DNA demethylation promotes endogenous DNA damage, a process that normally safeguards cell identity but can also provoke neurotoxicity after anticancer treatments.
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Affiliation(s)
- Dongpeng Wang
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Wei Wu
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Nicholas Zolnerowich
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Srikanth Kodali
- Stem Cells and Regenerative Medicine, Center for Cell and Gene Therapy, Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dali Zong
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Nancy Wong
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Santiago Noriega
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - William J. Nathan
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | | | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael J. Kruhlak
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ferenc Livak
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Michael Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Keith Caldecott
- Genome Damage and Stability Centre, University of Sussex, Falmer Brighton, UK
| | - Bruno Di Stefano
- Stem Cells and Regenerative Medicine, Center for Cell and Gene Therapy, Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
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22
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Abstract
Active DNA demethylation maintains enhancer activity in nonproliferating cells but can damage DNA.
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Affiliation(s)
- Isaac F López-Moyado
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
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23
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Georges RO, Sepulveda H, Angel JC, Johnson E, Palomino S, Nowak RB, Desai A, López-Moyado IF, Rao A. Acute deletion of TET enzymes results in aneuploidy in mouse embryonic stem cells through decreased expression of Khdc3. Nat Commun 2022; 13:6230. [PMID: 36266342 PMCID: PMC9584922 DOI: 10.1038/s41467-022-33742-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 09/29/2022] [Indexed: 02/06/2023] Open
Abstract
TET (Ten-Eleven Translocation) dioxygenases effect DNA demethylation through successive oxidation of the methyl group of 5-methylcytosine (5mC) in DNA. In humans and in mouse models, TET loss-of-function has been linked to DNA damage, genome instability and oncogenesis. Here we show that acute deletion of all three Tet genes, after brief exposure of triple-floxed, Cre-ERT2-expressing mouse embryonic stem cells (mESC) to 4-hydroxytamoxifen, results in chromosome mis-segregation and aneuploidy; moreover, embryos lacking all three TET proteins showed striking variation in blastomere numbers and nuclear morphology at the 8-cell stage. Transcriptional profiling revealed that mRNA encoding a KH-domain protein, Khdc3 (Filia), was downregulated in triple TET-deficient mESC, concomitantly with increased methylation of CpG dinucleotides in the vicinity of the Khdc3 gene. Restoring KHDC3 levels in triple Tet-deficient mESC prevented aneuploidy. Thus, TET proteins regulate Khdc3 gene expression, and TET deficiency results in mitotic infidelity and genome instability in mESC at least partly through decreased expression of KHDC3.
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Affiliation(s)
- Romain O Georges
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Hugo Sepulveda
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - J Carlos Angel
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Eric Johnson
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Susan Palomino
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Roberta B Nowak
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Arshad Desai
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Isaac F López-Moyado
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA.
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego; 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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24
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DNA Methylation in Regulatory T Cell Differentiation and Function: Challenges and Opportunities. Biomolecules 2022; 12:biom12091282. [PMID: 36139121 PMCID: PMC9496199 DOI: 10.3390/biom12091282] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/04/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
As a bona fide epigenetic marker, DNA methylation has been linked to the differentiation and function of regulatory T (Treg) cells, a subset of CD4 T cells that play an essential role in maintaining immune homeostasis and suppressing autoimmunity and antitumor immune response. DNA methylation undergoes dynamic regulation involving maintenance of preexisting patterns, passive and active demethylation, and de novo methylation. Scattered evidence suggests that these processes control different stages of Treg cell lifespan ranging from lineage induction to cell fate maintenance, suppression of effector T cells and innate immune cells, and transdifferentiation. Despite significant progress, it remains to be fully explored how differential DNA methylation regulates Treg cell fate and immunological function. Here, we review recent progress and discuss the questions and challenges for further understanding the immunological roles and mechanisms of dynamic DNA methylation in controlling Treg cell differentiation and function. We also explore the opportunities that these processes offer to manipulate Treg cell suppressive function for therapeutic purposes by targeting DNA methylation.
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25
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Kokubo K, Onodera A, Kiuchi M, Tsuji K, Hirahara K, Nakayama T. Conventional and pathogenic Th2 cells in inflammation, tissue repair, and fibrosis. Front Immunol 2022; 13:945063. [PMID: 36016937 PMCID: PMC9395650 DOI: 10.3389/fimmu.2022.945063] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/18/2022] [Indexed: 12/15/2022] Open
Abstract
Type 2 helper T (Th2) cells, a subset of CD4+ T cells, play an important role in the host defense against pathogens and allergens by producing Th2 cytokines, such as interleukin-4 (IL-4), IL-5, and IL-13, to trigger inflammatory responses. Emerging evidence reveals that Th2 cells also contribute to the repair of injured tissues after inflammatory reactions. However, when the tissue repair process becomes chronic, excessive, or uncontrolled, pathological fibrosis is induced, leading to organ failure and death. Thus, proper control of Th2 cells is needed for complete tissue repair without the induction of fibrosis. Recently, the existence of pathogenic Th2 (Tpath2) cells has been revealed. Tpath2 cells produce large amounts of Th2 cytokines and induce type 2 inflammation when activated by antigen exposure or tissue injury. In recent studies, Tpath2 cells are suggested to play a central role in the induction of type 2 inflammation whereas the role of Tpath2 cells in tissue repair and fibrosis has been less reported in comparison to conventional Th2 cells. In this review, we discuss the roles of conventional Th2 cells and pathogenic Th2 cells in the sequence of tissue inflammation, repair, and fibrosis.
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Affiliation(s)
- Kota Kokubo
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Onodera
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Institute for Advanced Academic Research, Chiba University, Chiba, Japan
| | - Masahiro Kiuchi
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kaori Tsuji
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kiyoshi Hirahara
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
- *Correspondence: Kiyoshi Hirahara, ; Toshinori Nakayama,
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
- AMED-CREST, AMED, Chiba, Japan
- *Correspondence: Kiyoshi Hirahara, ; Toshinori Nakayama,
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26
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Äijö T, Theofilatos D, Cheng M, Smith MD, Xiong Y, Baldwin AS, Tsagaratou A. TET proteins regulate T cell and iNKT cell lineage specification in a TET2 catalytic dependent manner. Front Immunol 2022; 13:940995. [PMID: 35990681 PMCID: PMC9389146 DOI: 10.3389/fimmu.2022.940995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/07/2022] [Indexed: 12/13/2022] Open
Abstract
TET proteins mediate DNA demethylation by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine (5hmC) and other oxidative derivatives. We have previously demonstrated a dynamic enrichment of 5hmC during T and invariant natural killer T cell lineage specification. Here, we investigate shared signatures in gene expression of Tet2/3 DKO CD4 single positive (SP) and iNKT cells in the thymus. We discover that TET proteins exert a fundamental role in regulating the expression of the lineage specifying factor Th-POK, which is encoded by Zbtb7b. We demonstrate that TET proteins mediate DNA demethylation - surrounding a proximal enhancer, critical for the intensity of Th-POK expression. In addition, TET proteins drive the DNA demethylation of site A at the Zbtb7b locus to facilitate GATA3 binding. GATA3 induces Th-POK expression in CD4 SP cells. Finally, by introducing a novel mouse model that lacks TET3 and expresses full length, catalytically inactive TET2, we establish a causal link between TET2 catalytic activity and lineage specification of both conventional and unconventional T cells.
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Affiliation(s)
- Tarmo Äijö
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Dimitris Theofilatos
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Meng Cheng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Matthew D. Smith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Albert S. Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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27
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Yang J, Gupta E, Horton JR, Blumenthal RM, Zhang X, Cheng X. Differential ETS1 binding to T:G mismatches within a CpG dinucleotide contributes to C-to-T somatic mutation rate of the IDH2 hotspot at codon Arg140. DNA Repair (Amst) 2022; 113:103306. [PMID: 35255310 PMCID: PMC9411267 DOI: 10.1016/j.dnarep.2022.103306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 12/16/2022]
Abstract
Cytosine to thymine (C>T) somatic mutation is highly enriched in certain types of cancer, and most commonly occurs via deamination of a 5-methylcytosine (5mC) to thymine, in the context of a CpG dinucleotide. In theory, deamination should occur at equal rates to both 5mC nucleotides on opposite strands. In most cases, the resulting T:G or G:T mismatch can be repaired by thymine DNA glycosylase activities. However, while some hotspot-associated CpG mutations have approximately equal numbers of mutations that resulted either from C>T or G>A in a CpG dinucleotide, many showed strand bias, being skewed toward C>T of the first base pair or G>A of the second base pair. Using the IDH2 Arg140 codon as a case study, we show that the two possible T:G mismatches at the codon-specific CpG site have differing effects on transcription factor ETS1 binding affinity, differentially affecting access of a repair enzyme (MBD4) to the deamination-caused T:G mismatch. Our study thus provides a plausible mechanism for exclusion of repair enzymes by the differential binding of transcription factors affecting the rate at which the antecedent opposite-strand mutations occur.
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Affiliation(s)
- Jie Yang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Esha Gupta
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA.
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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28
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Wang X, Sarver AL, Han Q, Seiler CL, Xie C, Lu H, Forster CL, Tretyakova NY, Hallstrom TC. UHRF2 regulates cell cycle, epigenetics and gene expression to control the timing of retinal progenitor and ganglion cell differentiation. Development 2022; 149:274710. [PMID: 35285483 PMCID: PMC8984156 DOI: 10.1242/dev.195644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 01/28/2022] [Indexed: 11/20/2022]
Abstract
Ubiquitin-like, containing PHD and RING finger domains 2 (UHRF2) regulates cell cycle and binds 5-hydroxymethylcytosine (5hmC) to promote completion of DNA demethylation. Uhrf2-/- mice are without gross phenotypic defects; however, the cell cycle and epigenetic regulatory functions of Uhrf2 during retinal tissue development are unclear. Retinal progenitor cells (RPCs) produce all retinal neurons and Müller glia in a predictable sequence controlled by the complex interplay between extrinsic signaling, cell cycle, epigenetic changes and cell-specific transcription factor activation. In this study, we find that UHRF2 accumulates in RPCs, and its conditional deletion from mouse RPCs reduced 5hmC, altered gene expressions and disrupted retinal cell proliferation and differentiation. Retinal ganglion cells were overproduced in Uhrf2-deficient retinae at the expense of VSX2+ RPCs. Most other cell types were transiently delayed in differentiation. Expression of each member of the Tet3/Uhrf2/Tdg active demethylation pathway was reduced in Uhrf2-deficient retinae, consistent with locally reduced 5hmC in their gene bodies. This study highlights a novel role of UHRF2 in controlling the transition from RPCs to differentiated cell by regulating cell cycle, epigenetic and gene expression decisions.
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Affiliation(s)
- Xiaohong Wang
- Department of Pediatrics, Division of Blood and Marrow Transplantation, 420 Delaware Street S.E., University of Minnesota, Minneapolis, MN 55455, USA
| | - Aaron L Sarver
- Institute for Health Informatics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Qiyuan Han
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christopher L Seiler
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chencheng Xie
- Department of Pediatrics, Division of Blood and Marrow Transplantation, 420 Delaware Street S.E., University of Minnesota, Minneapolis, MN 55455, USA
| | - Huarui Lu
- Department of Pediatrics, Division of Blood and Marrow Transplantation, 420 Delaware Street S.E., University of Minnesota, Minneapolis, MN 55455, USA
| | - Colleen L Forster
- BioNet, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Timothy C Hallstrom
- Department of Pediatrics, Division of Blood and Marrow Transplantation, 420 Delaware Street S.E., University of Minnesota, Minneapolis, MN 55455, USA
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29
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Tan L, Fu L, Zheng L, Fan W, Tan H, Tao Z, Xu Y. TET2 Regulates 5-Hydroxymethylcytosine Signature and CD4 + T-Cell Balance in Allergic Rhinitis. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2022; 14:254-272. [PMID: 35255541 PMCID: PMC8914607 DOI: 10.4168/aair.2022.14.2.254] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/03/2022] [Accepted: 01/16/2022] [Indexed: 11/23/2022]
Abstract
Purpose Previous studies have shown the role of ten-eleven translocation 2 (TET2) in CD4+ T cells. However, its function in CD4+ T cells under allergic inflammation is unclear. We aimed to investigate the epigenomic distribution of DNA 5-hydroxymethylcytosine (5hmC) and the role of TET2 in CD4+ T cells of allergic rhinitis (AR). Methods The hMeDIP-seq was performed to identify sequences with 5hmC deposition in CD4+ T cells of AR patients. Tet2-deficient or wild type mice were stimulated with ovalbumin (OVA) to develop an AR mouse model. The histopathology in nasal mucosae, Th1/Th2/Treg/Th17 cell percentage, concentrations of Th-related cytokines, expression of Tet and differential hydroxymethylated genes (DhMG), and the global deposition of 5hmC in sorted CD4+ T cells were detected. Results Epigenome-wide 5hmC landscape and DhMG in the CD4+ T cells of AR patients were identified. Tet2 depletion did not led to spontaneous inflammation. However, under the stimulation of allergen, OVA, loss of Tet2 resulted in the exacerbation of allergic inflammation, which was characterized by severer allergic symptoms, more inflammatory cells infiltrating the nasal lamina propria, sharper imbalances between Th1/Th2 and Treg/Th17 cells, and excessive secretion of OVA-specific IgE and Th2-related cytokines. Moreover, altered mRNA production of several DhMG and sharp decrease in 5hmC deposition were also observed in Tet2-deficient OVA-exposed mice. Conclusions TET2 may regulate DNA 5hmC, DhMG expressions, and CD4+ T cell balance in AR.
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Affiliation(s)
- Lu Tan
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lisheng Fu
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Li Zheng
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wenjun Fan
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hanyu Tan
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zezhang Tao
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yu Xu
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.
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30
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Saini A, Ghoneim HE, Lio CWJ, Collins PL, Oltz EM. Gene Regulatory Circuits in Innate and Adaptive Immune Cells. Annu Rev Immunol 2022; 40:387-411. [PMID: 35119910 DOI: 10.1146/annurev-immunol-101320-025949] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cell identity and function largely rely on the programming of transcriptomes during development and differentiation. Signature gene expression programs are orchestrated by regulatory circuits consisting of cis-acting promoters and enhancers, which respond to a plethora of cues via the action of transcription factors. In turn, transcription factors direct epigenetic modifications to revise chromatin landscapes, and drive contacts between distal promoter-enhancer combinations. In immune cells, regulatory circuits for effector genes are especially complex and flexible, utilizing distinct sets of transcription factors and enhancers, depending on the cues each cell type receives during an infection, after sensing cellular damage, or upon encountering a tumor. Here, we review major players in the coordination of gene regulatory programs within innate and adaptive immune cells, as well as integrative omics approaches that can be leveraged to decipher their underlying circuitry. Expected final online publication date for the Annual Review of Immunology, Volume 40 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ankita Saini
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Chan-Wang Jerry Lio
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Patrick L Collins
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
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31
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Cortés-Mancera FM, Sarno F, Goubert D, Rots MG. Gene-Targeted DNA Methylation: Towards Long-Lasting Reprogramming of Gene Expression? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:515-533. [DOI: 10.1007/978-3-031-11454-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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32
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Onodera A, Kiuchi M, Kokubo K, Nakayama T. Epigenetic regulation of inflammation by CxxC domain‐containing proteins*. Immunol Rev 2022. [DOI: 10.1111/imr.13056
expr 964170082 + 969516512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Affiliation(s)
- Atsushi Onodera
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
- Institute for Global Prominent Research Chiba University Chiba Japan
| | - Masahiro Kiuchi
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
| | - Kota Kokubo
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
| | - Toshinori Nakayama
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
- AMED‐CREST, AMED Chiba Japan
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33
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Onodera A, Kiuchi M, Kokubo K, Nakayama T. Epigenetic regulation of inflammation by CxxC domain-containing proteins. Immunol Rev 2021; 305:137-151. [PMID: 34935162 DOI: 10.1111/imr.13056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/03/2021] [Accepted: 11/12/2021] [Indexed: 12/14/2022]
Abstract
Epigenetic regulation of gene transcription in the immune system is important for proper control of protective and pathogenic inflammation. Aberrant epigenetic modifications are often associated with dysregulation of the immune cells, including lymphocytes and macrophages, leading to pathogenic inflammation and autoimmune diseases. Two classical epigenetic markers-histone modifications and DNA cytosine methylation, the latter is the 5 position of the cytosine base in the context of CpG dinucleotides-play multiple roles in the immune system. CxxC domain-containing proteins, which basically bind to the non-methylated CpG (i.e., epigenetic "readers"), often function as "writers" of the epigenetic markers via their catalytic domain within the proteins or by interacting with other epigenetic modifiers. We herein report the most recent advances in our understanding of the functions of CxxC domain-containing proteins in the immune system and inflammation, mainly focusing on T cells and macrophages.
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Affiliation(s)
- Atsushi Onodera
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Institute for Global Prominent Research, Chiba University, Chiba, Japan
| | - Masahiro Kiuchi
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kota Kokubo
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,AMED-CREST, AMED, Chiba, Japan
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34
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Yu G, Su Q, Chen Y, Wu L, Wu S, Li H. Epigenetics in neurodegenerative disorders induced by pesticides. Genes Environ 2021; 43:55. [PMID: 34893084 PMCID: PMC8662853 DOI: 10.1186/s41021-021-00224-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/21/2021] [Indexed: 12/15/2022] Open
Abstract
Neurodegenerative diseases are becoming major socio-economic burdens. However, most of them still have no effective treatment. Growing evidence indicates excess exposure to pesticides are involved in the development of various forms of neurodegenerative and neurological diseases through trigger epigenetic changes and inducing disruption of the epigenome. This review summaries studies on epigenetics alterations in nervous systems in relation to different kinds of pesticides, highlighting potential mechanism in the etiology, precision prevention and target therapy of various neurodegenerative diseases. In addition, the current gaps in research and future areas for study were also discussed.
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Affiliation(s)
- Guangxia Yu
- Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China.,Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China.,Key Lab of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Qianqian Su
- Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China.,Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Yao Chen
- Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China.,Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Lingyan Wu
- Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China.,Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Siying Wu
- Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China. .,Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China.
| | - Huangyuan Li
- Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China. .,Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China. .,Key Lab of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China.
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35
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Liu T, Guo L, Liu G, Hu X, Li X, Zhang J, Dai Z, Yu P, Jiang M, Wang J, Zhang J. Molecular Characterization of the Clinical and Tumor Immune Microenvironment Signature of 5-methylcytosine-Related Regulators in non-small Cell Lung Cancer. Front Cell Dev Biol 2021; 9:779367. [PMID: 34858994 PMCID: PMC8632062 DOI: 10.3389/fcell.2021.779367] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/19/2021] [Indexed: 12/28/2022] Open
Abstract
Background: DNA methylation is an important epigenetic modification, among which 5-methylcytosine methylation (5mC) is generally associated with tumorigenesis. Nonetheless, the potential roles of 5mC regulators in the tumor microenvironment (TME) remain unclear. Methods: The 5mC modification patterns of 1,374 lung adenocarcinoma samples were analyzed systematically. The correlation between the 5mC modification and tumor microenvironment cell infiltration was further assessed. The 5mCscore was developed to evaluate tumor mutation burden, immune check-point inhibitor response, and the clinical prognosis of individual tumors. Results: Three 5mC modification patterns were established based on the clinical characteristics of 21 5mC regulators. According to the differential expression of 5mC regulators, three distinct 5mC gene cluster were also identified, which showed distinct TME immune cell infiltration patterns and clinical prognoses. The 5mCscore was constructed to evaluate the tumor mutation burden, immune check-point inhibitor response, and prognosis characteristics. We found that patients with a low 5mCscore had significant immune cell infiltration and increased clinical benefit. Conclusion: This study indicated that the 5mC modification is involved in regulating TME infiltration remodeling. Targeting 5mC modification regulators might be a novel strategy to treat lung cancer.
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Affiliation(s)
- Taisheng Liu
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Liyi Guo
- The Sixth People's Hospital of Huizhou City, Huiyang Hospital Affiliated to Southern Medical University, Huizhou, China
| | - Guihong Liu
- Department of Radiation Oncology, DongGuan Tungwah Hospital, Dongguan, China
| | - Xiaoshan Hu
- Department of Internal Medicine of Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Xiaoning Li
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jinye Zhang
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Zili Dai
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou, China
| | - Peng Yu
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou, China
| | - Ming Jiang
- Department of Breast Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jian Wang
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou, China
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