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Unterman I, Avrahami D, Katsman E, Triche TJ, Glaser B, Berman BP. CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes. Genome Biol 2024; 25:151. [PMID: 38858759 PMCID: PMC11163775 DOI: 10.1186/s13059-024-03275-x] [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: 08/20/2023] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
Deconvolution methods infer quantitative cell type estimates from bulk measurement of mixed samples including blood and tissue. DNA methylation sequencing measures multiple CpGs per read, but few existing deconvolution methods leverage this within-read information. We develop CelFiE-ISH, which extends an existing method (CelFiE) to use within-read haplotype information. CelFiE-ISH outperforms CelFiE and other existing methods, achieving 30% better accuracy and more sensitive detection of rare cell types. We also demonstrate the importance of marker selection and of tailoring markers for haplotype-aware methods. While here we use gold-standard short-read sequencing data, haplotype-aware methods will be well-suited for long-read sequencing.
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Affiliation(s)
- Irene Unterman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dana Avrahami
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Efrat Katsman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Timothy J Triche
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Benjamin P Berman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Bradyanova S, Manoylov I, Boneva G, Kechidzhieva L, Tchorbanov A, Nikolova-Ganeva K. Methyl-supplemented nutrition delays the development of autoimmune disease in pristane-induced murine lupus. Immunology 2024; 172:269-278. [PMID: 38430118 DOI: 10.1111/imm.13774] [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: 05/25/2023] [Accepted: 02/22/2024] [Indexed: 03/03/2024] Open
Abstract
The aetiology and progression of systemic lupus erythematosus (SLE) resulted from a complex sequence of events generated both from genetic and epigenetic processes. In the current research, the effect of methyl-supplemented nutrition on the development of SLE was studied in the pristane-induced mouse model of the disease. The results clearly demonstrated decreased anti-dsDNA antibody and proteinuria levels, modulation of cytokines and protected renal structures in the group of treated mice. An additional increase in the DNA methylation of mouse B lymphocytes was also observed. The beneficial effect of the diet is due to the methyl-containing micronutrients with possible anti-inflammatory and immunomodulating effects on cell proliferation and gene expression. Since these components are responsible for maintaining the physiological methylation level of DNA, the results point to the central role of methylation processes in environmentally triggered lupus. As nutrition represents one of the major epigenetic factors, these micronutrients may be considered novel agents with significant therapeutic outcomes.
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Affiliation(s)
- Silviya Bradyanova
- Laboratory of Experimental Immunology, Department of Immunology, "The Stephan Angeloff" Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Iliyan Manoylov
- Laboratory of Experimental Immunology, Department of Immunology, "The Stephan Angeloff" Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Gabriela Boneva
- Laboratory of Experimental Immunology, Department of Immunology, "The Stephan Angeloff" Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Lidiya Kechidzhieva
- Laboratory of Experimental Immunology, Department of Immunology, "The Stephan Angeloff" Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Andrey Tchorbanov
- Laboratory of Experimental Immunology, Department of Immunology, "The Stephan Angeloff" Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
- National Institute of Immunology, Sofia, Bulgaria
| | - Kalina Nikolova-Ganeva
- Laboratory of Experimental Immunology, Department of Immunology, "The Stephan Angeloff" Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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Yao S, Prates K, Freydenzon A, Assante G, McRae AF, Morris MJ, Youngson NA. Liver-specific deletion of de novo DNA methyltransferases protects against glucose intolerance in high-fat diet-fed male mice. FASEB J 2024; 38:e23690. [PMID: 38795327 DOI: 10.1096/fj.202301546rr] [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: 08/03/2023] [Revised: 04/25/2024] [Accepted: 05/10/2024] [Indexed: 05/27/2024]
Abstract
Alterations to gene transcription and DNA methylation are a feature of many liver diseases including fatty liver disease and liver cancer. However, it is unclear whether the DNA methylation changes are a cause or a consequence of the transcriptional changes. It is even possible that the methylation changes are not required for the transcriptional changes. If DNA methylation is just a minor player in, or a consequence of liver transcriptional change, then future studies in this area should focus on other systems such as histone tail modifications. To interrogate the importance of de novo DNA methylation, we generated mice that are homozygous mutants for both Dnmt3a and Dnmt3b in post-natal liver. These mice are viable and fertile with normal sized livers. Males, but not females, showed increased adipose depots, yet paradoxically, improved glucose tolerance on both control diet and high-fat diets (HFD). Comparison of the transcriptome and methylome with RNA sequencing and whole-genome bisulfite sequencing in adult hepatocytes revealed that widespread loss of methylation in CpG-rich regions in the mutant did not induce loss of homeostatic transcriptional regulation. Similarly, extensive transcriptional changes induced by HFD did not require de novo DNA methylation. The improved metabolic phenotype of the Dnmt3a/3b mutant mice may be mediated through the dysregulation of a subset of glucose and fat metabolism genes which increase both glucose uptake and lipid export by the liver. However, further work is needed to confirm this.
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Affiliation(s)
- S Yao
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - K Prates
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Department of Biotechnology, Genetics, and Cellular Biology, State University of Maringá, Maringá, Brazil
| | - A Freydenzon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - G Assante
- Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - A F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - M J Morris
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - N A Youngson
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
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Kitazawa S, Haraguchi R, Takaoka Y, Kitazawa R. In situ sequence-specific visualization of single methylated cytosine on tissue sections using ICON probe and rolling-circle amplification. Histochem Cell Biol 2023; 159:263-273. [PMID: 36418613 PMCID: PMC10006048 DOI: 10.1007/s00418-022-02165-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2022] [Indexed: 11/25/2022]
Abstract
Since epigenetic modifications differ from cell to cell, detecting the DNA methylation status of individual cells is requisite. Therefore, it is important to conduct "morphology-based epigenetics research", in which the sequence-specific DNA methylation status is observed while maintaining tissue architecture. Here we demonstrate a novel histochemical technique that efficiently shows the presence of a single methylated cytosine in a sequence-dependent manner by applying ICON (interstrand complexation with osmium for nucleic acids) probes. By optimizing the concentration and duration of potassium osmate treatment, ICON probes selectively hybridize to methylated cytosine on tissue sections. Since the elongation process by rolling-circle amplification through the padlock probe and synchronous amplification by the hyperbranching reaction at a constant temperature efficiently amplifies the reaction, it is possible to specifically detect the presence of a single methylated cytosine. Since the ICON probe is cross-linked to the nuclear or mitochondrial DNA of the target cell, subsequent elongation and multiplication reactions proceed like a tree growing in soil with its roots firmly planted, thus facilitating the demonstration of methylated cytosine in situ. Using this novel ICON-mediated histochemical method, detection of the methylation of DNA in the regulatory region of the RANK gene in cultured cells and of mitochondrial DNA in paraffin sections of mouse cerebellar tissue was achievable. This combined ICON and rolling-circle amplification method is the first that shows evidence of the presence of a single methylated cytosine in a sequence-specific manner in paraffin sections, and is foreseen as applicable to a wide range of epigenetic studies.
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Affiliation(s)
- Sohei Kitazawa
- Department of Molecular Pathology, Ehime University Graduate School of Medicine, Shitsukawa 454, Toon, Ehime, 791-0295, Japan.
| | - Ryuma Haraguchi
- Department of Molecular Pathology, Ehime University Graduate School of Medicine, Shitsukawa 454, Toon, Ehime, 791-0295, Japan
| | - Yuki Takaoka
- Department of Molecular Pathology, Ehime University Graduate School of Medicine, Shitsukawa 454, Toon, Ehime, 791-0295, Japan
| | - Riko Kitazawa
- Division of Diagnostic Pathology, Ehime University Hospital, Shitsukawa 454, Toon, Ehime, 791-0295, Japan
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Wei A, Wu H. Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers. Development 2022; 149:dev182683. [PMID: 36519514 PMCID: PMC10108609 DOI: 10.1242/dev.182683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA methylation is a highly conserved epigenetic modification that plays essential roles in mammalian gene regulation, genome stability and development. Despite being primarily considered a stable and heritable epigenetic silencing mechanism at heterochromatic and repetitive regions, whole genome methylome analysis reveals that DNA methylation can be highly cell-type specific and dynamic within proximal and distal gene regulatory elements during early embryonic development, stem cell differentiation and reprogramming, and tissue maturation. In this Review, we focus on the mechanisms and functions of regulated DNA methylation and demethylation, highlighting how these dynamics, together with crosstalk between DNA methylation and histone modifications at distinct regulatory regions, contribute to mammalian development and tissue maturation. We also discuss how recent technological advances in single-cell and long-read methylome sequencing, along with targeted epigenome-editing, are enabling unprecedented high-resolution and mechanistic dissection of DNA methylome dynamics.
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Affiliation(s)
- Alex Wei
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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