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Yao YM, Miodownik I, O'Hagan MP, Jbara M, Afek A. Deciphering the dynamic code: DNA recognition by transcription factors in the ever-changing genome. Transcription 2024:1-25. [PMID: 39033307 DOI: 10.1080/21541264.2024.2379161] [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: 03/15/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
Transcription factors (TFs) intricately navigate the vast genomic landscape to locate and bind specific DNA sequences for the regulation of gene expression programs. These interactions occur within a dynamic cellular environment, where both DNA and TF proteins experience continual chemical and structural perturbations, including epigenetic modifications, DNA damage, mechanical stress, and post-translational modifications (PTMs). While many of these factors impact TF-DNA binding interactions, understanding their effects remains challenging and incomplete. This review explores the existing literature on these dynamic changes and their potential impact on TF-DNA interactions.
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Affiliation(s)
- Yumi Minyi Yao
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Irina Miodownik
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michael P O'Hagan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Muhammad Jbara
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ariel Afek
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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2
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Margalit S, Tulpová Z, Detinis Zur T, Michaeli Y, Deek J, Nifker G, Haldar R, Gnatek Y, Omer D, Dekel B, Feldman HB, Grunwald A, Ebenstein Y. Long-Read Structural and Epigenetic Profiling of a Kidney Tumor-Matched Sample with Nanopore Sequencing and Optical Genome Mapping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.587463. [PMID: 38915648 PMCID: PMC11195078 DOI: 10.1101/2024.03.31.587463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Carcinogenesis often involves significant alterations in the cancer genome architecture, marked by large structural and copy number variations (SVs and CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogenetic techniques are applied to detect such aberrations, but they are limited in resolution and do not cover features smaller than several hundred kilobases. Optical genome mapping and nanopore sequencing are attractive technologies that bridge this resolution gap and offer enhanced performance for cytogenetic applications. These methods profile native, individual DNA molecules, thus capturing epigenetic information. We applied both techniques to characterize a clear cell renal cell carcinoma (ccRCC) tumor's structural and copy number landscape, highlighting the relative strengths of each method in the context of variant size and average read length. Additionally, we assessed their utility for methylome and hydroxymethylome profiling, emphasizing differences in epigenetic analysis applicability.
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Affiliation(s)
- Sapir Margalit
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Zuzana Tulpová
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
- Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Tahir Detinis Zur
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yael Michaeli
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Jasline Deek
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Gil Nifker
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Rita Haldar
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yehudit Gnatek
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
| | - Dorit Omer
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
| | - Benjamin Dekel
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
- Pediatric Nephrology Unit, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Hagit Baris Feldman
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Assaf Grunwald
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yuval Ebenstein
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
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3
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Käver L, Hinney A, Rajcsanyi LS, Maier HB, Frieling H, Steiger H, Voelz C, Beyer C, Trinh S, Seitz J. Epigenetic alterations in patients with anorexia nervosa-a systematic review. Mol Psychiatry 2024:10.1038/s41380-024-02601-w. [PMID: 38849516 DOI: 10.1038/s41380-024-02601-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024]
Abstract
Anorexia nervosa (AN) is a complex metabolic and psychological disorder that is influenced by both heritable genetic components and environmental factors. Exposure to various environmental influences can lead to epigenetically induced changes in gene expression. Epigenetic research in AN is still in its infancy, and studies to date are limited in determining clear, valid links to disease onset and progression are limited. Therefore, the aim of this systematic review was to compile and critically evaluate the available results of epigenetic studies specifically in AN and to provide recommendations for future studies. In accordance with the PRISMA guidelines, a systematic literature search was performed in three different databases (PubMed, Embase, and Web of Science) through May 2023. Twenty-three original papers or conference abstracts on epigenetic studies in AN were collected. Epigenome-wide association studies (EWASs), which analyze DNA methylation across the genome in patients with AN and identify potential disease-relevant changes in promoter/regulatory regions of genes, are the most promising for future research. To date, five EWASs on AN have been published, suggesting a potential reversibility of malnutrition-induced epigenetic changes once patients recover. Hence, determining differential DNA methylation levels could serve as a biomarker for disease status or early diagnosis and might be involved in disease progression or chronification. For future research, EWASs with a larger sample size, longitudinal study design and uniform methods should be performed to contribute to the understanding of the pathophysiology of AN, the development of individual interventions and a better prognosis for affected patients.
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Affiliation(s)
- Larissa Käver
- Institute of Neuroanatomy, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany.
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, Virchowstrasse 174, 45147, Essen, Germany
- Center for Translational and Behavioral Neuroscience, University Hospital Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Luisa Sophie Rajcsanyi
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, Virchowstrasse 174, 45147, Essen, Germany
- Center for Translational and Behavioral Neuroscience, University Hospital Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Hannah Benedictine Maier
- Department of Psychiatry, Socialpsychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Helge Frieling
- Department of Psychiatry, Socialpsychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Howard Steiger
- Department of Psychiatry, McGill University, Montreal, QC, H3A 1A1, Canada
| | - Clara Voelz
- Institute of Neuroanatomy, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Cordian Beyer
- Institute of Neuroanatomy, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Stefanie Trinh
- Institute of Neuroanatomy, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Jochen Seitz
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, RWTH Aachen University, Neuenhofer Weg 21, 52074, Aachen, Germany
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, LVR University Hospital Essen, Virchowstrasse 174, 45147, Essen, Germany
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4
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Avraham S, Schütz L, Käver L, Dankers A, Margalit S, Michaeli Y, Zirkin S, Torchinsky D, Gilat N, Bahr O, Nifker G, Koren-Michowitz M, Weinhold E, Ebenstein Y. Chemo-Enzymatic Fluorescence Labeling Of Genomic DNA For Simultaneous Detection Of Global 5-Methylcytosine And 5-Hydroxymethylcytosine. Chembiochem 2023; 24:e202300400. [PMID: 37518671 DOI: 10.1002/cbic.202300400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/05/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
5-Methylcytosine and 5-hydroxymethylcytosine are epigenetic modifications involved in gene regulation and cancer. We present a new, simple, and high-throughput platform for multi-color epigenetic analysis. The novelty of our approach is the ability to multiplex methylation and de-methylation signals in the same assay. We utilize an engineered methyltransferase enzyme that recognizes and labels all unmodified CpG sites with a fluorescent cofactor. In combination with the already established labeling of the de-methylation mark 5-hydroxymethylcytosine via enzymatic glycosylation, we obtained a robust platform for simultaneous epigenetic analysis of these marks. We assessed the global epigenetic levels in multiple samples of colorectal cancer and observed a 3.5-fold reduction in 5hmC levels but no change in DNA methylation levels between sick and healthy individuals. We also measured epigenetic modifications in chronic lymphocytic leukemia and observed a decrease in both modification levels (5-hydroxymethylcytosine: whole blood 30 %; peripheral blood mononuclear cells (PBMCs) 40 %. 5-methylcytosine: whole blood 53 %; PBMCs 48 %). Our findings propose using a simple blood test as a viable method for analysis, simplifying sample handling in diagnostics. Importantly, our results highlight the assay's potential for epigenetic evaluation of clinical samples, benefiting research and patient management.
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Affiliation(s)
- Sigal Avraham
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Leonie Schütz
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Larissa Käver
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Andreas Dankers
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Sapir Margalit
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
| | - Yael Michaeli
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Shahar Zirkin
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Dmitry Torchinsky
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Noa Gilat
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Omer Bahr
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Gil Nifker
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | | | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Yuval Ebenstein
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
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5
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Chiu BCH, Zhang Z, Derman BA, Karpus J, Luo L, Zhang S, Langerman SS, Sukhanova M, Bhatti P, Jakubowiak A, He C, Zhang W. Genome-wide profiling of 5-hydroxymethylcytosines in circulating cell-free DNA reveals population-specific pathways in the development of multiple myeloma. J Hematol Oncol 2022; 15:106. [PMID: 35974364 PMCID: PMC9380317 DOI: 10.1186/s13045-022-01327-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/05/2022] [Indexed: 12/02/2022] Open
Abstract
Multiple myeloma (MM) and its precursors monoclonal gammopathy of undetermined significance (MGUS) and smoldering myeloma (SMM) are 2–3 times more common in African Americans (AA) than European Americans (EA). Although epigenetic changes are well recognized in the context of myeloma cell biology, the contribution of 5-hydroxymethylcytosines (5hmC) to racial disparities in MM is unknown. Using the 5hmC-Seal and next-generation sequencing, we profiled genome-wide 5hmC in circulating cell-free DNA (cfDNA) from 342 newly diagnosed patients with MM (n = 294), SMM (n = 18), and MGUS (n = 30). We compared differential 5hmC modifications between MM and its precursors among 227 EA and 115 AA patients. The captured 5hmC modifications in cfDNA were found to be enriched in B-cell and T-cell-derived histone modifications marking enhancers. Of the top 500 gene bodies with differential 5hmC levels between MM and SMM/MGUS, the majority (94.8%) were distinct between EA and AA and enriched with population-specific pathways, including amino acid metabolism in AA and mainly cancer-related signaling pathways in EA. These findings improved our understanding of the epigenetic contribution to racial disparities in MM and suggest epigenetic pathways that could be exploited as novel preventive strategies in high-risk populations.
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Affiliation(s)
- Brian C-H Chiu
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, 60637, USA.
| | - Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Benjamin A Derman
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Jason Karpus
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Liangzhi Luo
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Sheng Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Spencer S Langerman
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, 60637, USA
| | - Madina Sukhanova
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Parveen Bhatti
- Department of Cancer Control Research, BC Cancer Research Institute, Vancouver, BC, V5Z1L3 0611, Canada
| | - Andrzej Jakubowiak
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.,Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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6
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Gabrieli T, Michaeli Y, Avraham S, Torchinsky D, Margalit S, Schütz L, Juhasz M, Coruh C, Arbib N, Zhou ZS, Law JA, Weinhold E, Ebenstein Y. Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping. Nucleic Acids Res 2022; 50:e92. [PMID: 35657088 PMCID: PMC9458417 DOI: 10.1093/nar/gkac460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/12/2022] [Accepted: 06/01/2022] [Indexed: 12/15/2022] Open
Abstract
DNA methylation, specifically, methylation of cytosine (C) nucleotides at the 5-carbon position (5-mC), is the most studied and significant epigenetic modification. Here we developed a chemoenzymatic procedure to fluorescently label non-methylated cytosines in CpG context, allowing epigenetic profiling of single DNA molecules spanning hundreds of thousands of base pairs. We used a CpG methyltransferase with a synthetic S-adenosyl-l-methionine cofactor analog to transfer an azide to cytosines instead of the natural methyl group. A fluorophore was then clicked onto the DNA, reporting on the amount and position of non-methylated CpGs. We found that labeling efficiency was increased up to 2-fold by the addition of a nucleosidase, presumably by degrading the inactive by-product of the cofactor after labeling, preventing its inhibitory effect. We used the method to determine the decline in global DNA methylation in a chronic lymphocytic leukemia patient and then performed whole-genome methylation mapping of the model plant Arabidopsis thaliana. Our genome maps show high concordance with published bisulfite sequencing methylation maps. Although mapping resolution is limited by optical detection to 500–1000 bp, the labeled DNA molecules produced by this approach are hundreds of thousands of base pairs long, allowing access to long repetitive and structurally variable genomic regions.
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Affiliation(s)
- Tslil Gabrieli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Michaeli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Sigal Avraham
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Dmitry Torchinsky
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Sapir Margalit
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Leonie Schütz
- Institute of Organic Chemistry, RWTH Aachen University, D-52056Aachen, Germany
| | - Matyas Juhasz
- Institute of Organic Chemistry, RWTH Aachen University, D-52056Aachen, Germany
| | - Ceyda Coruh
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nissim Arbib
- Department of Obstetrics and Gynecology, Meir Hospital, Kfar Saba, Israel & Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, and Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts02115, USA
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, D-52056Aachen, Germany
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
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7
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Shang Y, Jiang T, Ran L, Hu W, Wu Y, Ye J, Peng Z, Chen L, Wang R. TET2-BCLAF1 transcription repression complex epigenetically regulates the expression of colorectal cancer gene Ascl2 via methylation of its promoter. J Biol Chem 2022; 298:102095. [PMID: 35660018 PMCID: PMC9251787 DOI: 10.1016/j.jbc.2022.102095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/08/2022] Open
Abstract
Ascl2 has been shown to be involved in tumorigenesis in colorectal cancer (CRC), although its epigenetic regulatory mechanism is largely unknown. Here, we found that methylation of the Ascl2 promoter (bp -1670 ∼ -1139) was significantly increased compared to the other regions of the Ascl2 locus in CRC cells and was associated with elevated Ascl2 mRNA expression. Furthermore, we found that promoter methylation was predictive of CRC patient survival after analyzing DNA methylation data, RNA-Seq data, and clinical data of 410 CRC patient samples from the MethHC database, the MEXPRESS database, and the Cbioportal website. Using the established TET methylcytosine dioxygenase 2 (TET2) knockdown and ectopic TET2 catalytic domain–expression cell models, we performed glucosylated hydroxymethyl–sensitive quatitative PCR (qPCR), real-time PCR, and Western blot assays to further confirm that hypermethylation of the Ascl2 promoter, and elevated Ascl2 expression in CRC cells was partly due to the decreased expression of TET2. Furthermore, BCLAF1 was identified as a TET2 interactor in CRC cells by LC-MS/MS, coimmunoprecipitation, immunofluorescence colocalization, and proximity ligation assays. Subsequently, we found the TET2–BCLAF1 complex bound to multiple elements around CCGG sites at the Ascl2 promoter and further restrained its hypermethylation by inducing its hydroxymethylation using chromatin immunoprecipitation-qPCR and glucosylated hydroxymethyl-qPCR assays. Finally, we demonstrate that TET2-modulated Ascl2-targeted stem gene expression in CRC cells was independent of Wnt signaling. Taken together, our data suggest an additional option for inhibiting Ascl2 expression in CRC cells through TET2–BCLAF1–mediated promoter methylation, Ascl2-dependent self-renewal of CRC progenitor cells, and TET2–BCLAF1–related CRC progression.
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Affiliation(s)
- Yangyang Shang
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Tao Jiang
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Lijian Ran
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Wenjing Hu
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Yun Wu
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Jun Ye
- Department of Gastroenterology of 958 Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Zhihong Peng
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Lei Chen
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Rongquan Wang
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China.
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8
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Lu MJ, Lu Y. 5-Hydroxymethylcytosine (5hmC) at or near cancer mutation hot spots as potential targets for early cancer detection. BMC Res Notes 2022; 15:143. [PMID: 35449110 PMCID: PMC9022237 DOI: 10.1186/s13104-022-06028-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Objective Universal noninvasive genomic screening to detect cancer and/or fetal DNA in plasma at all stages of development is highly warranted. Since 5-hydroxymethylcytosine (5hmC) emerged as an intermediate metabolite in active DNA demethylation, there have been increasing efforts to elucidate its function as a stable modification of the genome. In the current study, we demonstrate that discrete 5hmC sites within 80 bp hotspot regions exist in a greater proportion of cancer versus normal cells. Result 5hmC was detected in 16 of 17 known hotspots having C to T or G to A mutations. The results show the presence of two characteristically distinct 5hmC groups: Tier 1 Group with 3 to eightfold more 5hmCs detected in tumor-cells than in normal-cell derived DNA (as observed in 6 of 11 CpG sites). Tier 2 group with equal allele frequency of 5hmC among normal and tumor-cell derived DNA at 5 CpG hotspot sites as well as 5 non-CpG hotspots. Thus, detection and quantification of the Tier 1 group of 5hmC sites or its prevalence at or near cancer mutation hot spots in cells may enable early detection, screening and potentially prediction of the likelihood of cancer occurrence or the severity of the cancer.
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Affiliation(s)
| | - Yabin Lu
- Anchor Molecular Inc., New York, USA.
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9
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Yu Z, Tong Y, Liang Y, Li Y, Yang H, Liu SY, Xu Y, Dai Z, Zou X. Highly Sensitive Fluorescence Detection of Global 5-Hydroxymethylcytosine from Nanogram Input with Strongly Emitting Copper Nanotags. Anal Chem 2021; 93:14031-14035. [PMID: 34637276 DOI: 10.1021/acs.analchem.1c03266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Quantitative analysis of 5-hydroxymethylcytosine (5hmC) has remarkable clinical significance to early cancer diagnosis; however, it is limited by the requirement in current assays for large amounts of starting material and expensive instruments requring expertise. Herein, we present a highly sensitive fluorescence method, termed hmC-TACN, for global 5hmC quantification from several nanogram inputs based on terminal deoxynucleotide transferase (TdT)-assisted formation of fluorescent copper (Cu) nanotags. In this method, 5hmC is labeled with click tags by T4 phage β-glucosyltransferase (β-GT) and cross-linked with a random DNA primer via click chemistry. TdT initiates the template-free extension along the primer at the modified 5hmC site and then generates a long polythymine (T) tail, which can template the production of strongly emitting Cu nanoparticles (CuNPs). Consequently, an intensely fluorescent tag containing numerous CuNPs can be labeled onto the 5hmC site, providing the sensitive quantification of 5hmC with a limit of detection (LOD) as low as 0.021% of total nucleotides (S/N = 3). With only a 5 ng input (∼1000 cells) of genomic DNA, global 5hmC levels were accurately determined in mouse tissues, human cell lines (including normal and cancer cells of breast, lung, and liver), and urines of a bladder cancer patient and healthy control. Moreover, as few as 100 cells can also be distinguished between normal and cancer cells. The hmC-TACN method has great promise of being cost effective and easily mastered, with low-input clinical utility, and even for the microzone analysis of tumor models.
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Affiliation(s)
- Zhenning Yu
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yanli Tong
- Key Laboratory of Sensing Technology and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Yuling Liang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yunda Li
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Hongling Yang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Si-Yang Liu
- Key Laboratory of Sensing Technology and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Yuzhi Xu
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen 518107, China
| | - Zong Dai
- Key Laboratory of Sensing Technology and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
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10
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Zahid OK, Rivas F, Wang F, Sethi K, Reiss K, Bearden S, Hall AR. Solid-state nanopore analysis of human genomic DNA shows unaltered global 5-hydroxymethylcytosine content associated with early-stage breast cancer. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2021; 35:102407. [PMID: 33905828 PMCID: PMC8238847 DOI: 10.1016/j.nano.2021.102407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 01/31/2021] [Accepted: 04/05/2021] [Indexed: 01/08/2023]
Abstract
5-Hydroxymethylcytosine (5hmC), the first oxidized form of the well-known epigenetic modification 5-methylcytosine, is an independent regulator of gene expression and therefore a potential marker for disease. Here, we report on methods developed for a selective solid-state nanopore assay that enable direct analysis of global 5hmC content in human tissue. We first describe protocols for preparing genomic DNA derived from both healthy breast tissue and stage 1 breast tumor tissue and then use our approach to probe the net abundance of the modified base in each cohort. Then, we employ empirical data to adjust for the impact of nanopore diameter on the quantification. Correcting for variations in nanopore diameter among the devices used for analysis reveals no detectable difference in global 5hmC content between healthy and tumor tissue. These results suggest that 5hmC changes may not be associated with early-stage breast cancer and instead are a downstream consequence of the disease.
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Affiliation(s)
- Osama K Zahid
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Felipe Rivas
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Fanny Wang
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Komal Sethi
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Katherine Reiss
- Department of Engineering, Wake Forest University, Winston-Salem, NC, USA
| | - Samuel Bearden
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Adam R Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA; Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA.
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11
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Jeffet J, Margalit S, Michaeli Y, Ebenstein Y. Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale. Essays Biochem 2021; 65:51-66. [PMID: 33739394 PMCID: PMC8056043 DOI: 10.1042/ebc20200021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method's basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method's resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.
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Affiliation(s)
- Jonathan Jeffet
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sapir Margalit
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
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12
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Natural products in the reprogramming of cancer epigenetics. Toxicol Appl Pharmacol 2021; 417:115467. [PMID: 33631231 DOI: 10.1016/j.taap.2021.115467] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023]
Abstract
Owing to the technological advancements, including next generation sequencing, the significance of deregulated epigenetic mechanisms in cancer initiation, progression and treatment has become evident. The accumulating knowledge relating to the epigenetic markers viz. DNA methylation, Histone modifications and non-coding RNAs make them one of the most interesting candidates for developing anti-cancer therapies. The reversibility of deregulated epigenetic mechanisms through environmental and dietary factors opens numerous avenues in the field of chemoprevention and drug development. Recent studies have proven that plant-derived natural products encompass a great potential in targeting epigenetic signatures in cancer and numerous natural products are being explored for their possibility to be considered as "epi-drug". This review intends to highlight the major aberrant epigenetic mechanisms and summarizes the essential functions of natural products like Resveratrol, Quercetin, Genistein, EGCG, Curcumin, Sulforaphane, Apigenin, Parthenolide and Berberine in modulating these aberrations. This knowledge along with the challenges and limitations in this field has potential and wider implications in developing novel and successful therapeutic strategies. The increased focus in the area will possibly provide a better understanding for the development of dietary supplements and/or drugs either alone or in combination. The interaction of epigenetics with different hallmarks of cancer and how natural products can be utilized to target them will also be interesting in the future therapeutic approaches.
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13
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Velmanickam L, Jayasooriya V, Nawarathna D. Integrated dielectrophoretic and impedimetric biosensor provides a template for universal biomarker sensing in clinical samples. Electrophoresis 2021; 42:1060-1069. [PMID: 33506957 DOI: 10.1002/elps.202000347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 12/11/2022]
Abstract
The detection and quantification of nucleic acid and proteomic biomarkers in bodily fluids is a critical part of many medical screening and diagnoses. However, majority of the current detection platforms are not ideal for routine, rapid, and low-cost testing in point-of-care settings. To address this issue, we developed a concept for a disposable universal point-of-care biosensor that can detect and quantify nucleic acid and proteomic biomarkers in diluted serum samples. The central tenet of sensing is the use of dielectrophoresis, electrothermal effects, and thermophoresis to selectively and rapidly isolate the biomarkers of interest in electrodes and then quantify using electrical impedance. When the sensor was applied to quantify microRNA and antigen biomarker molecules directly in diluted serum samples, it produced a LOD values in the fM range and sensitivity values from 1012 to 1015 Ω/M with a 30 min assay time and assay cost of less than $50 per assay.
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Affiliation(s)
- Logeeshan Velmanickam
- Department of Electrical and Computer Engineering, North Dakota State University, Fargo, ND, USA
| | - Vidura Jayasooriya
- Department of Electrical and Computer Engineering, North Dakota State University, Fargo, ND, USA
| | - Dharmakeerthi Nawarathna
- Department of Electrical and Computer Engineering, North Dakota State University, Fargo, ND, USA.,Biomedical Engineering Program, North Dakota State University, Fargo, ND, USA
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14
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Liu YL, Zhu J, Weng GJ, Li JJ, Zhao JW. Gold nanotubes: synthesis, properties and biomedical applications. Mikrochim Acta 2020; 187:612. [PMID: 33064202 DOI: 10.1007/s00604-020-04460-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/16/2020] [Indexed: 11/25/2022]
Abstract
This review (with 106 references) summarizes the latest progress in the synthesis, properties and biomedical applications of gold nanotubes (AuNTs). Following an introduction into the field, a first large section covers two popular AuNTs synthesis methods. The hard template method introduces anodic alumina oxide template (AAO) and track-etched membranes (TeMs), while the sacrificial template method based on galvanic replacement introduces bimetallic, trimetallic AuNTs and AuNT-semiconductor hybrid materials. Then, the factors affecting the morphology of AuNTs are discussed. The next section covers their unique surface plasmon resonance (SPR), surface-enhanced Raman scattering (SERS) and their catalytic properties. This is followed by overviews on the applications of AuNTs in biosensors, protein transportation, photothermal therapy and imaging. Several tables are presented that give an overview on the wealth of synthetic methods, morphology factors and biological application. A concluding section summarizes the current status, addresses current challenges and gives an outlook on potential applications of AuNTs in biochemical detection and drug delivery.Graphical abstract.
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Affiliation(s)
- Yan-Ling Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Jian Zhu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.
| | - Guo-Jun Weng
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Jian-Jun Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Jun-Wu Zhao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.
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15
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Li Y, Ren Q, Wu D, Zhang M, Wang X, Zhu H, Sun S, Feng F. Combined 5-hydroxymethylcytosine content of human leucocyte antigen-B and human leucocyte antigen-DQB1 as novel biomarker for anti-tuberculosis drug-induced liver injury. Basic Clin Pharmacol Toxicol 2020; 127:234-240. [PMID: 32180347 DOI: 10.1111/bcpt.13401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/27/2022]
Abstract
This study investigated the diagnostic value of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) contents of human leucocyte antigen (HLA)-B and HLA-DQB1 in anti-tuberculosis drug-induced liver injury (ADLI). In total, 110 ADLI patients and 120 patients without ADLI controls were enrolled. Enzyme-linked immunosorbent assay (ELISA) was used to detect the 5-mC and 5-hmC content in DNA from peripheral blood leucocytes. The univariate analysis showed that smoking, drinking, and 5-mC and 5-hmC content of HLA-B and HLA-DQB1 were significantly associated with ADLI. After adjusting for drinking and smoking, we found that 5-mC content of HLA-B and HLA-DQB1 were associated with ADLI (odds ratio [OR] = 0.251 and 0.347, respectively) and 5-hmC contents of HLA-B and HLA-DQB1 were also associated with ADLI (OR = 1.848 and 4.705, respectively). Receiver operating characteristic (ROC) analysis indicated that the 5-hmC contents of both HLA-B and HLA-DQB1 were more clinically significant than the 5-mC contents were. The combined 5-hmC level of HLA-B and HLA-DQB1 was the best diagnostic biomarker for ADLI, with the highest areas under the curve (AUC) for 0.953, sensitivity for 0.900 and specificity for 0.875. Therefore, combined 5-hmC levels of HLA-B and HLA-DQB1 could be significant evidence for diagnosis of ADLI.
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Affiliation(s)
- Yuhong Li
- School of Public Health, North China University of Science and Technology, Tangshan, China
| | - Qi Ren
- School of Public Health, North China University of Science and Technology, Tangshan, China
| | - Dongxue Wu
- School of Public Health, North China University of Science and Technology, Tangshan, China
| | - Mi Zhang
- School of Public Health, North China University of Science and Technology, Tangshan, China
| | - Xue Wang
- School of Public Health, North China University of Science and Technology, Tangshan, China
| | - Hanyu Zhu
- School of Public Health, North China University of Science and Technology, Tangshan, China
| | - Shufeng Sun
- College of Nursing and Rehabilitation, North China University of Science and Technology, Tangshan, China
| | - Fumin Feng
- School of Public Health, North China University of Science and Technology, Tangshan, China.,College of Life Sciences, North China University of Science and Technology, Tangshan, China
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