1
|
Hench J, Hultschig C, Brugger J, Mariani L, Guzman R, Soleman J, Leu S, Benton M, Stec IM, Hench IB, Hoffmann P, Harter P, Weber KJ, Albers A, Thomas C, Hasselblatt M, Schüller U, Restelli L, Capper D, Hewer E, Diebold J, Kolenc D, Schneider UC, Rushing E, Della Monica R, Chiariotti L, Sill M, Schrimpf D, von Deimling A, Sahm F, Kölsche C, Tolnay M, Frank S. EpiDiP/NanoDiP: a versatile unsupervised machine learning edge computing platform for epigenomic tumour diagnostics. Acta Neuropathol Commun 2024; 12:51. [PMID: 38576030 PMCID: PMC10993614 DOI: 10.1186/s40478-024-01759-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 03/11/2024] [Indexed: 04/06/2024] Open
Abstract
DNA methylation analysis based on supervised machine learning algorithms with static reference data, allowing diagnostic tumour typing with unprecedented precision, has quickly become a new standard of care. Whereas genome-wide diagnostic methylation profiling is mostly performed on microarrays, an increasing number of institutions additionally employ nanopore sequencing as a faster alternative. In addition, methylation-specific parallel sequencing can generate methylation and genomic copy number data. Given these diverse approaches to methylation profiling, to date, there is no single tool that allows (1) classification and interpretation of microarray, nanopore and parallel sequencing data, (2) direct control of nanopore sequencers, and (3) the integration of microarray-based methylation reference data. Furthermore, no software capable of entirely running in routine diagnostic laboratory environments lacking high-performance computing and network infrastructure exists. To overcome these shortcomings, we present EpiDiP/NanoDiP as an open-source DNA methylation and copy number profiling suite, which has been benchmarked against an established supervised machine learning approach using in-house routine diagnostics data obtained between 2019 and 2021. Running locally on portable, cost- and energy-saving system-on-chip as well as gpGPU-augmented edge computing devices, NanoDiP works in offline mode, ensuring data privacy. It does not require the rigid training data annotation of supervised approaches. Furthermore, NanoDiP is the core of our public, free-of-charge EpiDiP web service which enables comparative methylation data analysis against an extensive reference data collection. We envision this versatile platform as a useful resource not only for neuropathologists and surgical pathologists but also for the tumour epigenetics research community. In daily diagnostic routine, analysis of native, unfixed biopsies by NanoDiP delivers molecular tumour classification in an intraoperative time frame.
Collapse
Affiliation(s)
- Jürgen Hench
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland.
| | - Claus Hultschig
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Jon Brugger
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Luigi Mariani
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Raphael Guzman
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Jehuda Soleman
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Severina Leu
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Miles Benton
- Human Genomics, Institute of Environmental Science and Research (ESR), 5022, Porirua, Wellington, New Zealand
| | - Irenäus Maria Stec
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Ivana Bratic Hench
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Per Hoffmann
- Life&Brain GmbH, Venusberg-Campus 1, Gebäude 76, 53127, Bonn, Germany
| | - Patrick Harter
- Institute of Neuropathology, Center for Neuropathology and Prion Research, Feodor- Lynen-Str. 23, 81377, München, Germany
| | - Katharina J Weber
- Neurological Institute (Edinger Institute), University Hospital, Heinrich-Hoffmann- Straße 7, 60528, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Anne Albers
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Ulrich Schüller
- Forschungsinstitut Kinderkrebszentrum, Martinistrasse 52, 20251, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital Hamburg- Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Department of Neuropathology, Department of Neuropathology, Charité- Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Lisa Restelli
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - David Capper
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
| | - Ekkehard Hewer
- Institut universitaire de pathologie, Lausanne University Hospital (CHUV), University of Lausanne, Rue du Bugnon 25, 1011, Lausanne, Switzerland
| | - Joachim Diebold
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
| | - Danijela Kolenc
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
| | - Ulf C Schneider
- Klinik für Neurochirurgie, Luzerner Kantonsspital, Haus 31, 6000, 16, Spitalstrasse, Luzern, Switzerland
| | - Elisabeth Rushing
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
- Medica Pathologie Zentrum Zürich, Hottingerstrasse 9 / 11, 8032, Zürich, Switzerland
| | - Rosa Della Monica
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486 - 80145, Napoli, Italy
| | - Lorenzo Chiariotti
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486 - 80145, Napoli, Italy
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- , 23. DKFZ, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Christian Kölsche
- Pathologisches Institut der LMU, Thalkirchner Str. 36, 80337, München, Germany
| | - Markus Tolnay
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Stephan Frank
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland.
| |
Collapse
|
2
|
Ehrlich M, Ehrlich KC, Lacey M, Baribault C, Sen S, Estève PO, Pradhan S. Epigenetics of Genes Preferentially Expressed in Dissimilar Cell Populations: Myoblasts and Cerebellum. Epigenomes 2024; 8:4. [PMID: 38390894 PMCID: PMC10885033 DOI: 10.3390/epigenomes8010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
While studying myoblast methylomes and transcriptomes, we found that CDH15 had a remarkable preference for expression in both myoblasts and cerebellum. To understand how widespread such a relationship was and its epigenetic and biological correlates, we systematically looked for genes with similar transcription profiles and analyzed their DNA methylation and chromatin state and accessibility profiles in many different cell populations. Twenty genes were expressed preferentially in myoblasts and cerebellum (Myob/Cbl genes). Some shared DNA hypo- or hypermethylated regions in myoblasts and cerebellum. Particularly striking was ZNF556, whose promoter is hypomethylated in expressing cells but highly methylated in the many cell populations that do not express the gene. In reporter gene assays, we demonstrated that its promoter's activity is methylation sensitive. The atypical epigenetics of ZNF556 may have originated from its promoter's hypomethylation and selective activation in sperm progenitors and oocytes. Five of the Myob/Cbl genes (KCNJ12, ST8SIA5, ZIC1, VAX2, and EN2) have much higher RNA levels in cerebellum than in myoblasts and displayed myoblast-specific hypermethylation upstream and/or downstream of their promoters that may downmodulate expression. Differential DNA methylation was associated with alternative promoter usage for Myob/Cbl genes MCF2L, DOK7, CNPY1, and ANK1. Myob/Cbl genes PAX3, LBX1, ZNF556, ZIC1, EN2, and VAX2 encode sequence-specific transcription factors, which likely help drive the myoblast and cerebellum specificity of other Myob/Cbl genes. This study extends our understanding of epigenetic/transcription associations related to differentiation and may help elucidate relationships between epigenetic signatures and muscular dystrophies or cerebellar-linked neuropathologies.
Collapse
Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center, Hayward Human Genetics Center, Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Kenneth C Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michelle Lacey
- Department of Mathematics, Tulane University, New Orleans, LA 70118, USA
| | - Carl Baribault
- Information Technology, Tulane University, New Orleans, LA 70118, USA
| | - Sagnik Sen
- Genome Biology Division, New England Biolabs, Ipswich, MA 01938, USA
| | | | - Sriharsa Pradhan
- Genome Biology Division, New England Biolabs, Ipswich, MA 01938, USA
| |
Collapse
|
3
|
Ito Y, Inoue S, Nakashima T, Zhang H, Li Y, Kasuya H, Matsukawa T, Wu Z, Yoshikawa T, Kataoka M, Ishikawa T, Kagoya Y. Epigenetic profiles guide improved CRISPR/Cas9-mediated gene knockout in human T cells. Nucleic Acids Res 2024; 52:141-153. [PMID: 37985205 PMCID: PMC10783505 DOI: 10.1093/nar/gkad1076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/22/2023] Open
Abstract
Genetic modification of specific genes is emerging as a useful tool to enhance the functions of antitumor T cells in adoptive immunotherapy. Current advances in CRISPR/Cas9 technology enable gene knockout during in vitro preparation of infused T-cell products through transient transfection of a Cas9-guide RNA (gRNA) ribonucleoprotein complex. However, selecting optimal gRNAs remains a major challenge for efficient gene ablation. Although multiple in silico tools to predict the targeting efficiency have been developed, their performance has not been validated in cultured human T cells. Here, we explored a strategy to select optimal gRNAs using our pooled data on CRISPR/Cas9-mediated gene knockout in human T cells. The currently available prediction tools alone were insufficient to accurately predict the indel percentage in T cells. We used data on the epigenetic profiles of cultured T cells obtained from transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Combining the epigenetic information with sequence-based prediction tools significantly improved the gene-editing efficiency. We further demonstrate that epigenetically closed regions can be targeted by designing two gRNAs in adjacent regions. Finally, we demonstrate that the gene-editing efficiency of unstimulated T cells can be enhanced through pretreatment with IL-7. These findings enable more efficient gene editing in human T cells.
Collapse
Affiliation(s)
- Yusuke Ito
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Satoshi Inoue
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Takahiro Nakashima
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Haosong Zhang
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yang Li
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hitomi Kasuya
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Tetsuya Matsukawa
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Zhiwen Wu
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Toshiaki Yoshikawa
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Mirei Kataoka
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
| | - Tetsuo Ishikawa
- Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Yokohama, Japan
- Collective Intelligence Research Laboratory, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuki Kagoya
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| |
Collapse
|
4
|
Schlichenmaier N, Zielinski A, Beneke S, Dietrich DR. PODO/TERT256 - A promising human immortalized podocyte cell line and its potential use for in vitro research at different oxygen levels. Chem Biol Interact 2024; 387:110813. [PMID: 38006960 DOI: 10.1016/j.cbi.2023.110813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/27/2023]
Abstract
Podocytes are of key interest for the prediction of nephrotoxicity as they are especially sensitive to toxic insults due to their central role in the glomerular filtration apparatus. However, currently, prediction of nephrotoxicity in humans remains insufficiently reliable, thus highlighting the need for advanced in vitro model systems using human cells with improved prediction capacity. Recent approaches for refining in vitro model systems focus on closely replicating physiological conditions as observed under the in vivo situation typical of the respective nephron section of interest. PODO/TERT256, a human immortalized podocyte cell line, were employed in a semi-static transwell system to evaluate its potential use as a human podocyte in vitro system for modelling potential human glomerular toxicity. Furthermore, the impact of routinely employed excessive oxygen tension (21 % - AtmOx), when compared to the physiological oxygen tensions (10 % - PhysOx) observed in vivo, was analyzed. Generally, cultured PODO/TERT256 formed a stable, contact-inhibited monolayer with typical podocyte morphology (large cell body, apical microvilli, finger-like cytoplasmic projections (reminiscent of foot processes), and interdigitating cell-cell junctions) and developed a size-selective filtration barrier. PhysOx, however, induced a more pronounced in vivo like phenotype, comprised of significantly larger cell bodies, significantly enhanced filtration barrier size-selectivity, and a remarkable re-localization of nephrin to the cell membrane, thus suggesting an improved in vitro replication of in vivo characteristics. Preliminary toxicity characterization with the known glomerulotoxin doxorubicin (DOX) suggested an increasing change in filtration permeability, already at the lowest DOX concentrations tested (0.01 μM) under PhysOx, whereas obvious changes under AtmOx were observed as of 0.16 μM and higher with a near all or nothing effect. The latter findings suggested that PODO/TERT256 could serve as an in vitro human podocyte model for studying glomerulotoxicity, whereby culturing at PhyOx tension appeared critical for an improved in vivo-like phenotype and functionality. Moreover, PODO/TERT256 could be incorporated into advanced human glomerulus systems in vitro, recapitulating microfluidic conditions and multiple cell types (endothelial and mesenchymal cells) that can even better predict human glomerular toxicity.
Collapse
Affiliation(s)
- Nadja Schlichenmaier
- Human and Environmental Toxicology, Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Alexander Zielinski
- Human and Environmental Toxicology, Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Sascha Beneke
- Human and Environmental Toxicology, Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Daniel R Dietrich
- Human and Environmental Toxicology, Department of Biology, University of Konstanz, Konstanz, Germany.
| |
Collapse
|
5
|
Krawczyk E, Kitlińska J. Preclinical Models of Neuroblastoma-Current Status and Perspectives. Cancers (Basel) 2023; 15:3314. [PMID: 37444423 PMCID: PMC10340830 DOI: 10.3390/cancers15133314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Preclinical in vitro and in vivo models remain indispensable tools in cancer research. These classic models, including two- and three-dimensional cell culture techniques and animal models, are crucial for basic and translational studies. However, each model has its own limitations and typically does not fully recapitulate the course of the human disease. Therefore, there is an urgent need for the development of novel, advanced systems that can allow for efficient evaluation of the mechanisms underlying cancer development and progression, more accurately reflect the disease pathophysiology and complexity, and effectively inform therapeutic decisions for patients. Preclinical models are especially important for rare cancers, such as neuroblastoma, where the availability of patient-derived specimens that could be used for potential therapy evaluation and screening is limited. Neuroblastoma modeling is further complicated by the disease heterogeneity. In this review, we present the current status of preclinical models for neuroblastoma research, discuss their development and characteristics emphasizing strengths and limitations, and describe the necessity of the development of novel, more advanced and clinically relevant approaches.
Collapse
Affiliation(s)
- Ewa Krawczyk
- Department of Pathology, Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Joanna Kitlińska
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20057, USA
| |
Collapse
|
6
|
Mircetic J, Camgöz A, Abohawya M, Ding L, Dietzel J, Tobar SG, Paszkowski-Rogacz M, Seidlitz T, Schmäche T, Mehnert MC, Sidorova O, Weitz J, Buchholz F, Stange DE. CRISPR/Cas9 Screen in Gastric Cancer Patient-Derived Organoids Reveals KDM1A-NDRG1 Axis as a Targetable Vulnerability. Small Methods 2023; 7:e2201605. [PMID: 36908010 DOI: 10.1002/smtd.202201605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/01/2023] [Indexed: 06/09/2023]
Abstract
Viability CRISPR screens have proven indispensable in parsing genome function. However, their application in new, more physiologically relevant culturing systems like patient-derived organoids (PDOs) has been much slower. To probe epigenetic contribution to gastric cancer (GC), the third leading cause of cancer-related deaths worldwide, the first negative selection CRISPR screen in GC PDOs that faithfully preserve primary tumor characteristics is performed. Extensive quality control measurements showing feasibility of CRISPR screens in primary organoid culture are provided. The screen reveals the histone lysine demethylase-1A (KDM1A) to constitute a GC vulnerability. Both genetic and pharmacological inhibition of KDM1A cause organoid growth retardation. Further, it is shown that most of KDM1A cancer-supporting functions center on repression of N-myc downstream regulates gene-1 (NDRG1). De-repression of NDRG1 by KDM1A inhibitors (KDM1Ai) causes inhibition of Wnt signaling and a strong G1 cell cycle arrest. Finally, by profiling 20 GC PDOs, it is shown that NDRG1 upregulation predicts KDM1Ai response with 100% sensitivity and 82% specificity in the tested cohort. Thus, this work pioneers the use of negative selection CRISPR screens in patient-derived organoids, identifies a marker of KDM1Ai response, and accordingly a cohort of patients who may benefit from such therapy.
Collapse
Affiliation(s)
- Jovan Mircetic
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), 01309, Dresden, Germany
- Mildred Scheel Early Career Center (MSNZ) P2, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Aylin Camgöz
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
| | - Moustafa Abohawya
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), 01309, Dresden, Germany
| | - Li Ding
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Julia Dietzel
- Mildred Scheel Early Career Center (MSNZ) P2, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Sebastián García Tobar
- Mildred Scheel Early Career Center (MSNZ) P2, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Therese Seidlitz
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Tim Schmäche
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Marie-Christin Mehnert
- Mildred Scheel Early Career Center (MSNZ) P2, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Olga Sidorova
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Experimental and Clinical Research Center (ECRC) of the Max Delbrück Center (MDC) and Charité Berlin, 10117, Berlin, Germany
| | - Jürgen Weitz
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Frank Buchholz
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Daniel E Stange
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), 01309, Dresden, Germany
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| |
Collapse
|
7
|
Cairns J, Leonard E, Khan K, Parks C, Maglennon G, Zhang B, Lazic SE, Ewart L, David R. Optimal experimental design for efficient toxicity testing in microphysiological systems: A bone marrow application. Front Pharmacol 2023; 14:1142581. [PMID: 37063297 PMCID: PMC10103791 DOI: 10.3389/fphar.2023.1142581] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/21/2023] [Indexed: 04/03/2023] Open
Abstract
Introduction: Microphysiological systems (MPS; organ-on-a-chip) aim to recapitulate the 3D organ microenvironment and improve clinical predictivity relative to previous approaches. Though MPS studies provide great promise to explore treatment options in a multifactorial manner, they are often very complex. It is therefore important to assess and manage technical confounding factors, to maximise power, efficiency and scalability.Methods: As an illustration of how MPS studies can benefit from a systematic evaluation of confounders, we developed an experimental design approach for a bone marrow (BM) MPS and tested it for a specified context of use, the assessment of lineage-specific toxicity.Results: We demonstrated the accuracy of our multicolour flow cytometry set-up to determine cell type and maturity, and the viability of a “repeated measures” design where we sample from chips repeatedly for increased scalability and robustness. Importantly, we demonstrated an optimal way to arrange technical confounders. Accounting for these confounders in a mixed-model analysis pipeline increased power, which meant that the expected lineage-specific toxicities following treatment with olaparib or carboplatin were detected earlier and at lower doses. Furthermore, we performed a sample size analysis to estimate the appropriate number of replicates required for different effect sizes. This experimental design-based approach will generalise to other MPS set-ups.Discussion: This design of experiments approach has established a groundwork for a reliable and reproducible in vitro analysis of BM toxicity in a MPS, and the lineage-specific toxicity data demonstrate the utility of this model for BM toxicity assessment. Toxicity data demonstrate the utility of this model for BM toxicity assessment.
Collapse
Affiliation(s)
- Jonathan Cairns
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
- *Correspondence: Jonathan Cairns, ; Rhiannon David,
| | - Emilyanne Leonard
- Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Kainat Khan
- Oncology Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Conor Parks
- Oncology Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Gareth Maglennon
- Pathology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Bairu Zhang
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Stanley E. Lazic
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Lorna Ewart
- Safety Platforms, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Rhiannon David
- Safety Innovation, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
- *Correspondence: Jonathan Cairns, ; Rhiannon David,
| |
Collapse
|
8
|
Heredia-Mendez AJ, Sánchez-Sánchez G, López-Camarillo C. Reprogramming of the Genome-Wide DNA Methylation Landscape in Three-Dimensional Cancer Cell Cultures. Cancers (Basel) 2023; 15:cancers15071991. [PMID: 37046652 PMCID: PMC10093594 DOI: 10.3390/cancers15071991] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/13/2023] [Accepted: 03/19/2023] [Indexed: 03/29/2023] Open
Abstract
During the last century, 2D cell cultures have been the tool most widely used to study cancer biology, drug discovery, genomics, and the regulation of gene expression at genetic/epigenetic levels. However, this experimental approach has limitations in faithfully recreating the microenvironment and cellular processes occurring in tumors. For these reasons, 3D cell cultures have recently been implemented to optimize the conditions that better recreate the biological and molecular features of tumors, including cell–cell and cell–extracellular matrix (ECM) interactions, growth kinetics, metabolic activities, and the development of gradients in the cellular microenvironment affecting the availability of oxygen and nutrients. In this sense, tumor cells receive stimuli from the local environment, resulting in significant changes in their signaling pathways, gene expression, and transcriptional and epigenetic patterns. In this review, we discuss how different types of 3D cell culture models can be applied to characterize the epigenetic footprints of cancer cell lines, emphasizing that DNA methylation patterns play an essential role in the emergence and development of cancer. However, how 3D cancer cell cultures remodel the epigenetic programs is poorly understood, with very few studies in this emerging topic. Here, we have summarized the studies on the reprogramming of the epigenetic landscape of DNA methylation during tumorigenesis and discuss how it may be affected by microenvironmental factors, specifically in 3D cell cultures.
Collapse
|
9
|
Desaulniers D, Cummings-Lorbetskie C, Leingartner K, Meier MJ, Pickles JC, Yauk CL. DNA methylation changes from primary cultures through senescence-bypass in Syrian hamster fetal cells initially exposed to benzo[a]pyrene. Toxicology 2023; 487:153451. [PMID: 36754249 DOI: 10.1016/j.tox.2023.153451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/27/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
Current chemical testing strategies are limited in their ability to detect non-genotoxic carcinogens (NGTxC). Epigenetic anomalies develop during carcinogenesis regardless of whether the molecular initiating event is associated with genotoxic (GTxC) or NGTxC events; therefore, epigenetic markers may be harnessed to develop new approach methodologies that improve the detection of both types of carcinogens. This study used Syrian hamster fetal cells to establish the chronology of carcinogen-induced DNA methylation changes from primary cells until senescence-bypass as an essential carcinogenic step. Cells exposed to solvent control for 7 days were compared to naïve primary cultures, to cells exposed for 7 days to benzo[a]pyrene, and to cells at the subsequent transformation stages: normal colonies, morphologically transformed colonies, senescence, senescence-bypass, and sustained proliferation in vitro. DNA methylation changes identified by reduced representation bisulphite sequencing were minimal at day-7. Profound DNA methylation changes arose during cellular senescence and some of these early differentially methylated regions (DMRs) were preserved through the final sustained proliferation stage. A set of these DMRs (e.g., Pou4f1, Aifm3, B3galnt2, Bhlhe22, Gja8, Klf17, and L1l) were validated by pyrosequencing and their reproducibility was confirmed across multiple clones obtained from a different laboratory. These DNA methylation changes could serve as biomarkers to enhance objectivity and mechanistic understanding of cell transformation and could be used to predict senescence-bypass and chemical carcinogenicity.
Collapse
Affiliation(s)
- Daniel Desaulniers
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
| | | | - Karen Leingartner
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
| | - Matthew J Meier
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
| | | | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
| |
Collapse
|
10
|
Sigin VO, Kalinkin AI, Nikolaeva AF, Ignatova EO, Kuznetsova EB, Chesnokova GG, Litviakov NV, Tsyganov MM, Ibragimova MK, Vinogradov II, Vinogradov MI, Vinogradov IY, Zaletaev DV, Nemtsova MV, Kutsev SI, Tanas AS, Strelnikov VV. DNA Methylation and Prospects for Predicting the Therapeutic Effect of Neoadjuvant Chemotherapy for Triple-Negative and Luminal B Breast Cancer. Cancers (Basel) 2023; 15:cancers15051630. [PMID: 36900421 PMCID: PMC10001080 DOI: 10.3390/cancers15051630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/24/2023] [Accepted: 03/05/2023] [Indexed: 03/09/2023] Open
Abstract
Despite advances in the diagnosis and treatment of breast cancer (BC), the main cause of deaths is resistance to existing therapies. An approach to improve the effectiveness of therapy in patients with aggressive BC subtypes is neoadjuvant chemotherapy (NACT). Yet, the response to NACT for aggressive subtypes is less than 65% according to large clinical trials. An obvious fact is the lack of biomarkers predicting the therapeutic effect of NACT. In a search for epigenetic markers, we performed genome-wide differential methylation screening by XmaI-RRBS in cohorts of NACT responders and nonresponders, for triple-negative (TN) and luminal B tumors. The predictive potential of the most discriminative loci was further assessed in independent cohorts by methylation-sensitive restriction enzyme quantitative PCR (MSRE-qPCR), a promising method for the implementation of DNA methylation markers in diagnostic laboratories. The selected most informative individual markers were combined into panels demonstrating cvAUC = 0.83 (TMEM132D and MYO15B markers panel) for TN tumors and cvAUC = 0.76 (TTC34, LTBR and CLEC14A) for luminal B tumors. The combination of methylation markers with clinical features that correlate with NACT effect (clinical stage for TN and lymph node status for luminal B tumors) produces better classifiers, with cvAUC = 0.87 for TN tumors and cvAUC = 0.83 for luminal B tumors. Thus, clinical characteristics predictive of NACT response are independently additive to the epigenetic classifier and in combination improve prediction.
Collapse
Affiliation(s)
- Vladimir O. Sigin
- Research Centre for Medical Genetics, 115522 Moscow, Russia
- Correspondence: ; Tel.: +7-916-279-5124
| | | | | | - Ekaterina O. Ignatova
- Research Centre for Medical Genetics, 115522 Moscow, Russia
- N. N. Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia
| | - Ekaterina B. Kuznetsova
- Research Centre for Medical Genetics, 115522 Moscow, Russia
- Laboratory of Medical Genetics, I. M. Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
| | | | - Nikolai V. Litviakov
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Matvey M. Tsyganov
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Marina K. Ibragimova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Ilya I. Vinogradov
- Regional Clinical Oncology Dispensary, 390011 Ryazan, Russia
- Department of Pathological Anatomy, Ryazan State Medical University, 390026 Ryazan, Russia
| | | | - Igor Y. Vinogradov
- Department of Pathological Anatomy, Ryazan State Medical University, 390026 Ryazan, Russia
| | | | - Marina V. Nemtsova
- Research Centre for Medical Genetics, 115522 Moscow, Russia
- Laboratory of Medical Genetics, I. M. Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
| | | | | | | |
Collapse
|
11
|
Lee J, Lee D, Kim HP, Kim TY, Bang D. EBS-seq: enrichment-based method for accurate analysis of 5-hydroxymethylcytosine at single-base resolution. Clin Epigenetics 2023; 15:34. [PMID: 36859282 PMCID: PMC9979530 DOI: 10.1186/s13148-023-01451-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/18/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND A growing body of research has emphasized 5-hydroxymethylcytosine (5hmC) as an important epigenetic mark. High-resolution methods to detect 5hmC require high sequencing depth and are therefore expensive. Many studies have used enrichment-based methods to detect 5hmC; however, conventional enrichment-based methods have limited resolution. To overcome these limitations, we developed EBS-seq, a cost-efficient method for 5hmC detection with single-base resolution that combines the advantages of high-resolution methods and enrichment-based methods. RESULTS EBS-seq uses selective labeling of 5hmC, deamination of cytosine and 5-methylcytosine, pull-down of labeled 5hmC, and C-to-T conversion during DNA amplification. Using this method, we profiled 5hmC in HEK293T cells and two colorectal cancer samples. Compared with conventional enrichment-based 5hmC detection, EBS-seq improved 5hmC signals by localizing them at single-base resolution. Furthermore, EBS-seq was able to determine 5hmC levels in CpG-dense regions where distortion of signals can occur, such as CpG islands and CpG shores. Comparing EBS-seq and conventional high-resolution 5hmC detection by ACE-seq, we showed that EBS-seq is more effective at finding 5hmC sites. Using EBS-seq, we found strong associations between gene expression and gene-body 5hmC content in both HEK293T cells and colorectal cancer samples. CONCLUSIONS EBS-seq is a reliable and cost-efficient method for 5hmC detection because it simultaneously enriches 5hmC-containing DNA fragments and localizes 5hmC signals at single-base resolution. This method is a promising choice for 5hmC detection in challenging clinical samples with low 5hmC levels, such as cancer tissues.
Collapse
Affiliation(s)
- Jaywon Lee
- Department of Chemistry, Yonsei University, Seoul, Korea
| | - Dongin Lee
- Department of Chemistry, Yonsei University, Seoul, Korea
| | | | - Tae-You Kim
- IMBdx, Seoul, Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul, Korea.
| |
Collapse
|
12
|
Robusti G, Vai A, Bonaldi T, Noberini R. Investigating pathological epigenetic aberrations by epi-proteomics. Clin Epigenetics 2022; 14:145. [PMID: 36371348 PMCID: PMC9652867 DOI: 10.1186/s13148-022-01371-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022] Open
Abstract
Epigenetics includes a complex set of processes that alter gene activity without modifying the DNA sequence, which ultimately determines how the genetic information common to all the cells of an organism is used to generate different cell types. Dysregulation in the deposition and maintenance of epigenetic features, which include histone posttranslational modifications (PTMs) and histone variants, can result in the inappropriate expression or silencing of genes, often leading to diseased states, including cancer. The investigation of histone PTMs and variants in the context of clinical samples has highlighted their importance as biomarkers for patient stratification and as key players in aberrant epigenetic mechanisms potentially targetable for therapy. Mass spectrometry (MS) has emerged as the most powerful and versatile tool for the comprehensive, unbiased and quantitative analysis of histone proteoforms. In recent years, these approaches-which we refer to as "epi-proteomics"-have demonstrated their usefulness for the investigation of epigenetic mechanisms in pathological conditions, offering a number of advantages compared with the antibody-based methods traditionally used to profile clinical samples. In this review article, we will provide a critical overview of the MS-based approaches that can be employed to study histone PTMs and variants in clinical samples, with a strong focus on the latest advances in this area, such as the analysis of uncommon modifications and the integration of epi-proteomics data into multi-OMICs approaches, as well as the challenges to be addressed to fully exploit the potential of this novel field of research.
Collapse
Affiliation(s)
- Giulia Robusti
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Alessandro Vai
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Tiziana Bonaldi
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Oncology and Hematology-Oncology, University of Milan, 20122 Milan, Italy
| | - Roberta Noberini
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy
| |
Collapse
|
13
|
Mangiavacchi PM, Caldas-Bussiere MC, Mendonça MDS, Rumpf R, Lemos Júnior PES, Alves CS, Carneiro WDS, Dias AJB, Rios ÁFL. Multi-locus DNA methylation analysis of imprinted genes in cattle from somatic cell nuclear transfer. Theriogenology 2022; 186:95-107. [DOI: 10.1016/j.theriogenology.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 10/18/2022]
|
14
|
Piossek F, Beneke S, Schlichenmaier N, Mucic G, Drewitz S, Dietrich DR. Physiological oxygen and co-culture with human fibroblasts facilitate in vivo-like properties in human renal proximal tubular epithelial cells. Chem Biol Interact 2022; 361:109959. [DOI: 10.1016/j.cbi.2022.109959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 11/28/2022]
|
15
|
Tost J. Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. Advances in Experimental Medicine and Biology 2022; 1389:395-469. [DOI: 10.1007/978-3-031-11454-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
16
|
Holloway PM. Novel, Emerging Chip Models of the Blood-Brain Barrier and Future Directions. Methods Mol Biol 2022; 2492:193-224. [PMID: 35733046 DOI: 10.1007/978-1-0716-2289-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The use of microfluidic chips is now allowing for more advanced modelling of the blood-brain barrier (BBB) in vitro, recapitulating heterotypic interactions, 3D architecture, and physiological flow. This chapter will give an introduction to these new technologies and how they are being applied to model the BBB and neurovascular unit (NVU). A foundational understanding of the fluid dynamics germane to the effective use of these chips will be set and an overview of how physical phenomena at the microscale can be exploited to enable new possibilities to control the cell culture environment. The four main approaches to construct microfluidic blood vessel mimetics will be discussed with examples of how these techniques are being applied to model the BBB and more recently to study specific neurovascular disease processes. Finally, practical guidance will be given for researchers wishing to adopt these new techniques along with a summary of the challenges, limitations faced, and new opportunities opened up by these advanced cell culture systems.
Collapse
Affiliation(s)
- Paul M Holloway
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
17
|
Luo Y, Lu H, Peng D, Ruan X, Chen YE, Guo Y. Liver-humanized mice: A translational strategy to study metabolic disorders. J Cell Physiol 2022; 237:489-506. [PMID: 34661916 PMCID: PMC9126562 DOI: 10.1002/jcp.30610] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/07/2021] [Accepted: 09/11/2021] [Indexed: 01/03/2023]
Abstract
The liver is the metabolic core of the whole body. Tools commonly used to study the human liver metabolism include hepatocyte cell lines, primary human hepatocytes, and pluripotent stem cells-derived hepatocytes in vitro, and liver genetically humanized mouse model in vivo. However, none of these systems can mimic the human liver in physiological and pathological states satisfactorily. Liver-humanized mice, which are established by reconstituting mouse liver with human hepatocytes, have emerged as an attractive animal model to study drug metabolism and evaluate the therapeutic effect in "human liver" in vivo because the humanized livers greatly replicate enzymatic features of human hepatocytes. The application of liver-humanized mice in studying metabolic disorders is relatively less common due to the largely uncertain replication of metabolic profiles compared to humans. Here, we summarize the metabolic characteristics and current application of liver-humanized mouse models in metabolic disorders that have been reported in the literature, trying to evaluate the pros and cons of using liver-humanized mice as novel mouse models to study metabolic disorders.
Collapse
Affiliation(s)
- Yonghong Luo
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, Michigan, USA.,Department of Cardiovascular Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Haocheng Lu
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Daoquan Peng
- Department of Cardiovascular Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Xiangbo Ruan
- Division of Endocrinology, Diabetes and Metabolism, Johns Hopkins School of Medicine, Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Y. Eugene Chen
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, Michigan, USA.,Center for Advanced Models and Translational Sciences and Therapeutics, University of Michigan, Ann Arbor, MI 48109, USA.,Address correspondence to: Yanhong Guo, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI 48109, Phone: 734-764-1405, . Or Y. Eugene Chen, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI 48109, USA. Phone: 734-936-9548,
| | - Yanhong Guo
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, Michigan, USA.,Address correspondence to: Yanhong Guo, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI 48109, Phone: 734-764-1405, . Or Y. Eugene Chen, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI 48109, USA. Phone: 734-936-9548,
| |
Collapse
|
18
|
Xu B, Wang H, Tan L. Dysregulated TET Family Genes and Aberrant 5mC Oxidation in Breast Cancer: Causes and Consequences. Cancers (Basel) 2021; 13:cancers13236039. [PMID: 34885145 PMCID: PMC8657367 DOI: 10.3390/cancers13236039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/27/2021] [Accepted: 11/27/2021] [Indexed: 02/08/2023] Open
Abstract
Simple Summary Both genetic and epigenetic mechanisms contribute to the pathogenesis of breast cancer. Since Tahiliani et al. identified TET1 as the first methyl-cytosine dioxygenase in 2009, accumulating evidence has shown that aberrant 5mC oxidation and dysregulated TET family genes are associated with diseases, including breast cancer. In this review we provide an overview on the diagnosis and prognosis values of aberrant 5mC oxidation in breast cancer and emphasize the causes and consequences of such epigenetic alterations. Abstract DNA methylation (5-methylcytosine, 5mC) was once viewed as a stable epigenetic modification until Rao and colleagues identified Ten-eleven translocation 1 (TET1) as the first 5mC dioxygenase in 2009. TET family genes (including TET1, TET2, and TET3) encode proteins that can catalyze 5mC oxidation and consequently modulate DNA methylation, not only regulating embryonic development and cellular differentiation, but also playing critical roles in various physiological and pathophysiological processes. Soon after the discovery of TET family 5mC dioxygenases, aberrant 5mC oxidation and dysregulation of TET family genes have been reported in breast cancer as well as other malignancies. The impacts of aberrant 5mC oxidation and dysregulated TET family genes on the different aspects (so-called cancer hallmarks) of breast cancer have also been extensively investigated in the past decade. In this review, we summarize current understanding of the causes and consequences of aberrant 5mC oxidation in the pathogenesis of breast cancer. The challenges and future perspectives of this field are also discussed.
Collapse
Affiliation(s)
- Bo Xu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China;
| | - Hao Wang
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Correspondence: (H.W.); (L.T.); Tel.: +86-21-54237876 (L.T.)
| | - Li Tan
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China;
- Correspondence: (H.W.); (L.T.); Tel.: +86-21-54237876 (L.T.)
| |
Collapse
|
19
|
Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
Collapse
Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
| |
Collapse
|
20
|
Milojević M, Rožanc J, Vajda J, Činč Ćurić L, Paradiž E, Stožer A, Maver U, Vihar B. In Vitro Disease Models of the Endocrine Pancreas. Biomedicines 2021; 9:1415. [PMID: 34680532 DOI: 10.3390/biomedicines9101415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/30/2021] [Accepted: 10/05/2021] [Indexed: 12/12/2022] Open
Abstract
The ethical constraints and shortcomings of animal models, combined with the demand to study disease pathogenesis under controlled conditions, are giving rise to a new field at the interface of tissue engineering and pathophysiology, which focuses on the development of in vitro models of disease. In vitro models are defined as synthetic experimental systems that contain living human cells and mimic tissue- and organ-level physiology in vitro by taking advantage of recent advances in tissue engineering and microfabrication. This review provides an overview of in vitro models and focuses specifically on in vitro disease models of the endocrine pancreas and diabetes. First, we briefly review the anatomy, physiology, and pathophysiology of the human pancreas, with an emphasis on islets of Langerhans and beta cell dysfunction. We then discuss different types of in vitro models and fundamental elements that should be considered when developing an in vitro disease model. Finally, we review the current state and breakthroughs in the field of pancreatic in vitro models and conclude with some challenges that need to be addressed in the future development of in vitro models.
Collapse
|
21
|
Yang Y, Shen S, Cai Y, Zeng K, Liu K, Li S, Zeng L, Chen L, Tang J, Hu Z, Xia Z, Zhang L. Dynamic Patterns of N6-Methyladenosine Profiles of Messenger RNA Correlated with the Cardiomyocyte Regenerability during the Early Heart Development in Mice. Oxid Med Cell Longev 2021; 2021:5537804. [PMID: 34413927 DOI: 10.1155/2021/5537804] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/13/2021] [Indexed: 12/16/2022]
Abstract
N6-Methyladenosine (m6A) plays important roles in regulating mRNA processing. Despite rapid progress in this field, little is known about the role and mechanism of m6A modification in myocardial development and cardiomyocyte regeneration. Existing studies have shown that the heart tissues of newborn mice have the capability of proliferation and regeneration, but its mechanism, particularly its relation to m6A methylation, remains unknown. Methods. To systematically profile the mRNA m6A modification pattern in the heart tissues of mice at different developmental stages, we jointly performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) of heart tissues of mice, respectively, aged 1 day old, 7 days old, and 28 days old. Results. We identified the linkages and association between differentially expressed mRNA transcripts and hyper or hypomethylated m6A peaks in C57BL/6J mice at different heart developmental stages. Results showed that the amount of m6A peaks and the level of m6A modification were the lowest in the heart of mice at 1 day old. By contrast, heart tissues from 7-day-old mice tended to possess the most m6A peaks and the highest global m6A level. However, the m6A characteristics of myocardial tissue changed little after 7 days old as compared to that of 1 day old. Specifically, we found 1269 downmethylated genes of 1434 methylated genes in 7-day-old mouse heart tissues as compared to those in 1-day-old mice. Hypermethylation of some specific genes may correlate with the heart's strong proliferative and regenerative capability at the first day after birth. In terms of m6A density, the tendency shifted from coding sequences (CDS) to 3′-untranslated regions (3′UTR) and stop codon with the progression of heart development. In addition, some genes demonstrated remarkable changes both in methylation and expression, like kiss1, plekha6, and megf6, which may play important roles in proliferation. Furthermore, signaling pathways highly related to proliferation such as “Wnt signaling pathway,” “ECM-receptor interaction,” and “cardiac chamber formation” were significantly enriched in 1-day-old methylated genes. Conclusions. Our results reveal a pattern that different m6A modifications are distributed in C57BL/6J heart tissue at different developmental stages, which provides new insights into a novel function of m6A methylation of mRNA in myocardial development and regeneration.
Collapse
|
22
|
McNeill RV, Palladino VS, Brunkhorst-Kanaan N, Grimm O, Reif A, Kittel-Schneider S. Expression of the adult ADHD-associated gene ADGRL3 is dysregulated by risk variants and environmental risk factors. World J Biol Psychiatry 2021; 22:335-349. [PMID: 32787626 DOI: 10.1080/15622975.2020.1809014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVES ADGRL3 is a well-replicated risk gene for adult ADHD, encoding the G protein-coupled receptor latrophilin-3 (LPHN3). However, LPHN3's potential role in pathogenesis is unclear. We aimed to determine whether ADGRL3 expression could be dysregulated by genetic risk variants and/or ADHD-associated environmental risk factors. METHODS Eighteen adult ADHD patients and healthy controls were genotyped for rs734644, rs1397547, rs1397548, rs2271338, rs2305339, rs2345039 and rs6551665 ADGRL3 SNPs, and fibroblast cells were derived from skin punches. The environmental ADHD risk factors 'low birthweight' and 'maternal smoking' were modelled in fibroblast cell culture using starvation and nicotine exposure, respectively. Quantitative real-time PCR and western blotting were performed to quantify ADGRL3 gene and protein expression under control, starvation and nicotine-exposed conditions. RESULTS Starvation was found to significantly decrease ADGRL3 expression, whereas nicotine exposure significantly increased ADGRL3 expression. rs1397547 significantly elevated ADGRL3 transcription and protein expression. rs6551665 and rs2345039 interacted with environment to modulate ADGRL3 transcription. ADGRL3 SNPs were significantly able to predict its transcription under both baseline and starvation conditions, and rs1397547 was identified as a significant independent predictor. CONCLUSIONS ADGRL3 SNPs and environmental risk factors can regulate ADGRL3 expression, providing a potential functional mechanism by which LPHN3 may play a role in ADHD pathogenesis.
Collapse
Affiliation(s)
- Rhiannon V McNeill
- Department of Psychiatry, Psychotherapy and Psychosomatic Medicine, University Hospital Frankfurt, Frankfurt, Germany.,Department of Psychiatry, Psychotherapy and Psychosomatic Medicine, University Hospital Würzburg, Würzburg, Germany
| | - Viola Stella Palladino
- Department of Psychiatry, Psychotherapy and Psychosomatic Medicine, University Hospital Frankfurt, Frankfurt, Germany
| | - Nathalie Brunkhorst-Kanaan
- Department of Psychiatry, Psychotherapy and Psychosomatic Medicine, University Hospital Frankfurt, Frankfurt, Germany
| | - Oliver Grimm
- Department of Psychiatry, Psychotherapy and Psychosomatic Medicine, University Hospital Frankfurt, Frankfurt, Germany
| | - Andreas Reif
- Department of Psychiatry, Psychotherapy and Psychosomatic Medicine, University Hospital Frankfurt, Frankfurt, Germany
| | - Sarah Kittel-Schneider
- Department of Psychiatry, Psychotherapy and Psychosomatic Medicine, University Hospital Frankfurt, Frankfurt, Germany.,Department of Psychiatry, Psychotherapy and Psychosomatic Medicine, University Hospital Würzburg, Würzburg, Germany
| |
Collapse
|
23
|
Huff TC, Sant DW, Camarena V, Van Booven D, Andrade NS, Mustafi S, Monje PV, Wang G. Vitamin C regulates Schwann cell myelination by promoting DNA demethylation of pro-myelinating genes. J Neurochem 2021; 157:1759-1773. [PMID: 32219848 PMCID: PMC7530063 DOI: 10.1111/jnc.15015] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/12/2022]
Abstract
Ascorbic acid (vitamin C) is critical for Schwann cells to myelinate peripheral nerve axons during development and remyelination after injury. However, its exact mechanism remains elusive. Vitamin C is a dietary nutrient that was recently discovered to promote active DNA demethylation. Schwann cell myelination is characterized by global DNA demethylation in vivo and may therefore be regulated by vitamin C. We found that vitamin C induces a massive transcriptomic shift (n = 3,848 genes) in primary cultured Schwann cells while simultaneously producing a global increase in genomic 5-hydroxymethylcytosine (5hmC), a DNA demethylation intermediate which regulates transcription. Vitamin C up-regulates 10 pro-myelinating genes which exhibit elevated 5hmC content in both the promoter and gene body regions of these loci following treatment. Using a mouse model of human vitamin C metabolism, we found that maternal dietary vitamin C deficiency causes peripheral nerve hypomyelination throughout early development in resulting offspring. Additionally, dietary vitamin C intake regulates the expression of myelin-related proteins such as periaxin (PRX) and myelin basic protein (MBP) during development and remyelination after injury in mice. Taken together, these results suggest that vitamin C cooperatively promotes myelination through 1) increased DNA demethylation and transcription of pro-myelinating genes, and 2) its known role in stabilizing collagen helices to form the basal lamina that is necessary for myelination.
Collapse
Affiliation(s)
- Tyler C. Huff
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - David W. Sant
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Vladimir Camarena
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Nadja S. Andrade
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sushmita Mustafi
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Paula V. Monje
- Department of Neurological Surgery, Indiana University, Indianapolis, IN, USA
| | - Gaofeng Wang
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| |
Collapse
|
24
|
Örd T, Õunap K, Stolze LK, Aherrahrou R, Nurminen V, Toropainen A, Selvarajan I, Lönnberg T, Aavik E, Ylä-Herttuala S, Civelek M, Romanoski CE, Kaikkonen MU. Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci. Circ Res 2021; 129:240-258. [PMID: 34024118 PMCID: PMC8260472 DOI: 10.1161/circresaha.121.318971] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Supplemental Digital Content is available in the text. Genome-wide association studies have identified hundreds of loci associated with coronary artery disease (CAD). Many of these loci are enriched in cisregulatory elements but not linked to cardiometabolic risk factors nor to candidate causal genes, complicating their functional interpretation.
Collapse
Affiliation(s)
- Tiit Örd
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| | - Kadri Õunap
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| | - Lindsey K. Stolze
- Department of Cellular and Molecular Medicine, The College of Medicine, The University of Arizona, Tucson, AZ (L.K.S., C.E.R.)
| | - Redouane Aherrahrou
- Center for Public Health Genomics (R.A., M.C.), University of Virginia, Charlottesville
| | - Valtteri Nurminen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| | - Anu Toropainen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| | - Ilakya Selvarajan
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Finland (T.L.)
| | - Einari Aavik
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| | - Seppo Ylä-Herttuala
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| | - Mete Civelek
- Center for Public Health Genomics (R.A., M.C.), University of Virginia, Charlottesville
- Department of Biomedical Engineering (M.C.), University of Virginia, Charlottesville
| | - Casey E. Romanoski
- Department of Cellular and Molecular Medicine, The College of Medicine, The University of Arizona, Tucson, AZ (L.K.S., C.E.R.)
| | - Minna U. Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| |
Collapse
|
25
|
Rodger EJ, Almomani SN, Ludgate JL, Stockwell PA, Baguley BC, Eccles MR, Chatterjee A. Comparison of Global DNA Methylation Patterns in Human Melanoma Tissues and Their Derivative Cell Lines. Cancers (Basel) 2021; 13:cancers13092123. [PMID: 33924927 PMCID: PMC8124222 DOI: 10.3390/cancers13092123] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/19/2021] [Accepted: 04/22/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Cancer cell lines are a defined population of cells, originally sourced from tumour tissue, that can be maintained in culture for an extended period of time. They are a critical laboratory-based model, and are frequently used to unravel mechanisms of cancer cell biology. In all cells, gene activity is in part regulated by DNA methylation, the epigenetic process by which methyl groups are added to DNA. In this study, we demonstrate that at a global level, DNA methylation profiles are globally well conserved, but we identify specific sites that are consistently more methylated in tumour-derived cell lines compared to the original tumour tissue. The genes associated with these common differentially methylated regions are involved in important cellular processes and are strongly enriched for epigenetic mechanisms associated with suppression of gene activity. This study provides a valuable resource for identifying false positives due to cell culture and for better interpretation of future cancer epigenetics studies. Abstract DNA methylation is a heritable epigenetic mark that is fundamental to mammalian development. Aberrant DNA methylation is an epigenetic hallmark of cancer cells. Cell lines are a critical in vitro model and very widely used to unravel mechanisms of cancer cell biology. However, limited data are available to assess whether DNA methylation patterns in tissues are retained when cell lines are established. Here, we provide the first genome-scale sequencing-based methylation map of metastatic melanoma tumour tissues and their derivative cell lines. We show that DNA methylation profiles are globally conserved in vitro compared to the tumour tissue of origin. However, we identify sites that are consistently hypermethylated in cell lines compared to their tumour tissue of origin. The genes associated with these common differentially methylated regions are involved in cell metabolism, cell cycle and apoptosis and are also strongly enriched for the H3K27me3 histone mark and PRC2 complex-related genes. Our data indicate that although global methylation patterns are similar between tissues and cell lines, there are site-specific epigenomic differences that could potentially impact gene expression. Our work provides a valuable resource for identifying false positives due to cell culture and for better interpretation of cancer epigenetics studies in the future.
Collapse
Affiliation(s)
- Euan J. Rodger
- Department of Pathology, Otago Medical School—Dunedin Campus, University of Otago, Dunedin 9054, New Zealand; (S.N.A.); (J.L.L.); (P.A.S.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1010, New Zealand;
- Correspondence: (E.J.R.); (M.R.E.); (A.C.)
| | - Suzan N. Almomani
- Department of Pathology, Otago Medical School—Dunedin Campus, University of Otago, Dunedin 9054, New Zealand; (S.N.A.); (J.L.L.); (P.A.S.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1010, New Zealand;
| | - Jackie L. Ludgate
- Department of Pathology, Otago Medical School—Dunedin Campus, University of Otago, Dunedin 9054, New Zealand; (S.N.A.); (J.L.L.); (P.A.S.)
| | - Peter A. Stockwell
- Department of Pathology, Otago Medical School—Dunedin Campus, University of Otago, Dunedin 9054, New Zealand; (S.N.A.); (J.L.L.); (P.A.S.)
| | - Bruce C. Baguley
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1010, New Zealand;
| | - Michael R. Eccles
- Department of Pathology, Otago Medical School—Dunedin Campus, University of Otago, Dunedin 9054, New Zealand; (S.N.A.); (J.L.L.); (P.A.S.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1010, New Zealand;
- Correspondence: (E.J.R.); (M.R.E.); (A.C.)
| | - Aniruddha Chatterjee
- Department of Pathology, Otago Medical School—Dunedin Campus, University of Otago, Dunedin 9054, New Zealand; (S.N.A.); (J.L.L.); (P.A.S.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1010, New Zealand;
- Correspondence: (E.J.R.); (M.R.E.); (A.C.)
| |
Collapse
|
26
|
Goldsmith C, Rodríguez-Aguilera JR, El-Rifai I, Jarretier-Yuste A, Hervieu V, Raineteau O, Saintigny P, Chagoya de Sánchez V, Dante R, Ichim G, Hernandez-Vargas H. Low biological fluctuation of mitochondrial CpG and non-CpG methylation at the single-molecule level. Sci Rep 2021; 11:8032. [PMID: 33850190 PMCID: PMC8044111 DOI: 10.1038/s41598-021-87457-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/30/2021] [Indexed: 12/16/2022] Open
Abstract
Mammalian cytosine DNA methylation (5mC) is associated with the integrity of the genome and the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is methylated and whether 5mC has a regulatory role in this context. Here, we used bisulfite-independent single-molecule sequencing of native human and mouse DNA to study mitochondrial 5mC across different biological conditions. We first validated the ability of long-read nanopore sequencing to detect 5mC in CpG (5mCpG) and non-CpG (5mCpH) context in nuclear DNA at expected genomic locations (i.e. promoters, gene bodies, enhancers, and cell type-specific transcription factor binding sites). Next, using high coverage nanopore sequencing we found low levels of mtDNA CpG and CpH methylation (with several exceptions) and little variation across biological processes: differentiation, oxidative stress, and cancer. 5mCpG and 5mCpH were overall higher in tissues compared to cell lines, with small additional variation between cell lines of different origin. Despite general low levels, global and single-base differences were found in cancer tissues compared to their adjacent counterparts, in particular for 5mCpG. In conclusion, nanopore sequencing is a useful tool for the detection of modified DNA bases on mitochondria that avoid the biases introduced by bisulfite and PCR amplification. Enhanced nanopore basecalling models will provide further resolution on the small size effects detected here, as well as rule out the presence of other DNA modifications such as oxidized forms of 5mC.
Collapse
Affiliation(s)
- Chloe Goldsmith
- Department of Tumor Escape, Resistance and Immunity, TGF-Beta and Immuno-Regulation Team, Cancer Research Centre of Lyon (CRCL), INSERM U 1052, CNRS UMR 5286, UCBL1, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France.
| | - Jesús Rafael Rodríguez-Aguilera
- Department of Cellular Biology and Development, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | - Ines El-Rifai
- Department of Tumor Escape, Resistance and Immunity, TGF-Beta and Immuno-Regulation Team, Cancer Research Centre of Lyon (CRCL), INSERM U 1052, CNRS UMR 5286, UCBL1, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France
| | - Adrien Jarretier-Yuste
- Department of Tumor Escape, Resistance and Immunity, TGF-Beta and Immuno-Regulation Team, Cancer Research Centre of Lyon (CRCL), INSERM U 1052, CNRS UMR 5286, UCBL1, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France
| | - Valérie Hervieu
- Department of Surgical Pathology, Hospices Civils de Lyon, Groupement Hospitalier Est, Lyon, France
| | - Olivier Raineteau
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, Bron, France
| | - Pierre Saintigny
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- Department of Translational Medicine, Centre Léon Bérard, Lyon, France
| | - Victoria Chagoya de Sánchez
- Department of Cellular Biology and Development, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | - Robert Dante
- Dependence Receptors Cancer and Development Laboratory, Department of Signaling of Tumoral Escape. Cancer Research. Center of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France
| | - Gabriel Ichim
- Cancer Cell Death Laboratory, Part of LabEx DEVweCAN, Université de Lyon, Lyon, France
- Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France
| | - Hector Hernandez-Vargas
- Department of Tumor Escape, Resistance and Immunity, TGF-Beta and Immuno-Regulation Team, Cancer Research Centre of Lyon (CRCL), INSERM U 1052, CNRS UMR 5286, UCBL1, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France.
- Department of Translational Medicine, Centre Léon Bérard, Lyon, France.
| |
Collapse
|
27
|
Holloway PM, Willaime-Morawek S, Siow R, Barber M, Owens RM, Sharma AD, Rowan W, Hill E, Zagnoni M. Advances in microfluidic in vitro systems for neurological disease modeling. J Neurosci Res 2021; 99:1276-1307. [PMID: 33583054 DOI: 10.1002/jnr.24794] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/21/2020] [Accepted: 12/19/2020] [Indexed: 12/19/2022]
Abstract
Neurological disorders are the leading cause of disability and the second largest cause of death worldwide. Despite significant research efforts, neurology remains one of the most failure-prone areas of drug development. The complexity of the human brain, boundaries to examining the brain directly in vivo, and the significant evolutionary gap between animal models and humans, all serve to hamper translational success. Recent advances in microfluidic in vitro models have provided new opportunities to study human cells with enhanced physiological relevance. The ability to precisely micro-engineer cell-scale architecture, tailoring form and function, has allowed for detailed dissection of cell biology using microphysiological systems (MPS) of varying complexities from single cell systems to "Organ-on-chip" models. Simplified neuronal networks have allowed for unique insights into neuronal transport and neurogenesis, while more complex 3D heterotypic cellular models such as neurovascular unit mimetics and "Organ-on-chip" systems have enabled new understanding of metabolic coupling and blood-brain barrier transport. These systems are now being developed beyond MPS toward disease specific micro-pathophysiological systems, moving from "Organ-on-chip" to "Disease-on-chip." This review gives an outline of current state of the art in microfluidic technologies for neurological disease research, discussing the challenges and limitations while highlighting the benefits and potential of integrating technologies. We provide examples of where such toolsets have enabled novel insights and how these technologies may empower future investigation into neurological diseases.
Collapse
Affiliation(s)
- Paul M Holloway
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Richard Siow
- King's British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Melissa Barber
- King's British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Róisín M Owens
- Department Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Anup D Sharma
- New Orleans BioInnovation Center, AxoSim Inc., New Orleans, LA, USA
| | - Wendy Rowan
- Novel Human Genetics Research Unit, GSK R&D, Stevenage, UK
| | - Eric Hill
- School of Life and Health sciences, Aston University, Birmingham, UK
| | - Michele Zagnoni
- Electronic and Electrical Engineering, University of Strathclyde, Glasgow, UK
| |
Collapse
|
28
|
Seumois G, Ramírez-Suástegui C, Schmiedel BJ, Liang S, Peters B, Sette A, Vijayanand P. Single-cell transcriptomic analysis of allergen-specific T cells in allergy and asthma. Sci Immunol 2021; 5:5/48/eaba6087. [PMID: 32532832 DOI: 10.1126/sciimmunol.aba6087] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/22/2020] [Indexed: 12/19/2022]
Abstract
CD4+ T helper (TH) cells and regulatory T (Treg) cells that respond to common allergens play an important role in driving and dampening airway inflammation in patients with asthma. Until recently, direct, unbiased molecular analysis of allergen-reactive TH and Treg cells has not been possible. To better understand the diversity of these T cell subsets in allergy and asthma, we analyzed the single-cell transcriptome of ~50,000 house dust mite (HDM) allergen-reactive TH cells and Treg cells from asthmatics with HDM allergy and from three control groups: asthmatics without HDM allergy and nonasthmatics with and without HDM allergy. Our analyses show that HDM allergen-reactive TH and Treg cells are highly heterogeneous and certain subsets are quantitatively and qualitatively different in individuals with HDM-reactive asthma. The number of interleukin-9 (IL-9)-expressing HDM-reactive TH cells is greater in asthmatics with HDM allergy compared with nonasthmatics with HDM allergy, and this IL-9-expressing TH subset displays enhanced pathogenic properties. More HDM-reactive TH and Treg cells expressing the interferon response signature (THIFNR and TregIFNR) are present in asthmatics without HDM allergy compared with those with HDM allergy. In cells from these subsets (THIFNR and TregIFNR), expression of TNFSF10 was enriched; its product, tumor necrosis factor-related apoptosis-inducing ligand, dampens activation of TH cells. These findings suggest that the THIFNR and TregIFNR subsets may dampen allergic responses, which may help explain why only some people develop TH2 responses to nearly ubiquitous allergens.
Collapse
Affiliation(s)
- Grégory Seumois
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
| | | | | | - Shu Liang
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.,Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.,Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Pandurangan Vijayanand
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA. .,Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA.,Clinical and Experimental Sciences, National Institute for Health Research Southampton Respiratory Biomedical Research Unit, Faculty of Medicine, University of Southampton, Southampton SO166YD, UK
| |
Collapse
|
29
|
Tsiouplis NJ, Bailey DW, Chiou LF, Wissink FJ, Tsagaratou A. TET-Mediated Epigenetic Regulation in Immune Cell Development and Disease. Front Cell Dev Biol 2021; 8:623948. [PMID: 33520997 PMCID: PMC7843795 DOI: 10.3389/fcell.2020.623948] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
TET proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidation products in DNA. The oxidized methylcytosines (oxi-mCs) facilitate DNA demethylation and are also novel epigenetic marks. TET loss-of-function is strongly associated with cancer; TET2 loss-of-function mutations are frequently observed in hematological malignancies that are resistant to conventional therapies. Importantly, TET proteins govern cell fate decisions during development of various cell types by activating a cell-specific gene expression program. In this review, we seek to provide a conceptual framework of the mechanisms that fine tune TET activity. Then, we specifically focus on the multifaceted roles of TET proteins in regulating gene expression in immune cell development, function, and disease.
Collapse
Affiliation(s)
- Nikolas James Tsiouplis
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States
| | - David Wesley Bailey
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States.,University of North Carolina Center of Translational Immunology, Chapel Hill, NC, United States.,University of North Carolina Institute of Inflammatory Disease, Chapel Hill, NC, United States
| | - Lilly Felicia Chiou
- University of North Carolina Curriculum in Genetics and Molecular Biology, Chapel Hill, NC, United States
| | - Fiona Jane Wissink
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States
| | - Ageliki Tsagaratou
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States.,University of North Carolina Center of Translational Immunology, Chapel Hill, NC, United States.,University of North Carolina Institute of Inflammatory Disease, Chapel Hill, NC, United States.,University of North Carolina Curriculum in Genetics and Molecular Biology, Chapel Hill, NC, United States.,University of North Carolina Department of Genetics, Chapel Hill, NC, United States.,University of North Carolina Department of Microbiology and Immunology, Chapel Hill, NC, United States
| |
Collapse
|
30
|
Noberini R, Robusti G, Bonaldi T. Mass spectrometry-based characterization of histones in clinical samples: applications, progresses, and challenges. FEBS J 2021; 289:1191-1213. [PMID: 33415821 PMCID: PMC9291046 DOI: 10.1111/febs.15707] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/24/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022]
Abstract
In the last 15 years, increasing evidence linking epigenetics to various aspects of cancer biology has prompted the investigation of histone post-translational modifications (PTMs) and histone variants in the context of clinical samples. The studies performed so far demonstrated the potential of this type of investigations for the discovery of both potential epigenetic biomarkers for patient stratification and novel epigenetic mechanisms potentially targetable for cancer therapy. Although traditionally the analysis of histones in clinical samples was performed through antibody-based methods, mass spectrometry (MS) has emerged as a more powerful tool for the unbiased, comprehensive, and quantitative investigation of histone PTMs and variants. MS has been extensively used for the analysis of epigenetic marks in cell lines and animal tissue and, thanks to recent technological advances, is now ready to be applied also to clinical samples. In this review, we will provide an overview on the quantitative MS-based analysis of histones, their PTMs and their variants in cancer clinical samples, highlighting current achievements and future perspectives for this novel field of research. Among the different MS-based approaches currently available for histone PTM profiling, we will focus on the 'bottom-up' strategy, namely the analysis of short proteolytic peptides, as it has been already successfully employed for the analysis of clinical samples.
Collapse
Affiliation(s)
- Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giulia Robusti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| |
Collapse
|
31
|
Tsagaratou A. Deciphering the multifaceted roles of TET proteins in T-cell lineage specification and malignant transformation. Immunol Rev 2021; 300:22-36. [PMID: 33410200 DOI: 10.1111/imr.12940] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/23/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022]
Abstract
TET proteins are DNA demethylases that can oxidize 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC) and other oxidized mC bases (oxi-mCs). Importantly, TET proteins govern cell fate decisions during development of various cell types by activating a cell-specific gene expression program. In this review, we focus on the role of TET proteins in T-cell lineage specification. We explore the multifaceted roles of TET proteins in regulating gene expression in the contexts of T-cell development, lineage specification, function, and disease. Finally, we discuss the future directions and experimental strategies required to decipher the precise mechanisms employed by TET proteins to fine-tune gene expression and safeguard cell identity.
Collapse
Affiliation(s)
- Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Center of Translational Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Institute of Inflammatory Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
32
|
Noberini R, Restellini C, Savoia EO, Bonaldi T. Enrichment of histones from patient samples for mass spectrometry-based analysis of post-translational modifications. Methods 2020; 184:19-28. [DOI: 10.1016/j.ymeth.2019.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/30/2019] [Accepted: 10/04/2019] [Indexed: 12/22/2022] Open
|
33
|
Abstract
PURPOSE OF REVIEW The aims of this review are to evaluate the methods used to measure 5-hydroxymethylcytosine (5-hmC), and then summarize the available data investigating the impact of environmental factors on 5-hydroxymethylcytosine (5-hmC) in the brain. RECENT FINDINGS Recent research has shown that some environmental factors, including exposure to exogenous chemicals, stress, altered diet, and exercise, are all associated with 5-hmC variation in the brain. However, due to a lack of specificity in the methods used to generate a majority of the available data, it cannot be determined whether environment-induced changes in 5-hmC occur in specific biological pathways. Environment appears to shape 5-hmC levels in the brain, but the available literature is hampered by limitations in measurement methods. The field of neuroepigenetics needs to adopt new tools to increase the specificity of its data and enhance biological interpretation of exposure-related changes in 5-hmC. This will help improve understanding of the potential roles for environmental factors and 5-hmC in neurological disease.
Collapse
Affiliation(s)
- Joseph Kochmanski
- Department of Translational Neuroscience, Grand Rapids Research Center, Michigan State University College of Human Medicine, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
| | - Alison I Bernstein
- Department of Translational Neuroscience, Grand Rapids Research Center, Michigan State University College of Human Medicine, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA.
| |
Collapse
|
34
|
Lu J, Jiang G, Wu Y, Antony S, Meitzler JL, Juhasz A, Liu H, Roy K, Makhlouf H, Chuaqui R, Butcher D, Konaté MM, Doroshow JH. NADPH oxidase 1 is highly expressed in human large and small bowel cancers. PLoS One 2020; 15:e0233208. [PMID: 32428030 PMCID: PMC7237001 DOI: 10.1371/journal.pone.0233208] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 04/30/2020] [Indexed: 12/21/2022] Open
Abstract
To facilitate functional investigation of the role of NADPH oxidase 1 (NOX1) and associated reactive oxygen species in cancer cell signaling, we report herein the development and characterization of a novel mouse monoclonal antibody that specifically recognizes the C-terminal region of the NOX1 protein. The antibody was validated in stable NOX1 overexpression and knockout systems, and demonstrates wide applicability for Western blot analysis, confocal microscopy, flow cytometry, and immunohistochemistry. We employed our NOX1 antibody to characterize NOX1 expression in a panel of 30 human colorectal cancer cell lines, and correlated protein expression with NOX1 mRNA expression and superoxide production in a subset of these cells. Although a significant correlation between oncogenic RAS status and NOX1 mRNA levels could not be demonstrated in colon cancer cell lines, RAS mutational status did correlate with NOX1 expression in human colon cancer surgical specimens. Immunohistochemical analysis of a comprehensive set of tissue microarrays comprising over 1,200 formalin-fixed, paraffin-embedded tissue cores from human epithelial tumors and inflammatory disease confirmed that NOX1 is overexpressed in human colon and small intestinal adenocarcinomas, as well as adenomatous polyps, compared to adjacent, uninvolved intestinal mucosae. In contradistinction to prior studies, we did not find evidence of NOX1 overexpression at the protein level in tumors versus histologically normal tissues in prostate, lung, ovarian, or breast carcinomas. This study constitutes the most comprehensive histopathological characterization of NOX1 to date in cellular models of colon cancer and in normal and malignant human tissues using a thoroughly evaluated monoclonal antibody. It also further establishes NOX1 as a clinically relevant therapeutic target in colorectal and small intestinal cancer.
Collapse
Affiliation(s)
- Jiamo Lu
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Guojian Jiang
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Yongzhong Wu
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Smitha Antony
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Jennifer L. Meitzler
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Agnes Juhasz
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Han Liu
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Krishnendu Roy
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Hala Makhlouf
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Rodrigo Chuaqui
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Donna Butcher
- Pathology/Histotechnology Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Mariam M. Konaté
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, United States of America
| | - James H. Doroshow
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, United States of America
| |
Collapse
|
35
|
Abstract
Trichloroethylene (TCE) is an industrial solvent and a common environmental contaminant detected in thousands of hazardous waste sites. Risk of exposure is a concern for workers in occupations that use TCE as well as for residents who live near industries that use TCE or who live near TCE-contaminated sites. Although renal, hepatic and carcinogenic effects of TCE have been documented, less is known about TCE impacts on reproductive functions despite epidemiology reports associating maternal TCE exposure with adverse pregnancy outcomes. Toxicological evidence suggests that the placenta mediates at least some of the adverse pregnancy outcomes associated with TCE exposure. Toxicology studies show that the TCE metabolite, S-(1,2-dichlorovinyl)-l-cysteine (DCVC) generates toxic effects such as mitochondrial dysfunction, apoptosis, oxidative stress, and release of prostaglandins and pro-inflammatory cytokines in placental cell lines. Each of these mechanisms of toxicity have significant implications for placental functions and, thus, ultimately the health of mother and developing child. Despite these findings there remain significant gaps in our knowledge about effects of TCE on the placenta, including effects on specific placental cell types and functions as well as sex differences in response to TCE exposure. Due to the critical role that the placenta plays in pregnancy, future research addressing some of these knowledge gaps could lead to significant gains in public health.
Collapse
Affiliation(s)
- Elana R Elkin
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109-2029, USA.
| | | | | | | | | |
Collapse
|
36
|
Kint S, Trypsteen W, De Spiegelaere W, Malatinkova E, Kinloch-de Loes S, De Meyer T, Van Criekinge W, Vandekerckhove L. Underestimated effect of intragenic HIV-1 DNA methylation on viral transcription in infected individuals. Clin Epigenetics 2020; 12:36. [PMID: 32111236 PMCID: PMC7049218 DOI: 10.1186/s13148-020-00829-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/16/2020] [Indexed: 12/13/2022] Open
Abstract
Background The HIV-1 proviral genome harbors multiple CpG islands (CpGIs), both in the promoter and intragenic regions. DNA methylation in the promoter region has been shown to be heavily involved in HIV-1 latency regulation in cultured cells. However, its exact role in proviral transcriptional regulation in infected individuals is poorly understood or characterized. Moreover, methylation at intragenic CpGIs has never been studied in depth. Results A large, well-characterized HIV-1 patient cohort (n = 72), consisting of 17 long-term non-progressors and 8 recent seroconverters (SRCV) without combination antiretroviral therapy (cART), 15 early cART-treated, and 32 late cART-treated patients, was analyzed using a next-generation bisulfite sequencing DNA methylation method. In general, we observed low level of promoter methylation and higher levels of intragenic methylation. Additionally, SRCV showed increased promoter methylation and decreased intragenic methylation compared with the other patient groups. This data indicates that increased intragenic methylation could be involved in proviral transcriptional regulation. Conclusions Contrasting in vitro studies, our results indicate that intragenic hypermethylation of HIV-1 proviral DNA is an underestimated factor in viral control in HIV-1-infected individuals, showing the importance of analyzing the complete proviral genome in future DNA methylation studies.
Collapse
Affiliation(s)
- Sam Kint
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, Medical Research Building 2, 9000, Ghent, Belgium.,Biobix, Department of Data Analysis and Mathematical Modelling, Faculty of Bio-science Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, Medical Research Building 2, 9000, Ghent, Belgium
| | - Ward De Spiegelaere
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Eva Malatinkova
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, Medical Research Building 2, 9000, Ghent, Belgium
| | - Sabine Kinloch-de Loes
- Division of Infection and Immunity, Royal Free Hospital, Royal Free Campus, University College London, Pont St, Hampstead, London, NW3 2QG, UK
| | - Tim De Meyer
- Biobix, Department of Data Analysis and Mathematical Modelling, Faculty of Bio-science Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wim Van Criekinge
- Biobix, Department of Data Analysis and Mathematical Modelling, Faculty of Bio-science Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, Medical Research Building 2, 9000, Ghent, Belgium.
| |
Collapse
|
37
|
Labitzky V, Baranowsky A, Maar H, Hanika S, Starzonek S, Ahlers AK, Stübke K, Koziolek EJ, Heine M, Schäfer P, Windhorst S, Jücker M, Riecken K, Amling M, Schinke T, Schumacher U, Valentiner U, Lange T. Modeling Spontaneous Bone Metastasis Formation of Solid Human Tumor Xenografts in Mice. Cancers (Basel) 2020; 12:E385. [PMID: 32046143 DOI: 10.3390/cancers12020385] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/02/2020] [Accepted: 02/05/2020] [Indexed: 12/18/2022] Open
Abstract
The majority of cancer-related deaths are due to hematogenous metastases, and the bone marrow (BM) represents one of the most frequent metastatic sites. To study BM metastasis formation in vivo, the most efficient approach is based on intracardiac injection of human tumor cells into immunodeficient mice. However, such a procedure circumvents the early steps of the metastatic cascade. Here we describe the development of xenograft mouse models (balb/c rag2-/- and severe combined immunodeficient (SCID)), in which BM metastases are spontaneously derived from subcutaneous (s.c.) primary tumors (PTs). As verified by histology, the described methodology including ex vivo bioluminescence imaging (BLI) even enabled the detection of micrometastases in the BM. Furthermore, we established sublines from xenograft primary tumors (PTs) and corresponding BM (BM) metastases using LAN-1 neuroblastoma xenografts as a first example. In vitro "metastasis" assays (viability, proliferation, transmigration, invasion, colony formation) partially indicated pro-metastatic features of the LAN-1-BM compared to the LAN-1-PT subline. Unexpectedly, after s.c. re-injection into mice, LAN-1-BM xenografts developed spontaneous BM metastases less frequently than LAN-1-PT xenografts. This study provides a novel methodologic approach for modelling the spontaneous metastatic cascade of human BM metastasis formation in mice. Moreover, our data indicate that putative bone-metastatic features get rapidly lost upon routine cell culture.
Collapse
|
38
|
Reus JB, Trivino-Soto GS, Wu LI, Kokott K, Lim ES. SV40 Large T Antigen Is Not Responsible for the Loss of STING in 293T Cells but Can Inhibit cGAS-STING Interferon Induction. Viruses 2020; 12:v12020137. [PMID: 31991682 PMCID: PMC7077178 DOI: 10.3390/v12020137] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 01/05/2023] Open
Abstract
Several DNA viruses have evolved antagonists to inhibit the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) DNA-sensing immune pathway. This includes DNA viral oncogenes that antagonize the cGAS-STING pathway by binding STING through the LxCxE motif. The 293T human cells are widely used in biology studies as they are highly transfectable. While parental 293 cells express high levels of STING, 293T cells lack STING and are unable to induce interferon antiviral responses to cytosolic DNA. Additionally, 293T cells express the SV40 polyomavirus large T antigen (LT) which enhances the replication of transfected DNA plasmids carrying the SV40 origin of replication. Since SV40 LT also encodes the LxCxE motif, the lack of STING expression in 293T cells is commonly assumed to be due to SV40 large T antigen. We find that SV40 LT does not alter exogenously expressed and endogenous levels of STING protein. We show that STING transcription is suppressed in 293T cells but is not driven by SV40. This study also revealed that SV40 LT does indeed inhibit cGAS-STING interferon induction, but through a mechanism distinct from other DNA virus oncogenes. Collectively, these results indicate that while SV40 LT can inhibit cGAS-STING interferon induction, it does so in an unanticipated manner.
Collapse
Affiliation(s)
- Joshua B. Reus
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Guillermo S. Trivino-Soto
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Lily I. Wu
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Kristiana Kokott
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Efrem S. Lim
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Correspondence:
| |
Collapse
|
39
|
Uribe-Lewis S, Carroll T, Menon S, Nicholson A, Manasterski PJ, Winton DJ, Buczacki SJA, Murrell A. 5-hydroxymethylcytosine and gene activity in mouse intestinal differentiation. Sci Rep 2020; 10:546. [PMID: 31953501 PMCID: PMC6969059 DOI: 10.1038/s41598-019-57214-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/19/2019] [Indexed: 12/17/2022] Open
Abstract
Cytosine hydroxymethylation (5hmC) in mammalian DNA is the product of oxidation of methylated cytosines (5mC) by Ten-Eleven-Translocation (TET) enzymes. While it has been shown that the TETs influence 5mC metabolism, pluripotency and differentiation during early embryonic development, the functional relationship between gene expression and 5hmC in adult (somatic) stem cell differentiation is still unknown. Here we report that 5hmC levels undergo highly dynamic changes during adult stem cell differentiation from intestinal progenitors to differentiated intestinal epithelium. We profiled 5hmC and gene activity in purified mouse intestinal progenitors and differentiated progeny to identify 43425 differentially hydroxymethylated regions and 5325 differentially expressed genes. These differentially marked regions showed both losses and gains of 5hmC after differentiation, despite lower global levels of 5hmC in progenitor cells. In progenitors, 5hmC did not correlate with gene transcript levels, however, upon differentiation the global increase in 5hmC content showed an overall positive correlation with gene expression level as well as prominent associations with histone modifications that typify active genes and enhancer elements. Our data support a gene regulatory role for 5hmC that is predominant over its role in controlling DNA methylation states.
Collapse
Affiliation(s)
- Santiago Uribe-Lewis
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University New York, New York, NY, 10065, USA
| | - Suraj Menon
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Anna Nicholson
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Piotr J Manasterski
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Douglas J Winton
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Simon J A Buczacki
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Addenbrookes Biomedical Campus, Cambridge, CB2 0AF, UK
| | - Adele Murrell
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| |
Collapse
|
40
|
Abstract
Epigenomic mapping of tissue samples generates critical insights into genome-wide regulations of gene activities and expressions during normal development and disease processes. Epigenomic profiling using a low number of cells produced by patient and mouse samples presents new challenges to biotechnologists. In this review, we first discuss the rationale and premise behind profiling epigenomes for precision medicine. We then examine the existing literature on applying microfluidics to facilitate low-input and high-throughput epigenomic profiling, with emphasis on technologies enabling interfacing with next-generation sequencing. We detail assays on studies of histone modifications, DNA methylation, 3D chromatin structures and non-coding RNAs. Finally, we discuss what the future may hold in terms of method development and translational potential.
Collapse
Affiliation(s)
- Chengyu Deng
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| |
Collapse
|
41
|
Çelik-Uzuner S. Enhanced immunological detection of epigenetic modifications of DNA in healthy and cancerous cells by fluorescence microscopy. Microsc Res Tech 2019; 82:1962-1972. [PMID: 31429164 DOI: 10.1002/jemt.23365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022]
Abstract
Epigenetic modifications of DNA, including methylation, hydroxymethylation, formylation, and carboxylation of cytosines, are proposed to function in gene regulation during reproduction and development. Changes in cytosine methylation are associated with a range of diseases, such as cancer. Immunofluorescence uses specific antibodies to quantitatively detect the global amount of cytosine modifications by fluorescence microscopy. The most critical stage of immunofluorescence is the antigen retrieval to remove the protein content around the DNA, allowing specific antibodies to bind to DNA epitopes. Acid treatments have commonly been used for antigen retrieval. Previously, trypsin was added after acid in the protocol, which increased the amount of detectable DNA methylation. In this study, the protocol was further enhanced by the addition of pepsin, which is able to target charged hydrophobic amino acids in proteins, unlike trypsin, which breaks positive hydrophilic amino acids. The global levels of cytosine modifications in CF-1, HeLa, and AR42J cells were compared using this protocol. In all cells, the sequential treatment of trypsin and pepsin increased the specificity of the staining. With the synergistic effect of the two enzymes, it is possible to target different protein groups packaging DNA molecules and removing them effectively. The findings suggest that this revised protocol can be conveniently used for each cytosine modification in the cells examined, and should be optimized for other cells. These new antigen retrieval conditions may more accurately detect the changes in cytosine modifications during development and in diseases.
Collapse
Affiliation(s)
- Selcen Çelik-Uzuner
- Faculty of Science, Department of Molecular Biology and Genetics, Karadeniz Technical University, Trabzon, Turkey
| |
Collapse
|
42
|
Losi L, Lauriola A, Tazzioli E, Gozzi G, Scurani L, D'Arca D, Benhattar J. Involvement of epigenetic modification of TERT promoter in response to all-trans retinoic acid in ovarian cancer cell lines. J Ovarian Res 2019; 12:62. [PMID: 31291979 PMCID: PMC6617683 DOI: 10.1186/s13048-019-0536-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 07/01/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND All-trans retinoic acid (ATRA) is currently being used to treat hematological malignancies, given the ability to inhibit cell proliferation. This effect seems to be related to epigenetic changes of the TERT (Telomerase Reverse Transcriptase) promoter. When hypomethylated, ATRA-inducible TERT repressors can bind the promoter, repressing transcription of TERT, the rate-limiting component of telomerase. Ovarian carcinomas are heterogeneous tumors characterized by several aberrantly methylated genes among which is TERT. We recently found a hypomethylation of TERT promoter in about one third of serous carcinoma, the most lethal histotype. Our aim was to investigate the potential role of ATRA as an anticancer drug in a sub-group of ovarian carcinoma where the TERT promoter was hypomethylated. METHODS The potential antiproliferative and cytotoxic effect of ATRA was investigated in seven serous ovarian carcinoma and one teratocarcinoma cell lines and the results were compared to the methylation status of their TERT promoter. RESULTS The serous ovarian carcinoma cell line OVCAR3, harboring a hypomethylated TERT promoter, was the best and fastest responder. PA1 and SKOV3, two cell lines with an intermediate methylated promoter, revealed a weaker and delayed response. On the contrary, the other 5 cell lines with a highly methylated promoter did not respond to ATRA, indicative of ATRA-resistant cells. CONCLUSIONS Our results demonstrate an inverse correlation between the methylation level of TERT promoter and ATRA efficacy in ovarian carcinoma cell lines. Although these results are preliminary, ATRA treatment could become a new powerful, personalized therapy in serous ovarian carcinoma patients, but only in those with tumors harboring a hypomethylated TERT promoter.
Collapse
Affiliation(s)
- Lorena Losi
- Department of Life Sciences, Unit of Pathology, University of Modena and Reggio Emilia, Largo del Pozzo 71, 41124, Modena, Italy.
| | - Angela Lauriola
- Department of Life Sciences, Unit of Pathology, University of Modena and Reggio Emilia, Largo del Pozzo 71, 41124, Modena, Italy.,Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Erica Tazzioli
- Department of Life Sciences, Unit of Pathology, University of Modena and Reggio Emilia, Largo del Pozzo 71, 41124, Modena, Italy.,Institute of Pathology, Lausanne University Hospital, Lausanne, Switzerland
| | - Gaia Gozzi
- Department of Life Sciences, Unit of Pathology, University of Modena and Reggio Emilia, Largo del Pozzo 71, 41124, Modena, Italy
| | - Letizia Scurani
- Department of Life Sciences, Unit of Pathology, University of Modena and Reggio Emilia, Largo del Pozzo 71, 41124, Modena, Italy
| | - Domenico D'Arca
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Jean Benhattar
- Institute of Pathology, Lausanne University Hospital, Lausanne, Switzerland. .,Aurigen, Centre de Génétique et Pathologie, Avenue de Sévelin 18, 1004, Lausanne, Switzerland.
| |
Collapse
|
43
|
Noberini R, Restellini C, Savoia EO, Raimondi F, Ghiani L, Jodice MG, Bertalot G, Bonizzi G, Capra M, Maffini FA, Tagliabue M, Ansarin M, Lupia M, Giordano M, Osti D, Pelicci G, Chiocca S, Bonaldi T. Profiling of Epigenetic Features in Clinical Samples Reveals Novel Widespread Changes in Cancer. Cancers (Basel) 2019; 11:E723. [PMID: 31137727 DOI: 10.3390/cancers11050723] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/09/2019] [Accepted: 05/20/2019] [Indexed: 12/31/2022] Open
Abstract
Aberrations in histone post-translational modifications (PTMs), as well as in the histone modifying enzymes (HMEs) that catalyze their deposition and removal, have been reported in many tumors and many epigenetic inhibitors are currently under investigation for cancer treatment. Therefore, profiling epigenetic features in cancer could have important implications for the discovery of both biomarkers for patient stratification and novel epigenetic targets. In this study, we employed mass spectrometry-based approaches to comprehensively profile histone H3 PTMs in a panel of normal and tumoral tissues for different cancer types, identifying various changes, some of which appear to be a consequence of the increased proliferation rate of tumors, while others are cell-cycle independent. Histone PTM changes found in tumors partially correlate with alterations of the gene expression profiles of HMEs obtained from publicly available data and are generally lost in culture conditions. Through this analysis, we identified tumor- and subtype-specific histone PTM changes, but also widespread changes in the levels of histone H3 K9me3 and K14ac marks. In particular, H3K14ac showed a cell-cycle independent decrease in all the seven tumor/tumor subtype models tested and could represent a novel epigenetic hallmark of cancer. .
Collapse
|
44
|
Wang P, Yan Y, Yu W, Zhang H. Role of ten-eleven translocation proteins and 5-hydroxymethylcytosine in hepatocellular carcinoma. Cell Prolif 2019; 52:e12626. [PMID: 31033072 PMCID: PMC6668972 DOI: 10.1111/cpr.12626] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/26/2019] [Accepted: 04/03/2019] [Indexed: 12/13/2022] Open
Abstract
In mammals, methylation of the 5th position of cytosine (5mC) seems to be a major epigenetic modification of DNA. This process can be reversed (resulting in cytosine) with high efficiency by dioxygenases of the ten‐eleven translocation (TET) family, which perform oxidation of 5mC to 5‐hydroxymethylcytosine (5hmC), 5‐formylcytosine and 5‐carboxylcytosine. It has been demonstrated that these 5mC oxidation derivatives are in a dynamic state and have pivotal regulatory functions. Here, we comprehensively summarized the recent research progress in the understanding of the physiological functions of the TET proteins and their mechanisms of regulation of DNA methylation and transcription. Among the three TET genes, TET1 and TET2 expression levels have frequently been shown to be low in hepatocellular carcinoma (HCC) tissues and received most attention. The modulation of TET1 also correlates with microRNAs in a post‐transcriptional regulatory process. Additionally, recent studies revealed that global genomic 5hmC levels are down‐regulated in HCC tissues and cell lines. Combined with the reported results, identification of 5hmC signatures in HCC tissues and in circulating cell‐free DNA will certainly contribute to early detection and should help to design therapeutic strategies against HCC. 5hmC might also be a novel prognostic biomarker of HCC. Thus, a detailed understanding of the molecular mechanisms resulting in the premalignant and aggressive transformation of TET proteins and cells with 5hmC disruption might help to develop novel epigenetic therapies for HCC.
Collapse
Affiliation(s)
- Penghui Wang
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yunmeng Yan
- Key Clinical Laboratory of Henan Province, Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Yu
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hongyi Zhang
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
45
|
Walters BJ, Cox BC. Approaches for the study of epigenetic modifications in the inner ear and related tissues. Hear Res 2019; 376:69-85. [PMID: 30679030 DOI: 10.1016/j.heares.2019.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/12/2018] [Accepted: 01/11/2019] [Indexed: 12/12/2022]
Abstract
DNA methylation and histone modifications such as methylation, acetylation, and phosphorylation, are two types of epigenetic modifications that alter gene expression. These additions to DNA regulatory elements or to the tails of histones can be inherited or can also occur de novo. Since epigenetic modifications can have significant effects on various processes at both the cellular and organismal level, there has been a rapid increase in research on this topic throughout all fields of biology in recent years. However, epigenetic research is relativity new for the inner ear field, likely due to the limited number of cells present and their quiescent nature. Here, we provide an overview of methods used to detect DNA methylation and histone modifications with a focus on those that have been validated for use with limited cell numbers and a discussion of the strengths and limitations for each. We also provide examples for how these methods have been used to investigate the epigenetic landscape in the inner ear and related tissues.
Collapse
Affiliation(s)
- Bradley J Walters
- Departments of Neurobiology and Anatomical Sciences, and of Otolaryngology and Communicative Sciences, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Brandon C Cox
- Departments of Pharmacology and Surgery, Division of Otolaryngology, Southern Illinois University School of Medicine, Springfield, IL 62711, USA.
| |
Collapse
|
46
|
Bronner C, Alhosin M, Hamiche A, Mousli M. Coordinated Dialogue between UHRF1 and DNMT1 to Ensure Faithful Inheritance of Methylated DNA Patterns. Genes (Basel) 2019; 10:E65. [PMID: 30669400 DOI: 10.3390/genes10010065] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/22/2018] [Accepted: 01/11/2019] [Indexed: 12/19/2022] Open
Abstract
DNA methylation, catalyzed by DNA methyltransferases (DNMTs), is an epigenetic mark that needs to be faithfully replicated during mitosis in order to maintain cell phenotype during successive cell divisions. This epigenetic mark is located on the 5′-carbon of the cytosine mainly within cytosine–phosphate–guanine (CpG) dinucleotides. DNA methylation is asymmetrically positioned on both DNA strands, temporarily generating a hemi-methylated state after DNA replication. Hemi-methylation is a particular status of DNA that is recognized by ubiquitin-like containing plant homeodomain (PHD) and really interesting new gene (RING) finger domains 1 (UHRF1) through its SET- (Su(var)3-9, Enhancer-of-zeste and Trithorax) and RING-associated (SRA) domain. This interaction is considered to be involved in the recruitment of DNMT1 to chromatin in order to methylate the adequate cytosine on the newly synthetized DNA strand. The UHRF1/DNMT1 tandem plays a pivotal role in the inheritance of DNA methylation patterns, but the fine-tuning mechanism remains a mystery. Indeed, because DNMT1 experiences difficulties in finding the cytosine to be methylated, it requires the help of a guide, i.e., of UHRF1, which exhibits higher affinity for hemi-methylated DNA vs. non-methylated DNA. Two models of the UHRF1/DNMT1 dialogue were suggested to explain how DNMT1 is recruited to chromatin: (i) an indirect communication via histone H3 ubiquitination, and (ii) a direct interaction of UHRF1 with DNMT1. In the present review, these two models are discussed, and we try to show that they are compatible with each other.
Collapse
|
47
|
Grova N, Schroeder H, Olivier JL, Turner JD. Epigenetic and Neurological Impairments Associated with Early Life Exposure to Persistent Organic Pollutants. Int J Genomics 2019; 2019:2085496. [PMID: 30733955 DOI: 10.1155/2019/2085496] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/14/2018] [Accepted: 10/31/2018] [Indexed: 12/31/2022] Open
Abstract
The incidence of neurodevelopmental and neurodegenerative diseases worldwide has dramatically increased over the last decades. Although the aetiology remains uncertain, evidence is now growing that exposure to persistent organic pollutants during sensitive neurodevelopmental periods such as early life may be a strong risk factor, predisposing the individual to disease development later in life. Epidemiological studies have associated environmentally persistent organic pollutant exposure to brain disorders including neuropathies, cognitive, motor, and sensory impairments; neurodevelopmental disorders such as autism spectrum disorder (ASD) and attention-deficit hyperactivity disorder (ADHD); and neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis (ALS). In many ways, this expands the classical “Developmental Origins of Health and Disease” paradigm to include exposure to pollutants. This model has been refined over the years to give the current “three-hit” model that considers the individual's genetic factors as a first “hit.” It has an immediate interaction with the early-life exposome (including persistent organic pollutants) that can be considered to be a second “hit.” Together, these first two “hits” produce a quiescent or latent phenotype, most probably encoded in the epigenome, which has become susceptible to a third environmental “hit” in later life. It is only after the third “hit” that the increased risk of disease symptoms is crystallised. However, if the individual is exposed to a different environment in later life, they would be expected to remain healthy. In this review, we examine the effect of exposure to persistent organic pollutants and particulate matters in early life and the relationship to subsequent neurodevelopmental and neurodegenerative disorders. The roles of those environmental factors which may affect epigenetic DNA methylation and therefore influence normal neurodevelopment are then evaluated.
Collapse
|
48
|
Németh CE, Nemoda Z, Lőw P, Szabó P, Horváth EZ, Willaert A, Boel A, Callewaert BL, Coucke PJ, Colombi M, Bánhegyi G, Margittai É. Decreased Nuclear Ascorbate Accumulation Accompanied with Altered Genomic Methylation Pattern in Fibroblasts from Arterial Tortuosity Syndrome Patients. Oxid Med Cell Longev 2019; 2019:8156592. [PMID: 30800210 DOI: 10.1155/2019/8156592] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022]
Abstract
Ascorbate requiring Fe2+/2-oxoglutarate-dependent dioxygenases located in the nucleoplasm have been shown to participate in epigenetic regulation of gene expression via histone and DNA demethylation. Transport of dehydroascorbic acid is impaired in the endomembranes of fibroblasts from arterial tortuosity syndrome (ATS) patients, due to the mutation in the gene coding for glucose transporter GLUT10. We hypothesized that altered nuclear ascorbate concentration might be present in ATS fibroblasts, affecting dioxygenase activity and DNA demethylation. Therefore, our aim was to characterize the subcellular distribution of vitamin C, the global and site-specific changes in 5-methylcytosine and 5-hydroxymethylcytosine levels, and the effect of ascorbate supplementation in control and ATS fibroblast cultures. Diminished nuclear accumulation of ascorbate was found in ATS fibroblasts upon ascorbate or dehydroascorbic acid addition. Analyzing DNA samples of cultured fibroblasts from controls and ATS patients, a lower global 5-hydroxymethylcytosine level was found in ATS fibroblasts, which could not be significantly modified by ascorbate addition. Investigation of the (hydroxy)methylation status of specific regions in six candidate genes related to ascorbate metabolism and function showed that ascorbate addition could stimulate hydroxymethylation and active DNA demethylation at the PPAR-γ gene region in control fibroblasts only. The altered DNA hydroxymethylation patterns in patient cells both at the global level and at specific gene regions accompanied with decreased nuclear accumulation of ascorbate suggests the epigenetic role of vitamin C in the pathomechanism of ATS. The present findings represent the first example for the role of vitamin C transport in epigenetic regulation suggesting that ATS is a compartmentalization disease.
Collapse
|
49
|
Pennings S, Revuelta A, McLaughlin KA, Abd Hadi NA, Petchreing P, Ottaviano R, Meehan RR. Dynamics and Mechanisms of DNA Methylation Reprogramming. Epigenetics and Regeneration 2019:19-45. [DOI: 10.1016/b978-0-12-814879-2.00002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
|
50
|
Bonvin E, Radaelli E, Bizet M, Luciani F, Calonne E, Putmans P, Nittner D, Singh NK, Santagostino SF, Petit V, Larue L, Marine JC, Fuks F. TET2-Dependent Hydroxymethylome Plasticity Reduces Melanoma Initiation and Progression. Cancer Res 2018; 79:482-494. [PMID: 30538121 DOI: 10.1158/0008-5472.can-18-1214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 10/03/2018] [Accepted: 12/06/2018] [Indexed: 11/16/2022]
Abstract
Although numerous epigenetic aberrancies accumulate in melanoma, their contribution to initiation and progression remain unclear. The epigenetic mark 5-hydroxymethylcytosine (5hmC), generated through TET-mediated DNA modification, is now referred to as the sixth base of DNA and has recently been reported as a potential biomarker for multiple types of cancer. Loss of 5hmC is an epigenetic hallmark of melanoma, but whether a decrease in 5hmc levels contributes directly to pathogenesis or whether it merely results from disease progression-associated epigenetic remodeling remains to be established. Here, we show that NRAS-driven melanomagenesis in mice is accompanied by an overall decrease in 5hmC and specific 5hmC gains in selected gene bodies. Strikingly, genetic ablation of Tet2 in mice cooperated with oncogenic NRASQ61K to promote melanoma initiation while suppressing specific gains in 5hmC. We conclude that TET2 acts as a barrier to melanoma initiation and progression, partly by promoting 5hmC gains in specific gene bodies. SIGNIFICANCE: This work emphasizes the importance of epigenome plasticity in cancer development and highlights the involvement of druggable epigenetic factors in cancer.
Collapse
Affiliation(s)
- Elise Bonvin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Enrico Radaelli
- Mouse Histopathology Core Facility, VIB Center for Brain & Disease Research, Leuven, Belgium.,Comparative Pathology Core, University of Pennsylvania, School of Veterinary Medicine, Department of Pathobiology, Philadelphia, Pennsylvania
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Flavie Luciani
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - David Nittner
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium.,Histopathology Expertise Center, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
| | - Nitesh Kumar Singh
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Sara Francesca Santagostino
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, The Rockefeller University, Weill Cornell Medicine, New York, New York.,Department of Safety Assessment, Genentech, Inc., South San Francisco, California
| | - Valérie Petit
- Normal and Pathological Development of Melanocytes, CNRS UMR3347, INSERM U1021, Institut Curie, Orsay, France
| | - Lionel Larue
- Normal and Pathological Development of Melanocytes, CNRS UMR3347, INSERM U1021, Institut Curie, Orsay, France
| | - Jean Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium. .,Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium.
| |
Collapse
|