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Herwig-Carl MC, Sharma A, Tischler V, Pelusi N, Loeffler KU, Holz FG, Zeschnigk M, Landreville S, Auw-Haedrich C, Noberini R, Bonaldi T. Mass Spectrometry-Based Profiling of Histone Post-Translational Modifications in Uveal Melanoma Tissues, Human Melanocytes, and Uveal Melanoma Cell Lines - A Pilot Study. Invest Ophthalmol Vis Sci 2024; 65:27. [PMID: 38349785 PMCID: PMC10868634 DOI: 10.1167/iovs.65.2.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/31/2024] [Indexed: 02/15/2024] Open
Abstract
Purpose Epigenetic alterations in uveal melanoma (UM) are still neither well characterized, nor understood. In this pilot study, we sought to provide a deeper insight into the possible role of epigenetic alterations in the pathogenesis of UM and their potential prognostic relevance. To this aim, we comprehensively profiled histone post-translational modifications (PTMs), which represent epigenetic features regulating chromatin accessibility and gene transcription, in UM formalin-fixed paraffin-embedded (FFPE) tissues, control tissues, UM cell lines, and healthy melanocytes. Methods FFPE tissues of UM (n = 24), normal choroid (n = 4), human UM cell lines (n = 7), skin melanocytes (n = 6), and uveal melanocytes (n = 2) were analyzed through a quantitative liquid chromatography-mass spectrometry (LC-MS) approach. Results Hierarchical clustering showed a clear separation with several histone PTMs that changed significantly in a tumor compared to normal samples, in both tissues and cell lines. In addition, several acetylations and H4K20me1 showed lower levels in BAP1 mutant tumors. Some of these changes were also observed when we compared GNA11 mutant tumors with GNAQ tumors. The epigenetic profiling of cell lines revealed that the UM cell lines MP65 and UPMM1 have a histone PTM pattern closer to the primary tissues than the other cell lines analyzed. Conclusions Our results suggest the existence of different histone PTM patterns that may be important for diagnosis and prognosis in UM. However, further analyses are needed to confirm these findings in a larger cohort. The epigenetic characterization of a panel of UM cell lines suggested which cellular models are more suitable for epigenetic investigations.
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Affiliation(s)
- Martina C. Herwig-Carl
- Department of Ophthalmology, University Hospital Bonn, Bonn, Germany
- Division of Ophthalmic Pathology, University Hospital Bonn, Bonn, Germany
- Centrum for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Germany
| | - Amit Sharma
- Department of Ophthalmology, University Hospital Bonn, Bonn, Germany
- Department of Neurosurgery, University Hospital Bonn, Bonn, Germany
| | - Verena Tischler
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Natalie Pelusi
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Karin U. Loeffler
- Department of Ophthalmology, University Hospital Bonn, Bonn, Germany
- Division of Ophthalmic Pathology, University Hospital Bonn, Bonn, Germany
| | - Frank G. Holz
- Department of Ophthalmology, University Hospital Bonn, Bonn, Germany
- Centrum for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Germany
| | - Michael Zeschnigk
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Solange Landreville
- Department of Ophthalmology and Otolaryngology-Cervicofacial Surgery, Université Laval, Quebec City, Quebec, Canada
| | | | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Department of Oncology and Haematology-Oncology (DIPO), University of Milan, Milan, Italy
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Chatzikyriakou P, Brempou D, Quinn M, Fishbein L, Noberini R, Anastopoulos IN, Tufton N, Lim ES, Obholzer R, Hubbard JG, Moonim M, Bonaldi T, Nathanson KL, Izatt L, Oakey RJ. A comprehensive characterisation of phaeochromocytoma and paraganglioma tumours through histone protein profiling, DNA methylation and transcriptomic analysis genome wide. Clin Epigenetics 2023; 15:196. [PMID: 38124114 PMCID: PMC10734084 DOI: 10.1186/s13148-023-01598-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/08/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Phaeochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumours. Pathogenic variants have been identified in more than 15 susceptibility genes; associated tumours are grouped into three Clusters, reinforced by their transcriptional profiles. Cluster 1A PPGLs have pathogenic variants affecting enzymes of the tricarboxylic acid cycle, including succinate dehydrogenase. Within inherited PPGLs, these are the most common. PPGL tumours are known to undergo epigenetic reprograming, and here, we report on global histone post-translational modifications and DNA methylation levels, alongside clinical phenotypes. RESULTS Out of the 25 histone post-translational modifications examined, Cluster 1A PPGLs were distinguished from other tumours by a decrease in hyper-acetylated peptides and an increase in H3K4me2. DNA methylation was compared between tumours from individuals who developed metastatic disease versus those that did not. The majority of differentially methylated sites identified tended to be completely methylated or unmethylated in non-metastatic tumours, with low inter-sample variance. Metastatic tumours by contrast consistently had an intermediate DNA methylation state, including the ephrin receptor EPHA4 and its ligand EFNA3. Gene expression analyses performed to identify genes involved in metastatic tumour behaviour pin-pointed a number of genes previously described as mis-regulated in Cluster 1A tumours, as well as highlighting the tumour suppressor RGS22 and the pituitary tumour-transforming gene PTTG1. CONCLUSIONS Combined transcriptomic and DNA methylation analyses revealed aberrant pathways, including ones that could be implicated in metastatic phenotypes and, for the first time, we report a decrease in hyper-acetylated histone marks in Cluster 1 PPGLs.
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Affiliation(s)
- Prodromos Chatzikyriakou
- Department of Medical and Molecular Genetics, King's College London, London, SE1 9RT, UK
- Comprehensive Cancer Centre, King's College London, London, SE5 8AF, UK
| | - Dimitria Brempou
- Department of Medical and Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Mark Quinn
- Department of Medical and Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Lauren Fishbein
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, Perelman School of Medicine, Philadelphia, PA, USA
- Division of Endocrinology, Diabetes and Metabolism in the Department of Medicine Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Ioannis N Anastopoulos
- Department of Biomolecular Engineering, UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Nicola Tufton
- Department of Endocrinology, St. Bartholomew's Hospital, Barts Health NHS Trust, and William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Eugenie S Lim
- Department of Endocrinology, St. Bartholomew's Hospital, Barts Health NHS Trust, and William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Rupert Obholzer
- Department of ENT and Skull Base Surgery, Guy's and St Thomas' NHS Foundation Trust, London, SE1 9RT, UK
| | - Johnathan G Hubbard
- Department of Endocrine Surgery, Guy's and St Thomas' NHS Foundation Trust, London, SE1 9RT, UK
| | - Mufaddal Moonim
- Department of Cellular Pathology, Guy's and St Thomas' NHS Foundation Trust, London, SE1 9RT, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milano, Via Festa del Perdono 7, 20122, Milan, Italy
| | - Katherine L Nathanson
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, Perelman School of Medicine, Philadelphia, PA, USA
| | - Louise Izatt
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, SE1 9RT, UK
| | - Rebecca J Oakey
- Department of Medical and Molecular Genetics, King's College London, London, SE1 9RT, UK.
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Noberini R, Bonaldi T. Proteomics contributions to epigenetic drug discovery. Proteomics 2023; 23:e2200435. [PMID: 37727062 DOI: 10.1002/pmic.202200435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023]
Abstract
The combined activity of epigenetic features, which include histone post-translational modifications, DNA methylation, and nucleosome positioning, regulates gene expression independently from changes in the DNA sequence, defining how the shared genetic information of an organism is used to generate different cell phenotypes. Alterations in epigenetic processes have been linked with a multitude of diseases, including cancer, fueling interest in the discovery of drugs targeting the proteins responsible for writing, erasing, or reading histone and DNA modifications. Mass spectrometry (MS)-based proteomics has emerged as a versatile tool that can assist drug discovery pipelines from target validation, through target deconvolution, to monitoring drug efficacy in vivo. Here, we provide an overview of the contributions of MS-based proteomics to epigenetic drug discovery, describing the main approaches that can be used to support different drug discovery pipelines and highlighting how they contributed to the development and characterization of epigenetic drugs.
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Affiliation(s)
- Roberta Noberini
- 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
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
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Zhao Y, Xiong W, Li C, Zhao R, Lu H, Song S, Zhou Y, Hu Y, Shi B, Ge J. Hypoxia-induced signaling in the cardiovascular system: pathogenesis and therapeutic targets. Signal Transduct Target Ther 2023; 8:431. [PMID: 37981648 PMCID: PMC10658171 DOI: 10.1038/s41392-023-01652-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 11/21/2023] Open
Abstract
Hypoxia, characterized by reduced oxygen concentration, is a significant stressor that affects the survival of aerobic species and plays a prominent role in cardiovascular diseases. From the research history and milestone events related to hypoxia in cardiovascular development and diseases, The "hypoxia-inducible factors (HIFs) switch" can be observed from both temporal and spatial perspectives, encompassing the occurrence and progression of hypoxia (gradual decline in oxygen concentration), the acute and chronic manifestations of hypoxia, and the geographical characteristics of hypoxia (natural selection at high altitudes). Furthermore, hypoxia signaling pathways are associated with natural rhythms, such as diurnal and hibernation processes. In addition to innate factors and natural selection, it has been found that epigenetics, as a postnatal factor, profoundly influences the hypoxic response and progression within the cardiovascular system. Within this intricate process, interactions between different tissues and organs within the cardiovascular system and other systems in the context of hypoxia signaling pathways have been established. Thus, it is the time to summarize and to construct a multi-level regulatory framework of hypoxia signaling and mechanisms in cardiovascular diseases for developing more therapeutic targets and make reasonable advancements in clinical research, including FDA-approved drugs and ongoing clinical trials, to guide future clinical practice in the field of hypoxia signaling in cardiovascular diseases.
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Affiliation(s)
- Yongchao Zhao
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
| | - Weidong Xiong
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, 200032, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, 200032, China
| | - Chaofu Li
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
| | - Ranzun Zhao
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Hao Lu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Shuai Song
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - You Zhou
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Yiqing Hu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China.
| | - Bei Shi
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China.
| | - Junbo Ge
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China.
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China.
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, 200032, China.
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, 200032, China.
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China.
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China.
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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Zhang X, Noberini R, Vai A, Bonaldi T, Seidl MF, Collemare J. Detection and quantification of the histone code in the fungal genus Aspergillus. Fungal Genet Biol 2023; 167:103800. [PMID: 37146898 DOI: 10.1016/j.fgb.2023.103800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/30/2023] [Accepted: 04/24/2023] [Indexed: 05/07/2023]
Abstract
In eukaryotes, the combination of different histone post-translational modifications (PTMs) - the histone code - impacts the chromatin organization as compact and transcriptionally silent heterochromatin or accessible and transcriptionally active euchromatin. Although specific histone PTMs have been studied in fungi, an overview of histone PTMs and their relative abundance is still lacking. Here, we used mass spectrometry to detect and quantify histone PTMs in three fungal species belonging to three distinct taxonomic sections of the genus Aspergillus (Aspergillus niger, Aspergillus nidulans (two strains), and Aspergillus fumigatus). We overall detected 23 different histone PTMs, including a majority of lysine methylations and acetylations, and 23 co-occurrence patterns of multiple histone PTMs. Among those, we report for the first time the detection of H3K79me1, H3K79me2, and H4K31ac in Aspergilli. Although all three species harbour the same PTMs, we found significant differences in the relative abundance of H3K9me1/2/3, H3K14ac, H3K36me1 and H3K79me1, as well as the co-occurrence of acetylation on both K18 and K23 of histone H3 in a strain-specific manner. Our results provide novel insights about the underexplored complexity of the histone code in filamentous fungi, and its functional implications on genome architecture and gene regulation.
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Affiliation(s)
- Xin Zhang
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Alessandro Vai
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Haematology-Oncology, University of Milano, Via Santa Sofia 9/1, 20122 Milano, Italy.
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Jérȏme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
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Pham K, Ho L, D'Incal CP, De Cock A, Berghe WV, Goethals P. Epigenetic analytical approaches in ecotoxicological aquatic research. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 330:121737. [PMID: 37121302 DOI: 10.1016/j.envpol.2023.121737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/15/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Environmental epigenetics has become a key research focus in global climate change studies and environmental pollutant investigations impacting aquatic ecosystems. Specifically, triggered by environmental stress conditions, intergenerational DNA methylation changes contribute to biological adaptive responses and survival of organisms to increase their tolerance towards these conditions. To critically review epigenetic analytical approaches in ecotoxicological aquatic research, we evaluated 78 publications reported over the past five years (2016-2021) that applied these methods to investigate the responses of aquatic organisms to environmental changes and pollution. The results show that DNA methylation appears to be the most robust epigenetic regulatory mark studied in aquatic animals. As such, multiple DNA methylation analysis methods have been developed in aquatic organisms, including enzyme restriction digestion-based and methyl-specific immunoprecipitation methods, and bisulfite (in)dependent sequencing strategies. In contrast, only a handful of aquatic studies, i.e. about 15%, have been focusing on histone variants and post-translational modifications due to the lack of species-specific affinity based immunological reagents, such as specific antibodies for chromatin immunoprecipitation applications. Similarly, ncRNA regulation remains as the least popular method used in the field of environmental epigenetics. Insights into the opportunities and challenges of the DNA methylation and histone variant analysis methods as well as decreasing costs of next generation sequencing approaches suggest that large-scale epigenetic environmental studies in model and non-model organisms will soon become available in the near future. Moreover, antibody-dependent and independent methods, such as mass spectrometry-based methods, can be used as an alternative epigenetic approach to characterize global changes of chromatin histone modifications in future aquatic research. Finally, a systematic guide for DNA methylation and histone variant methods is offered for ecotoxicological aquatic researchers to select the most relevant epigenetic analytical approach in their research.
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Affiliation(s)
- Kim Pham
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium.
| | - Long Ho
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
| | - Claudio Peter D'Incal
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Andrée De Cock
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
| | - Wim Vanden Berghe
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Peter Goethals
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
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7
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Noberini R, Bonaldi T. Mass Spectrometry-Based Analysis of Histone Posttranslational Modifications from Laser Microdissected Samples. Methods Mol Biol 2023; 2718:271-283. [PMID: 37665465 DOI: 10.1007/978-1-0716-3457-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The analysis of histone posttranslational modifications (PTMs) in clinical samples has gained considerable interest due to the increasing knowledge about the implication of epigenetics in a multitude of physiological and pathological processes. Mass spectrometry (MS) has emerged as the most accurate and versatile tool to detect and quantify histone PTMs and has also been applied to clinical specimens, thanks to protocols developed during the past years. However, the requirement for relatively large amounts of material has so far impaired the application of these approaches to samples available in limited amounts. To address this issue, we have recently streamlined the protein extraction procedure from low-amount clinical samples and optimized the digestion step, obtaining a protocol suitable for the analysis of the most common histone PTMs from laser microdissected tissue areas containing down to 1000 cells, which we will describe in this chapter.
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Affiliation(s)
- Roberta Noberini
- 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.
- Department of Oncology and Haematology-Oncology, University of Milano, Milan, Italy.
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Noberini R, Longhi E, Bonaldi T. A Super-SILAC Approach for Profiling Histone Posttranslational Modifications. Methods Mol Biol 2023; 2603:87-102. [PMID: 36370272 DOI: 10.1007/978-1-0716-2863-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Histone posttranslational modifications (PTMs) play an important role in the regulation of gene expression and have been implicated in a multitude of physiological and pathological processes. During the last decade, mass spectrometry (MS) has emerged as the most accurate and versatile tool to quantitate histone PTMs. Stable-isotope labeling by amino acids in cell culture (SILAC) is an MS-based quantitation strategy involving metabolic labeling of cells, which has been applied to global protein profiling as well as histone PTM analysis. The classical SILAC approach is associated with reduced experimental variability and high quantitation accuracy, but provides limited multiplexing capabilities and can be applied only to actively dividing cells, thus excluding clinical samples. Both limitations are overcome by an evolution of classical SILAC involving the use of a mix of heavy-labeled cell lines as a spike-in standard, known as "super-SILAC". In this chapter, we will provide a detailed description of the optimized protocol used in our laboratory to generate a histone-focused super-SILAC mix and employ it as an internal standard for histone PTM quantitation.
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Affiliation(s)
- Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.
| | - Elisa Longhi
- 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.
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Amatori S, Persico G, Cantatore F, Rusin M, Formica M, Giorgi L, Macedi E, Casciaro F, Errico Provenzano A, Gambardella S, Noberini R, Bonaldi T, Fusi V, Giorgio M, Fanelli M. Small molecule-induced epigenomic reprogramming of APL blasts leading to antiviral-like response and c-MYC downregulation. Cancer Gene Ther 2022; 30:671-682. [PMID: 36536122 DOI: 10.1038/s41417-022-00576-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
AbstractAcute promyelocytic leukemia (APL) is an aggressive subtype of acute myeloid leukemia (AML) in which the PML/RARα fusion protein exerts oncogenic activities by recruiting repressive complexes to the promoter of specific target genes. Other epigenetic perturbations, as alterations of histone H3 lysine 9 trimethylation (H3K9me3), have been frequently found in AMLs and are associated with leukemogenesis and leukemia progression. Here, we characterized the epigenomic effects of maltonis, a novel maltol-derived molecule, in APL cells. We demonstrate that maltonis treatments induce a profound remodulation of the histone code, reducing global H3K9me3 signal and modulating other histone post-translational modifications. Transcriptomic and epigenomic analyses revealed that maltonis exposure induces changes of genes expression associated with a genomic redistribution of histone H3 lysine 4 trimethylation (H3K4me3) and lysine 27 acetylation (H3K27ac). Upregulation of interferon alpha and gamma response and downregulation of c-MYC target genes, in function of c-MYC reduced expression (monitored in all the hematopoietic neoplasms tested), represent the most significant modulated pathways. These data demonstrate the ability of maltonis to epigenetically reprogram the gene expression profile of APL cells, inducing an intriguing antiviral-like response, concomitantly with the downregulation of c-MYC-related pathways, thus making it an attractive candidate for antileukemic therapy.
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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] [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.
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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
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Radzikowska U, Baerenfaller K, Cornejo‐Garcia JA, Karaaslan C, Barletta E, Sarac BE, Zhakparov D, Villaseñor A, Eguiluz‐Gracia I, Mayorga C, Sokolowska M, Barbas C, Barber D, Ollert M, Chivato T, Agache I, Escribese MM. Omics technologies in allergy and asthma research: An EAACI position paper. Allergy 2022; 77:2888-2908. [PMID: 35713644 PMCID: PMC9796060 DOI: 10.1111/all.15412] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 01/27/2023]
Abstract
Allergic diseases and asthma are heterogenous chronic inflammatory conditions with several distinct complex endotypes. Both environmental and genetic factors can influence the development and progression of allergy. Complex pathogenetic pathways observed in allergic disorders present a challenge in patient management and successful targeted treatment strategies. The increasing availability of high-throughput omics technologies, such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics allows studying biochemical systems and pathophysiological processes underlying allergic responses. Additionally, omics techniques present clinical applicability by functional identification and validation of biomarkers. Therefore, finding molecules or patterns characteristic for distinct immune-inflammatory endotypes, can subsequently influence its development, progression, and treatment. There is a great potential to further increase the effectiveness of single omics approaches by integrating them with other omics, and nonomics data. Systems biology aims to simultaneously and longitudinally understand multiple layers of a complex and multifactorial disease, such as allergy, or asthma by integrating several, separated data sets and generating a complete molecular profile of the condition. With the use of sophisticated biostatistics and machine learning techniques, these approaches provide in-depth insight into individual biological systems and will allow efficient and customized healthcare approaches, called precision medicine. In this EAACI Position Paper, the Task Force "Omics technologies in allergic research" broadly reviewed current advances and applicability of omics techniques in allergic diseases and asthma research, with a focus on methodology and data analysis, aiming to provide researchers (basic and clinical) with a desk reference in the field. The potential of omics strategies in understanding disease pathophysiology and key tools to reach unmet needs in allergy precision medicine, such as successful patients' stratification, accurate disease prognosis, and prediction of treatment efficacy and successful prevention measures are highlighted.
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Affiliation(s)
- Urszula Radzikowska
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Christine‐Kühne Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - Katja Baerenfaller
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - José Antonio Cornejo‐Garcia
- Research LaboratoryIBIMA, ARADyAL Instituto de Salud Carlos III, Regional University Hospital of Málaga, UMAMálagaSpain
| | - Cagatay Karaaslan
- Department of Biology, Molecular Biology SectionFaculty of ScienceHacettepe UniversityAnkaraTurkey
| | - Elena Barletta
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - Basak Ezgi Sarac
- Department of Biology, Molecular Biology SectionFaculty of ScienceHacettepe UniversityAnkaraTurkey
| | - Damir Zhakparov
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - Alma Villaseñor
- Centre for Metabolomics and Bioanalysis (CEMBIO)Department of Chemistry and BiochemistryFacultad de FarmaciaUniversidad San Pablo‐CEU, CEU UniversitiesMadridSpain,Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | - Ibon Eguiluz‐Gracia
- Allergy UnitHospital Regional Universitario de MálagaMálagaSpain,Allergy Research GroupInstituto de Investigación Biomédica de Málaga‐IBIMAMálagaSpain
| | - Cristobalina Mayorga
- Allergy UnitHospital Regional Universitario de MálagaMálagaSpain,Allergy Research GroupInstituto de Investigación Biomédica de Málaga‐IBIMAMálagaSpain,Andalusian Centre for Nanomedicine and Biotechnology – BIONANDMálagaSpain
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Christine‐Kühne Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO)Department of Chemistry and BiochemistryFacultad de FarmaciaUniversidad San Pablo‐CEU, CEU UniversitiesMadridSpain
| | - Domingo Barber
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | - Markus Ollert
- Department of Infection and ImmunityLuxembourg Institute of HealthyEsch‐sur‐AlzetteLuxembourg,Department of Dermatology and Allergy CenterOdense Research Center for AnaphylaxisOdense University Hospital, University of Southern DenmarkOdenseDenmark
| | - Tomas Chivato
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain,Department of Clinic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | | | - Maria M. Escribese
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
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12
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Philips O, Sultonova M, Blackmore B, Murphy JP. Understanding emerging bioactive metabolites with putative roles in cancer biology. Front Oncol 2022; 12:1014748. [PMID: 36249070 PMCID: PMC9557195 DOI: 10.3389/fonc.2022.1014748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Dysregulated metabolism in cancers is, by now, well established. Although metabolic adaptations provide cancers with the ability to synthesize the precursors required for rapid biosynthesis, some metabolites have direct functional, or bioactive, effects in human cells. Here we summarize recently identified metabolites that have bioactive roles either as post-translational modifications (PTMs) on proteins or in, yet unknown ways. We propose that these metabolites could play a bioactive role in promoting or inhibiting cancer cell phenotypes in a manner that is mostly unexplored. To study these potentially important bioactive roles, we discuss several novel metabolomic and proteomic approaches aimed at defining novel PTMs and metabolite-protein interactions. Understanding metabolite PTMs and protein interactors of bioactive metabolites may provide entirely new therapeutic targets for cancer.
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13
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Zhang X, Noberini R, Bonaldi T, Collemare J, Seidl MF. The histone code of the fungal genus Aspergillus uncovered by evolutionary and proteomic analyses. Microb Genom 2022; 8. [PMID: 36129736 PMCID: PMC9676040 DOI: 10.1099/mgen.0.000856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chemical modifications of DNA and histone proteins impact the organization of chromatin within the nucleus. Changes in these modifications, catalysed by different chromatin-modifying enzymes, influence chromatin organization, which in turn is thought to impact the spatial and temporal regulation of gene expression. While combinations of different histone modifications, the histone code, have been studied in several model species, we know very little about histone modifications in the fungal genus Aspergillus, whose members are generally well studied due to their importance as models in cell and molecular biology as well as their medical and biotechnological relevance. Here, we used phylogenetic analyses in 94 Aspergilli as well as other fungi to uncover the occurrence and evolutionary trajectories of enzymes and protein complexes with roles in chromatin modifications or regulation. We found that these enzymes and complexes are highly conserved in Aspergilli, pointing towards a complex repertoire of chromatin modifications. Nevertheless, we also observed few recent gene duplications or losses, highlighting Aspergillus species to further study the roles of specific chromatin modifications. SET7 (KMT6) and other components of PRC2 (Polycomb Repressive Complex 2), which is responsible for methylation on histone H3 at lysine 27 in many eukaryotes including fungi, are absent in Aspergilli as well as in closely related Penicillium species, suggesting that these lost the capacity for this histone modification. We corroborated our computational predictions by performing untargeted MS analysis of histone post-translational modifications in Aspergillus nidulans. This systematic analysis will pave the way for future research into the complexity of the histone code and its functional implications on genome architecture and gene regulation in fungi.
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Affiliation(s)
- Xin Zhang
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.,Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy.,Department of Oncology and Haematology-Oncology, University of Milano, Via Santa Sofia 9/1, 20122 Milano, Italy
| | - Jerome Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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14
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Faletti S, Osti D, Ceccacci E, Richichi C, Costanza B, Nicosia L, Noberini R, Marotta G, Furia L, Faretta MR, Brambillasca S, Quarto M, Bertero L, Boldorini R, Pollo B, Gandini S, Cora D, Minucci S, Mercurio C, Varasi M, Bonaldi T, Pelicci G. LSD1-directed therapy affects glioblastoma tumorigenicity by deregulating the protective ATF4-dependent integrated stress response. Sci Transl Med 2021; 13:eabf7036. [PMID: 34878824 DOI: 10.1126/scitranslmed.abf7036] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Stefania Faletti
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy
| | - Daniela Osti
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy
| | - Elena Ceccacci
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy
| | - Cristina Richichi
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy
| | - Brunella Costanza
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy
| | - Luciano Nicosia
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy
| | - Giulia Marotta
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy
| | - Laura Furia
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy
| | - Mario R Faretta
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy
| | - Silvia Brambillasca
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), Milan 20139, Italy
| | - Micaela Quarto
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), Milan 20139, Italy
| | - Luca Bertero
- Department of Medical Sciences, University of Turin, Turin 10126, Italy
| | - Renzo Boldorini
- Department of Health Science, University of Piemonte Orientale (UPO), Novara 28100, Italy
| | - Bianca Pollo
- Unit of Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | - Sara Gandini
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy
| | - Davide Cora
- Department of Translational Medicine, Center for Translational Research on Autoimmune and Allergic Disease (CAAD), University of Piemonte Orientale, Novara 28100, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy
| | - Ciro Mercurio
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), Milan 20139, Italy
| | - Mario Varasi
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy
| | - Giuliana Pelicci
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan 20139, Italy.,Department of Translational Medicine, University of Piemonte Orientale, Novara 28100, Italy
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15
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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] [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.
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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;
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16
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Hua Y, Yue Y, Zhao D, Ma Y, Xiong Y, Xiong X, Li J. Ablation of KDM2A Inhibits Preadipocyte Proliferation and Promotes Adipogenic Differentiation. Int J Mol Sci 2021; 22:9759. [PMID: 34575926 PMCID: PMC8467897 DOI: 10.3390/ijms22189759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/01/2021] [Accepted: 09/06/2021] [Indexed: 12/11/2022] Open
Abstract
Epigenetic signals and chromatin-modifying proteins play critical roles in adipogenesis, which determines the risk of obesity and which has recently attracted increasing interest. Histone demethylase 2A (KDM2A) is an important component of histone demethylase; however, its direct effect on fat deposition remains unclear. Here, a KDM2A loss of function was performed using two unbiased methods, small interfering RNA (siRNA) and Cre-Loxp recombinase systems, to reveal its function in adipogenesis. The results show that the knockdown of KDM2A by siRNAs inhibited the proliferation capacity of 3T3-L1 preadipocytes. Furthermore, the promotion of preadipocyte differentiation was observed in siRNA-treated cells, manifested by the increasing content of lipid droplets and the expression level of adipogenic-related genes. Consistently, the genetic deletion of KDM2A by Adipoq-Cre in primary adipocytes exhibited similar phenotypes to those of 3T3-L1 preadipocytes. Interestingly, the knockdown of KDM2A upregulates the expression level of Transportin 1(TNPO1), which in turn may induce the nuclear translocation of PPARγ and the accumulation of lipid droplets. In conclusion, the ablation of KDM2A inhibits preadipocyte proliferation and promotes its adipogenic differentiation. This work provides direct evidence of the exact role of KDM2A in fat deposition and provides theoretical support for obesity therapy that targets KDM2A.
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Affiliation(s)
- Yonglin Hua
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China; (Y.H.); (Y.Y.); (D.Z.); (Y.M.); (X.X.)
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Yongqi Yue
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China; (Y.H.); (Y.Y.); (D.Z.); (Y.M.); (X.X.)
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Dan Zhao
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China; (Y.H.); (Y.Y.); (D.Z.); (Y.M.); (X.X.)
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Yan Ma
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China; (Y.H.); (Y.Y.); (D.Z.); (Y.M.); (X.X.)
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Yan Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China; (Y.H.); (Y.Y.); (D.Z.); (Y.M.); (X.X.)
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Southwest Minzu University, Chengdu 610041, China
| | - Xianrong Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China; (Y.H.); (Y.Y.); (D.Z.); (Y.M.); (X.X.)
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Southwest Minzu University, Chengdu 610041, China
| | - Jian Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China; (Y.H.); (Y.Y.); (D.Z.); (Y.M.); (X.X.)
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Southwest Minzu University, Chengdu 610041, China
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17
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Noberini R, Savoia EO, Brandini S, Greco F, Marra F, Bertalot G, Pruneri G, McDonnell LA, Bonaldi T. Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples. Clin Epigenetics 2021; 13:145. [PMID: 34315505 PMCID: PMC8317427 DOI: 10.1186/s13148-021-01120-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/18/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Increasing evidence linking epigenetic mechanisms and different diseases, including cancer, has prompted in the last 15 years the investigation of histone post-translational modifications (PTMs) in clinical samples. Methods allowing the isolation of histones from patient samples followed by the accurate and comprehensive quantification of their PTMs by mass spectrometry (MS) have been developed. However, the applicability of these methods is limited by the requirement for substantial amounts of material. RESULTS To address this issue, in this study we streamlined the protein extraction procedure from low-amount clinical samples and tested and implemented different in-gel digestion strategies, obtaining a protocol that allows the MS-based analysis of the most common histone PTMs from laser microdissected tissue areas containing as low as 1000 cells, an amount approximately 500 times lower than what is required by available methods. We then applied this protocol to breast cancer patient laser microdissected tissues in two proof-of-concept experiments, identifying differences in histone marks in heterogeneous regions selected by either morphological evaluation or MALDI MS imaging. CONCLUSIONS These results demonstrate that analyzing histone PTMs from very small tissue areas and detecting differences from adjacent tumor regions is technically feasible. Our method opens the way for spatial epi-proteomics, namely the investigation of epigenetic features in the context of tissue and tumor heterogeneity, which will be instrumental for the identification of novel epigenetic biomarkers and aberrant epigenetic mechanisms.
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Affiliation(s)
- Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.
| | - Evelyn Oliva Savoia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Stefania Brandini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Francesco Greco
- Institute of Life Sciences, Sant'Anna School of Advanced Studies, 56127, Pisa, Italy
- Fondazione Pisana Per La Scienza ONLUS, 56107, San Giuliano Terme, PI, Italy
| | - Francesca Marra
- Department of Pathology, Fondazione IRCCS-Istituto Nazionale Tumori, Milan, Italy
| | - Giovanni Bertalot
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giancarlo Pruneri
- Department of Pathology, Fondazione IRCCS-Istituto Nazionale Tumori, Milan, Italy
| | - Liam A McDonnell
- Fondazione Pisana Per La Scienza ONLUS, 56107, San Giuliano Terme, PI, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.
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18
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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] [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.
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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
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19
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Lu C, Coradin M, Porter EG, Garcia BA. Accelerating the Field of Epigenetic Histone Modification Through Mass Spectrometry-Based Approaches. Mol Cell Proteomics 2020; 20:100006. [PMID: 33203747 PMCID: PMC7950153 DOI: 10.1074/mcp.r120.002257] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/15/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
Histone post-translational modifications (PTMs) are one of the main mechanisms of epigenetic regulation. Dysregulation of histone PTMs leads to many human diseases, such as cancer. Because of its high throughput, accuracy, and flexibility, mass spectrometry (MS) has emerged as a powerful tool in the epigenetic histone modification field, allowing the comprehensive and unbiased analysis of histone PTMs and chromatin-associated factors. Coupled with various techniques from molecular biology, biochemistry, chemical biology, and biophysics, MS has been used to characterize distinct aspects of histone PTMs in the epigenetic regulation of chromatin functions. In this review, we will describe advancements in the field of MS that have facilitated the analysis of histone PTMs and chromatin biology. Middle–down is the most suitable to study histone combinatorial post-translational modifications. Crosslinking MS has a variety of potential applications in exploring histone post-translational modifications. Hydrogen–deuterium exchange MS holds great promise to study the compaction of nucleosome. Multi-omics approaches are useful to study complex regulatory networks.
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Affiliation(s)
- Congcong Lu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mariel Coradin
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth G Porter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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Abshiru NA, Sikora JW, Camarillo JM, Morris JA, Compton PD, Lee T, Neelamraju Y, Haddox S, Sheridan C, Carroll M, Cripe LD, Tallman MS, Paietta EM, Melnick AM, Thomas PM, Garrett-Bakelman FE, Kelleher NL. Targeted detection and quantitation of histone modifications from 1,000 cells. PLoS One 2020; 15:e0240829. [PMID: 33104722 PMCID: PMC7588077 DOI: 10.1371/journal.pone.0240829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/02/2020] [Indexed: 01/30/2023] Open
Abstract
Histone post-translational modifications (PTMs) create a powerful regulatory mechanism for maintaining chromosomal integrity in cells. Histone acetylation and methylation, the most widely studied histone PTMs, act in concert with chromatin-associated proteins to control access to genetic information during transcription. Alterations in cellular histone PTMs have been linked to disease states and have crucial biomarker and therapeutic potential. Traditional bottom-up mass spectrometry of histones requires large numbers of cells, typically one million or more. However, for some cell subtype-specific studies, it is difficult or impossible to obtain such large numbers of cells and quantification of rare histone PTMs is often unachievable. An established targeted LC-MS/MS method was used to quantify the abundance of histone PTMs from cell lines and primary human specimens. Sample preparation was modified by omitting nuclear isolation and reducing the rounds of histone derivatization to improve detection of histone peptides down to 1,000 cells. In the current study, we developed and validated a quantitative LC-MS/MS approach tailored for a targeted histone assay of 75 histone peptides with as few as 10,000 cells. Furthermore, we were able to detect and quantify 61 histone peptides from just 1,000 primary human stem cells. Detection of 37 histone peptides was possible from 1,000 acute myeloid leukemia patient cells. We anticipate that this revised method can be used in many applications where achieving large cell numbers is challenging, including rare human cell populations.
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Affiliation(s)
- Nebiyu A. Abshiru
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Jacek W. Sikora
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Jeannie M. Camarillo
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Juliette A. Morris
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Philip D. Compton
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Tak Lee
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States of America
| | - Samuel Haddox
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States of America
| | - Caroline Sheridan
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States of America
| | - Larry D. Cripe
- Indiana University/Melvin and Bren Simon Cancer Center, Indianapolis, IN, United States of America
| | - Martin S. Tallman
- Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | | | - Ari M. Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
| | - Paul M. Thomas
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Francine E. Garrett-Bakelman
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States of America
- Division of Hematology/Medical Oncology, Department of Medicine, University of Virginia, Charlottesville, VA, United States of America
- * E-mail: (FEGB); (NLK)
| | - Neil L. Kelleher
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
- * E-mail: (FEGB); (NLK)
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Label-Free Mass Spectrometry-Based Quantification of Linker Histone H1 Variants in Clinical Samples. Int J Mol Sci 2020; 21:ijms21197330. [PMID: 33020374 PMCID: PMC7582528 DOI: 10.3390/ijms21197330] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/21/2022] Open
Abstract
Epigenetic aberrations have been recognized as important contributors to cancer onset and development, and increasing evidence suggests that linker histone H1 variants may serve as biomarkers useful for patient stratification, as well as play an important role as drivers in cancer. Although traditionally histone H1 levels have been studied using antibody-based methods and RNA expression, these approaches suffer from limitations. Mass spectrometry (MS)-based proteomics represents the ideal tool to accurately quantify relative changes in protein abundance within complex samples. In this study, we used a label-free quantification approach to simultaneously analyze all somatic histone H1 variants in clinical samples and verified its applicability to laser micro-dissected tissue areas containing as low as 1000 cells. We then applied it to breast cancer patient samples, identifying differences in linker histone variants patters in primary triple-negative breast tumors with and without relapse after chemotherapy. This study highlights how label-free quantitation by MS is a valuable option to accurately quantitate histone H1 levels in different types of clinical samples, including very low-abundance patient tissues.
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