1
|
Rosano D, Sofyali E, Dhiman H, Ghirardi C, Ivanoiu D, Heide T, Vingiani A, Bertolotti A, Pruneri G, Canale E, Dewhurst HF, Saha D, Slaven N, Barozzi I, Li T, Zemlyanskiy G, Phillips H, James C, Győrffy B, Lynn C, Cresswell GD, Rehman F, Noberini R, Bonaldi T, Sottoriva A, Magnani L. Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells. Cancer Discov 2024; 14:866-889. [PMID: 38527495 PMCID: PMC11061610 DOI: 10.1158/2159-8290.cd-23-1161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/10/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
Abstract
Patients with estrogen receptor-positive breast cancer receive adjuvant endocrine therapies (ET) that delay relapse by targeting clinically undetectable micrometastatic deposits. Yet, up to 50% of patients relapse even decades after surgery through unknown mechanisms likely involving dormancy. To investigate genetic and transcriptional changes underlying tumor awakening, we analyzed late relapse patients and longitudinally profiled a rare cohort treated with long-term neoadjuvant ETs until progression. Next, we developed an in vitro evolutionary study to record the adaptive strategies of individual lineages in unperturbed parallel experiments. Our data demonstrate that ETs induce nongenetic cell state transitions into dormancy in a stochastic subset of cells via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably in the absence of recurrent genetic alterations. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs. SIGNIFICANCE This study advances the understanding of therapy-induced dormancy with potential clinical implications for breast cancer. Estrogen receptor-positive breast cancer cells adapt to endocrine treatment by entering a dormant state characterized by strong heterochromatinization with no recurrent genetic changes. Targeting the epigenetic rewiring impairs the adaptation of cancer cells to ETs. See related commentary by Llinas-Bertran et al., p. 704. This article is featured in Selected Articles from This Issue, p. 695.
Collapse
Affiliation(s)
- Dalia Rosano
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| | - Emre Sofyali
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Heena Dhiman
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| | - Chiara Ghirardi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Diana Ivanoiu
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Timon Heide
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | | | | | - Giancarlo Pruneri
- Istituto Nazionale Tumori, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Milano, Italy
| | - Eleonora Canale
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Hannah F. Dewhurst
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Debjani Saha
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Neil Slaven
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Centre for Cancer Research, Medical University of Vienna, Austria
| | - Tong Li
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Grigory Zemlyanskiy
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Henry Phillips
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Chela James
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- RCNS Cancer Biomarker Research Group, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
| | - Claire Lynn
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - George D. Cresswell
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Farah Rehman
- Charing Cross Hospital, Imperial College NHS Trust, London, United Kingdom
| | - 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, Milano, Italy
| | - Andrea Sottoriva
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| |
Collapse
|
2
|
Liu C, Xu M, Li W, Cao X, Wang Y, Chen H, Zhang T, Lu M, Xie H, Chen Y. Quantitative Pattern of hPTMs by Mass Spectrometry-Based Proteomics with Implications for Triple-Negative Breast Cancer. J Proteome Res 2024; 23:1495-1505. [PMID: 38576392 DOI: 10.1021/acs.jproteome.4c00034] [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: 04/06/2024]
Abstract
Triple-negative breast cancer (TNBC) is known for its aggressive nature, and TNBC management is currently challenging due to the lack of effective targets. Despite the importance of histone post-translational modifications (hPTMs) in breast cancer, their associations with molecular subtypes of breast cancer, especially TNBC, are poorly understood. In this study, a combination of untargeted and targeted proteomics approaches, supplemented by a derivatization method, was applied to breast cancer cells and tissue samples. Untargeted proteomics of eight breast cancer cell lines belonging to different molecular subtypes revealed 36 modified peptides with 12 lysine modification sites in histone H3, and the most frequently reported top 5 histone H3 methylation and acetylation sites were covered. Then, targeted proteomics was carried out to quantify the total 20 target hPTMs at the covered modification sites (i.e., mono-, di-, trimethylation, and acetylation for each site), indicating the difficulty in distinguishing TNBC cells from normal cells. Subsequently, the analysis in TNBC patients revealed significant expression differences in 4 specific hPTMs (H3K14ac, H3K27me1, H3K36me2, and H3K36me3) between TNBC and adjacent normal tissue samples. These unique hPTM patterns allowed for the differentiation of TNBC from normal cases. This finding provides promising implications for advancing targeted treatment strategies for TNBC in the future.
Collapse
Affiliation(s)
- Chunyan Liu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Mengying Xu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Wan Li
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Xiao Cao
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Yan Wang
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Haoran Chen
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Tianqi Zhang
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Meiyan Lu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Hui Xie
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing 211166, China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Nanjing 211166, China
| |
Collapse
|
3
|
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.
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
|
4
|
Borkiewicz L. Histone 3 Lysine 27 Trimethylation Signature in Breast Cancer. Int J Mol Sci 2021; 22:12853. [PMID: 34884658 PMCID: PMC8657745 DOI: 10.3390/ijms222312853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer development and progression rely on complicated genetic and also epigenetic changes which regulate gene expression without altering the DNA sequence. Epigenetic mechanisms such as DNA methylation, histone modifications, and regulation by lncRNAs alter protein expression by either promoting gene transcription or repressing it. The presence of so-called chromatin modification marks at various gene promoters and gene bodies is associated with normal cell development but also with tumorigenesis and progression of different types of cancer, including the most frequently diagnosed breast cancer. This review is focused on the significance of one of the abundant post-translational modifications of histone 3- trimethylation of lysine 27 (H3K27me3), which was shown to participate in tumour suppressor genes' silencing. Unlike other reviews in the field, here the overview of existing evidence linking H3K27me3 status with breast cancer biology and the tumour outcome is presented especially in the context of diverse breast cancer subtypes. Moreover, the potential of agents that target H3K27me3 for the treatment of this complex disease as well as H3K27 methylation in cross-talk with other chromatin modifications and lncRNAs are discussed.
Collapse
Affiliation(s)
- Lidia Borkiewicz
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-059 Lublin, Poland
| |
Collapse
|
5
|
Babu N, Bhat MY, John AE, Chatterjee A. The role of proteomics in the multiplexed analysis of gene alterations in human cancer. Expert Rev Proteomics 2021; 18:737-756. [PMID: 34602018 DOI: 10.1080/14789450.2021.1984884] [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: 10/20/2022]
Abstract
INTRODUCTION Proteomics has played a pivotal role in identifying proteins perturbed in disease conditions when compared with healthy samples. Study of dysregulated proteins aids in identifying diagnostic markers and potential therapeutic targets. Cancer is an outcome of interplay of several such disarrayed proteins and molecular pathways which perturb cellular homeostasis, resulting in transformation. In this review, we discuss various facets of proteomic approaches, including tools and technological advancements, aiding in understanding differentially expressed molecules and signaling mechanisms. AREAS COVERED In this review, we have taken the approach of documenting the different methods of proteomic studies, ranging from labeling techniques, data analysis methods, and the nature of molecule detected. We summarize each technique and provide a glimpse of cancer research carried out using them, highlighting the advantages and drawbacks in comparison with others. Literature search using online resources, such as PubMed and Google Scholar were carried out for this approach. EXPERT OPINION Technological advancements in proteomics studies have come a long way from the study of two-dimensional mapping of proteins separated on gels in the early 1970s. Higher precision in molecular identification and quantification (high throughput), and greater number of samples analyzed have been the focus of researchers.
Collapse
Affiliation(s)
- Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Mohd Younis Bhat
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | | | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| |
Collapse
|
6
|
Su M, Zhang Z, Zhou L, Han C, Huang C, Nice EC. Proteomics, Personalized Medicine and Cancer. Cancers (Basel) 2021; 13:2512. [PMID: 34063807 PMCID: PMC8196570 DOI: 10.3390/cancers13112512] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
As of 2020 the human genome and proteome are both at >90% completion based on high stringency analyses. This has been largely achieved by major technological advances over the last 20 years and has enlarged our understanding of human health and disease, including cancer, and is supporting the current trend towards personalized/precision medicine. This is due to improved screening, novel therapeutic approaches and an increased understanding of underlying cancer biology. However, cancer is a complex, heterogeneous disease modulated by genetic, molecular, cellular, tissue, population, environmental and socioeconomic factors, which evolve with time. In spite of recent advances in treatment that have resulted in improved patient outcomes, prognosis is still poor for many patients with certain cancers (e.g., mesothelioma, pancreatic and brain cancer) with a high death rate associated with late diagnosis. In this review we overview key hallmarks of cancer (e.g., autophagy, the role of redox signaling), current unmet clinical needs, the requirement for sensitive and specific biomarkers for early detection, surveillance, prognosis and drug monitoring, the role of the microbiome and the goals of personalized/precision medicine, discussing how emerging omics technologies can further inform on these areas. Exemplars from recent onco-proteogenomic-related publications will be given. Finally, we will address future perspectives, not only from the standpoint of perceived advances in treatment, but also from the hurdles that have to be overcome.
Collapse
Affiliation(s)
- Miao Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Chao Han
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| |
Collapse
|
7
|
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.
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
|
8
|
Capitoli G, Piga I, Clerici F, Brambilla V, Mahajneh A, Leni D, Garancini M, Pincelli AI, L'Imperio V, Galimberti S, Magni F, Pagni F. Analysis of Hashimoto's thyroiditis on fine needle aspiration samples by MALDI-Imaging. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140481. [PMID: 32645440 DOI: 10.1016/j.bbapap.2020.140481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/04/2020] [Accepted: 06/27/2020] [Indexed: 12/11/2022]
Abstract
Matrix-Assisted Laser Desorption/Ionization (MALDI)-Mass Spectrometry imaging (MSI) has been applied in various diseases aimed to biomarkers discovery. In this study diagnosis and prognosis of Hashimoto Thyroiditis (HT) in cytopathology by MALDI-MSI has been investigated. Specimens from a routine series of subjects who underwent UltraSound-guided thyroid Fine Needle Aspirations (FNAs) were used. The molecular classifier trained in a previous study was modified to include HT as a separate entity in the group of benign lesions, in the diagnostic proteomic triage of thyroid nodules. The statistical analysis confirmed the existence of signals that HT shares with hyperplastic lesions and others that are specific and characterize this subgroup. Statistically relevant HT-related peaks were included in the model. Then, the discriminatory capability of the classifier was tested in a second validation phase, showing a good agreement with cytological diagnoses. The possibility to overlap the molecular signatures of both the lymphocytes and epithelial cells components (ROIs or pixel-by-pixel analysis) confirmed the composite proteomic background of HT. These results open the way to their possible translation as alternative serum biomarkers of this autoimmune condition.
Collapse
Affiliation(s)
- Giulia Capitoli
- Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, School of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Isabella Piga
- Proteomics and Metabolomics, School of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Francesca Clerici
- Proteomics and Metabolomics, School of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Virginia Brambilla
- Pathology, Department of Medicine and Surgery, University of Milano-Bicocca, San Gerardo Hospital, ASST, Monza, Italy
| | - Allia Mahajneh
- Proteomics and Metabolomics, School of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Davide Leni
- Department of radiology, San Gerardo Hospital, ASST, Monza, Italy
| | | | | | - Vincenzo L'Imperio
- Pathology, Department of Medicine and Surgery, University of Milano-Bicocca, San Gerardo Hospital, ASST, Monza, Italy
| | - Stefania Galimberti
- Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, School of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Fulvio Magni
- Proteomics and Metabolomics, School of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro, Italy.
| | - Fabio Pagni
- Pathology, Department of Medicine and Surgery, University of Milano-Bicocca, San Gerardo Hospital, ASST, Monza, Italy.
| |
Collapse
|
9
|
Profiling of Epigenetic Features in Clinical Samples Reveals Novel Widespread Changes in Cancer. Cancers (Basel) 2019; 11:cancers11050723. [PMID: 31137727 PMCID: PMC6562406 DOI: 10.3390/cancers11050723] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [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
|
10
|
Hoedt E, Zhang G, Neubert TA. Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) for Quantitative Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:531-539. [PMID: 31347069 DOI: 10.1007/978-3-030-15950-4_31] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful approach for high-throughput quantitative proteomics. SILAC allows highly accurate protein quantitation through metabolic encoding of whole cell proteomes using stable isotope labeled amino acids. Since its introduction in 2002, SILAC has become increasingly popular. In this chapter we review the methodology and application of SILAC, with an emphasis on three research areas: dynamics of posttranslational modifications, protein-protein interactions, and protein turnover.
Collapse
Affiliation(s)
- Esthelle Hoedt
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Guoan Zhang
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
| |
Collapse
|
11
|
Abstract
Introduction: Epigenetic dysregulation drives or supports numerous human cancers. The chromatin landscape in cancer cells is often marked by abnormal histone post-translational modification (PTM) patterns and by aberrant assembly and recruitment of protein complexes to specific genomic loci. Mass spectrometry-based proteomic analyses can support the discovery and characterization of both phenomena. Areas covered: We broadly divide this literature into two parts: 'modification-centric' analyses that link histone PTMs to cancer biology; and 'complex-centric' analyses that examine protein-protein interactions that occur de novo as a result of oncogenic mutations. We also discuss proteomic studies of oncohistones. We highlight relevant examples, discuss limitations, and speculate about forthcoming innovations regarding each application. Expert commentary: 'Modification-centric' analyses have been used to further understanding of cancer's histone code and to identify associated therapeutic vulnerabilities. 'Complex-centric' analyses have likewise revealed insights into mechanisms of oncogenesis and suggested potential therapeutic targets, particularly in MLL-associated leukemia. Proteomic experiments have also supported some of the pioneering studies of oncohistone-mediated tumorigenesis. Additional applications of proteomics that may benefit cancer epigenetics research include middle-down and top-down histone PTM analysis, chromatin reader profiling, and genomic locus-specific protein identification. In the coming years, proteomic approaches will remain powerful ways to interrogate the biology of cancer.
Collapse
Affiliation(s)
- Dylan M Marchione
- a Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - Benjamin A Garcia
- a Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - John Wojcik
- b Department of Pathology and Laboratory Medicine, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| |
Collapse
|
12
|
Wu M, Fan B, Guo Q, Li Y, Chen R, Lv N, Diao Y, Luo Y. Knockdown of SETDB1 inhibits breast cancer progression by miR-381-3p-related regulation. Biol Res 2018; 51:39. [PMID: 30309377 PMCID: PMC6180515 DOI: 10.1186/s40659-018-0189-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/03/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND SET domain bifurcated 1 (SETDB1) has been widely considered as an oncogene playing a critical role in many human cancers, including breast cancer. Nevertheless, the molecular mechanism by which SETDB1 regulates breast cancer tumorigenesis is still unknown. METHODS qRT-PCR assay or western blot analysis was performed to assess the expression level of SETDB1 mRNA or protein, respectively. siSETDB1, pCMV6-XL5-SETDB1, miR-381-3p mimic, or miR-381-3p inhibitor was transfected into cells to regulate the expression of SETDB1 or miR-381-3p. MiRNA directly interacted with SETDB1 was verified by luciferase reporter assay and RNA immunoprecipitation. CCK-8 assay, colony formation assay, flow cytometric analysis, and transwell assay were used to detect the abilities of cell proliferation, cell cycle progression and migration, respectively. Animal model of xenograft tumor was used to observe the regulatory effect of SETDB1 on tumor growth in vivo. RESULTS We verified that SETDB1 mRNA level was upregulated in breast cancer tissues and cell lines, and SETDB1 depletion led to a suppression of cell proliferation, cell cycle progression and migration in vitro, as well as tumor growth in vivo. SETDB1 was verified to be a target of miR-381-3p. Moreover, miR-381-3p overexpression suppressed cell proliferation, cell cycle progression and migration, whereas SETDB1 abated miR-381-3p-mediated regulatory function on breast cancer cells. CONCLUSIONS This study revealed that SETDB1 knockdown might suppress breast cancer progression at least partly by miR-381-3p-related regulation, providing a novel prospect in breast cancer therapy.
Collapse
Affiliation(s)
- Milu Wu
- grid.459333.bDepartment of Oncology, The Affiliated Hospital of Qinghai University, No. 29, Tongren Rd, Xining, 810001 Qinghai China
| | - Baohua Fan
- grid.459333.bDepartment of Oncology, The Affiliated Hospital of Qinghai University, No. 29, Tongren Rd, Xining, 810001 Qinghai China
| | - Qijing Guo
- grid.459333.bDepartment of Oncology, The Affiliated Hospital of Qinghai University, No. 29, Tongren Rd, Xining, 810001 Qinghai China
| | - Yan Li
- grid.459333.bDepartment of Oncology, The Affiliated Hospital of Qinghai University, No. 29, Tongren Rd, Xining, 810001 Qinghai China
| | - Rong Chen
- grid.459333.bDepartment of Oncology, The Affiliated Hospital of Qinghai University, No. 29, Tongren Rd, Xining, 810001 Qinghai China
| | - Nannan Lv
- grid.459333.bDepartment of Oncology, The Affiliated Hospital of Qinghai University, No. 29, Tongren Rd, Xining, 810001 Qinghai China
| | - Yinzhuo Diao
- grid.459333.bDepartment of Oncology, The Affiliated Hospital of Qinghai University, No. 29, Tongren Rd, Xining, 810001 Qinghai China
| | - Yushuang Luo
- grid.459333.bDepartment of Oncology, The Affiliated Hospital of Qinghai University, No. 29, Tongren Rd, Xining, 810001 Qinghai China
| |
Collapse
|
13
|
Wang X, He Y, Ye Y, Zhao X, Deng S, He G, Zhu H, Xu N, Liang S. SILAC-based quantitative MS approach for real-time recording protein-mediated cell-cell interactions. Sci Rep 2018; 8:8441. [PMID: 29855483 PMCID: PMC5981645 DOI: 10.1038/s41598-018-26262-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/04/2018] [Indexed: 02/05/2023] Open
Abstract
In tumor microenvironment, interactions among multiple cell types are critical for cancer progression. To understand the molecular mechanisms of these complex interplays, the secreted protein analysis between malignant cancer cells and the surrounding nonmalignant stroma is a good viewpoint to investigate cell-cell interactions. Here, we developed two stable isotope labeling of amino acids in cell culture (SILAC)-based mass spectrometry (MS)/MS approaches termed spike-in SILAC and triple-SILAC to quantify changes of protein secretion level in a cell co-cultured system. Within the co-culture system of CT26 and Ana-1 cells, the spike-in SILAC and triple-SILAC MS approaches are sensitive to quantitatively measure protein secretion changes. Three representative quantified proteins (Galectin-1, Cathepsin L1 and Thrombospondin-1) by two SILAC-based MS methods were further validated by Western blotting, and the coming result matched well with SILACs’. We further applied these two SILACs to human cell lines, NCM460 and HT29 co-culture system, for evaluating the feasibility, which confirmed the spike-in and triple SILAC were capable of monitoring the changed secreted proteins of human cell lines. Considering these two strategies in time consuming, sample complexity and proteome coverage, the triple-SILAC way shows more efficiency and economy for real-time recording secreted protein levels in tumor microenvironment.
Collapse
Affiliation(s)
- Xixi Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China.,Chengdu Center for Disease Control and Prevention, Chengdu, 610041, P. R. China
| | - Yu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Yang Ye
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Xinyu Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Shi Deng
- Department of Urinary Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, P. R. China
| | - Gu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Hongxia Zhu
- Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular Oncology, Cancer Institute & Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, 100021, P. R. China
| | - Ningzhi Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China.,Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular Oncology, Cancer Institute & Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, 100021, P. R. China
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China.
| |
Collapse
|
14
|
Noberini R, Osti D, Miccolo C, Richichi C, Lupia M, Corleone G, Hong SP, Colombo P, Pollo B, Fornasari L, Pruneri G, Magnani L, Cavallaro U, Chiocca S, Minucci S, Pelicci G, Bonaldi T. Extensive and systematic rewiring of histone post-translational modifications in cancer model systems. Nucleic Acids Res 2018; 46:3817-3832. [PMID: 29618087 PMCID: PMC5934616 DOI: 10.1093/nar/gky224] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 03/09/2018] [Accepted: 03/16/2018] [Indexed: 01/04/2023] Open
Abstract
Histone post-translational modifications (PTMs) generate a complex combinatorial code that regulates gene expression and nuclear functions, and whose deregulation has been documented in different types of cancers. Therefore, the availability of relevant culture models that can be manipulated and that retain the epigenetic features of the tissue of origin is absolutely crucial for studying the epigenetic mechanisms underlying cancer and testing epigenetic drugs. In this study, we took advantage of quantitative mass spectrometry to comprehensively profile histone PTMs in patient tumor tissues, primary cultures and cell lines from three representative tumor models, breast cancer, glioblastoma and ovarian cancer, revealing an extensive and systematic rewiring of histone marks in cell culture conditions, which includes a decrease of H3K27me2/me3, H3K79me1/me2 and H3K9ac/K14ac, and an increase of H3K36me1/me2. While some changes occur in short-term primary cultures, most of them are instead time-dependent and appear only in long-term cultures. Remarkably, such changes mostly revert in cell line- and primary cell-derived in vivo xenograft models. Taken together, these results support the use of xenografts as the most representative models of in vivo epigenetic processes, suggesting caution when using cultured cells, in particular cell lines and long-term primary cultures, for epigenetic investigations.
Collapse
Affiliation(s)
- Roberta Noberini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan 20139, Italy
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Daniela Osti
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Claudia Miccolo
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Cristina Richichi
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Michela Lupia
- Unit of Gynecological Oncology Research, European Institute of Oncology, Milan 20141, Italy
| | - Giacomo Corleone
- Department of Surgery and Cancer, Imperial College Hammersmith, London W12, UK
| | - Sung-Pil Hong
- Department of Surgery and Cancer, Imperial College Hammersmith, London W12, UK
| | - Piergiuseppe Colombo
- Department of Pathology, Humanitas Clinical and Research Center, Rozzano, Milan 20089, Italy
| | - Bianca Pollo
- Department of Neuropathology, IRCCS Foundation Neurological Institute 'C. Besta', Milan 20133, Italy
| | - Lorenzo Fornasari
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Giancarlo Pruneri
- Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Milano 20141, Italy
- School of Medicine, University of Milan, Milan 20122, Italy
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College Hammersmith, London W12, UK
| | - Ugo Cavallaro
- Unit of Gynecological Oncology Research, European Institute of Oncology, Milan 20141, Italy
| | - Susanna Chiocca
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
- New Drugs Program, European Institute of Oncology, Milan 20139, Italy
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Giuliana Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
- Department of Translational Medicine, Piemonte Orientale University 'Amedeo Avogadro', Novara 28100, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| |
Collapse
|
15
|
Fellows R, Denizot J, Stellato C, Cuomo A, Jain P, Stoyanova E, Balázsi S, Hajnády Z, Liebert A, Kazakevych J, Blackburn H, Corrêa RO, Fachi JL, Sato FT, Ribeiro WR, Ferreira CM, Perée H, Spagnuolo M, Mattiuz R, Matolcsi C, Guedes J, Clark J, Veldhoen M, Bonaldi T, Vinolo MAR, Varga-Weisz P. Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases. Nat Commun 2018; 9:105. [PMID: 29317660 PMCID: PMC5760624 DOI: 10.1038/s41467-017-02651-5] [Citation(s) in RCA: 306] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 12/18/2017] [Indexed: 01/01/2023] Open
Abstract
The recently discovered histone post-translational modification crotonylation connects cellular metabolism to gene regulation. Its regulation and tissue-specific functions are poorly understood. We characterize histone crotonylation in intestinal epithelia and find that histone H3 crotonylation at lysine 18 is a surprisingly abundant modification in the small intestine crypt and colon, and is linked to gene regulation. We show that this modification is highly dynamic and regulated during the cell cycle. We identify class I histone deacetylases, HDAC1, HDAC2, and HDAC3, as major executors of histone decrotonylation. We show that known HDAC inhibitors, including the gut microbiota-derived butyrate, affect histone decrotonylation. Consistent with this, we find that depletion of the gut microbiota leads to a global change in histone crotonylation in the colon. Our results suggest that histone crotonylation connects chromatin to the gut microbiota, at least in part, via short-chain fatty acids and HDACs.
Collapse
Affiliation(s)
- Rachel Fellows
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Jérémy Denizot
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK.,Université Clermont Auvergne, Inserm U1071, INRA USC2018, M2iSH, Clermont-Ferrand, F-63000, France
| | | | - Alessandro Cuomo
- Department of Experimental Oncology, Istituto Europeo di Oncologia, 20139, Milano, Italy
| | - Payal Jain
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Elena Stoyanova
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Szabina Balázsi
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Zoltán Hajnády
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Anke Liebert
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Juri Kazakevych
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | | | - Renan Oliveira Corrêa
- Laboratory of Immunoinflammation, Institute of Biology, UNICAMP, Campinas, 13083-862, Brazil
| | - José Luís Fachi
- Laboratory of Immunoinflammation, Institute of Biology, UNICAMP, Campinas, 13083-862, Brazil
| | - Fabio Takeo Sato
- Laboratory of Immunoinflammation, Institute of Biology, UNICAMP, Campinas, 13083-862, Brazil
| | - Willian R Ribeiro
- Department of Pharmaceutical Sciences, Institute of Environmental, Chemistry and Pharmaceutical Sciences, Universidade Federal de São Paulo, Diadema, SP, 09913-03, Brazil.,Chemical Biology Graduate Program, Universidade Federal de São Paulo, Diadema, SP, 09913-03, Brazil
| | - Caroline Marcantonio Ferreira
- Department of Pharmaceutical Sciences, Institute of Environmental, Chemistry and Pharmaceutical Sciences, Universidade Federal de São Paulo, Diadema, SP, 09913-03, Brazil
| | - Hélène Perée
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | | | - Raphaël Mattiuz
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Csaba Matolcsi
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Joana Guedes
- Lymphocyte Signalling and Development, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Jonathan Clark
- Biological Chemistry, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Marc Veldhoen
- Lymphocyte Signalling and Development, Babraham Institute, Cambridge, CB22 3AT, UK.,Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, 1649-028, Portugal
| | - Tiziana Bonaldi
- Department of Experimental Oncology, Istituto Europeo di Oncologia, 20139, Milano, Italy.
| | | | - Patrick Varga-Weisz
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK. .,School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK.
| |
Collapse
|
16
|
Soldi M, Mari T, Nicosia L, Musiani D, Sigismondo G, Cuomo A, Pavesi G, Bonaldi T. Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers. Nucleic Acids Res 2017; 45:12195-12213. [PMID: 28981749 PMCID: PMC5716071 DOI: 10.1093/nar/gkx821] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 09/06/2017] [Indexed: 01/09/2023] Open
Abstract
The integrated activity of cis-regulatory elements fine-tunes transcriptional programs of mammalian cells by recruiting cell type–specific as well as ubiquitous transcription factors (TFs). Despite their key role in modulating transcription, enhancers are still poorly characterized at the molecular level, and their limited DNA sequence conservation in evolution and variable distance from target genes make their unbiased identification challenging. The coexistence of high mono-methylation and low tri-methylation levels of lysine 4 of histone H3 is considered a signature of enhancers, but a comprehensive view of histone modifications associated to enhancers is still lacking. By combining chromatin immunoprecipitation (ChIP) with mass spectrometry, we investigated cis-regulatory regions in macrophages to comprehensively identify histone marks specifically associated with enhancers, and to profile their dynamics after transcriptional activation elicited by an inflammatory stimulation. The intersection of the proteomics data with ChIP-seq and RNA-seq analyses revealed the existence of novel subpopulations of enhancers, marked by specific histone modification signatures: specifically, H3K4me1/K36me2 marks transcribed enhancers, while H3K4me1/K36me3 and H3K4me1/K79me2 combinations mark distinct classes of intronic enhancers. Thus, our MS analysis of functionally distinct genomic regions revealed the combinatorial code of histone modifications, highlighting the potential of proteomics in addressing fundamental questions in epigenetics.
Collapse
Affiliation(s)
- Monica Soldi
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Tommaso Mari
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Luciano Nicosia
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Daniele Musiani
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Gianluca Sigismondo
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Giulio Pavesi
- Department of Biosciences, Milan University, Milan 20133, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| |
Collapse
|
17
|
Zavialova MG, Zgoda VG, Nikolaev EN. [Analysis of contribution of protein phosphorylation in the development of the diseases]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2017; 63:101-114. [PMID: 28414281 DOI: 10.18097/pbmc20176302101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In recent decades, studies in the molecular origins of socially significant diseases have made a big step forward with the development and using of high-performance methods in genomics and proteomics. Numerous studies in the framework of the global program "Human Proteome" were aimed at the identification of all possible proteins in various cell cultures and tissues, including cancer. One of the objectives was to identify biomarkers - proteins with high specificity to certain pathologies. However, in many cases, it is shown that the development of the disease is not associated with the appearance of new proteins, but depends on the level of gene expression or forming of proteoforms - splice variants, single amino acid substitutions (SAP variants), and post-translational modifications (PTM) of proteins. PTM may play a key role in the development of pathology because they activate a variety of regulatory or structural proteins in the majority of cell physiological processes. Phosphorylation is among the most significant of these protein modifications.This review will describe methods for analysis of protein phosphorylation used in the studies of such diseases as cancer and neurodegenerative diseases, as well as examples of cases when the modified proteins are involved directly to their development, and screening such significant PTM is used for the diagnosis and choice of treatment.
Collapse
Affiliation(s)
| | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
| | - E N Nikolaev
- Institute of Biomedical Chemistry, Moscow, Russia; Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia
| |
Collapse
|
18
|
Ferry L, Fournier A, Tsusaka T, Adelmant G, Shimazu T, Matano S, Kirsh O, Amouroux R, Dohmae N, Suzuki T, Filion GJ, Deng W, de Dieuleveult M, Fritsch L, Kudithipudi S, Jeltsch A, Leonhardt H, Hajkova P, Marto JA, Arita K, Shinkai Y, Defossez PA. Methylation of DNA Ligase 1 by G9a/GLP Recruits UHRF1 to Replicating DNA and Regulates DNA Methylation. Mol Cell 2017; 67:550-565.e5. [PMID: 28803780 DOI: 10.1016/j.molcel.2017.07.012] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/24/2017] [Accepted: 07/10/2017] [Indexed: 01/02/2023]
Abstract
DNA methylation is an essential epigenetic mark in mammals that has to be re-established after each round of DNA replication. The protein UHRF1 is essential for this process; it has been proposed that the protein targets newly replicated DNA by cooperatively binding hemi-methylated DNA and H3K9me2/3, but this model leaves a number of questions unanswered. Here, we present evidence for a direct recruitment of UHRF1 by the replication machinery via DNA ligase 1 (LIG1). A histone H3K9-like mimic within LIG1 is methylated by G9a and GLP and, compared with H3K9me2/3, more avidly binds UHRF1. Interaction with methylated LIG1 promotes the recruitment of UHRF1 to DNA replication sites and is required for DNA methylation maintenance. These results further elucidate the function of UHRF1, identify a non-histone target of G9a and GLP, and provide an example of a histone mimic that coordinates DNA replication and DNA methylation maintenance.
Collapse
Affiliation(s)
- Laure Ferry
- Epigenetics and Cell Fate, University Paris Diderot, Sorbonne Paris Cité, UMR 7216 CNRS, 75013 Paris, France
| | - Alexandra Fournier
- Epigenetics and Cell Fate, University Paris Diderot, Sorbonne Paris Cité, UMR 7216 CNRS, 75013 Paris, France
| | - Takeshi Tsusaka
- Cellular Memory Laboratory, RIKEN Wako, Saitama 351-0198, Japan; Graduate School of Medicine, Diabetes, Endocrinology, and Nutrition, Kyoto University, Kyoto 606-8507, Japan
| | - Guillaume Adelmant
- The Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Shohei Matano
- Department of Medical Life Sciences, Yokohama City University, Yokohama 230-0045, Japan
| | - Olivier Kirsh
- Epigenetics and Cell Fate, University Paris Diderot, Sorbonne Paris Cité, UMR 7216 CNRS, 75013 Paris, France
| | - Rachel Amouroux
- MRC Clinical Sciences Centre (CSC), Du Cane Road, London W12 0NN, UK; Faculty of Medicine, Institute of Clinical Sciences (ICS), Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Center for Sustainable Resource Science, RIKEN, Wako, Saitama 351-0198, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Center for Sustainable Resource Science, RIKEN, Wako, Saitama 351-0198, Japan
| | - Guillaume J Filion
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Wen Deng
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Maud de Dieuleveult
- Epigenetics and Cell Fate, University Paris Diderot, Sorbonne Paris Cité, UMR 7216 CNRS, 75013 Paris, France
| | - Lauriane Fritsch
- Epigenetics and Cell Fate, University Paris Diderot, Sorbonne Paris Cité, UMR 7216 CNRS, 75013 Paris, France
| | | | - Albert Jeltsch
- Institut für Biochemie, Stuttgart University, 70569 Stuttgart, Germany
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Petra Hajkova
- MRC Clinical Sciences Centre (CSC), Du Cane Road, London W12 0NN, UK; Faculty of Medicine, Institute of Clinical Sciences (ICS), Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Jarrod A Marto
- The Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kyohei Arita
- Department of Medical Life Sciences, Yokohama City University, Yokohama 230-0045, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Wako, Saitama 351-0198, Japan.
| | - Pierre-Antoine Defossez
- Epigenetics and Cell Fate, University Paris Diderot, Sorbonne Paris Cité, UMR 7216 CNRS, 75013 Paris, France.
| |
Collapse
|
19
|
Noberini R, Longuespée R, Richichi C, Pruneri G, Kriegsmann M, Pelicci G, Bonaldi T. PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples. Clin Epigenetics 2017; 9:69. [PMID: 28702092 PMCID: PMC5504751 DOI: 10.1186/s13148-017-0369-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/28/2017] [Indexed: 12/22/2022] Open
Abstract
Background Aberrations in histone post-translational modifications (hPTMs) have been linked with various pathologies, including cancer, and could not only represent useful biomarkers but also suggest possible targetable epigenetic mechanisms. We have recently developed an approach, termed pathology tissue analysis of histones by mass spectrometry (PAT-H-MS), that allows performing a comprehensive and quantitative analysis of histone PTMs from formalin-fixed paraffin-embedded pathology samples. Despite its great potential, the application of this technique is limited by tissue heterogeneity. Methods In this study, we further implemented the PAT-H-MS approach by coupling it with techniques aimed at reducing sample heterogeneity and selecting specific portions or cell populations within the samples, such as manual macrodissection and laser microdissection (LMD). Results When applied to the analysis of a small set of breast cancer samples, LMD-PAT-H-MS allowed detecting more marked changes between luminal A-like and triple negative patients as compared with the classical approach. These changes included not only the already known H3 K27me3 and K9me3 marks, but also H3 K36me1, which was found increased in triple negative samples and validated on a larger cohort of patients, and could represent a potential novel marker distinguishing breast cancer subtypes. Conclusions These results show the feasibility of applying techniques to reduce sample heterogeneity, including laser microdissection, to the PAT-H-MS protocol, providing new tools in clinical epigenetics and opening new avenues for the comprehensive analysis of histone post-translational modifications in selected cell populations. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0369-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Roberta Noberini
- Center for Genomic Science of IIT@ SEMM, Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy
| | - Rémi Longuespée
- Institute of Pathology, University of Heidelberg, Im Neuenheimer Feld 224, 69620 Heidelberg, Germany
| | - Cristina Richichi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Giancarlo Pruneri
- Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Via Ripamonti 435, 20141 Milan, Italy.,School of Medicine, University of Milan, 20122 Milan, Italy
| | - Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, Im Neuenheimer Feld 224, 69620 Heidelberg, Germany
| | - Giuliana Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.,Department of Translational Medicine, Piemonte Orientale University "Amedeo Avogadro", 28100 Novara, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| |
Collapse
|
20
|
Cuomo A, Soldi M, Bonaldi T. SILAC-Based Quantitative Strategies for Accurate Histone Posttranslational Modification Profiling Across Multiple Biological Samples. Methods Mol Biol 2017; 1528:97-119. [PMID: 27854018 DOI: 10.1007/978-1-4939-6630-1_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone posttranslational modifications (hPTMs) play a key role in regulating chromatin dynamics and fine-tuning DNA-based processes. Mass spectrometry (MS) has emerged as a versatile technology for the analysis of histones, contributing to the dissection of hPTMs, with special strength in the identification of novel marks and in the assessment of modification cross talks. Stable isotope labeling by amino acid in cell culture (SILAC), when adapted to histones, permits the accurate quantification of PTM changes among distinct functional states; however, its application has been mainly confined to actively dividing cell lines. A spike-in strategy based on SILAC can be used to overcome this limitation and profile hPTMs across multiple samples. We describe here the adaptation of SILAC to the analysis of histones, in both standard and spike-in setups. We also illustrate its coupling to an implemented "shotgun" workflow, by which heavy arginine-labeled histone peptides, produced upon Arg-C digestion, are qualitatively and quantitatively analyzed in an LC-MS/MS system that combines ultrahigh-pressure liquid chromatography (UHPLC) with new-generation Orbitrap high-resolution instrument.
Collapse
Affiliation(s)
- Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Monica Soldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy.
| |
Collapse
|
21
|
Noberini R, Bonaldi T. A Super-SILAC Strategy for the Accurate and Multiplexed Profiling of Histone Posttranslational Modifications. Methods Enzymol 2016; 586:311-332. [PMID: 28137569 DOI: 10.1016/bs.mie.2016.09.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone posttranslational modifications (hPTMs) generate a complex combinatorial code that plays a critical role in the regulation of gene activity and nuclear architecture during physiological and pathological processes. Mass spectrometry (MS) offers an unbiased, comprehensive, and quantitative view on hPTM patterns, and has emerged as a powerful tool in epigenetic research. Stable isotope labeling by amino acid in cell culture (SILAC) is a MS-based quantitative method that relies on the metabolic labeling of cell populations, which has been widely applied in global proteomic studies and can also be exploited for the accurate quantitation of hPTM changes among distinct functional states. However, the classical SILAC strategy has two main limits: it cannot be applied to more than three cell populations at the time and excludes samples that cannot be metabolically labeled, such as clinical samples. These limitations can be overcome by using a super-SILAC strategy, where a mix of heavy-labeled cell lines is used as a spike-in to analyze any types of samples with high accuracy and high multiplexing capabilities. In this chapter, we will provide a detailed description of a protocol to set up a histone-focused super-SILAC strategy and exploit it to accurately profile hPTMs across multiple samples. As a case study, we will describe a breast cancer-focused super-SILAC approach, which we used in a recent publication to profile hPTMs in frozen and formalin-fixed paraffin-embedded human samples, revealing previously unknown marks that differentiate breast cancer subtypes.
Collapse
Affiliation(s)
- R Noberini
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milano, Italy
| | - T Bonaldi
- European Institute of Oncology, Milano, Italy.
| |
Collapse
|
22
|
Önder Ö, Sidoli S, Carroll M, Garcia BA. Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations. Expert Rev Proteomics 2016; 12:499-517. [PMID: 26400466 DOI: 10.1586/14789450.2015.1084231] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chromatin biology and epigenetics are scientific fields that are rapid expanding due to their fundamental role in understanding cell development, heritable characters and progression of diseases. Histone post-translational modifications (PTMs) are major regulators of the epigenetic machinery due to their ability to modulate gene expression, DNA repair and chromosome condensation. Large-scale strategies based on mass spectrometry have been impressively improved in the last decade, so that global changes of histone PTM abundances are quantifiable with nearly routine proteomics analyses and it is now possible to determine combinatorial patterns of modifications. Presented here is an overview of the most utilized and newly developed proteomics strategies for histone PTM characterization and a number of case studies where epigenetic mechanisms have been comprehensively characterized. Moreover, a number of current epigenetic therapies are illustrated, with an emphasis on cancer.
Collapse
Affiliation(s)
- Özlem Önder
- a 1 Division of Hematology and Oncology, Philadelphia, 19104, USA.,b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simone Sidoli
- b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Martin Carroll
- a 1 Division of Hematology and Oncology, Philadelphia, 19104, USA
| | - Benjamin A Garcia
- b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| |
Collapse
|
23
|
Sowers JL, Mirfattah B, Xu P, Tang H, Park IY, Walker C, Wu P, Laezza F, Sowers LC, Zhang K. Quantification of histone modifications by parallel-reaction monitoring: a method validation. Anal Chem 2016; 87:10006-14. [PMID: 26356480 DOI: 10.1021/acs.analchem.5b02615] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abnormal epigenetic reprogramming is one of the major causes leading to irregular gene expression and regulatory pathway perturbations, in the cells, resulting in unhealthy cell development or diseases. Accurate measurements of these changes of epigenetic modifications, especially the complex histone modifications, are very important, and the methods for these measurements are not trivial. By following our previous introduction of PRM to targeting histone modifications (Tang, H.; Fang, H.; Yin, E.; Brasier, A. R.; Sowers, L. C.; Zhang, K. Multiplexed parallel reaction monitoring targeting histone modifications on the QExactive mass spectrometer. Anal. Chem. 2014, 86 (11), 5526-34), herein we validated this method by varying the protein/trypsin ratios via serial dilutions. Our data demonstrated that PRM with SILAC histones as the internal standards allowed reproducible measurements of histone H3/H4 acetylation and methylation in the samples whose histone contents differ at least one-order of magnitude. The method was further validated by histones isolated from histone H3 K36 trimethyltransferase SETD2 knockout mouse embryonic fibroblasts (MEF) cells. Furthermore, histone acetylation and methylation in human neural stem cells (hNSC) treated with ascorbic acid phosphate (AAP) were measured by this method, revealing that H3 K36 trimethylation was significantly down-regulated by 6 days of treatment with vitamin C.
Collapse
Affiliation(s)
| | | | | | | | - In Young Park
- Institute of Biosciences and Technology, Texas A&M Health Sciences Center , Houston, Texas 77030, United States
| | - Cheryl Walker
- Institute of Biosciences and Technology, Texas A&M Health Sciences Center , Houston, Texas 77030, United States
| | | | | | | | | |
Collapse
|
24
|
Noberini R, Sigismondo G, Bonaldi T. The contribution of mass spectrometry-based proteomics to understanding epigenetics. Epigenomics 2016; 8:429-45. [DOI: 10.2217/epi.15.108] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Chromatin is a macromolecular complex composed of DNA and histones that regulate gene expression and nuclear architecture. The concerted action of DNA methylation, histone post-translational modifications and chromatin-associated proteins control the epigenetic regulation of the genome, ultimately determining cell fate and the transcriptional outputs of differentiated cells. Deregulation of this complex machinery leads to disease states, and exploiting epigenetic drugs is becoming increasingly attractive for therapeutic intervention. Mass spectrometry (MS)-based proteomics emerged as a powerful tool complementary to genomic approaches for epigenetic research, allowing the unbiased and comprehensive analysis of histone post-translational modifications and the characterization of chromatin constituents and chromatin-associated proteins. Furthermore, MS holds great promise for epigenetic biomarker discovery and represents a useful tool for deconvolution of epigenetic drug targets. Here, we will provide an overview of the applications of MS-based proteomics in various areas of chromatin biology.
Collapse
Affiliation(s)
- Roberta Noberini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, via Adamello 16, Milano, Italy
| | - Gianluca Sigismondo
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milano, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milano, Italy
| |
Collapse
|
25
|
Bonaldi T, Noberini R. Recent advances in mass spectrometry analysis of histone post-translational modifications: potential clinical impact of the PAT-H-MS approach. Expert Rev Proteomics 2016; 13:245-50. [DOI: 10.1586/14789450.2016.1147960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
26
|
Noberini R, Pruneri G, Minucci S, Bonaldi T. Mass-spectrometry analysis of histone post-translational modifications in pathology tissue using the PAT-H-MS approach. Data Brief 2016; 7:188-94. [PMID: 27408908 PMCID: PMC4927966 DOI: 10.1016/j.dib.2016.02.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/09/2016] [Accepted: 02/09/2016] [Indexed: 11/24/2022] Open
Abstract
Aberrant histone post-translational modifications (hPTMs) have been implicated with various pathologies, including cancer, and may represent useful epigenetic biomarkers. The data described here provide a mass spectrometry-based quantitative analysis of hPTMs from formalin-fixed paraffin-embedded (FFPE) tissues, from which histones were extracted through the recently developed PAT-H-MS method. First, we analyzed FFPE samples from mouse spleen and liver or human breast cancer up to six years old, together with their corresponding fresh frozen tissue. We then combined the PAT-H-MS approach with a histone-focused version of the super-SILAC strategy-using a mix of histones from four breast cancer cell lines as a spike-in standard- to accurately quantify hPTMs from breast cancer specimens belonging to different subtypes. The data, which are associated with a recent publication (Pathology tissue-quantitative mass spectrometry analysis to profile histone post-translational modification patterns in patient samples (Noberini, 2015) [1]), are deposited at the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD002669.
Collapse
Affiliation(s)
- Roberta Noberini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy
| | - Giancarlo Pruneri
- School of Medicine, University of Milan, 20122 Milan, Italy; Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Via Ripamonti 435, 20141 Milan, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; Drug Development Program, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; Department of Bioscience, University of Milan, 20133 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| |
Collapse
|
27
|
Noberini R, Uggetti A, Pruneri G, Minucci S, Bonaldi T. Pathology Tissue-quantitative Mass Spectrometry Analysis to Profile Histone Post-translational Modification Patterns in Patient Samples. Mol Cell Proteomics 2015; 15:866-77. [PMID: 26463340 PMCID: PMC4813706 DOI: 10.1074/mcp.m115.054510] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Indexed: 12/18/2022] Open
Abstract
Histone post-translational modifications (hPTMs) generate a complex combinatorial code that has been implicated with various pathologies, including cancer. Dissecting such a code in physiological and diseased states may be exploited for epigenetic biomarker discovery, but hPTM analysis in clinical samples has been hindered by technical limitations. Here, we developed a method (PAThology tissue analysis of Histones by Mass Spectrometry - PAT-H-MS) that allows to perform a comprehensive, unbiased and quantitative MS-analysis of hPTM patterns on formalin-fixed paraffin-embedded (FFPE) samples. In pairwise comparisons, histone extracted from formalin-fixed paraffin-embedded tissues showed patterns similar to fresh frozen samples for 24 differentially modified peptides from histone H3. In addition, when coupled with a histone-focused version of the super-SILAC approach, this method allows the accurate quantification of modification changes among breast cancer patient samples. As an initial application of the PAThology tissue analysis of Histones by Mass Spectrometry method, we analyzed breast cancer samples, revealing significant changes in histone H3 methylation patterns among Luminal A-like and Triple Negative disease subtypes. These results pave the way for retrospective epigenetic studies that combine the power of MS-based hPTM analysis with the extensive clinical information associated with formalin-fixed paraffin-embedded archives.
Collapse
Affiliation(s)
- Roberta Noberini
- From the ‡Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy
| | - Andrea Uggetti
- §Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Via Ripamonti 435, 20141 Milano
| | - Giancarlo Pruneri
- §Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Via Ripamonti 435, 20141 Milano; ¶School of Medicine, University of Milan, 20122 Milan, Italy
| | - Saverio Minucci
- ‖Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; **Drug Development Program, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; ‡‡Department of Bioscience, University of Milan, 20133 Milan, Italy
| | - Tiziana Bonaldi
- ‖Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy;
| |
Collapse
|
28
|
|
29
|
Chen X, Wei S, Ji Y, Guo X, Yang F. Quantitative proteomics using SILAC: Principles, applications, and developments. Proteomics 2015; 15:3175-92. [DOI: 10.1002/pmic.201500108] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/24/2015] [Accepted: 06/08/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Shasha Wei
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Yanlong Ji
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
| | - Xiaojing Guo
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| |
Collapse
|
30
|
Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
31
|
Wingens M, Gätgens J, Schmidt A, Albaum SP, Büntemeyer H, Noll T, Hoffrogge R. 2D-DIGE screening of high-productive CHO cells under glucose limitation--basic changes in the proteome equipment and hints for epigenetic effects. J Biotechnol 2015; 201:86-97. [PMID: 25612871 DOI: 10.1016/j.jbiotec.2015.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 12/23/2014] [Accepted: 01/09/2015] [Indexed: 01/21/2023]
Abstract
CHO derivates (Chinese hamster ovary) belong to the most important mammalian cells for industrial recombinant protein production. Many efforts have been made to improve productivity and stability of CHO cells in bioreactor processes. Here, we followed up one barely understood phenomenon observed with process optimizations: a significantly increased cell-specific productivity in late phases of glucose-limited perfusion cultivations, when glucose (and lactate) reserves are exhausted. Our aim was to elucidate the cellular activities connected to the metabolic shift from glucose surplus to glucose limitation phase. With 2D-DIGE, we compared three stages in a perfusion culture of CHO cells: the initial growth with high glucose concentration and low lactate production, the second phase with glucose going to limitation and high lactate level, and finally the state of glucose limitation and also low lactate concentration but increased cell-specific productivity. With our proteomic approach we were able to demonstrate consequences of glucose limitation for the protein expression machinery which also could play a role for a higher recombinant protein production. Most interestingly, we detected epigenetic effects on the level of proteins involved in histone modification (HDAC1/-2, SET, RBBP7, DDX5). Together with shifts in the protein inventory of energy metabolism, cytoskeleton and protein expression, a picture emerges of basic changes in the cellular equipment under long-term glucose limitation of CHO cells.
Collapse
Affiliation(s)
- Marc Wingens
- Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany
| | - Jochem Gätgens
- IBG-1: Biotechnology; Bioprocesses and Bioanalytics, Research Center Jülich, Germany
| | - Anica Schmidt
- Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany
| | - Stefan P Albaum
- Bioinformatics Resource Facility, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Heino Büntemeyer
- Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany
| | - Thomas Noll
- Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany
| | - Raimund Hoffrogge
- Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany.
| |
Collapse
|
32
|
Najam-ul-Haq M, Saeed A, Jabeen F, Hussain D, Khan N, Shabir M, Raza N, Ashiq MN, Malana MA, Zafar ZI. Development of new multifunctional terpolymer sorbent for proteomics applications. Biomed Chromatogr 2014; 29:981-9. [DOI: 10.1002/bmc.3382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 10/05/2014] [Accepted: 10/08/2014] [Indexed: 01/29/2023]
Affiliation(s)
- Muhammad Najam-ul-Haq
- Institute of Chemical Sciences; Bahauddin Zakariya University; Multan 60800 Pakistan
| | - Adeela Saeed
- Institute of Chemical Sciences; Bahauddin Zakariya University; Multan 60800 Pakistan
| | - Fahmida Jabeen
- Institute of Chemical Sciences; Bahauddin Zakariya University; Multan 60800 Pakistan
| | - Dilshad Hussain
- Institute of Chemical Sciences; Bahauddin Zakariya University; Multan 60800 Pakistan
| | - Naseem Khan
- Institute of Chemical Sciences; Bahauddin Zakariya University; Multan 60800 Pakistan
| | - Maryam Shabir
- Institute of Chemical Sciences; Bahauddin Zakariya University; Multan 60800 Pakistan
| | - Nadeem Raza
- Institute of Chemical Sciences; Bahauddin Zakariya University; Multan 60800 Pakistan
| | - Muhammad Naeem Ashiq
- Institute of Chemical Sciences; Bahauddin Zakariya University; Multan 60800 Pakistan
| | - Muhammad Aslam Malana
- Institute of Chemical Sciences; Bahauddin Zakariya University; Multan 60800 Pakistan
| | - Zafar Iqbal Zafar
- Institute of Chemical Sciences; Bahauddin Zakariya University; Multan 60800 Pakistan
| |
Collapse
|
33
|
Soldi M, Cuomo A, Bonaldi T. Improved bottom-up strategy to efficiently separate hypermodified histone peptides through ultra-HPLC separation on a bench top Orbitrap instrument. Proteomics 2014; 14:2212-25. [DOI: 10.1002/pmic.201400075] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 06/06/2014] [Accepted: 07/28/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Monica Soldi
- Department of Experimental Oncology; European Institute of Oncology; Milano Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology; European Institute of Oncology; Milano Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology; European Institute of Oncology; Milano Italy
| |
Collapse
|
34
|
Soldi M, Bonaldi T. The ChroP approach combines ChIP and mass spectrometry to dissect locus-specific proteomic landscapes of chromatin. J Vis Exp 2014. [PMID: 24747196 DOI: 10.3791/51220] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Chromatin is a highly dynamic nucleoprotein complex made of DNA and proteins that controls various DNA-dependent processes. Chromatin structure and function at specific regions is regulated by the local enrichment of histone post-translational modifications (hPTMs) and variants, chromatin-binding proteins, including transcription factors, and DNA methylation. The proteomic characterization of chromatin composition at distinct functional regions has been so far hampered by the lack of efficient protocols to enrich such domains at the appropriate purity and amount for the subsequent in-depth analysis by Mass Spectrometry (MS). We describe here a newly designed chromatin proteomics strategy, named ChroP (Chromatin Proteomics), whereby a preparative chromatin immunoprecipitation is used to isolate distinct chromatin regions whose features, in terms of hPTMs, variants and co-associated non-histonic proteins, are analyzed by MS. We illustrate here the setting up of ChroP for the enrichment and analysis of transcriptionally silent heterochromatic regions, marked by the presence of tri-methylation of lysine 9 on histone H3. The results achieved demonstrate the potential of ChroP in thoroughly characterizing the heterochromatin proteome and prove it as a powerful analytical strategy for understanding how the distinct protein determinants of chromatin interact and synergize to establish locus-specific structural and functional configurations.
Collapse
Affiliation(s)
- Monica Soldi
- Department of Experimental Oncology, European Institute of Oncology
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology;
| |
Collapse
|
35
|
Soldi M, Bremang M, Bonaldi T. Biochemical systems approaches for the analysis of histone modification readout. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:657-68. [PMID: 24681439 DOI: 10.1016/j.bbagrm.2014.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 03/06/2014] [Accepted: 03/18/2014] [Indexed: 11/28/2022]
Abstract
Chromatin is the macromolecular nucleoprotein complex that governs the organization of genetic material in the nucleus of eukaryotic cells. In chromatin, DNA is packed with histone proteins into nucleosomes. Core histones are prototypes of hyper-modified proteins, being decorated by a large number of site-specific reversible and irreversible post-translational modifications (PTMs), which contribute to the maintenance and modulation of chromatin plasticity, gene activation, and a variety of other biological processes and disease states. The observations of the variety, frequency and co-occurrence of histone modifications in distinct patterns at specific genomic loci have led to the idea that hPTMs can create a molecular barcode, read by effector proteins that translate it into a specific transcriptional state, or process, on the underlying DNA. However, despite the fact that this histone-code hypothesis was proposed more than 10 years ago, the molecular details of its working mechanisms are only partially characterized. In particular, two questions deserve specific investigation: how the different modifications associate and synergize into patterns and how these PTM configurations are read and translated by multi-protein complexes into a specific functional outcome on the genome. Mass spectrometry (MS) has emerged as a versatile tool to investigate chromatin biology, useful for both identifying and validating hPTMs, and to dissect the molecular determinants of histone modification readout systems. We review here the MS techniques and the proteomics methods that have been developed to address these fundamental questions in epigenetics research, emphasizing approaches based on the proteomic dissection of distinct native chromatin regions, with a critical evaluation of their present challenges and future potential. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
Collapse
Affiliation(s)
- Monica Soldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.
| |
Collapse
|
36
|
Bremang M, Cuomo A, Agresta AM, Stugiewicz M, Spadotto V, Bonaldi T. Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome. MOLECULAR BIOSYSTEMS 2014; 9:2231-47. [PMID: 23748837 DOI: 10.1039/c3mb00009e] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein methylation is a post-translational modification (PTM) by which a variable number of methyl groups are transferred to lysine and arginine residues within proteins. Despite increased interest in this modification due to its reversible nature and its emerging role in a diverse set of biological pathways beyond chromatin, global identification of protein methylation has remained an unachieved goal. To characterise sites of lysine and arginine methylation beyond histones, we employed an approach that combines heavy methyl stable isotope labelling by amino acids in cell culture (hmSILAC) with high-resolution mass spectrometry-based proteomics. Through a broad evaluation of immuno-affinity enrichment and the application of two classical protein separation techniques prior to mass spectrometry, to nucleosolic and cytosolic fractions separately, we identified a total of 501 different methylation types, on 397 distinct lysine and arginine sites, present on 139 unique proteins. Our results considerably extend the number of known in vivo methylation sites and indicate their significant presence on several protein complexes involved at all stages of gene expression, from chromatin remodelling and transcription to splicing and translation. In addition, we describe the potential of the hmSILAC approach for accurate relative quantification of methylation levels between distinct functional states.
Collapse
Affiliation(s)
- Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | | | | | | | | | | |
Collapse
|
37
|
Chen L, Fischer R, Peng Y, Reeves E, McHugh K, Ternette N, Hanke T, Dong T, Elliott T, Shastri N, Kollnberger S, James E, Kessler B, Bowness P. Critical role of endoplasmic reticulum aminopeptidase 1 in determining the length and sequence of peptides bound and presented by HLA-B27. Arthritis Rheumatol 2014; 66:284-94. [PMID: 24504800 DOI: 10.1002/art.38249] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 10/22/2013] [Indexed: 12/16/2022]
Abstract
OBJECTIVE HLA-B27 and endoplasmic reticulum aminopeptidase 1 (ERAP1) are the two strongest genetic factors predisposing to ankylosing spondylitis (AS). A key aminopeptidase in class I major histocompatibility complex presentation, ERAP1 potentially contributes to the pathogenesis of AS by altering HLA-B27 peptide presentation. The aim of this study was to analyze the effects of ERAP1 on the HLA-B27 peptide repertoire and peptide presentation to cytotoxic T lymphocytes (CTLs). METHODS ERAP1-silenced and -competent HeLa.B27 and C1R.B27 cells were isotope-labeled, mixed, lysed, and then immunoprecipitated using W6/32 or ME1 antibodies. Peptides bound to HLA-B27 were eluted and analyzed by tandem mass spectrometry. Selected peptides were synthesized and tested for HLA-B27 binding ability. The effect of ERAP1 silencing/mutation on presentation of an immunodominant viral HLA-B27 epitope, KK10, to CTLs was also studied. RESULTS In both HeLa.B27 and C1R.B27 cells, the proportion of 9-mer HLA-B27-bound peptides was decreased by ERAP1 silencing, whereas the percentages of longer peptides (11-13 mer) were increased. Surprisingly, following ERAP1 silencing, C-terminally extended peptides were readily identified. These were better able to bind to HLA-B27 than were N-terminally extended peptides lacking an arginine at position 2. In both HeLa.B27 cells and mouse fibroblasts expressing HLA-B27, the absence of ERAP1 reduced peptide recognition by HLA-B27-restricted KK10-specific CTLs following infection with recombinant vaccinia virus or transfection with minigenes expressing KK10 precursors. Presence of an AS-protective variant of ERAP1, K528R, as compared to wild-type ERAP1, reduced the peptide recognition by KK10 CTLs following transfection with extended KK10 minigenes. CONCLUSION These results show that ERAP1 directly alters peptide binding and presentation by HLA-B27, thus demonstrating a potential pathogenic mechanism in AS. Inhibition of ERAP1 could potentially be used for treatment of AS and other ERAP1-associated diseases.
Collapse
|
38
|
Hoedt E, Zhang G, Neubert TA. Stable isotope labeling by amino acids in cell culture (SILAC) for quantitative proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:93-106. [PMID: 24952180 DOI: 10.1007/978-3-319-06068-2_5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful approach for high-throughput quantitative proteomics. SILAC allows highly accurate protein quantitation through metabolic encoding of whole cell proteomes using stable isotope labeled amino acids. Since its introduction in 2002, SILAC has become increasingly popular. In this chapter we review the methodology and application of SILAC, with an emphasis on three research areas: dynamics of posttranslational modifications, protein-protein interactions, and protein turnover.
Collapse
Affiliation(s)
- Esthelle Hoedt
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 540 First Avenue, New York, NY, 10016, USA
| | | | | |
Collapse
|
39
|
Lau HT, Lewis KA, Ong SE. Quantifying in vivo, site-specific changes in protein methylation with SILAC. Methods Mol Biol 2014; 1188:161-175. [PMID: 25059611 DOI: 10.1007/978-1-4939-1142-4_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Interest in protein methylation has grown rapidly in recent years. Mass spectrometry-based proteomics is ideally suited to characterize protein modifications, but the multiplicity of methylated residues and the lack of efficient methods to enrich methylated proteins have limited the proteomic identification of protein methylation sites. In this protocol, we compare two metabolic labeling approaches, stable isotope labeling by amino acids in cell culture (SILAC) and its variant heavy methyl SILAC, for studying protein methylation. Instead of heavy lysine and arginine in the typical SILAC experiment, heavy methyl SILAC uses (13)C, (2)H methionine as the labeling amino acid. As cells convert methionine to S-adenosylmethionine, heavy methyl SILAC encodes a 4 Da mass tag for each methyl group, distinguishing between degrees of methylation is possible from mass difference alone. We provide a protocol for SILAC-based analyses of protein methylation and highlight the strengths and weaknesses of each method for targeted and proteomic analyses.
Collapse
Affiliation(s)
- Ho-Tak Lau
- Department of Pharmacology, University of Washington, 1959 NE Pacific Street, 357280, Seattle, WA, 98195, USA
| | | | | |
Collapse
|
40
|
Karch KR, Denizio JE, Black BE, Garcia BA. Identification and interrogation of combinatorial histone modifications. Front Genet 2013; 4:264. [PMID: 24391660 PMCID: PMC3868920 DOI: 10.3389/fgene.2013.00264] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 11/15/2013] [Indexed: 11/13/2022] Open
Abstract
Histone proteins are dynamically modified to mediate a variety of cellular processes including gene transcription, DNA damage repair, and apoptosis. Regulation of these processes occurs through the recruitment of non-histone proteins to chromatin by specific combinations of histone post-translational modifications (PTMs). Mass spectrometry has emerged as an essential tool to discover and quantify histone PTMs both within and between samples in an unbiased manner. Developments in mass spectrometry that allow for characterization of large histone peptides or intact protein has made it possible to determine which modifications occur simultaneously on a single histone polypeptide. A variety of techniques from biochemistry, biophysics, and chemical biology have been employed to determine the biological relevance of discovered combinatorial codes. This review first describes advancements in the field of mass spectrometry that have facilitated histone PTM analysis and then covers notable approaches to probe the biological relevance of these modifications in their nucleosomal context.
Collapse
Affiliation(s)
- Kelly R Karch
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Jamie E Denizio
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Ben E Black
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| |
Collapse
|
41
|
Guan X, Rastogi N, Parthun MR, Freitas MA. Discovery of histone modification crosstalk networks by stable isotope labeling of amino acids in cell culture mass spectrometry (SILAC MS). Mol Cell Proteomics 2013; 12:2048-59. [PMID: 23592332 DOI: 10.1074/mcp.m112.026716] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this paper we describe an approach that combines stable isotope labeling of amino acids in cells culture, high mass accuracy liquid chromatography tandem mass spectrometry and a novel data analysis approach to accurately determine relative peptide post-translational modification levels. This paper describes the application of this approach to the discovery of novel histone modification crosstalk networks in Saccharomyces cerevisiae. Yeast histone mutants were generated to mimic the presence/absence of 44 well-known modifications on core histones H2A, H2B, H3, and H4. In each mutant strain the relative change in H3 K79 methylation and H3 K56 acetylation were determined using stable isotope labeling of amino acids in cells culture. This approach showed relative changes in H3 K79 methylation and H3 K56 acetylation that are consistent with known histone crosstalk networks. More importantly, this study revealed additional histone modification sites that affect H3 K79 methylation and H3 K56 acetylation.
Collapse
Affiliation(s)
- Xiaoyan Guan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | | | | |
Collapse
|
42
|
Mass spectrometry-based proteomics in molecular diagnostics: discovery of cancer biomarkers using tissue culture. BIOMED RESEARCH INTERNATIONAL 2013; 2013:783131. [PMID: 23586059 PMCID: PMC3613068 DOI: 10.1155/2013/783131] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 01/30/2013] [Indexed: 12/14/2022]
Abstract
Accurate diagnosis and proper monitoring of cancer patients remain a key obstacle for successful cancer treatment and prevention. Therein comes the need for biomarker discovery, which is crucial to the current oncological and other clinical practices having the potential to impact the diagnosis and prognosis. In fact, most of the biomarkers have been discovered utilizing the proteomics-based approaches. Although high-throughput mass spectrometry-based proteomic approaches like SILAC, 2D-DIGE, and iTRAQ are filling up the pitfalls of the conventional techniques, still serum proteomics importunately poses hurdle in overcoming a wide range of protein concentrations, and also the availability of patient tissue samples is a limitation for the biomarker discovery. Thus, researchers have looked for alternatives, and profiling of candidate biomarkers through tissue culture of tumor cell lines comes up as a promising option. It is a rich source of tumor cell-derived proteins, thereby, representing a wide array of potential biomarkers. Interestingly, most of the clinical biomarkers in use today (CA 125, CA 15.3, CA 19.9, and PSA) were discovered through tissue culture-based system and tissue extracts. This paper tries to emphasize the tissue culture-based discovery of candidate biomarkers through various mass spectrometry-based proteomic approaches.
Collapse
|
43
|
Mass spectrometry-based proteomics for the analysis of chromatin structure and dynamics. Int J Mol Sci 2013; 14:5402-31. [PMID: 23466885 PMCID: PMC3634404 DOI: 10.3390/ijms14035402] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/24/2013] [Accepted: 02/20/2013] [Indexed: 12/22/2022] Open
Abstract
Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs) and DNA methylation, which act in a concerted manner to enforce a specific "chromatin landscape", with a regulatory effect on gene expression. Mass Spectrometry (MS) has emerged as a powerful analytical strategy to detect histone PTMs, revealing interplays between neighbouring PTMs and enabling screens for their readers in a comprehensive and quantitative fashion. Here we provide an overview of the recent achievements of state-of-the-art mass spectrometry-based proteomics for the detailed qualitative and quantitative characterization of histone post-translational modifications, histone variants, and global interactomes at specific chromatin regions. This synopsis emphasizes how the advances in high resolution MS, from "Bottom Up" to "Top Down" analysis, together with the uptake of quantitative proteomics methods by chromatin biologists, have made MS a well-established method in the epigenetics field, enabling the acquisition of original information, highly complementary to that offered by more conventional, antibody-based, assays.
Collapse
|
44
|
Zhang C, Liu Y, Andrews PC. Quantification of histone modifications using ¹⁵N metabolic labeling. Methods 2013; 61:236-43. [PMID: 23454290 DOI: 10.1016/j.ymeth.2013.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 02/11/2013] [Accepted: 02/13/2013] [Indexed: 11/27/2022] Open
Abstract
Mass spectrometry has made major contributions to recent discoveries in the field of epigenetics, particularly in the characterization of the myriad post-translational modifications (PTMs) of histones which are technically challenging to analyze. These new developments have further aroused great interest in development of robust, new mass spectrometric methods to quantitatively study the dynamics of histone modifications. This review covers quantitative analysis of histone PTMs and discuss an ¹⁵N metabolic labeling procedure for quantifying histone PTMs applied to the analysis of methyltransferase knockouts in the model organism, Tetrahymena thermophila.
Collapse
Affiliation(s)
- Chunchao Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, USA
| | | | | |
Collapse
|
45
|
Bartke T, Borgel J, DiMaggio PA. Proteomics in epigenetics: new perspectives for cancer research. Brief Funct Genomics 2013; 12:205-18. [PMID: 23401080 PMCID: PMC3662889 DOI: 10.1093/bfgp/elt002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The involvement of epigenetic processes in the origin and progression of cancer is now widely appreciated. Consequently, targeting the enzymatic machinery that controls the epigenetic regulation of the genome has emerged as an attractive new strategy for therapeutic intervention. The development of epigenetic drugs requires a detailed knowledge of the processes that govern chromatin regulation. Over the recent years, mass spectrometry (MS) has become an indispensable tool in epigenetics research. In this review, we will give an overview of the applications of MS-based proteomics in studying various aspects of chromatin biology. We will focus on the use of MS in the discovery and mapping of histone modifications and how novel proteomic approaches are being utilized to identify and study chromatin-associated proteins and multi-subunit complexes. Finally, we will discuss the application of proteomic methods in the diagnosis and prognosis of cancer based on epigenetic biomarkers and comment on their future impact on cancer epigenetics.
Collapse
Affiliation(s)
- Till Bartke
- MRC Clinical Sciences Centre, Imperial College London Faculty of Medicine, Hammersmith Hospital Campus, London W12 0NN, UK.
| | | | | |
Collapse
|
46
|
Abstract
Stable isotope labeling with amino acids in cell culture (SILAC) has become an extremely valuable tool in quantitative proteomics and in biomarker discovery. Incorporation of SILAC labels occurs when cells are passaged multiple times in media where the endogenous amino acids are replaced with the heavy isotope ones. During a typical experiment, cells from heavy and light strains are combined in equal ratios and all steps of protein extraction and digestion occur on these cells together, minimizing the number of external variables introduced during sample processing. Potential biomarkers are revealed during liquid chromatography-tandem mass spectrometry analysis by peptides that differ considerably in intensity between the two strains as revealed by the mass shift from the incorporated SILAC label. The protocol presented here describes how to perform a typical experiment using the SILAC technology for the search for biomarkers as revealed by differences in protein expression levels, as well as by phosphorylation, a common posttranslational modification.
Collapse
|
47
|
Britton LMP, Gonzales-Cope M, Zee BM, Garcia BA. Breaking the histone code with quantitative mass spectrometry. Expert Rev Proteomics 2012; 8:631-43. [PMID: 21999833 DOI: 10.1586/epr.11.47] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Histone post-translational modifications (PTMs) comprise one of the most intricate nuclear signaling networks that govern gene expression in a long-term and dynamic fashion. These PTMs are considered to be 'epigenetic' or heritable from one cell generation to the next and help establish genomic expression patterns. While much of the analyses of histones have historically been performed using site-specific antibodies, these methods are replete with technical obstacles (i.e., cross-reactivity and epitope occlusion). Mass spectrometry-based proteomics has begun to play a significant role in the interrogation of histone PTMs, revealing many new aspects of these modifications that cannot be easily determined with standard biological approaches. Here, we review the accomplishments of mass spectrometry in the histone field, and outline the future roadblocks that must be overcome for mass spectrometry-based proteomics to become the method of choice for chromatin biologists.
Collapse
Affiliation(s)
- Laura-Mae P Britton
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | | | | | |
Collapse
|
48
|
Stratmann A, Haendler B. Histone demethylation and steroid receptor function in cancer. Mol Cell Endocrinol 2012; 348:12-20. [PMID: 21958694 DOI: 10.1016/j.mce.2011.09.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 09/05/2011] [Accepted: 09/13/2011] [Indexed: 10/17/2022]
Abstract
Steroid receptors recruit various cofactors to form multi-protein complexes which locally alter chromatin structure and control DNA accessibility in order to regulate gene transcription. Some of these factors are enzymes that add or remove histone marks in the vicinity of regulatory regions of target genes. Numerous histone modifications added by specific writer enzymes and removed by eraser enzymes have been identified. Histone methylation is a modification with a complex outcome, as it can lead to gene activation or repression, depending on the modified residue and the context. Methylation marks are added by different enzyme families displaying exquisite substrate specificity. Lysine methylation is reversible and two different demethylase families have been identified in humans, the Jumonji C and the lysine-specific demethylase families. A regulatory role of histone demethylases in fine-tuning the function of steroid receptors, especially the androgen receptor and estrogen receptor, has emerged in recent years. This is mostly inferred from in vitro studies, but more recently first in vivo data have further supported this concept. This and the deregulated expression observed for several histone demethylases suggest a role in tumours such as prostate and breast cancer.
Collapse
Affiliation(s)
- Antje Stratmann
- Therapeutic Research Group Oncology/Gynecological Therapies and Global Biomarker, Bayer Pharma AG, Bayer HealthCare, D-13342 Berlin, Germany
| | | |
Collapse
|
49
|
Proteomic databases and tools to decipher post-translational modifications. J Proteomics 2011; 75:127-44. [DOI: 10.1016/j.jprot.2011.09.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 09/14/2011] [Accepted: 09/18/2011] [Indexed: 01/10/2023]
|
50
|
|