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Bi B, Qiu M, Liu P, Wang Q, Wen Y, Li Y, Li B, Li Y, He Y, Zhao J. Protein post-translational modifications: A key factor in colorectal cancer resistance mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194977. [PMID: 37625568 DOI: 10.1016/j.bbagrm.2023.194977] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/16/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer-related death. Despite advances in treatment, drug resistance remains a critical impediment. Post-translational modifications (PTMs) regulate protein stability, localization, and activity, impacting vital cellular processes. Recent research has highlighted the essential role of PTMs in the development of CRC resistance. This review summarizes recent advancements in understanding PTMs' roles in CRC resistance, focusing on the latest discoveries. We discuss the functional impact of PTMs on signaling pathways and molecules involved in CRC resistance, progress in drug development, and potential therapeutic targets. We also summarize the primary enrichment methods for PTMs. Finally, we discuss current challenges and future directions, including the need for more comprehensive PTM analysis methods and PTM-targeted therapies. This review identifies potential therapeutic interventions for addressing medication resistance in CRC, proposes prospective therapeutic options, and gives an overview of the function of PTMs in CRC resistance.
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Affiliation(s)
- Bo Bi
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Miaojuan Qiu
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Peng Liu
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Qiang Wang
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Yingfei Wen
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - You Li
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Binbin Li
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Yongshu Li
- Hubei Normal University, College of Life Sciences Huangshi, Hubei, China.
| | - Yulong He
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China.
| | - Jing Zhao
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China.
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Noberini R, Bonaldi T. Proteomics contributions to epigenetic drug discovery. Proteomics 2023; 23:e2200435. [PMID: 37727062 DOI: 10.1002/pmic.202200435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023]
Abstract
The combined activity of epigenetic features, which include histone post-translational modifications, DNA methylation, and nucleosome positioning, regulates gene expression independently from changes in the DNA sequence, defining how the shared genetic information of an organism is used to generate different cell phenotypes. Alterations in epigenetic processes have been linked with a multitude of diseases, including cancer, fueling interest in the discovery of drugs targeting the proteins responsible for writing, erasing, or reading histone and DNA modifications. Mass spectrometry (MS)-based proteomics has emerged as a versatile tool that can assist drug discovery pipelines from target validation, through target deconvolution, to monitoring drug efficacy in vivo. Here, we provide an overview of the contributions of MS-based proteomics to epigenetic drug discovery, describing the main approaches that can be used to support different drug discovery pipelines and highlighting how they contributed to the development and characterization of epigenetic drugs.
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Affiliation(s)
- Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
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Massignani E, Maniaci M, Bonaldi T. Heavy Methyl SILAC Metabolic Labeling of Human Cell Lines for High-Confidence Identification of R/K-Methylated Peptides by High-Resolution Mass Spectrometry. Methods Mol Biol 2023; 2603:173-186. [PMID: 36370279 DOI: 10.1007/978-1-0716-2863-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein methylation is a widespread post-translational modification (PTM) involved in several important biological processes including, but not limited to, RNA splicing, signal transduction, translation, and DNA repair. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is considered today the most versatile and accurate technique to profile PTMs with high precision and proteome-wide depth; however, the identification of protein methylations by MS is still prone to high false discovery rates. In this chapter, we describe the heavy methyl SILAC metabolic labeling strategy that allows high-confidence identification of in vivo methyl-peptides by MS-based proteomics. We provide a general protocol that covers the steps of heavy methyl labeling of cultured cells, protein sample preparation, LC-MS/MS analysis, and downstream computational analysis of the acquired MS data.
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Affiliation(s)
- Enrico Massignani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- European School of Molecular Medicine (SEMM), Milan, Italy
| | - Marianna Maniaci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- European School of Molecular Medicine (SEMM), Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.
- Department of Oncology and Haemathology-Oncology, University of MIlan, Milano, Italy.
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Brodbelt JS. Deciphering combinatorial post-translational modifications by top-down mass spectrometry. Curr Opin Chem Biol 2022; 70:102180. [PMID: 35779351 PMCID: PMC9489649 DOI: 10.1016/j.cbpa.2022.102180] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 12/15/2022]
Abstract
Post-translational modifications (PTMs) create vast structural and functional diversity of proteins, ultimately modulating protein function and degradation, influencing cellular signaling, and regulating transcription. The combinatorial patterns of PTMs increase the heterogeneity of proteins and further mediates their interactions. Advances in mass spectrometry-based proteomics have resulted in identification of thousands of proteins and allowed characterization of numerous types and sites of PTMs. Examination of intact proteins, termed the top-down approach, offers the potential to map protein sequences and localize multiple PTMs on each protein, providing the most comprehensive cataloging of proteoforms. This review describes some of the dividends of using mass spectrometry to analyze intact proteins and showcases innovative strategies that have enhanced the promise of top-down proteomics for exploring the impact of combinatorial PTMs in unsurpassed detail.
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
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Brandi J, Noberini R, Bonaldi T, Cecconi D. Advances in enrichment methods for mass spectrometry-based proteomics analysis of post-translational modifications. J Chromatogr A 2022; 1678:463352. [PMID: 35896048 DOI: 10.1016/j.chroma.2022.463352] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/08/2022] [Accepted: 07/17/2022] [Indexed: 10/17/2022]
Abstract
Post-translational modifications (PTMs) occur during or after protein biosynthesis and increase the functional diversity of proteome. They comprise phosphorylation, acetylation, methylation, glycosylation, ubiquitination, sumoylation (among many other modifications), and influence all aspects of cell biology. Mass-spectrometry (MS)-based proteomics is the most powerful approach for PTM analysis. Despite this, it is challenging due to low abundance and labile nature of many PTMs. Hence, enrichment of modified peptides is required for MS analysis. This review provides an overview of most common PTMs and a discussion of current enrichment methods for MS-based proteomics analysis. The traditional affinity strategies, including immunoenrichment, chromatography and protein pull-down, are outlined together with their strengths and shortcomings. Moreover, a special attention is paid to chemical enrichment strategies, such as capture by chemoselective probes, metabolic and chemoenzymatic labelling, which are discussed with an emphasis on their recent progress. Finally, the challenges and future trends in the field are discussed.
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Affiliation(s)
- Jessica Brandi
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milano, Italy.
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milano, Italy; Department of Oncology and Haemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122 Milano, Italy.
| | - Daniela Cecconi
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
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Zhu G, Jin L, Sun W, Wang S, Liu N. Proteomics of post-translational modifications in colorectal cancer: Discovery of new biomarkers. Biochim Biophys Acta Rev Cancer 2022; 1877:188735. [PMID: 35577141 DOI: 10.1016/j.bbcan.2022.188735] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the costliest health problems and ranks second in cancer-related mortality in developed countries. With the aid of proteomics, many protein biomarkers for the diagnosis, prognosis, and precise management of CRC have been identified. Furthermore, some protein biomarkers exhibit structural diversity after modifications. Post-translational modifications (PTMs), most of which are catalyzed by a variety of enzymes, extensively increase protein diversity and are involved in many complex and dynamic cellular processes through the regulation of protein function. Accumulating evidence suggests that abnormal PTM events are associated with a variety of human diseases, such as CRC, thus highlighting the need for studying PTMs to discover both the molecular mechanisms and therapeutic targets of CRC. In this review, we begin with a brief overview of the importance of protein PTMs, discuss the general strategies for proteomic profiling of several key PTMs (including phosphorylation, acetylation, glycosylation, ubiquitination, methylation, and citrullination), shift the emphasis to describing the specific methods used for delineating the global landscapes of each of these PTMs, and summarize the recent applications of these methods to explore the potential roles of the PTMs in CRC. Finally, we discuss the current status of PTM research on CRC and provide future perspectives on how PTM regulation can play an essential role in translational medicine for early diagnosis, prognosis stratification, and therapeutic intervention in CRC.
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Affiliation(s)
- Gengjun Zhu
- Department Oncology and Hematology, The Second Hospital of Jilin University, Changchun, China
| | - Lifang Jin
- Department Oncology and Hematology, The Second Hospital of Jilin University, Changchun, China
| | - Wanchun Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Shuang Wang
- Dermatological department, The Second Hospital of Jilin University, Changchun, China.
| | - Ning Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China; Central Laboratory, The Second Hospital of Jilin University, Changchun, China.
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Samuel SF, Barry A, Greenman J, Beltran-Alvarez P. Arginine methylation: the promise of a 'silver bullet' for brain tumours? Amino Acids 2021; 53:489-506. [PMID: 33404912 PMCID: PMC8107164 DOI: 10.1007/s00726-020-02937-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Despite intense research efforts, our pharmaceutical repertoire against high-grade brain tumours has not been able to increase patient survival for a decade and life expectancy remains at less than 16 months after diagnosis, on average. Inhibitors of protein arginine methyltransferases (PRMTs) have been developed and investigated over the past 15 years and have now entered oncology clinical trials, including for brain tumours. This review collates recent advances in the understanding of the role of PRMTs and arginine methylation in brain tumours. We provide an up-to-date literature review on the mechanisms for PRMT regulation. These include endogenous modulators such as alternative splicing, miRNA, post-translational modifications and PRMT-protein interactions, and synthetic inhibitors. We discuss the relevance of PRMTs in brain tumours with a particular focus on PRMT1, -2, -5 and -8. Finally, we include a future perspective where we discuss possible routes for further research on arginine methylation and on the use of PRMT inhibitors in the context of brain tumours.
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Affiliation(s)
| | - Antonia Barry
- Department of Biomedical Sciences, University of Hull, Hull, UK
| | - John Greenman
- Department of Biomedical Sciences, University of Hull, Hull, UK
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Salvi M. Non-Histone Protein Methylation: Molecular Mechanisms and Physiopathological Relevance. Curr Protein Pept Sci 2021; 21:640-641. [PMID: 32571200 DOI: 10.2174/138920372107200620152550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mauro Salvi
- Department of Biomedical Sciences University of Padova Via U. Bassi 58/B 35131 Padova, Italy
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