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Mabunda IG, Zinyemba NK, Pillay S, Offor BC, Muller B, Piater LA. The geographical distribution of scorpions, implication of venom toxins, envenomation, and potential therapeutics in Southern and Northern Africa. Toxicol Res (Camb) 2024; 13:tfae118. [PMID: 39100857 PMCID: PMC11298049 DOI: 10.1093/toxres/tfae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/01/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024] Open
Abstract
Scorpions are predatory arachnids whose venomous sting primarily affects people in tropical and subtropical regions. Most scorpion stings can only cause localized pain without severe envenomation. Less than one-third of the stings cause systemic envenoming and possibly lead to death. About 350,000 scorpion stings in Northern Africa are recorded yearly, resulting in about 810 deaths. In Eastern/Southern Africa, there are about 79,000 stings recorded yearly, resulting in 245 deaths. Farmers and those living in poverty-stricken areas are among the most vulnerable to getting stung by scorpions. However, compared to adults, children are at greater risk of severe envenomation. Scorpion venom is made up of complex mixtures dominated by peptides and proteins that confer its potency and toxicity. These venom toxins have intra- and interspecies variations associated with the scorpion's habitat, sex, diet, and age. These variations alter the activity of antivenoms used to treat scorpion sting envenomation. Thus, the study of the proteome composition of medically important scorpion venoms needs to be scaled up along their geographical distribution and contributions to envenomation in Southern and Northern Africa. This will help the production of safer, more effective, and broad-spectrum antivenoms within these regions. Here, we review the clinical implications of scorpion sting envenomation in Southern and Northern Africa. We further highlight the compositions of scorpion venoms and tools used in scorpion venomics. We discuss current antivenoms used against scorpion sting envenomation and suggestions for future production of better antivenoms or alternatives. Finally, we discuss the therapeutic properties of scorpion venom.
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Affiliation(s)
- Isac G Mabunda
- Department of Biochemistry, Corner of Kingsway and University Road, Auckland Park Campus, University of Johannesburg, Auckland Park, 2006, Gauteng, South Africa
| | - Nodji K Zinyemba
- Department of Biochemistry, Corner of Kingsway and University Road, Auckland Park Campus, University of Johannesburg, Auckland Park, 2006, Gauteng, South Africa
| | - Shanelle Pillay
- Department of Biochemistry, Corner of Kingsway and University Road, Auckland Park Campus, University of Johannesburg, Auckland Park, 2006, Gauteng, South Africa
| | - Benedict C Offor
- Department of Biochemistry, Corner of Kingsway and University Road, Auckland Park Campus, University of Johannesburg, Auckland Park, 2006, Gauteng, South Africa
| | - Beric Muller
- South Africa Venom Suppliers cc, 41 Louis, Trichardt 0920, South Africa
| | - Lizelle A Piater
- Department of Biochemistry, Corner of Kingsway and University Road, Auckland Park Campus, University of Johannesburg, Auckland Park, 2006, Gauteng, South Africa
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Hernández ÁP, Chaparro-González L, Garzo-Sánchez O, Arias-Hidalgo C, Juanes-Velasco P, García PA, Castro MÁ, Fuentes M. Podophyllic Aldehyde, a Podophyllotoxin Derivate, Elicits Different Cell Cycle Profiles Depending on the Tumor Cell Line: A Systematic Proteomic Analysis. Int J Mol Sci 2024; 25:4631. [PMID: 38731850 PMCID: PMC11083757 DOI: 10.3390/ijms25094631] [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: 03/15/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
When new antitumor therapy drugs are discovered, it is essential to address new target molecules from the point of view of chemical structure and to carry out efficient and systematic evaluation. In the case of natural products and derived compounds, it is of special importance to investigate chemomodulation to further explore antitumoral pharmacological activities. In this work, the compound podophyllic aldehyde, a cyclolignan derived from the chemomodulation of the natural product podophyllotoxin, has been evaluated for its viability, influence on the cell cycle, and effects on intracellular signaling. We used functional proteomics characterization for the evaluation. Compared with the FDA-approved drug etoposide (another podophyllotoxin derivative), we found interesting results regarding the cytotoxicity of podophyllic aldehyde. In addition, we were able to observe the effect of mitotic arrest in the treated cells. The use of podophyllic aldehyde resulted in increased cytotoxicity in solid tumor cell lines, compared to etoposide, and blocked the cycle more successfully than etoposide. High-throughput analysis of the deregulated proteins revealed a selective antimitotic mechanism of action of podophyllic aldehyde in the HT-29 cell line, in contrast with other solid and hematological tumor lines. Also, the apoptotic profile of podophyllic aldehyde was deciphered. The cell death mechanism is activated independently of the cell cycle profile. The results of these targeted analyses have also shown a significant response to the signaling of kinases, key proteins involved in signaling cascades for cell proliferation or metastasis. Thanks to this comprehensive analysis of podophyllic aldehyde, remarkable cytotoxic, antimitotic, and other antitumoral features have been discovered that will repurpose this compound for further chemical transformations and antitumoral analysis.
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Affiliation(s)
- Ángela-Patricia Hernández
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno s/n, 37007 Salamanca, Spain; (L.C.-G.); (O.G.-S.); (C.A.-H.); (P.J.-V.); (M.F.)
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, Faculty of Pharmacy, University of Salamanca, Campus Miguel de Unamuno s/n, 37007 Salamanca, Spain; (P.A.G.); (M.Á.C.)
| | - Lorea Chaparro-González
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno s/n, 37007 Salamanca, Spain; (L.C.-G.); (O.G.-S.); (C.A.-H.); (P.J.-V.); (M.F.)
| | - Olga Garzo-Sánchez
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno s/n, 37007 Salamanca, Spain; (L.C.-G.); (O.G.-S.); (C.A.-H.); (P.J.-V.); (M.F.)
| | - Carlota Arias-Hidalgo
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno s/n, 37007 Salamanca, Spain; (L.C.-G.); (O.G.-S.); (C.A.-H.); (P.J.-V.); (M.F.)
| | - Pablo Juanes-Velasco
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno s/n, 37007 Salamanca, Spain; (L.C.-G.); (O.G.-S.); (C.A.-H.); (P.J.-V.); (M.F.)
| | - Pablo A. García
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, Faculty of Pharmacy, University of Salamanca, Campus Miguel de Unamuno s/n, 37007 Salamanca, Spain; (P.A.G.); (M.Á.C.)
| | - Mª Ángeles Castro
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, Faculty of Pharmacy, University of Salamanca, Campus Miguel de Unamuno s/n, 37007 Salamanca, Spain; (P.A.G.); (M.Á.C.)
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno s/n, 37007 Salamanca, Spain; (L.C.-G.); (O.G.-S.); (C.A.-H.); (P.J.-V.); (M.F.)
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
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Verma A, Patel R, Mahale A, Thorat RV, Rath SL, Sridhar E, Moiyadi A, Srivastava S. Multitarget Potential Drug Candidates for High-Grade Gliomas Identified by Multiple Reaction Monitoring Coupled with In Silico Drug Repurposing. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:59-75. [PMID: 38320249 DOI: 10.1089/omi.2023.0256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
High-grade gliomas (HGGs) are extremely aggressive primary brain tumors with high mortality rates. Despite notable progress achieved by clinical research and biomarkers emerging from proteomics studies, efficacious drugs and therapeutic targets are limited. This study used targeted proteomics, in silico molecular docking, and simulation-based drug repurposing to identify potential drug candidates for HGGs. Importantly, we performed multiple reaction monitoring (MRM) on differentially expressed proteins with putative roles in the development and progression of HGGs based on our previous work and the published literature. Furthermore, in silico molecular docking-based drug repurposing was performed with a customized library of FDA-approved drugs to identify multitarget-directed ligands. The top drug candidates such as Pazopanib, Icotinib, Entrectinib, Regorafenib, and Cabozantinib were explored for their drug-likeness properties using the SwissADME. Pazopanib exhibited binding affinities with a maximum number of proteins and was considered for molecular dynamic simulations and cell toxicity assays. HGG cell lines showed enhanced cytotoxicity and cell proliferation inhibition with Pazopanib and Temozolomide combinatorial treatment compared to Temozolomide alone. To the best of our knowledge, this is the first study combining MRM with molecular docking and simulation-based drug repurposing to identify potential drug candidates for HGG. While the present study identified five multitarget-directed potential drug candidates, future clinical studies in larger cohorts are crucial to evaluate the efficacy of these molecular candidates. The research strategy and methodology used in the present study offer new avenues for innovation in drug discovery and development which may prove useful, particularly for cancers with low cure rates.
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Affiliation(s)
- Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Rushda Patel
- Sinhgad College of Pharmacy, Savitribai Phule Pune University, Pune, India
| | - Atharva Mahale
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Rujuta Vijay Thorat
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Soumya Lipsa Rath
- Department of Biotechnology, National Institute of Technology, Warangal, India
| | - Epari Sridhar
- Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Aliasgar Moiyadi
- Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Zelanis A, Barcick U, Racorti NDV, Salardani M. Heterotypic communication as the promoter of phenotypic plasticity of cancer cells: The role of cancer secretomes. Proteomics 2023; 23:e2200243. [PMID: 37474490 DOI: 10.1002/pmic.202200243] [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: 10/27/2022] [Revised: 04/24/2023] [Accepted: 07/03/2023] [Indexed: 07/22/2023]
Abstract
Cellular communication relies on signaling circuits whose statuses are mainly modulated by soluble biomolecules such as carbohydrates, lipids, proteins, and metabolites as well as extracellular vesicles (EVs). Therefore, the active secretion of such biomolecules is critical for both cell homeostasis and proper pathophysiological responses in a timely fashion. In this context, proteins are among the main modulators of such biological responses. Hence, profiling cell line secretomes may be an opportunity for the identification of "signatures" of specific cell types (i.e., stromal or metastatic cells) with important prognostic/therapeutic value. This review will focus on the biological implications of cell secretomes in the context of cancer, as well as their functional roles in shaping the tumoral microenvironment (TME) and communication status of participating cells.
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Affiliation(s)
- André Zelanis
- Functional Proteomics Laboratory, Institute of Science and Technology, Federal University of São Paulo, UNIFESP, São José dos Campos, São Paulo, Brazil
| | - Uilla Barcick
- Functional Proteomics Laboratory, Institute of Science and Technology, Federal University of São Paulo, UNIFESP, São José dos Campos, São Paulo, Brazil
| | - Nathália de Vasconcellos Racorti
- Functional Proteomics Laboratory, Institute of Science and Technology, Federal University of São Paulo, UNIFESP, São José dos Campos, São Paulo, Brazil
| | - Murilo Salardani
- Functional Proteomics Laboratory, Institute of Science and Technology, Federal University of São Paulo, UNIFESP, São José dos Campos, São Paulo, Brazil
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Bothrops Jararaca Snake Venom Modulates Key Cancer-Related Proteins in Breast Tumor Cell Lines. Toxins (Basel) 2021; 13:toxins13080519. [PMID: 34437390 PMCID: PMC8402457 DOI: 10.3390/toxins13080519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/19/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer is characterized by the development of abnormal cells that divide in an uncontrolled way and may spread into other tissues where they may infiltrate and destroy normal body tissue. Several previous reports have described biochemical anti-tumorigenic properties of crude snake venom or its components, including their capability of inhibiting cell proliferation and promoting cell death. However, to the best of our knowledge, there is no work describing cancer cell proteomic changes following treatment with snake venoms. In this work we describe the quantitative changes in proteomics of MCF7 and MDA-MB-231 breast tumor cell lines following treatment with Bothrops jararaca snake venom, as well as the functional implications of the proteomic changes. Cell lines were treated with sub-toxic doses at either 0.63 μg/mL (low) or 2.5 μg/mL (high) of B. jararaca venom for 24 h, conditions that cause no cell death per se. Proteomics analysis was conducted on a nano-scale liquid chromatography coupled on-line with mass spectrometry (nLC-MS/MS). More than 1000 proteins were identified and evaluated from each cell line treated with either the low or high dose of the snake venom. Protein profiling upon venom treatment showed differential expression of several proteins related to cancer cell metabolism, immune response, and inflammation. Among the identified proteins we highlight histone H3, SNX3, HEL-S-156an, MTCH2, RPS, MCC2, IGF2BP1, and GSTM3. These data suggest that sub-toxic doses of B. jararaca venom have potential to modulate cancer-development related protein targets in cancer cells. This work illustrates a novel biochemical strategy to identify therapeutic targets against cancer cell growth and survival.
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6
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Comprehensive serum proteomic analysis in early endometrial cancer. J Proteomics 2021; 234:104099. [PMID: 33412313 DOI: 10.1016/j.jprot.2020.104099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 12/19/2020] [Accepted: 12/29/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Endometrial cancer is the most common gynecologic cancer and yet much is still unknown about this disease. Our goal was to identify unique biomarkers of disease by performing a comprehensive proteomic analysis of early stage, low-grade endometrial cancer through analysis of serum collected from patients pre- and post-definitive surgery. METHODS We used mass spectrometry (MS)-based proteomics to identify serum proteins from these patients. Serum samples from women undergoing hysterectomy with bilateral salpingo-oophorectomy for benign reasons served as control samples for the correlative studies. We then correlated our findings with The Cancer Genome Atlas (TCGA) database for additional confirmation. RESULTS The Ingenuity Pathway Analysis of proteins that were differentially expressed in endometrial cancer showed increased cell survival and decreased organismal death, the most common hallmarks of cancer. We identified over expression of FAM83D (family with sequence similarity 83, member D) in the serum of patients with early stage low-grade endometrial cancer and verified the same in the endometrial cancer cell lines and patient tumors. We also confirmed our hypothesis that FAM83D may serve as a biomarker for endometrial cancer in a cohort of patients with endometrial cancer from The Cancer Genome Atlas (TCGA) project. CONCLUSION Comprehensive proteomic analysis is a feasible strategy for potential biomarker identification. Using this technique, FAM83D was identified as a candidate biomarker in early endometrial cancer in our patient samples and was not present in benign control samples. FAM83D has been associated with poor clinical outcomes in several human malignancies. SIGNIFICANCE Our manuscript describes an alternative approach to comprehensive protein analysis in a model pre and post tumor removal for a sample of patients with early endometrial cancer. The model is innovative and the findings of over expression FAM83D in this population of early cancer may be useful in the study of a disease where there are few biomarkers or targetable therapies.
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Proteomic approaches to investigate gammaherpesvirus biology and associated tumorigenesis. Adv Virus Res 2020; 109:201-254. [PMID: 33934828 DOI: 10.1016/bs.aivir.2020.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The DNA viruses, Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV), are members of the gammaherpesvirus subfamily, a group of viruses whose infection is associated with multiple malignancies, including cancer. The primary host for these viruses is humans and, like all herpesviruses, infection with these pathogens is lifelong. Due to the persistence of gammaherpesvirus infection and the potential for cancer formation in infected individuals, there is a driving need to understand not only the biology of these viruses and how they remain undetected in host cells but also the mechanism(s) by which tumorigenesis occurs. One of the methods that has provided much insight into these processes is proteomics. Proteomics is the study of all the proteins that are encoded by a genome and allows for (i) identification of existing and novel proteins derived from a given genome, (ii) interrogation of protein-protein interactions within a system, and (iii) discovery of druggable targets for the treatment of malignancies. In this chapter, we explore how proteomics has contributed to our current understanding of gammaherpesvirus biology and their oncogenic processes, as well as the clinical applications of proteomics for the detection and treatment of gammaherpesvirus-associated cancers.
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Li Z, Li X, He X, Jia X, Zhang X, Lu B, Zhao J, Lu J, Chen L, Dong Z, Liu K, Dong Z. Proteomics Reveal the Inhibitory Mechanism of Levodopa Against Esophageal Squamous Cell Carcinoma. Front Pharmacol 2020; 11:568459. [PMID: 33101026 PMCID: PMC7546765 DOI: 10.3389/fphar.2020.568459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/04/2020] [Indexed: 12/22/2022] Open
Abstract
High recurrence rates and poor survival of patients with esophageal squamous cell carcinoma (ESCC) after treatment make ongoing research on chemoprevention drugs for ESCC particularly important. In this study, we screened a large number of FDA-approved drugs and found levodopa, a drug used to treat Parkinson's disease, had an inhibitory effect on the growth of ESCC cells. To elucidate the molecular mechanisms involved, we applied quantitative proteomics to investigate the anti-tumor activity of levodopa on ESCC. The results suggest that levodopa could down-regulate oxidative phosphorylation, non-alcoholic fatty liver disease, and Parkinson's disease pathways. Major mitochondrial respiratory compounds were involved in the pathways, including succinate dehydrogenase subunit D, NADH-ubiquinone oxidoreductase Fe-S protein 4, and mitochondrial cytochrome c oxidase subunit 3. Down-regulation of these proteins was associated with mitochondrial dysfunction. Western blotting and immunofluorescence results confirmed the proteomics findings. Cell viability assays indicated mitochondrial activity was suppressed after levodopa treatment. Reduced mitochondrial membrane potential was detected using JC-1 staining and TMRE assays. Transmission electron microscopy revealed changes in the morphology of mitochondria. Taken together, these results indicate that levodopa inhibited the growth of ESCC through restraining mitochondria function.
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Affiliation(s)
- Zhenzhen Li
- Department of Pathophysiology, School of Basic Medical Sciences, AMS, College of Medicine, Zhengzhou University, Zhengzhou, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, China
| | - Xin Li
- Department of Pathophysiology, School of Basic Medical Sciences, AMS, College of Medicine, Zhengzhou University, Zhengzhou, China
| | - Xinyu He
- Department of Pathophysiology, School of Basic Medical Sciences, AMS, College of Medicine, Zhengzhou University, Zhengzhou, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, China
| | - Xuechao Jia
- Department of Pathophysiology, School of Basic Medical Sciences, AMS, College of Medicine, Zhengzhou University, Zhengzhou, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, China
| | - Xiaofan Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, AMS, College of Medicine, Zhengzhou University, Zhengzhou, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, China
| | - Bingbing Lu
- Department of Pathophysiology, School of Basic Medical Sciences, AMS, College of Medicine, Zhengzhou University, Zhengzhou, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, China
| | - Jimin Zhao
- Department of Pathophysiology, School of Basic Medical Sciences, AMS, College of Medicine, Zhengzhou University, Zhengzhou, China.,Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou, China
| | - Jing Lu
- Department of Pathophysiology, School of Basic Medical Sciences, AMS, College of Medicine, Zhengzhou University, Zhengzhou, China.,Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou, China
| | - Lexia Chen
- Department of Pathophysiology, School of Basic Medical Sciences, AMS, College of Medicine, Zhengzhou University, Zhengzhou, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, China
| | - Ziming Dong
- Department of Pathophysiology, School of Basic Medical Sciences, AMS, College of Medicine, Zhengzhou University, Zhengzhou, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, China.,Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou, China
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, AMS, College of Medicine, Zhengzhou University, Zhengzhou, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, China.,Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou, China.,Cancer Chemoprevention International Collaboration Laboratory, Zhengzhou, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, AMS, College of Medicine, Zhengzhou University, Zhengzhou, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou, China.,Cancer Chemoprevention International Collaboration Laboratory, Zhengzhou, China
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Pessotti DS, Andrade-Silva D, Serrano SMT, Zelanis A. Heterotypic signaling between dermal fibroblasts and melanoma cells induces phenotypic plasticity and proteome rearrangement in malignant cells. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140525. [PMID: 32866629 DOI: 10.1016/j.bbapap.2020.140525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/11/2022]
Abstract
The signaling events triggered by soluble mediators released from both transformed and stromal cells shape the phenotype of tumoral cells and have significant implications in cancer development and progression. In this study we performed an in vitro heterotypic signaling assays by evaluating the proteome diversity of human dermal fibroblasts after stimulation with the conditioned media obtained from malignant melanoma cells. In addition, we also evaluated the changes in the proteome of melanoma cells after stimulation with their own conditioned media as well as with the conditioned medium from melanoma-stimulated fibroblasts. Our results revealed a clear rearrangement in the proteome of stromal and malignant cells upon crosstalk of soluble mediators. The main proteome signature of fibroblasts stimulated with melanoma conditioned medium was related to protein synthesis, which indicates that this process might be an early response of stromal cells. In addition, the conditioned medium derived from 'primed' stromal cells (melanoma-stimulated fibroblasts) was more effective in altering the functional phenotype (cell migration) of malignant cells than the conditioned medium from non-stimulated fibroblasts. Collectively, self- and cross-stimulation may play a key role in shaping the tumor microenvironment and enable tumoral cells to succeed in the process of melanoma progression and metastasis. Although the proteome landscape of cells participating in such a heterotypic signaling represents a snapshot of a highly dynamic state, understanding the diversity of proteins and enriched biological pathways resulting from stimulated cell states may allow for targeting specific cell regulatory motifs involved in melanoma progression and metastasis.
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Affiliation(s)
- Dayelle S Pessotti
- Functional Proteomics Laboratory, Department of Science and Technology, Federal University of São Paulo, (ICT-UNIFESP), São José dos Campos, SP, Brazil
| | - Débora Andrade-Silva
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Solange M T Serrano
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - André Zelanis
- Functional Proteomics Laboratory, Department of Science and Technology, Federal University of São Paulo, (ICT-UNIFESP), São José dos Campos, SP, Brazil..
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Cao C, Xiao Z, Ge C, Wu Y. Application and Research Progress of Proteomics in Chicken Meat Quality and Identification: A Review. FOOD REVIEWS INTERNATIONAL 2020. [DOI: 10.1080/87559129.2020.1733594] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Changwei Cao
- College of Food Science, Sichuan Agricultural University, Ya’ An, Sichuan, China
| | - Zhichao Xiao
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Changrong Ge
- Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yinglong Wu
- College of Food Science, Sichuan Agricultural University, Ya’ An, Sichuan, China
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11
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Carvalho A, Viaene J, Vandenbussche G, De Braekeleer K, Masereel B, Wouters J, Souard F, Vander Heyden Y, Van Antwerpen P, Delporte C, Mathieu V. A new potential anti-cancer beta-carboline derivative decreases the expression levels of key proteins involved in glioma aggressiveness: A proteomic investigation. Drug Dev Res 2019; 81:32-42. [PMID: 31498913 DOI: 10.1002/ddr.21600] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/08/2019] [Accepted: 08/14/2019] [Indexed: 12/15/2022]
Abstract
Gliomas remain highly fatal due to their high resistance to current therapies. Deregulation of protein synthesis contributes to cancer onset and progression and is a source of rising interest for new drugs. CM16, a harmine derivative with predicted high blood-brain barrier penetration, exerts antiproliferative effects partly through translation inhibition. We evaluated herein how CM16 alters the proteome of glioma cells. The analysis of the gel-free LC/MS and auto-MS/MS data showed that CM16 induces time- and concentration-dependent significant changes in the total ion current chromatograms. In addition, we observed spontaneous clustering of the samples according to their treatment condition and their proper classification by unsupervised and supervised analyses, respectively. A two-dimensional gel-based approach analysis allowed us to identify that treatment with CM16 may downregulate four key proteins involved in glioma aggressiveness and associated with poor patient survival (HspB1, BTF3, PGAM1, and cofilin), while it may upregulate galectin-1 and Ebp1. Consistently with the protein synthesis inhibition properties of CM16, HspB1, Ebp1, and BTF3 exert known roles in protein synthesis. In conclusion, the downregulation of HspB1, BTF3, PGAM1 and cofilin bring new insights in CM16 antiproliferative effects, further supporting CM16 as an interesting protein synthesis inhibitor to combat glioma.
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Affiliation(s)
- Annelise Carvalho
- Department of Pharmacotherapy and Pharmaceutics, Faculté de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium.,ULB Cancer Research Center, Université Libre de Bruxelles, Brussels, Belgium
| | - Johan Viaene
- VUB - Analytical Chemistry, Applied Chemometrics and Molecular Modeling, Pharmaceutical Institute, Vrije Universiteit Brussel - VUB, Brussels, Belgium
| | - Guy Vandenbussche
- Laboratory for the Structure and Function of Biological Membranes, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Kris De Braekeleer
- Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Department of Research in Drug Development (RD3), Faculté de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium
| | - Bernard Masereel
- NAMEDIC, Department of Pharmacy, University of Namur, Namur, Belgium
| | - Johan Wouters
- NAMEDIC, Department of Pharmacy, University of Namur, Namur, Belgium
| | - Florence Souard
- Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Department of Research in Drug Development (RD3), Faculté de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium.,Université Grenoble Alpes, CNRS, DPM, Grenoble, France
| | - Yvan Vander Heyden
- VUB - Analytical Chemistry, Applied Chemometrics and Molecular Modeling, Pharmaceutical Institute, Vrije Universiteit Brussel - VUB, Brussels, Belgium
| | - Pierre Van Antwerpen
- Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Department of Research in Drug Development (RD3), Faculté de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium.,Analytical Platform of the Faculty of Pharmacy and Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Université Libre de Bruxelles, Brussels, Belgium
| | - Cédric Delporte
- Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Department of Research in Drug Development (RD3), Faculté de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium.,Analytical Platform of the Faculty of Pharmacy and Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, Université Libre de Bruxelles, Brussels, Belgium
| | - Véronique Mathieu
- Department of Pharmacotherapy and Pharmaceutics, Faculté de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium.,ULB Cancer Research Center, Université Libre de Bruxelles, Brussels, Belgium
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12
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Celebi R, Bear Don't Walk O, Movva R, Alpsoy S, Dumontier M. In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data. Sci Rep 2019; 9:8949. [PMID: 31222109 PMCID: PMC6586895 DOI: 10.1038/s41598-019-45236-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/29/2019] [Indexed: 12/14/2022] Open
Abstract
Chemotherapy is a routine treatment approach for early-stage cancers, but the effectiveness of such treatments is often limited by drug resistance, toxicity, and tumor heterogeneity. Combination chemotherapy, in which two or more drugs are applied simultaneously, offers one promising approach to address these concerns, since two single-target drugs may synergize with one another through interconnected biological processes. However, the identification of effective dual therapies has been particularly challenging; because the search space is large, combination success rates are low. Here, we present our method for DREAM AstraZeneca-Sanger Drug Combination Prediction Challenge to predict synergistic drug combinations. Our approach involves using biologically relevant drug and cell line features with machine learning. Our machine learning model obtained the primary metric = 0.36 and the tie-breaker metric = 0.37 in the extension round of the challenge which was ranked in top 15 out of 76 submissions. Our approach also achieves a mean primary metric of 0.39 with ten repetitions of 10-fold cross-validation. Further, we analyzed our model's predictions to better understand the molecular processes underlying synergy and discovered that key regulators of tumorigenesis such as TNFA and BRAF are often targets in synergistic interactions, while MYC is often duplicated. Through further analysis of our predictions, we were also ble to gain insight into mechanisms and potential biomarkers of synergistic drug pairs.
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Affiliation(s)
- Remzi Celebi
- Maastricht University, Institute of Data Science, Maastricht, Netherlands.
| | | | - Rajiv Movva
- Stanford University, Department of Genetics, Palo Alto, USA
| | - Semih Alpsoy
- Turkish-German University, Department of Molecular Biotechnology, Istanbul, Turkey
| | - Michel Dumontier
- Maastricht University, Institute of Data Science, Maastricht, Netherlands
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13
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Liberato T, Fukushima I, Kitano ES, Serrano SM, Chammas R, Zelanis A. Proteomic profiling of the proteolytic events in the secretome of the transformed phenotype of melanocyte-derived cells using Terminal Amine Isotopic Labeling of Substrates. J Proteomics 2019; 192:291-298. [DOI: 10.1016/j.jprot.2018.09.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/15/2018] [Accepted: 09/21/2018] [Indexed: 12/27/2022]
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14
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Luteolin attenuates Wnt signaling via upregulation of FZD6 to suppress prostate cancer stemness revealed by comparative proteomics. Sci Rep 2018; 8:8537. [PMID: 29867083 PMCID: PMC5986741 DOI: 10.1038/s41598-018-26761-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/15/2018] [Indexed: 12/28/2022] Open
Abstract
The mechanisms underlying luteolin-induced inhibition of prostate cancer (PCa) stemness have remained elusive. Here, we report that luteolin suppresses PCa stemness through Wnt signaling by upregulation of FZD6 (frizzled class receptor 6). Luteolin inhibits PCa cell proliferation, migration, self-renewal as well as the expression of prostate cancer stem cell markers in vitro. Through iTRAQ-based quantitative proteomics study, we identified 208 differentially expressed proteins in luteolin-treated PC-3 cells. Subsequent mechanistic analysis revealed that luteolin inhibits Wnt signaling by transcriptional upregulation of FZD6, and thereby suppressing the stemness of PCa cells. Furthermore, we identified FZD6 as a tumor suppressor that can abolish PCa stemness. In summary, our findings demonstrate that suppression of Wnt signaling by upregulation of FZD6 is a mechanism underlying luteolin-induced inhibition of PCa stemness. Our work suggests a new therapeutic strategy against human prostate cancer caused by aberrant activation of Wnt signaling.
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15
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Signatures of protein expression revealed by secretome analyses of cancer associated fibroblasts and melanoma cell lines. J Proteomics 2018; 174:1-8. [DOI: 10.1016/j.jprot.2017.12.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/11/2017] [Accepted: 12/18/2017] [Indexed: 02/07/2023]
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16
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Ahmed AA, Abedalthagafi M. Cancer diagnostics: The journey from histomorphology to molecular profiling. Oncotarget 2018; 7:58696-58708. [PMID: 27509178 PMCID: PMC5295463 DOI: 10.18632/oncotarget.11061] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/19/2016] [Indexed: 12/15/2022] Open
Abstract
Although histomorphology has made significant advances into the understanding of cancer etiology, classification and pathogenesis, it is sometimes complicated by morphologic ambiguities, and other shortcomings that necessitate the development of ancillary tests to complement its diagnostic value. A new approach to cancer patient management consists of targeting specific molecules or gene mutations in the cancer genome by inhibitory therapy. Molecular diagnostic tests and genomic profiling methods are increasingly being developed to identify tumor targeted molecular profile that is the basis of targeted therapy. Novel targeted therapy has revolutionized the treatment of gastrointestinal stromal tumor, renal cell carcinoma and other cancers that were previously difficult to treat with standard chemotherapy. In this review, we discuss the role of histomorphology in cancer diagnosis and management and the rising role of molecular profiling in targeted therapy. Molecular profiling in certain diagnostic and therapeutic difficulties may provide a practical and useful complement to histomorphology and opens new avenues for targeted therapy and alternative methods of cancer patient management.
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Affiliation(s)
- Atif A Ahmed
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Malak Abedalthagafi
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,The Saudi Human Genome Laboratory, Department of Pathology, King Fahad Medical City, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
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17
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Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer. Cell Rep 2017; 18:3242-3256. [PMID: 28355574 PMCID: PMC5382236 DOI: 10.1016/j.celrep.2017.03.015] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/04/2017] [Accepted: 03/02/2017] [Indexed: 12/20/2022] Open
Abstract
Our understanding of the molecular determinants of cancer is still inadequate because of cancer heterogeneity. Here, using epithelial ovarian cancer (EOC) as a model system, we analyzed a minute amount of patient-derived epithelial cells from either healthy or cancerous tissues by single-shot mass-spectrometry-based phosphoproteomics. Using a multi-disciplinary approach, we demonstrated that primary cells recapitulate tissue complexity and represent a valuable source of differentially expressed proteins and phosphorylation sites that discriminate cancer from healthy cells. Furthermore, we uncovered kinase signatures associated with EOC. In particular, CDK7 targets were characterized in both EOC primary cells and ovarian cancer cell lines. We showed that CDK7 controls cell proliferation and that pharmacological inhibition of CDK7 selectively represses EOC cell proliferation. Our approach defines the molecular landscape of EOC, paving the way for efficient therapeutic approaches for patients. Finally, we highlight the potential of phosphoproteomics to identify clinically relevant and druggable pathways in cancer. We analyze ex-vivo-cultured primary cells using phosphoproteomics We investigate epithelial ovarian cancer (EOC) and healthy tissue We uncover expression of cancer-specific proteins and kinase signatures The kinase CDK7 phosphorylates POLR2A and regulates EOC cell proliferation
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18
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Ohmori KH, Ooya T, Takeuchi T. Crosslinked Network with Rotatable Binding Sites Based on Monocarboxylated α-Cyclodextrin [2]Rotaxane Capable of Angiotensin III Recognition. Chemistry 2017; 23:4708-4712. [PMID: 28185437 DOI: 10.1002/chem.201700206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Indexed: 12/22/2022]
Abstract
Synthetic receptors selective for target peptides or proteins have received attention because of their potential applications in the separation of biomolecules and biomedical diagnostics. Herein, a [2]rotaxane-based functional monomer containing monocarboxylated α-cyclodextrin (α-CD) was synthesized, and its crosslinked polymers were evaluated to determine their binding ability to a model peptide, angiotensin III (Arg-Val-Tyr-Ile-His-Pro-Phe), containing an arginine (Arg) residue. The binding ability of the resulting polymers toward angiotensin III, angiotensin IV (Val-Tyr-Ile-His-Pro-Phe), and FMRF-amide (Phe-Met-Arg-Phe) was examined by the batch-binding assay and compared with that of control polymers, in which maleic acid-introduced α-CD was chemically crosslinked. The results suggest that the [2]rotaxane-based functional monomer in the crosslinked polymer contributes to the high affinity toward angiotensin III. The α-CD motion and rotation within the [2]rotaxane-based crosslinked polymer may be applicable for designing molecular recognition materials.
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Affiliation(s)
- Ko-Hei Ohmori
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Tooru Ooya
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Toshifumi Takeuchi
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
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19
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Lu S, Zhang J. Designed covalent allosteric modulators: an emerging paradigm in drug discovery. Drug Discov Today 2017; 22:447-453. [DOI: 10.1016/j.drudis.2016.11.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/04/2016] [Accepted: 11/15/2016] [Indexed: 12/11/2022]
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20
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Kreutz D, Bileck A, Plessl K, Wolrab D, Groessl M, Keppler BK, Meier SM, Gerner C. Response Profiling Using Shotgun Proteomics Enables Global Metallodrug Mechanisms of Action To Be Established. Chemistry 2017; 23:1881-1890. [PMID: 28071820 DOI: 10.1002/chem.201604516] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Indexed: 12/23/2022]
Abstract
Response profiling using shotgun proteomics for establishing global metallodrug mechanisms of action in two colon carcinoma cell lines, HCT116 and SW480, has been applied and evaluated with the clinically approved arsenic trioxide. Surprisingly, the complete established mechanism of action of arsenic trioxide was observed by protein regulations in SW480, but not HCT116 cells. Comparing the basal protein expression in the two cell lines revealed an 80 % convergence of protein identification, but with significant expression differences, which in turn seem to affect the extent of protein regulation. A clear-cut redox response was observed in SW480 cells upon treatment with arsenic, but hardly in HCT116 cells. Response profiling was then used to investigate four anti-cancer metallodrugs (KP46, KP772, KP1339 and KP1537). Proteome alterations were mapped to selected functional groups, including DNA repair, endocytosis, protection from oxidative stress, protection from endoplasmatic reticulum (ER) stress, cell adhesion and mitochondrial function. The present data suggest that knowledge of the mechanism of action of anti-cancer metallodrugs and improved patient stratification strategies are imperative for the design of clinical studies.
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Affiliation(s)
- Dominique Kreutz
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Kerstin Plessl
- Department of Obstetrics and Fetal-Maternal Medicine, Reproductive Biology Unit, Medical University of Vienna, Waehringer Guertel 18-20, 5Q, 1090, Vienna, Austria
| | - Denise Wolrab
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Michael Groessl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Bernhard K Keppler
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 42, 1090, Vienna, Austria
| | - Samuel M Meier
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
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21
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Weigt D, Hopf C, Médard G. Studying epigenetic complexes and their inhibitors with the proteomics toolbox. Clin Epigenetics 2016; 8:76. [PMID: 27437033 PMCID: PMC4950666 DOI: 10.1186/s13148-016-0244-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/05/2016] [Indexed: 12/27/2022] Open
Abstract
Some epigenetic modifier proteins have become validated clinical targets. With a few small molecule inhibitors already approved by national health administrations and many more in the pharmaceutical industry pipelines, there is a need for technologies that can promote full comprehension of the molecular action of these drugs. Proteomics, with its relatively unbiased nature, can contribute to a thorough understanding of the complexity of the megadalton complexes, which write, read and erase the histone code, and it can help study the on-target and off-target effect of the drugs designed to modulate their action. This review on the one hand gathers the published affinity probes able to decipher small molecule targets and off-targets in a close-to-native environment. These are small molecule analogues of epigenetic drugs conceived as protein target enrichment tools after they have engaged them in cells or lysates. Such probes, which have been designed for deacetylases, bromodomains, demethylases, and methyltransferases not only enrich their direct protein targets but also their stable interactors, which can be identified by mass spectrometry. Hence, they constitute a tool to study the epigenetic complexes together with other techniques also reviewed here: immunoaffinity purification with antibodies against native protein complex constituents or epitope tags, affinity matrices designed to bind recombinantly tagged protein, and enrichment of the complexes using histone tail peptides as baits. We expect that this toolbox will be adopted by more and more researchers willing to harness the spectacular advances in mass spectrometry to the epigenetic field.
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Affiliation(s)
- David Weigt
- />Center for Applied Research in Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- />HBIGS International Graduate School of Molecular and Cellular Biology, Heidelberg University, Im Neuenheimer Feld 501, 69120 Heidelberg, Germany
| | - Carsten Hopf
- />Center for Applied Research in Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- />HBIGS International Graduate School of Molecular and Cellular Biology, Heidelberg University, Im Neuenheimer Feld 501, 69120 Heidelberg, Germany
| | - Guillaume Médard
- />Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
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