1
|
Spanò DP, Bonelli S, Calligaris M, Carreca AP, Carcione C, Zito G, Nicosia A, Rizzo S, Scilabra SD. High-Resolution Secretome Analysis of Chemical Hypoxia Treated Cells Identifies Putative Biomarkers of Chondrosarcoma. Proteomes 2022; 10:proteomes10030025. [PMID: 35893766 PMCID: PMC9326515 DOI: 10.3390/proteomes10030025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/08/2022] [Accepted: 07/10/2022] [Indexed: 11/16/2022] Open
Abstract
Chondrosarcoma is the second most common bone tumor, accounting for 20% of all cases. Little is known about the pathology and molecular mechanisms involved in the development and in the metastatic process of chondrosarcoma. As a consequence, there are no approved therapies for this tumor and surgical resection is the only treatment currently available. Moreover, there are no available biomarkers for this type of tumor, and chondrosarcoma classification relies on operator-dependent histopathological assessment. Reliable biomarkers of chondrosarcoma are urgently needed, as well as greater understanding of the molecular mechanisms of its development for translational purposes. Hypoxia is a central feature of chondrosarcoma progression. The hypoxic tumor microenvironment of chondrosarcoma triggers a number of cellular events, culminating in increased invasiveness and migratory capability. Herein, we analyzed the effects of chemically-induced hypoxia on the secretome of SW 1353, a human chondrosarcoma cell line, using high-resolution quantitative proteomics. We found that hypoxia induced unconventional protein secretion and the release of proteins associated to exosomes. Among these proteins, which may be used to monitor chondrosarcoma development, we validated the increased secretion in response to hypoxia of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme well-known for its different functional roles in a wide range of tumors. In conclusion, by analyzing the changes induced by hypoxia in the secretome of chondrosarcoma cells, we identified molecular mechanisms that can play a role in chondrosarcoma progression and pinpointed proteins, including GAPDH, that may be developed as potential biomarkers for the diagnosis and therapeutic management of chondrosarcoma.
Collapse
Affiliation(s)
- Donatella Pia Spanò
- Proteomics Group of Fondazione Ri.MED, Department of Research IRCCS ISMETT, via Ernesto Tricomi 5, 90145 Palermo, Italy; (D.P.S.); (S.B.); (M.C.); (A.P.C.)
- STEBICEF (Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche), Università degli Studi di Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy
| | - Simone Bonelli
- Proteomics Group of Fondazione Ri.MED, Department of Research IRCCS ISMETT, via Ernesto Tricomi 5, 90145 Palermo, Italy; (D.P.S.); (S.B.); (M.C.); (A.P.C.)
- STEBICEF (Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche), Università degli Studi di Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy
| | - Matteo Calligaris
- Proteomics Group of Fondazione Ri.MED, Department of Research IRCCS ISMETT, via Ernesto Tricomi 5, 90145 Palermo, Italy; (D.P.S.); (S.B.); (M.C.); (A.P.C.)
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Anna Paola Carreca
- Proteomics Group of Fondazione Ri.MED, Department of Research IRCCS ISMETT, via Ernesto Tricomi 5, 90145 Palermo, Italy; (D.P.S.); (S.B.); (M.C.); (A.P.C.)
| | - Claudia Carcione
- Fondazione Ri.MED, Department of Research IRCCS ISMETT, via Ernesto Tricomi 5, 90145 Palermo, Italy;
| | - Giovanni Zito
- Research Department, IRCSS ISMETT (Instituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione), 90127 Palermo, Italy;
| | - Aldo Nicosia
- Institute for Biomedical Research and Innovation-National Research Council (IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy;
| | - Sergio Rizzo
- Medical Oncology Unit, IRCCS ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione), 90127 Palermo, Italy;
| | - Simone Dario Scilabra
- Proteomics Group of Fondazione Ri.MED, Department of Research IRCCS ISMETT, via Ernesto Tricomi 5, 90145 Palermo, Italy; (D.P.S.); (S.B.); (M.C.); (A.P.C.)
- Correspondence:
| |
Collapse
|
2
|
Chan YY, Chan MC. Pharmacological Activation of the HIF Pathway Exerts Distinct Proliferative Effects in MDA‐MB‐231 and MCF7 cells**. ChemistrySelect 2022. [DOI: 10.1002/slct.202200698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yan Ying Chan
- Department of Molecular Medicine Faculty of Medicine Universiti Malaya 50603 Kuala Lumpur Malaysia
| | - Mun Chiang Chan
- Department of Molecular Medicine Faculty of Medicine Universiti Malaya 50603 Kuala Lumpur Malaysia
| |
Collapse
|
3
|
Altered RBP1 Gene Expression Impacts Epithelial Cell Retinoic Acid, Proliferation, and Microenvironment. Cells 2022; 11:cells11050792. [PMID: 35269414 PMCID: PMC8909206 DOI: 10.3390/cells11050792] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 02/12/2022] [Accepted: 02/16/2022] [Indexed: 11/17/2022] Open
Abstract
Vitamin A is an essential diet-derived nutrient that has biological activity affected through an active metabolite, all-trans retinoic acid (atRA). Retinol-binding protein type 1 (RBP1) is an intracellular chaperone that binds retinol and retinal with high affinity, protects retinoids from non-specific oxidation, and delivers retinoids to specific enzymes to facilitate biosynthesis of RA. RBP1 expression is reduced in many of the most prevalent cancers, including breast cancer. Here, we sought to understand the relationship between RBP1 expression and atRA biosynthesis in mammary epithelial cells, as well as RBP1 expression and atRA levels in human mammary tissue. We additionally aimed to investigate the impact of RBP1 expression and atRA on the microenvironment as well as the potential for therapeutic restoration of RBP1 expression and endogenous atRA production. Using human mammary ductal carcinoma samples and a series of mammary epithelial cell lines representing different stages of tumorigenesis, we investigated the relationship between RBP1 expression as determined by QPCR and atRA via direct liquid chromatography-multistage-tandem mass spectrometry-based quantification. The functional effect of RBP1 expression and atRA in epithelial cells was investigated via the expression of direct atRA targets using QPCR, proliferation using Ki-67 staining, and collagen deposition via picrosirius red staining. We also investigated the atRA content of stromal cells co-cultured with normal and tumorigenic epithelial cells. Results show that RBP1 and atRA are reduced in mammary tumor tissue and tumorigenic epithelial cell lines. Knock down of RBP1 expression using shRNA or overexpression of RBP1 supported a direct relationship between RBP1 expression with atRA. Increases in cellular atRA were able to activate atRA direct targets, inhibit proliferation and inhibit collagen deposition in epithelial cell lines. Conditions encountered in tumor microenvironments, including low glucose and hypoxia, were able to reduce RBP1 expression and atRA. Treatment with either RARα agonist AM580 or demethylating agent Decitabine were able to increase RBP1 expression and atRA. Cellular content of neighboring fibroblasts correlated with the RA producing capacity of epithelial cells in co-culture. This work establishes a direct relationship between RBP1 expression and atRA, which is maintained when RBP1 expression is restored therapeutically. The results demonstrate diseases with reduced RBP1 could potentially benefit from therapeutics that restore RBP1 expression and endogenous atRA.
Collapse
|
4
|
Baby S, Gurukkala Valapil D, Shankaraiah N. Unravelling KDM4 histone demethylase inhibitors for cancer therapy. Drug Discov Today 2021; 26:1841-1856. [PMID: 34051367 DOI: 10.1016/j.drudis.2021.05.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/06/2021] [Accepted: 05/21/2021] [Indexed: 12/15/2022]
Abstract
Epigenetic enzyme-targeted therapy is a promising new development in the field of drug discovery. To date, histone deacetylases and DNA methyltransferases have been investigated as druggable epigenetic enzyme targets in cancer therapeutics. Histone methyltransferases and lysine demethylase inhibitors are the latest groups of epi-drugs being actively studied in clinical trials. KDM4s are JmjC domain-containing histone H3 lysine 9/36 demethylase enzymes, belonging to the 2-OG-dependent oxygenases, which are upregulated in multiple malignancies. In the recent years, these enzymes have captured much attention as a novel target in cancer therapy. Herein, we traverse the discovery path and current challenges in designing potent KDM4 inhibitors as potential anticancer agents. We discuss the considerable efforts and proposed future strategies to develop selective small molecule inhibitors of KDM4s, highlighting scaffold candidates and cyclic skeletons for which activity data, selectivity profiles and structure-activity relationships (SARs) have been studied.
Collapse
Affiliation(s)
- Stephin Baby
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India
| | - Durgesh Gurukkala Valapil
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India
| | - Nagula Shankaraiah
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India.
| |
Collapse
|
5
|
Quantitative Proteomic Approach Reveals Altered Metabolic Pathways in Response to the Inhibition of Lysine Deacetylases in A549 Cells under Normoxia and Hypoxia. Int J Mol Sci 2021; 22:ijms22073378. [PMID: 33806075 PMCID: PMC8036653 DOI: 10.3390/ijms22073378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/24/2022] Open
Abstract
Growing evidence is showing that acetylation plays an essential role in cancer, but studies on the impact of KDAC inhibition (KDACi) on the metabolic profile are still in their infancy. Here, we analyzed, by using an iTRAQ-based quantitative proteomics approach, the changes in the proteome of KRAS-mutated non-small cell lung cancer (NSCLC) A549 cells in response to trichostatin-A (TSA) and nicotinamide (NAM) under normoxia and hypoxia. Part of this response was further validated by molecular and biochemical analyses and correlated with the proliferation rates, apoptotic cell death, and activation of ROS scavenging mechanisms in opposition to the ROS production. Despite the differences among the KDAC inhibitors, up-regulation of glycolysis, TCA cycle, oxidative phosphorylation and fatty acid synthesis emerged as a common metabolic response underlying KDACi. We also observed that some of the KDACi effects at metabolic levels are enhanced under hypoxia. Furthermore, we used a drug repositioning machine learning approach to list candidate metabolic therapeutic agents for KRAS mutated NSCLC. Together, these results allow us to better understand the metabolic regulations underlying KDACi in NSCLC, taking into account the microenvironment of tumors related to hypoxia, and bring new insights for the future rational design of new therapies.
Collapse
|
6
|
Hsu KF, Wilkins SE, Hopkinson RJ, Sekirnik R, Flashman E, Kawamura A, McCullagh JS, Walport LJ, Schofield CJ. Hypoxia and hypoxia mimetics differentially modulate histone post-translational modifications. Epigenetics 2021; 16:14-27. [PMID: 32609604 PMCID: PMC7889154 DOI: 10.1080/15592294.2020.1786305] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/07/2020] [Accepted: 05/22/2020] [Indexed: 12/13/2022] Open
Abstract
Post-translational modifications (PTMs) to the tails of the core histone proteins are critically involved in epigenetic regulation. Hypoxia affects histone modifications by altering the activities of histone-modifying enzymes and the levels of hypoxia-inducible factor (HIF) isoforms. Synthetic hypoxia mimetics promote a similar response, but how accurately the hypoxia mimetics replicate the effects of limited oxygen availability on the levels of histone PTMs is uncertain. Here we report studies on the profiling of the global changes to PTMs on intact histones in response to hypoxia/hypoxia-related stresses using liquid chromatography-mass spectrometry (LC-MS). We demonstrate that intact protein LC-MS profiling is a relatively simple and robust method for investigating potential effects of drugs on histone modifications. The results provide insights into the profiles of PTMs associated with hypoxia and inform on the extent to which hypoxia and hypoxia mimetics cause similar changes to histones. These findings imply chemically-induced hypoxia does not completely replicate the substantial effects of physiological hypoxia on histone PTMs, highlighting that caution should be used in interpreting data from their use.
Collapse
Affiliation(s)
- Kuo-Feng Hsu
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Sarah E. Wilkins
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Richard J. Hopkinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- Leicester Institute of Structural and Chemical Biology and School of Chemistry, University of Leicester, Leicester, UK
| | - Rok Sekirnik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Emily Flashman
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust Centre for Human Genetics, Oxford, UK
- Chemistry - School of Natural and Environmental Sciences, Newcastle University, UK
| | - James S.O. McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Louise J. Walport
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
| | | |
Collapse
|
7
|
Bush JT, Pogany P, Pickett SD, Barker M, Baxter A, Campos S, Cooper AWJ, Hirst D, Inglis G, Nadin A, Patel VK, Poole D, Pritchard J, Washio Y, White G, Green DVS. A Turing Test for Molecular Generators. J Med Chem 2020; 63:11964-11971. [PMID: 32955254 DOI: 10.1021/acs.jmedchem.0c01148] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Machine learning approaches promise to accelerate and improve success rates in medicinal chemistry programs by more effectively leveraging available data to guide a molecular design. A key step of an automated computational design algorithm is molecule generation, where the machine is required to design high-quality, drug-like molecules within the appropriate chemical space. Many algorithms have been proposed for molecular generation; however, a challenge is how to assess the validity of the resulting molecules. Here, we report three Turing-inspired tests designed to evaluate the performance of molecular generators. Profound differences were observed between the performance of molecule generators in these tests, highlighting the importance of selection of the appropriate design algorithms for specific circumstances. One molecule generator, based on match molecular pairs, performed excellently against all tests and thus provides a valuable component for machine-driven medicinal chemistry design workflows.
Collapse
Affiliation(s)
- Jacob T Bush
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Peter Pogany
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Stephen D Pickett
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Mike Barker
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Andrew Baxter
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Sebastien Campos
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Anthony W J Cooper
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - David Hirst
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Graham Inglis
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Alan Nadin
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Vipulkumar K Patel
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Darren Poole
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - John Pritchard
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Yoshiaki Washio
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Gemma White
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Darren V S Green
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| |
Collapse
|
8
|
Bush JT, Chan MC, Mohammed S, Schofield CJ. Quantitative MS-Based Proteomics: Comparing the MCF-7 Cellular Response to Hypoxia and a 2-Oxoglutarate Analogue. Chembiochem 2020; 21:1647-1655. [PMID: 31919953 PMCID: PMC7317498 DOI: 10.1002/cbic.201900719] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 12/19/2022]
Abstract
The hypoxia-inducible factors (HIFs) are key transcription factors in determining cellular responses involving alterations in protein levels in response to limited oxygen availability in animal cells. 2-Oxoglutarate-dependent oxygenases play key roles in regulating levels of HIF and its transcriptional activity. We describe MS-based proteomics studies in which we compared the results of subjecting human breast cancer MCF-7 cells to hypoxia or treating them with a cell-penetrating derivative (dimethyl N-oxalylglycine; DMOG) of the stable 2OG analogue N-oxalylglycine. The proteomic results are consistent with reported transcriptomic analyses and support the proposed key roles of 2OG-dependent HIF prolyl- and asparaginyl-hydroxylases in the hypoxic response. Differences between the data sets for hypoxia and DMOG might reflect context-dependent effects or HIF-independent effects of DMOG.
Collapse
Affiliation(s)
- Jacob T. Bush
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Current address: GSKMedicines Research CentreGunnels Wood RoadStevenageSG1 2NYUK
| | - Mun Chiang Chan
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Current address: Department of Molecular MedicineFaculty of MedicineUniversity of Malaya, Jalan Universiti50603Kuala LumpurMalaysia
| | - Shabaz Mohammed
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Christopher J. Schofield
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| |
Collapse
|