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Woods K, Rants'o TA, Chan AM, Sapre T, Mastin GE, Maguire KM, Ong SE, Golkowski M. diaPASEF-Powered Chemoproteomics Enables Deep Kinome Interaction Profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.22.624841. [PMID: 39605566 PMCID: PMC11601655 DOI: 10.1101/2024.11.22.624841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Protein-protein interactions (PPIs) underlie most biological functions. Devastating human conditions like cancers, neurological disorders, and infections, hijack PPI networks to initiate disease, and to drive disease progression. Understanding precisely how diseases remodel PPI networks can, therefore, help clarify disease mechanisms and identify therapeutic targets. Protein kinases control most cellular processes through protein phosphorylation. The 518 human kinases, known as the kinome, are frequently dysregulated in disease and highly druggable with ATP-competitive inhibitors. Kinase activity, localization, and substrate recognition are regulated by dynamic PPI networks composed of scaffolding and adapter proteins, other signaling enzymes like small GTPases and E3 ligases, and phospho-substrates. Accordingly, mapping kinase PPI networks can help determine kinome activation states, and, in turn, cellular activation states; this information can be used for studying kinase-mediated cell signaling, and for prioritizing kinases for drug discovery. Previously, we have developed a high-throughput method for kinome PPI mapping based on mass spectrometry (MS)-based chemoproteomics that we named kinobead competition and correlation analysis (kiCCA). Here, we introduce 2 nd generation (gen) kiCCA which utilizes data-independent acquisition (dia) with parallel accumulation serial fragmentation (PASEF) MS and a re-designed CCA algorithm with improved selection criteria and the ability to predict multiple kinase interaction partners of the same proteins. Using neuroblastoma cell line models of the noradrenergic-mesenchymal transition (NMT), we demonstrate that 2 nd gen kiCCA (1) identified 6.1-times more kinase PPIs in native cell extracts compared to our 1 st gen approach, (2) determined kinase-mediated signaling pathways that underly the neuroblastoma NMT, and (3) accurately predicted pharmacological targets for manipulating NMT states. Our 2 nd gen kiCCA method is broadly useful for cell signaling research and kinase drug discovery.
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2
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East MP, Sprung RW, Okumu DO, Olivares-Quintero JF, Joisa CU, Chen X, Zhang Q, Erdmann-Gilmore P, Mi Y, Sciaky N, Malone JP, Bhatia S, McCabe IC, Xu Y, Sutcliffe MD, Luo J, Spears PA, Perou CM, Earp HS, Carey LA, Yeh JJ, Spector DL, Gomez SM, Spanheimer PM, Townsend RR, Johnson GL. Quantitative proteomic mass spectrometry of protein kinases to determine dynamic heterogeneity of the human kinome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.04.614143. [PMID: 39464086 PMCID: PMC11507871 DOI: 10.1101/2024.10.04.614143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
The kinome is a dynamic system of kinases regulating signaling networks in cells and dysfunction of protein kinases contributes to many diseases. Regulation of the protein expression of kinases alters cellular responses to environmental changes and perturbations. We configured a library of 672 proteotypic peptides to quantify >300 kinases in a single LC-MS experiment using ten micrograms protein from human tissues including biopsies. This enables absolute quantitation of kinase protein abundance at attomole-femtomole expression levels, requiring no kinase enrichment and less than ten micrograms of starting protein from flash-frozen and formalin fixed paraffin embedded tissues. Breast cancer biopsies, organoids, and cell lines were analyzed using the SureQuant method, demonstrating the heterogeneity of kinase protein expression across and within breast cancer clinical subtypes. Kinome quantitation was coupled with nanoscale phosphoproteomics, providing a feasible method for novel clinical diagnosis and understanding of patient kinome responses to treatment.
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3
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Shen J, Chen L, Liu J, Li A, Zheng L, Chen S, Li Y. EGFR degraders in non-small-cell lung cancer: Breakthrough and unresolved issue. Chem Biol Drug Des 2024; 103:e14517. [PMID: 38610074 DOI: 10.1111/cbdd.14517] [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: 11/01/2023] [Revised: 03/02/2024] [Accepted: 03/16/2024] [Indexed: 04/14/2024]
Abstract
The epidermal growth factor receptor (EGFR) has been well validated as a therapeutic target for anticancer drug discovery. Osimertinib has become the first globally accessible third-generation EGFR inhibitor, representing one of the most advanced developments in non-small-cell lung cancer (NSCLC) therapy. However, a tertiary Cys797 to Ser797 (C797S) point mutation has hampered osimertinib treatment in patients with advanced EGFR-mutated NSCLC. Several classes of fourth-generation EGFR inhibitors were consequently discovered with the aim of overcoming the EGFRC797S mutation-mediated resistance. However, no clinical efficacy data of the fourth-generation EGFR inhibitors were reported to date, and EGFRC797S mutation-mediated resistance remains an "unmet clinical need." Proteolysis-targeting chimeric molecules (PROTACs) obtained from EGFR-TKIs have been developed to target drug resistance EGFR in NSCLC. Some PROTACs are from nature products. These degraders compared with EGFR inhibitors showed better efficiency in their cellular potency, inhibition, and toxicity profiles. In this review, we first introduce the structural properties of EGFR, the resistance, and mutations of EGFR, and then mainly focus on the recent advances of EGFR-targeting degraders along with its advantages and outstanding challenges.
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Affiliation(s)
- Jiayi Shen
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Liping Chen
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Jihu Liu
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Anzhi Li
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Lüyin Zheng
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Sheng Chen
- Jiangxi Chiralsyn Biological Medicine Co., Ltd, Ganzhou, Jiangxi, China
| | - Yongdong Li
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Gannan Normal University, Ganzhou, Jiangxi, China
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4
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Liang X, Ren H, Han F, Liang R, Zhao J, Liu H. The new direction of drug development: Degradation of undruggable targets through targeting chimera technology. Med Res Rev 2024; 44:632-685. [PMID: 37983964 DOI: 10.1002/med.21992] [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: 11/30/2022] [Revised: 06/13/2023] [Accepted: 10/29/2023] [Indexed: 11/22/2023]
Abstract
Imbalances in protein and noncoding RNA levels in vivo lead to the occurrence of many diseases. In addition to the use of small molecule inhibitors and agonists to restore these imbalances, recently emerged targeted degradation technologies provide a new direction for disease treatment. Targeted degradation technology directly degrades target proteins or RNA by utilizing the inherent degradation pathways, thereby eliminating the functions of pathogenic proteins (or RNA) to treat diseases. Compared with traditional therapies, targeted degradation technology which avoids the principle of traditional inhibitor occupation drive, has higher efficiency and selectivity, and widely expands the range of drug targets. It is one of the most promising and hottest areas for future drug development. Herein, we systematically introduced the in vivo degradation systems applied to degrader design: ubiquitin-proteasome system, lysosomal degradation system, and RNA degradation system. We summarized the development progress, structural characteristics, and limitations of novel chimeric design technologies based on different degradation systems. In addition, due to the lack of clear ligand-binding pockets, about 80% of disease-associated proteins cannot be effectively intervened with through traditional therapies. We deeply elucidated how to use targeted degradation technology to discover and design molecules for representative undruggable targets including transcription factors, small GTPases, and phosphatases. Overall, this review provides a comprehensive and systematic overview of targeted degradation technology-related research advances and a new guidance for the chimeric design of undruggable targets.
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Affiliation(s)
- Xuewu Liang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hairu Ren
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Fengyang Han
- School of Pharmacy, Fudan University, Shanghai, China
| | - Renwen Liang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jiayan Zhao
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Hong Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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5
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Gomez SM, Axtman AD, Willson TM, Major MB, Townsend RR, Sorger PK, Johnson GL. Illuminating function of the understudied druggable kinome. Drug Discov Today 2024; 29:103881. [PMID: 38218213 PMCID: PMC11262466 DOI: 10.1016/j.drudis.2024.103881] [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: 10/01/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The human kinome, with more than 500 proteins, is crucial for cell signaling and disease. Yet, about one-third of kinases lack in-depth study. The Data and Resource Generating Center for Understudied Kinases has developed multiple resources to address this challenge including creation of a heavy amino acid peptide library for parallel reaction monitoring and quantitation of protein kinase expression, use of understudied kinases tagged with a miniTurbo-biotin ligase to determine interaction networks by proximity-dependent protein biotinylation, NanoBRET probe development for screening chemical tool target specificity in live cells, characterization of small molecule chemical tools inhibiting understudied kinases, and computational tools for defining kinome architecture. These resources are available through the Dark Kinase Knowledgebase, supporting further research into these understudied protein kinases.
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Affiliation(s)
- Shawn M Gomez
- University of North Carolina School of Medicine, Chapel Hill, NC, USA.
| | - Alison D Axtman
- University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Timothy M Willson
- University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Michael B Major
- Washington University School of Medicine in St. Louis, MO, USA
| | - Reid R Townsend
- Washington University School of Medicine in St. Louis, MO, USA
| | | | - Gary L Johnson
- University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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6
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Wells JA, Kumru K. Extracellular targeted protein degradation: an emerging modality for drug discovery. Nat Rev Drug Discov 2024; 23:126-140. [PMID: 38062152 DOI: 10.1038/s41573-023-00833-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2023] [Indexed: 02/08/2024]
Abstract
Targeted protein degradation (TPD) has emerged in the past decade as a major new drug modality to remove intracellular proteins with bispecific small molecules that recruit the protein of interest (POI) to an E3 ligase for degradation in the proteasome. Unlike classic occupancy-based drugs, intracellular TPD (iTPD) eliminates the target and works catalytically, and so can be more effective and sustained, with lower dose requirements. Recently, this approach has been expanded to the extracellular proteome, including both secreted and membrane proteins. Extracellular targeted protein degradation (eTPD) uses bispecific antibodies, conjugates or small molecules to degrade extracellular POIs by trafficking them to the lysosome for degradation. Here, we focus on recent advances in eTPD, covering degrader systems, targets, molecular designs and parameters to advance them. Now almost any protein, intracellular or extracellular, is addressable in principle with TPD.
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Affiliation(s)
- James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
| | - Kaan Kumru
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
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7
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Stephenson EH, Higgins JMG. Pharmacological approaches to understanding protein kinase signaling networks. Front Pharmacol 2023; 14:1310135. [PMID: 38164473 PMCID: PMC10757940 DOI: 10.3389/fphar.2023.1310135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Protein kinases play vital roles in controlling cell behavior, and an array of kinase inhibitors are used successfully for treatment of disease. Typical drug development pipelines involve biological studies to validate a protein kinase target, followed by the identification of small molecules that effectively inhibit this target in cells, animal models, and patients. However, it is clear that protein kinases operate within complex signaling networks. These networks increase the resilience of signaling pathways, which can render cells relatively insensitive to inhibition of a single kinase, and provide the potential for pathway rewiring, which can result in resistance to therapy. It is therefore vital to understand the properties of kinase signaling networks in health and disease so that we can design effective multi-targeted drugs or combinations of drugs. Here, we outline how pharmacological and chemo-genetic approaches can contribute to such knowledge, despite the known low selectivity of many kinase inhibitors. We discuss how detailed profiling of target engagement by kinase inhibitors can underpin these studies; how chemical probes can be used to uncover kinase-substrate relationships, and how these tools can be used to gain insight into the configuration and function of kinase signaling networks.
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Affiliation(s)
| | - Jonathan M. G. Higgins
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle uponTyne, United Kingdom
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8
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Hua WJ, Yeh H, Lin ZH, Tseng AJ, Huang LC, Qiu WL, Tu TH, Wang DH, Hsu WH, Hwang WL, Lin TY. Ganoderma microsporum immunomodulatory protein as an extracellular epidermal growth factor receptor (EGFR) degrader for suppressing EGFR-positive lung cancer cells. Cancer Lett 2023; 578:216458. [PMID: 37865161 DOI: 10.1016/j.canlet.2023.216458] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/28/2023] [Accepted: 10/17/2023] [Indexed: 10/23/2023]
Abstract
Epidermal growth factor receptor (EGFR) abnormalities relevant to tumor progression. A newly developed strategy for cancer therapy is induction of EGFR degradation. GMI, an immunomodulatory protein from the medicinal mushroom Ganoderma microsporum, exhibits anticancer activity. However, its role in the intracellular trafficking and degradation of EGFR remains unclear. In this study, we discovered that GMI inhibits the phosphorylation of multiple tyrosine kinases. Specifically, GMI was discovered to suppress lung cancer cells harboring both wild-type and mutant EGFR by inhibiting EGFR dimerization and eliminating EGFR-mediated signaling. Functional studies revealed that GMI binds to the extracellular segment of EGFR. GMI interacts with EGFR to induce phosphorylation of EGFR at tyrosine1045, which triggers clathrin-dependent endocytosis and degradation of EGFR. Furthermore, in the mouse models, GMI was discovered to suppress tumor growth. Knockdown of EGFR in lung cancer cells abolishes GMI's anticancer activity in vivo and in vitro. Our results reveal the interaction mechanisms through which GMI induces EGFR degradation and abolishes EGFR-mediated intracellular pathway. Our study indicates that GMI is an EGFR degrader for inhibiting EGFR-expressing tumor growth.
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Affiliation(s)
- Wei-Jyun Hua
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan; Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsin Yeh
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Zhi-Hu Lin
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ai-Jung Tseng
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Li-Chen Huang
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wei-Lun Qiu
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tsung-Hsi Tu
- Faculty of Medicine, National Yang Ming Chiao Tung University, Taiwan; Department of Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taiwan
| | - Ding-Han Wang
- College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wei-Hung Hsu
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; LO-Sheng Hospital Ministry of Health and Welfare, Taipei, Taiwan; School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wei-Lun Hwang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Cancer and Immunology Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tung-Yi Lin
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan; Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Biomedical Industry Ph.D. Program, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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9
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Eggermont C, Gutierrez GJ, De Grève J, Giron P. Inhibition of PLK1 Destabilizes EGFR and Sensitizes EGFR-Mutated Lung Cancer Cells to Small Molecule Inhibitor Osimertinib. Cancers (Basel) 2023; 15:cancers15092589. [PMID: 37174055 PMCID: PMC10177332 DOI: 10.3390/cancers15092589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Tyrosine kinase inhibitors (TKI) targeting the epidermal growth factor receptor (EGFR) have significantly prolonged survival in EGFR-mutant non-small cell lung cancer patients. However, the development of resistance mechanisms prohibits the curative potential of EGFR TKIs. Combination therapies emerge as a valuable approach to preventing or delaying disease progression. Here, we investigated the combined inhibition of polo-like kinase 1 (PLK1) and EGFR in TKI-sensitive EGFR-mutant NSCLC cells. The pharmacological inhibition of PLK1 destabilized EGFR levels and sensitized NSCLC cells to Osimertinib through induction of apoptosis. In addition, we found that c-Cbl, a ubiquitin ligase of EGFR, is a direct phosphorylation target of PLK1 and PLK1 impacts the stability of c-Cbl in a kinase-dependent manner. In conclusion, we describe a novel interaction between mutant EGFR and PLK1 that may be exploited in the clinic. Co-targeting PLK1 and EGFR may improve and prolong the clinical response to EGFR TKI in patients with an EGFR-mutated NSCLC.
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Affiliation(s)
- Carolien Eggermont
- Laboratory of Medical and Molecular Oncology, Oncology Research Center, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Gustavo J Gutierrez
- Laboratory of Pathophysiological Cell Signaling, Department of Biology, Faculty of Science and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jacques De Grève
- Laboratory of Medical and Molecular Oncology, Oncology Research Center, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
- Centre for Medical Genetics, Research Group Reproduction and Genetics, Clinical Sciences, UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Philippe Giron
- Laboratory of Medical and Molecular Oncology, Oncology Research Center, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
- Centre for Medical Genetics, Research Group Reproduction and Genetics, Clinical Sciences, UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
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10
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De Robertis M, Greco MR, Cardone RA, Mazza T, Marzano F, Mehterov N, Kazakova M, Belev N, Tullo A, Pesole G, Sarafian V, Signori E. Upregulation of YKL-40 Promotes Metastatic Phenotype and Correlates with Poor Prognosis and Therapy Response in Patients with Colorectal Cancer. Cells 2022; 11:cells11223568. [PMID: 36428997 PMCID: PMC9688424 DOI: 10.3390/cells11223568] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/28/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
YKL-40 is a heparin- and chitin-binding glycoprotein that belongs to the family of glycosyl hydrolases but lacks enzymatic properties. It affects different (patho)physiological processes, including cancer. In different tumors, YKL-40 gene overexpression has been linked to higher cell proliferation, angiogenesis, and vasculogenic mimicry, migration, and invasion. Because, in colorectal cancer (CRC), the serological YKL-40 level may serve as a risk predictor and prognostic biomarker, we investigated the underlying mechanisms by which it may contribute to tumor progression and the clinical significance of its tissue expression in metastatic CRC. We demonstrated that high-YKL-40-expressing HCT116 and Caco2 cells showed increased motility, invasion, and proliferation. YKL-40 upregulation was associated with EMT signaling activation. In the AOM/DSS mouse model, as well as in tumors and sera from CRC patients, elevated YKL-40 levels correlated with high-grade tumors. In retrospective analyses of six independent cohorts of CRC patients, elevated YKL-40 expression correlated with shorter survival in patients with advanced CRC. Strikingly, high YKL-40 tissue levels showed a predictive value for a better response to cetuximab, even in patients with stage IV CRC and mutant KRAS, and worse sensitivity to oxaliplatin. Taken together, our findings establish that tissue YKL-40 overexpression enhances CRC metastatic potential, highlighting this gene as a novel prognostic candidate, a predictive biomarker for therapy response, and an attractive target for future therapy in CRC.
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Affiliation(s)
- Mariangela De Robertis
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari ‘A. Moro’, 70125 Bari, Italy
- Correspondence: (M.D.R.); (E.S.); Tel.: +39-06-4993-4232 (E.S.)
| | - Maria Raffaella Greco
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari ‘A. Moro’, 70125 Bari, Italy
| | - Rosa Angela Cardone
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari ‘A. Moro’, 70125 Bari, Italy
| | - Tommaso Mazza
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | - Flaviana Marzano
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Nikolay Mehterov
- Department of Medical Biology, Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
- Research Institute at Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
| | - Maria Kazakova
- Department of Medical Biology, Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
- Research Institute at Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
| | - Nikolay Belev
- University Hospital Eurohospital, 4000 Plovdiv, Bulgaria
- Department of Propedeutics of Surgical Diseases, Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
| | - Apollonia Tullo
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari ‘A. Moro’, 70125 Bari, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Victoria Sarafian
- Department of Medical Biology, Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
- Research Institute at Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
| | - Emanuela Signori
- Laboratory of Molecular Pathology and Experimental Oncology, Institute of Translational Pharmacology, Consiglio Nazionale delle Ricerche, 00133 Rome, Italy
- Correspondence: (M.D.R.); (E.S.); Tel.: +39-06-4993-4232 (E.S.)
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11
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Egawa J, Arta RK, Lemmon VP, Muños-Barrero M, Shi Y, Igarashi M, Someya T. The cyclin G-associated kinase (GAK) inhibitor SGC-GAK-1 inhibits neurite outgrowth and synapse formation. Mol Brain 2022; 15:68. [PMID: 35883152 PMCID: PMC9327206 DOI: 10.1186/s13041-022-00951-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/09/2022] [Indexed: 11/10/2022] Open
Abstract
Protein kinases are responsible for protein phosphorylation and are involved in important signal transduction pathways; however, a considerable number of poorly characterized kinases may be involved in neuronal development. Here, we considered cyclin G-associated kinase (GAK) as a candidate regulator of neurite outgrowth and synaptogenesis by examining the effects of the selective GAK inhibitor SGC-GAK-1. SGC-GAK-1 treatment of cultured neurons reduced neurite length and decreased synapse number and phosphorylation of neurofilament 200-kDa subunits relative to the control. In addition, the related kinase inhibitor erlotinib, which has distinct specificity and potency from SGC-GAK-1, had no effect on neurite growth, unlike SGC-GAK-1. These results suggest that GAK may be physiologically involved in normal neuronal development, and that decreased GAK function and the resultant impaired neurite outgrowth and synaptogenesis may be related to neurodevelopmental disorders.
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Affiliation(s)
- Jun Egawa
- Department of Psychiatry, School of Medicine, and Graduate School of Medical and Dental Sciences, Niigata University, 757 Asahimachi Dori-Ichibancho, Chuo-ku, Niigata, 951-8510, Japan. .,Department of Neurochemistry and Molecular Cell Biology, School of Medicine, and Graduate School of Medical and Dental Sciences, Niigata University, 757 Asahimachi Dori-Ichibancho, Chuo-ku, Niigata, 951-8510, Japan.
| | - Reza K Arta
- Department of Psychiatry, School of Medicine, and Graduate School of Medical and Dental Sciences, Niigata University, 757 Asahimachi Dori-Ichibancho, Chuo-ku, Niigata, 951-8510, Japan
| | - Vance P Lemmon
- Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, FL, USA.,Institute for Data Science and Computing, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Melissa Muños-Barrero
- Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Yan Shi
- Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michihiro Igarashi
- Department of Neurochemistry and Molecular Cell Biology, School of Medicine, and Graduate School of Medical and Dental Sciences, Niigata University, 757 Asahimachi Dori-Ichibancho, Chuo-ku, Niigata, 951-8510, Japan.
| | - Toshiyuki Someya
- Department of Psychiatry, School of Medicine, and Graduate School of Medical and Dental Sciences, Niigata University, 757 Asahimachi Dori-Ichibancho, Chuo-ku, Niigata, 951-8510, Japan
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12
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Chen PH, Hu Z, An E, Okeke IO, Zheng S, Luo X, Gong A, Jaime-Figueroa S, Crews CM. Modulation of Phosphoprotein Activity by Phosphorylation Targeting Chimeras (PhosTACs). ACS Chem Biol 2021; 16:2808-2815. [PMID: 34780684 PMCID: PMC10437008 DOI: 10.1021/acschembio.1c00693] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Protein phosphorylation, which regulates many critical aspects of cell biology, is dynamically governed by kinases and phosphatases. Many diseases are associated with dysregulated hyperphosphorylation of critical proteins, such as retinoblastoma protein in cancer. Although kinase inhibitors have been widely applied in the clinic, growing evidence of off-target effects and increasing drug resistance prompts the need to develop a new generation of drugs. Here, we propose a proof-of-concept study of phosphorylation targeting chimeras (PhosTACs). Similar to PROTACs in their ability to induce ternary complexes, PhosTACs focus on recruiting a Ser/Thr phosphatase to a phosphosubstrate to mediate its dephosphorylation. However, distinct from PROTACs, PhosTACs can uniquely provide target gain-of-function opportunities to manipulate protein activity. In this study, we applied a chemical biology approach to evaluate the feasibility of PhosTACs by recruiting the scaffold and catalytic subunits of the PP2A holoenzyme to protein substrates such as PDCD4 and FOXO3a for targeted protein dephosphorylation. For FOXO3a, this dephosphorylation resulted in the transcriptional activation of a FOXO3a-responsive reporter gene.
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Affiliation(s)
- Po-Han Chen
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
| | - Zhenyi Hu
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
| | - Elvira An
- Department of Pharmacology, Yale University, New Haven, Connecticut, 06511, United States
| | - Ifunanya Ozioma Okeke
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
| | - Sijin Zheng
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
- Yale University School of Medicine, New Haven, Connecticut, 06511, United States
| | - Xuanmeng Luo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
| | - Angela Gong
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
| | - Saul Jaime-Figueroa
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
| | - Craig M. Crews
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
- Department of Chemistry, Yale University, New Haven, Connecticut, 06511, United States
- Department of Pharmacology, Yale University, New Haven, Connecticut, 06511, United States
- Yale University School of Medicine, New Haven, Connecticut, 06511, United States
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13
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Yesilkanal AE, Johnson GL, Ramos AF, Rosner MR. New strategies for targeting kinase networks in cancer. J Biol Chem 2021; 297:101128. [PMID: 34461089 PMCID: PMC8449055 DOI: 10.1016/j.jbc.2021.101128] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 12/18/2022] Open
Abstract
Targeted strategies against specific driver molecules of cancer have brought about many advances in cancer treatment since the early success of the first small-molecule inhibitor Gleevec. Today, there are a multitude of targeted therapies approved by the Food and Drug Administration for the treatment of cancer. However, the initial efficacy of virtually every targeted treatment is often reversed by tumor resistance to the inhibitor through acquisition of new mutations in the target molecule, or reprogramming of the epigenome, transcriptome, or kinome of the tumor cells. At the core of this clinical problem lies the assumption that targeted treatments will only be efficacious if the inhibitors are used at their maximum tolerated doses. Such aggressive regimens create strong selective pressure on the evolutionary progression of the tumor, resulting in resistant cells. High-dose single agent treatments activate alternative mechanisms that bypass the inhibitor, while high-dose combinatorial treatments suffer from increased toxicity resulting in treatment cessation. Although there is an arsenal of targeted agents being tested clinically and preclinically, identifying the most effective combination treatment plan remains a challenge. In this review, we discuss novel targeted strategies with an emphasis on the recent cross-disciplinary studies demonstrating that it is possible to achieve antitumor efficacy without increasing toxicity by adopting low-dose multitarget approaches to treatment of cancer and metastasis.
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Affiliation(s)
- Ali E Yesilkanal
- Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois, USA.
| | - Gary L Johnson
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alexandre F Ramos
- Instituto do Câncer do Estado de São Paulo, Faculdade de Medicina and Escola de Artes, Ciências e Humanidades, University of São Paulo, Brazil
| | - Marsha Rich Rosner
- Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois, USA.
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14
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Elmore LW, Greer SF, Daniels EC, Saxe CC, Melner MH, Krawiec GM, Cance WG, Phelps WC. Blueprint for cancer research: Critical gaps and opportunities. CA Cancer J Clin 2021; 71:107-139. [PMID: 33326126 DOI: 10.3322/caac.21652] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
We are experiencing a revolution in cancer. Advances in screening, targeted and immune therapies, big data, computational methodologies, and significant new knowledge of cancer biology are transforming the ways in which we prevent, detect, diagnose, treat, and survive cancer. These advances are enabling durable progress in the goal to achieve personalized cancer care. Despite these gains, more work is needed to develop better tools and strategies to limit cancer as a major health concern. One persistent gap is the inconsistent coordination among researchers and caregivers to implement evidence-based programs that rely on a fuller understanding of the molecular, cellular, and systems biology mechanisms underpinning different types of cancer. Here, the authors integrate conversations with over 90 leading cancer experts to highlight current challenges, encourage a robust and diverse national research portfolio, and capture timely opportunities to advance evidence-based approaches for all patients with cancer and for all communities.
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Affiliation(s)
- Lynne W Elmore
- Office of the Chief Medical and Scientific Officer, American Cancer Society, Atlanta, Georgia
| | - Susanna F Greer
- Office of the Chief Medical and Scientific Officer, American Cancer Society, Atlanta, Georgia
| | - Elvan C Daniels
- Office of the Chief Medical and Scientific Officer, American Cancer Society, Atlanta, Georgia
| | - Charles C Saxe
- Office of the Chief Medical and Scientific Officer, American Cancer Society, Atlanta, Georgia
| | - Michael H Melner
- Office of the Chief Medical and Scientific Officer, American Cancer Society, Atlanta, Georgia
| | - Ginger M Krawiec
- Office of the Chief Medical and Scientific Officer, American Cancer Society, Atlanta, Georgia
| | - William G Cance
- Office of the Chief Medical and Scientific Officer, American Cancer Society, Atlanta, Georgia
| | - William C Phelps
- Office of the Chief Medical and Scientific Officer, American Cancer Society, Atlanta, Georgia
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15
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Fuchs O, Bokorova R. Preclinical Studies of PROTACs in Hematological Malignancies. Cardiovasc Hematol Disord Drug Targets 2021; 21:7-22. [PMID: 33687890 DOI: 10.2174/1871529x21666210308111546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/01/2021] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
Abstract
Incorrectly expressed or mutated proteins associated with hematologic malignancies have been generally targeted by chemotherapy using small-molecule inhibitors or monoclonal antibodies. But the majority of these intracellular proteins are without active sites and antigens. PROTACs, proteolysis targeting chimeras, are bifunctional molecules designed to polyubiquitinate and degrade specific pathological proteins of interest (POIs) by hijacking the activity of E3-ubiquitin ligases for POI polyubiquitination and subsequent degradation by the proteasome. This strategy utilizes the ubiquitin-proteasome system for the degradation of specific proteins in the cell. In many cases, including hematologic malignancies, inducing protein degradation as a therapeutic strategy offers therapeutic benefits over classical enzyme inhibition connected with resistance to inhibitors. Limitations of small-molecule inhibitors are shown. PROTACs can polyubiquitinate and mark for degradation of "undruggable"proteins, e.g. transcription factor STAT3 and scaffold proteins. Today, this technology is used in preclinical studies in various hematologic malignancies, mainly for targeting drug-resistant bromodomain and extraterminal proteins and Bruton tyrosine kinase. Several mechanisms limiting selectivity and safety of PROTAC molecules function are also discussed.
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Affiliation(s)
- Ota Fuchs
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Radka Bokorova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
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16
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Hao Q, Wang P, Dutta P, Chung S, Li Q, Wang K, Li J, Cao W, Deng W, Geng Q, Schrode K, Shaheen M, Wu K, Zhu D, Chen QH, Chen G, Elshimali Y, Vadgama J, Wu Y. Comp34 displays potent preclinical antitumor efficacy in triple-negative breast cancer via inhibition of NUDT3-AS4, a novel oncogenic long noncoding RNA. Cell Death Dis 2020; 11:1052. [PMID: 33311440 PMCID: PMC7733521 DOI: 10.1038/s41419-020-03235-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/03/2020] [Indexed: 01/12/2023]
Abstract
The abnormal PI3K/AKT/mTOR pathway is one of the most common genomic abnormalities in breast cancers including triple-negative breast cancer (TNBC), and pharmacologic inhibition of these aberrations has shown activity in TNBC patients. Here, we designed and identified a small-molecule Comp34 that suppresses both AKT and mTOR protein expression and exhibits robust cytotoxicity towards TNBC cells but not nontumorigenic normal breast epithelial cells. Mechanically, long noncoding RNA (lncRNA) AL354740.1-204 (also named as NUDT3-AS4) acts as a microRNA sponge to compete with AKT1/mTOR mRNAs for binding to miR-99s, leading to decrease in degradation of AKT1/mTOR mRNAs and subsequent increase in AKT1/mTOR protein expression. Inhibition of lncRNA-NUDT3-AS4 and suppression of the NUDT3-AS4/miR-99s association contribute to Comp34-affected biologic pathways. In addition, Comp34 alone is effective in cells with secondary resistance to rapamycin, the best-known inhibitor of mTOR, and displays a greater in vivo antitumor efficacy and lower toxicity than rapamycin in TNBC xenografted models. In conclusion, NUDT3-AS4 may play a proproliferative role in TNBC and be considered a relevant therapeutic target, and Comp34 presents promising activity as a single agent to inhibit TNBC through regulation of NUDT3-AS4 and miR-99s.
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Affiliation(s)
- Qiongyu Hao
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Piwen Wang
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Pranabananda Dutta
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Seyung Chung
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Qun Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, 200120, Shanghai, China
| | - Kun Wang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, 510080, Guangzhou, China
| | - Jieqing Li
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, 510080, Guangzhou, China
| | - Wei Cao
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Wenhong Deng
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
- Department of General Surgery, Renmin Hospital of Wuhan University, 430060, Wuhan, China
| | - Qing Geng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, 430060, Wuhan, China
| | - Katrina Schrode
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Magda Shaheen
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Ke Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Donghui Zhu
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Qiao-Hong Chen
- Department of Chemistry, California State University, Fresno, 2555 E. San Ramon Avenue, M/S SB70, Fresno, CA, 93740, USA
| | - Guanglin Chen
- Department of Chemistry, California State University, Fresno, 2555 E. San Ramon Avenue, M/S SB70, Fresno, CA, 93740, USA
| | - Yahya Elshimali
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA
| | - Jay Vadgama
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA.
| | - Yong Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, 90095, USA.
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17
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Yao N, Wang CR, Liu MQ, Li YJ, Chen WM, Li ZQ, Qi Q, Lu JJ, Fan CL, Chen MF, Qi M, Li XB, Hong J, Zhang DM, Ye WC. Discovery of a novel EGFR ligand DPBA that degrades EGFR and suppresses EGFR-positive NSCLC growth. Signal Transduct Target Ther 2020; 5:214. [PMID: 33033232 PMCID: PMC7544691 DOI: 10.1038/s41392-020-00251-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/25/2020] [Accepted: 06/15/2020] [Indexed: 12/22/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) activation plays a pivotal role in EGFR-driven non-small cell lung cancer (NSCLC) and is considered as a key target of molecular targeted therapy. EGFR tyrosine kinase inhibitors (TKIs) have been canonically used in NSCLC treatment. However, prevalent innate and acquired resistances and EGFR kinase-independent pro-survival properties limit the clinical efficacy of EGFR TKIs. Therefore, the discovery of novel EGFR degraders is a promising approach towards improving therapeutic efficacy and overcoming drug resistance. Here, we identified a 23-hydroxybetulinic acid derivative, namely DPBA, as a novel EGFR small-molecule ligand. It exerted potent in vitro and in vivo anticancer activity in both EGFR wild type and mutant NSCLC by degrading EGFR. Mechanistic studies disclosed that DPBA binds to the EGFR extracellular domain at sites differing from those of EGF and EGFR. DPBA did not induce EGFR dimerization, phosphorylation, and ubiquitination, but it significantly promoted EGFR degradation and repressed downstream survival pathways. Further analyses showed that DPBA induced clathrin-independent EGFR endocytosis mediated by flotillin-dependent lipid rafts and unaffected by EGFR TKIs. Activation of the early and late endosome markers rab5 and rab7 but not the recycling endosome marker rab11 was involved in DPBA-induced EGFR lysosomal degradation. The present study offers a new EGFR ligand for EGFR pharmacological degradation and proposes it as a potential treatment for EGFR-positive NSCLC, particularly NSCLC with innate or acquired EGFR TKI resistance. DPBA can also serve as a chemical probe in the studies on EGFR trafficking and degradation.
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Affiliation(s)
- Nan Yao
- College of Pharmacy, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, Jinan University, Guangzhou, China
| | - Chen-Ran Wang
- College of Pharmacy, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, Jinan University, Guangzhou, China
| | - Ming-Qun Liu
- College of Pharmacy, Jinan University, Guangzhou, China
| | - Ying-Jie Li
- College of Pharmacy, Jinan University, Guangzhou, China
| | - Wei-Min Chen
- College of Pharmacy, Jinan University, Guangzhou, China
| | - Zheng-Qiu Li
- College of Pharmacy, Jinan University, Guangzhou, China
| | - Qi Qi
- School of Medicine, Jinan University, Guangzhou, China
| | - Jin-Jian Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Chun-Lin Fan
- College of Pharmacy, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, Jinan University, Guangzhou, China
| | - Min-Feng Chen
- College of Pharmacy, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, Jinan University, Guangzhou, China
| | - Ming Qi
- College of Pharmacy, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, Jinan University, Guangzhou, China
| | - Xiao-Bo Li
- College of Pharmacy, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, Jinan University, Guangzhou, China
| | - Jian Hong
- School of Medicine, Jinan University, Guangzhou, China
| | - Dong-Mei Zhang
- College of Pharmacy, Jinan University, Guangzhou, China. .,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, Jinan University, Guangzhou, China.
| | - Wen-Cai Ye
- College of Pharmacy, Jinan University, Guangzhou, China. .,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, Jinan University, Guangzhou, China.
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18
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Mohanty V, Pinto SM, Subbannayya Y, Najar MA, Murthy KB, Prasad TSK, Murthy KR. Digging Deeper for the Eye Proteome in Vitreous Substructures: A High-Resolution Proteome Map of the Normal Human Vitreous Base. ACTA ACUST UNITED AC 2020; 24:379-389. [DOI: 10.1089/omi.2020.0020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sneha M. Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Mohd. Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Kalpana Babu Murthy
- Department of vitreo retina, Vittala International Institute of Ophthalmology, Bangalore, India
- Department of vitreo retina, Prabha Eye Clinic and Research Centre, Bangalore, India
| | | | - Krishna R. Murthy
- Department of vitreo retina, Vittala International Institute of Ophthalmology, Bangalore, India
- Department of vitreo retina, Prabha Eye Clinic and Research Centre, Bangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education, Manipal, India
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19
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Rahman SMT, Zhou W, Deiters A, Haugh JM. Optical control of MAP kinase kinase 6 (MKK6) reveals that it has divergent roles in pro-apoptotic and anti-proliferative signaling. J Biol Chem 2020; 295:8494-8504. [PMID: 32371393 DOI: 10.1074/jbc.ra119.012079] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/21/2020] [Indexed: 12/24/2022] Open
Abstract
The selective pressure imposed by extrinsic death signals and stressors adds to the challenge of isolating and interpreting the roles of proteins in stress-activated signaling networks. By expressing a kinase with activating mutations and a caged lysine blocking the active site, we can rapidly switch on catalytic activity with light and monitor the ensuing dynamics. Applying this approach to MAP kinase 6 (MKK6), which activates the p38 subfamily of MAPKs, we found that decaging active MKK6 in fibroblasts is sufficient to trigger apoptosis in a p38-dependent manner. Both in fibroblasts and in a murine melanoma cell line expressing mutant B-Raf, MKK6 activation rapidly and potently inhibited the pro-proliferative extracellular signal-regulated kinase (ERK) pathway; to our surprise, this negative cross-regulation was equally robust when all p38 isoforms were inhibited. These results position MKK6 as a new pleiotropic signal transducer that promotes both pro-apoptotic and anti-proliferative signaling, and they highlight the utility of caged, light-activated kinases for dissecting stress-activated signaling networks.
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Affiliation(s)
- Shah Md Toufiqur Rahman
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Wenyuan Zhou
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jason M Haugh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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20
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McDonald IM, Graves LM. Enigmatic MELK: The controversy surrounding its complex role in cancer. J Biol Chem 2020; 295:8195-8203. [PMID: 32350113 DOI: 10.1074/jbc.rev120.013433] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Ser/Thr protein kinase MELK (maternal embryonic leucine zipper kinase) has been considered an attractive therapeutic target for managing cancer since 2005. Studies using expression analysis have indicated that MELK expression is higher in numerous cancer cells and tissues than in their normal, nonneoplastic counterparts. Further, RNAi-mediated MELK depletion impairs proliferation of multiple cancers, including triple-negative breast cancer (TNBC), and these growth defects can be rescued with exogenous WT MELK, but not kinase-dead MELK complementation. Pharmacological MELK inhibition with OTS167 (alternatively called OTSSP167) and NVS-MELK8a, among other small molecules, also impairs cancer cell growth. These collective results led to MELK being classified as essential for cancer proliferation. More recently, in 2017, the proliferation of TNBC and other cancer cell lines was reported to be unaffected by genetic CRISPR/Cas9-mediated MELK deletion, calling into question the essentiality of this kinase in cancer. To date, the requirement of MELK in cancer remains controversial, and mechanisms underlying the disparate growth effects observed with RNAi, pharmacological inhibition, and CRISPR remain unclear. Our objective with this review is to highlight the evidence on both sides of this controversy, to provide commentary on the purported requirement of MELK in cancer, and to emphasize the need for continued elucidation of the functions of MELK.
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Affiliation(s)
- Ian M McDonald
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Lee M Graves
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA .,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA.,UNC Michael Hooker Proteomics Core Facility, University of North Carolina, Chapel Hill, North Carolina, USA
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21
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c-MYC Expression Is a Possible Keystone in the Colorectal Cancer Resistance to EGFR Inhibitors. Cancers (Basel) 2020; 12:cancers12030638. [PMID: 32164324 PMCID: PMC7139615 DOI: 10.3390/cancers12030638] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/26/2020] [Accepted: 03/05/2020] [Indexed: 12/26/2022] Open
Abstract
Alterations in the transcriptional factor c-MYC could be involved in the anti-EGFR resistance in metastatic colorectal cancer (mCRC). The c-MYC expression was evaluated in 121 RAS and BRAF wild-type mCRC before treatment with anti-EGFR+Folfiri therapy and in 33 subsequent metastases collected during target therapy (TT) or in TT resistance phase. We analyzed the expression and the functional role of some c-MYC linked miRNAs (miR-31-3p, miR-143 and miR-145) in our patient group and in two CRC cell lines, also performing a c-MYC target PCR array. Patients with higher c-MYC expression (HME) showed a significant lower PFS and OS when compared to those with low c-MYC expression (LME). HME pattern was significantly more frequent in the metastases after TT and significantly associated to anti-EGFR molecular resistance alterations. We also found a significant correlation between the expression of the above-mentioned c-MYC linked miRNAs, c-MYC level and anti-EGFR resistance. Moreover, expression gene profiling pointed out the pivotal role of c-MYC in CRC-related cell-cycle, apoptosis, signal transduction and cell-growth pathways. c-MYC expression might distinguish patients with a lower PFS and OS in anti-EGFR treated mCRC. The individuation of some miRNAs involved in the c-MYC pathway regulation and the downstream c-MYC effector genes could provide a new possible target to overcome the anti-EGFR resistance in mCRC.
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22
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Kurimchak AM, Herrera-Montávez C, Brown J, Johnson KJ, Sodi V, Srivastava N, Kumar V, Deihimi S, O'Brien S, Peri S, Mantia-Smaldone GM, Jain A, Winters RM, Cai KQ, Chernoff J, Connolly DC, Duncan JS. Functional proteomics interrogation of the kinome identifies MRCKA as a therapeutic target in high-grade serous ovarian carcinoma. Sci Signal 2020; 13:13/619/eaax8238. [PMID: 32071169 DOI: 10.1126/scisignal.aax8238] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
High-grade serous ovarian carcinoma (HGSOC) is the most lethal gynecological cancer with few effective, targeted therapies. HGSOC tumors exhibit genomic instability with frequent alterations in the protein kinome; however, only a small fraction of the kinome has been therapeutically targeted in HGSOC. Using multiplexed inhibitor beads and mass spectrometry, we mapped the kinome landscape of HGSOC tumors from patients and patient-derived xenograft models. The data revealed a prevalent signature consisting of established HGSOC driver kinases, as well as several kinases previously unexplored in HGSOC. Loss-of-function analysis of these kinases in HGSOC cells indicated MRCKA (also known as CDC42BPA) as a putative therapeutic target. Characterization of the effects of MRCKA knockdown in established HGSOC cell lines demonstrated that MRCKA was integral to signaling that regulated the cell cycle checkpoint, focal adhesion, and actin remodeling, as well as cell migration, proliferation, and survival. Moreover, inhibition of MRCKA using the small-molecule BDP9066 decreased cell proliferation and spheroid formation and induced apoptosis in HGSOC cells, suggesting that MRCKA may be a promising therapeutic target for the treatment of HGSOC.
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Affiliation(s)
- Alison M Kurimchak
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | | | - Jennifer Brown
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Katherine J Johnson
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.,Thermo Fisher Scientific, 168 Third Ave., Waltham, MA 02451, USA
| | - Valerie Sodi
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Nishi Srivastava
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Vikas Kumar
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Safoora Deihimi
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Shane O'Brien
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Suraj Peri
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, PA. 19111, USA
| | - Gina M Mantia-Smaldone
- Division of Gynecologic Oncology, Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Angela Jain
- Division of Gynecologic Oncology, Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Ryan M Winters
- Biosample Repository Facility, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Kathy Q Cai
- Histopathology Facility, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jonathan Chernoff
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Denise C Connolly
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - James S Duncan
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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23
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Sun X, Gao H, Yang Y, He M, Wu Y, Song Y, Tong Y, Rao Y. PROTACs: great opportunities for academia and industry. Signal Transduct Target Ther 2019; 4:64. [PMID: 31885879 PMCID: PMC6927964 DOI: 10.1038/s41392-019-0101-6] [Citation(s) in RCA: 370] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/17/2019] [Accepted: 11/21/2019] [Indexed: 02/07/2023] Open
Abstract
Although many kinds of therapies are applied in the clinic, drug-resistance is a major and unavoidable problem. Another disturbing statistic is the limited number of drug targets, which are presently only 20-25% of all protein targets that are currently being studied. Moreover, the focus of current explorations of targets are their enzymatic functions, which ignores the functions from their scaffold moiety. As a promising and appealing technology, PROteolysis TArgeting Chimeras (PROTACs) have attracted great attention both from academia and industry for finding available approaches to solve the above problems. PROTACs regulate protein function by degrading target proteins instead of inhibiting them, providing more sensitivity to drug-resistant targets and a greater chance to affect the nonenzymatic functions. PROTACs have been proven to show better selectivity compared to classic inhibitors. PROTACs can be described as a chemical knockdown approach with rapidity and reversibility, which presents new and different biology compared to other gene editing tools by avoiding misinterpretations that arise from potential genetic compensation and/or spontaneous mutations. PRTOACs have been widely explored throughout the world and have outperformed not only in cancer diseases, but also in immune disorders, viral infections and neurodegenerative diseases. Although PROTACs present a very promising and powerful approach for crossing the hurdles of present drug discovery and tool development in biology, more efforts are needed to gain to get deeper insight into the efficacy and safety of PROTACs in the clinic. More target binders and more E3 ligases applicable for developing PROTACs are waiting for exploration.
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Affiliation(s)
- Xiuyun Sun
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Hongying Gao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Yiqing Yang
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Ming He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yue Wu
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yugang Song
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yan Tong
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yu Rao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001 China
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24
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Kurimchak AM, Shelton C, Herrera-Montávez C, Duncan KE, Chernoff J, Duncan JS. Intrinsic Resistance to MEK Inhibition through BET Protein-Mediated Kinome Reprogramming in NF1-Deficient Ovarian Cancer. Mol Cancer Res 2019; 17:1721-1734. [PMID: 31043489 DOI: 10.1158/1541-7786.mcr-18-1332] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/14/2019] [Accepted: 04/29/2019] [Indexed: 11/16/2022]
Abstract
Mutation or deletion of Neurofibromin 1 (NF1), an inhibitor of RAS signaling, frequently occurs in epithelial ovarian cancer (EOC), supporting therapies that target downstream RAS effectors, such as the RAF-MEK-ERK pathway. However, no comprehensive studies have been carried out testing the efficacy of MEK inhibition in NF1-deficient EOC. Here, we performed a detailed characterization of MEK inhibition in NF1-deficient EOC cell lines using kinome profiling and RNA sequencing. Our studies showed MEK inhibitors (MEKi) were ineffective at providing durable growth inhibition in NF1-deficient cells due to kinome reprogramming. MEKi-mediated destabilization of FOSL1 resulted in induced expression of receptor tyrosine kinases (RTK) and their downstream RAF and PI3K signaling, thus overcoming MEKi therapy. MEKi synthetic enhancement screens identified BRD2 and BRD4 as integral mediators of the MEKi-induced RTK signatures. Inhibition of bromo and extra terminal (BET) proteins using BET bromodomain inhibitors blocked MEKi-induced RTK reprogramming, indicating that BRD2 and BRD4 represent promising therapeutic targets in combination with MEKi to block resistance due to kinome reprogramming in NF1-deficient EOC. IMPLICATIONS: Our findings suggest MEK inhibitors will likely not be effective as single-agent therapies in NF1-deficient EOC due to kinome reprogramming. Cotargeting BET proteins in combination with MEKis to block reprogramming at the transcriptional level may provide an epigenetic strategy to overcome MEKi resistance in NF1-deficient EOC.
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Affiliation(s)
- Alison M Kurimchak
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Claude Shelton
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | - Kelly E Duncan
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jonathan Chernoff
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - James S Duncan
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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25
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Roy SM, Minasov G, Arancio O, Chico LW, Van Eldik LJ, Anderson WF, Pelletier JC, Watterson DM. A Selective and Brain Penetrant p38αMAPK Inhibitor Candidate for Neurologic and Neuropsychiatric Disorders That Attenuates Neuroinflammation and Cognitive Dysfunction. J Med Chem 2019; 62:5298-5311. [PMID: 30978288 PMCID: PMC6580366 DOI: 10.1021/acs.jmedchem.9b00058] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The p38αMAPK
is a serine/threonine protein kinase and a key
node in the intracellular signaling networks that transduce and amplify
stress signals into physiological changes. A preponderance of preclinical
data and clinical observations established p38αMAPK as a brain
drug discovery target involved in neuroinflammatory responses and
synaptic dysfunction in multiple degenerative and neuropsychiatric
brain disorders. We summarize the discovery of highly selective, brain-penetrant,
small molecule p38αMAPK inhibitors that are efficacious in diverse
animal models of neurologic disorders. A crystallography and pharmacoinformatic
approach to fragment expansion enabled the discovery of an efficacious
hit. The addition of secondary pharmacology screens to refinement
delivered lead compounds with improved selectivity, appropriate pharmacodynamics,
and efficacy. Safety considerations and additional secondary pharmacology
screens drove optimization that delivered the drug candidate MW01-18-150SRM
(MW150), currently in early stage clinical trials.
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Affiliation(s)
- Saktimayee M Roy
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | - George Minasov
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | - Ottavio Arancio
- Columbia University , New York , New York 10032 , United States
| | - Laura W Chico
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | | | - Wayne F Anderson
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | - Jeffrey C Pelletier
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
| | - D Martin Watterson
- Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States
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26
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Xi M, Chen Y, Yang H, Xu H, Du K, Wu C, Xu Y, Deng L, Luo X, Yu L, Wu Y, Gao X, Cai T, Chen B, Shen R, Sun H. Small molecule PROTACs in targeted therapy: An emerging strategy to induce protein degradation. Eur J Med Chem 2019; 174:159-180. [PMID: 31035238 DOI: 10.1016/j.ejmech.2019.04.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/13/2019] [Accepted: 04/13/2019] [Indexed: 01/01/2023]
Abstract
Inhibitors and nucleic acid based techniques were two main approaches to interfere with protein signaling and respective cascade in the past. Until recently, a new class of small molecules named proteolysis-targeting chimeras (PROTACs) have emerged. Each contains a target warhead, a linker and an E3 ligand. These bifunctional molecules recruit E3 ligases and target specific proteins for degradation via the ubiquitin (Ub) proteasome system (UPS). The degradation provides several advantages over inhibition in potency, selectivity and drug resistance. Thus, a variety of small molecule PROTACs have been discovered so far. In this review, we summarize the biological mechanism, advantages and recent progress of PROTACs, trying to offer an outlook in development of drugs targeting degradation in future.
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Affiliation(s)
- Meiyang Xi
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Yi Chen
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Hongyu Yang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China
| | - Huiting Xu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Kui Du
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Chunlei Wu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Yanfei Xu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Liping Deng
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Xiang Luo
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Lemao Yu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Yonghua Wu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Xiaozhong Gao
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Tao Cai
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Bin Chen
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Runpu Shen
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China.
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China.
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27
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Lima ZS, Ghadamzadeh M, Arashloo FT, Amjad G, Ebadi MR, Younesi L. Recent advances of therapeutic targets based on the molecular signature in breast cancer: genetic mutations and implications for current treatment paradigms. J Hematol Oncol 2019; 12:38. [PMID: 30975222 PMCID: PMC6460547 DOI: 10.1186/s13045-019-0725-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/27/2019] [Indexed: 02/07/2023] Open
Abstract
Breast cancer is the most common malignancy in women all over the world. Genetic background of women contributes to her risk of having breast cancer. Certain inherited DNA mutations can dramatically increase the risk of developing certain cancers and are responsible for many of the cancers that run in some families. Regarding the widespread multigene panels, whole exome sequencing is capable of providing the evaluation of genetic function mutations for development novel strategy in clinical trials. Targeting the mutant proteins involved in breast cancer can be an effective therapeutic approach for developing novel drugs. This systematic review discusses gene mutations linked to breast cancer, focusing on signaling pathways that are being targeted with investigational therapeutic strategies, where clinical trials could be potentially initiated in the future are being highlighted.
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Affiliation(s)
- Zeinab Safarpour Lima
- Shahid Akbar Abadi Clinical Research Development Unit (ShCRDU), Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Mostafa Ghadamzadeh
- Departement of Radiology, Hasheminejad Kidney Centre (HKC), Iran University of Medical Sciences, Tehran, Iran
| | | | - Ghazaleh Amjad
- Shahid Akbar Abadi Clinical Research Development Unit (ShCRDU), Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Mohammad Reza Ebadi
- Shohadaye Haft-e-tir Hospital, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Ladan Younesi
- Shahid Akbar Abadi Clinical Research Development Unit (ShCRDU), Iran University of Medical Sciences (IUMS), Tehran, Iran
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28
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Noel BM, Ouellette SB, Marholz L, Dickey D, Navis C, Yang TY, Nguyen V, Parker SJ, Bernlohr D, Sachs Z, Parker LL. Multiomic Profiling of Tyrosine Kinase Inhibitor-Resistant K562 Cells Suggests Metabolic Reprogramming To Promote Cell Survival. J Proteome Res 2019; 18:1842-1856. [PMID: 30730747 DOI: 10.1021/acs.jproteome.9b00028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Resistance to chemotherapy can occur through a wide variety of mechanisms. Resistance to tyrosine kinase inhibitors (TKIs) often arises from kinase mutations-however, "off-target" resistance occurs but is poorly understood. Previously, we established cell line resistance models for three TKIs used in chronic myeloid leukemia treatment, and found that resistance was not attributed entirely to failure of kinase inhibition. Here, we performed global, integrated proteomic and transcriptomic profiling of these cell lines to describe mechanisms of resistance at the protein and gene expression level. We used whole transcriptome sequencing and SWATH-based data-independent acquisition mass spectrometry (DIA-MS), which does not require isotopic labels and provides quantitative measurements of proteins in a comprehensive, unbiased fashion. The proteomic and transcriptional data were correlated to generate an integrated understanding of the gene expression and protein alterations associated with TKI resistance. We defined mechanisms of resistance and two novel markers, CA1 and alpha-synuclein, that were common to all TKIs tested. Resistance to all of the TKIs was associated with oxidative stress responses, hypoxia signatures, and apparent metabolic reprogramming of the cells. Metabolite profiling and glucose-dependence experiments showed that resistant cells had routed their metabolism through glycolysis (particularly through the pentose phosphate pathway) and exhibited disruptions in mitochondrial metabolism. These experiments are the first to report a global, integrated proteomic, transcriptomic, and metabolic analysis of TKI resistance. These data suggest that although the mechanisms are complex, targeting metabolic pathways along with TKI treatment may overcome pan-TKI resistance.
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Affiliation(s)
- Brett M Noel
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States.,Department of Medicinal Chemistry and Molecular Pharmacology , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Steven B Ouellette
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Laura Marholz
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Deborah Dickey
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Connor Navis
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Tzu-Yi Yang
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Vinh Nguyen
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Sarah J Parker
- Smidt Heart Institute , Cedars Sinai , Los Angeles , California 90048 , United States
| | - David Bernlohr
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Zohar Sachs
- Department of Medicine , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Laurie L Parker
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
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29
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Wang X, Zhang M, Ping F, Liu H, Sun J, Wang Y, Shen A, Ding J, Geng M. Identification and Therapeutic Intervention of Coactivated Anaplastic Lymphoma Kinase, Fibroblast Growth Factor Receptor 2, and Ephrin Type-A Receptor 5 Kinases in Hepatocellular Carcinoma. Hepatology 2019; 69:573-586. [PMID: 29356025 PMCID: PMC6586030 DOI: 10.1002/hep.29792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/17/2018] [Indexed: 12/15/2022]
Abstract
Though kinase inhibitors have been heavily investigated in the clinic to combat advanced hepatocellular carcinoma (HCC), clinical outcomes have been disappointing overall, which may be due to the absence of kinase-addicted subsets in HCC patients. Recently, strategies that simultaneously inhibit multiple kinases are increasingly appreciated in HCC treatment, yet they are challenged by the dynamic nature of the kinase networks. This study aims to identify clustered kinases that may cooperate to drive the malignant growth of HCC. We show that anaplastic lymphoma kinase, fibroblast growth factor receptor 2, and ephrin type-A receptor 5 are the essential kinases that assemble into a functional cluster to sustain the viability of HCC cells through downstream protein kinase B-dependent, extracellular signal-regulated kinase-dependent, and p38-dependent signaling pathways. Their coactivation is associated with poor prognosis for overall survival in about 13% of HCC patients. Moreover, their activities are tightly regulated by heat shock protein 90 (Hsp90). Thereby Combined kinase inhibition or targeting of heat shock protein 90 led to significant therapeutic responses both in vitro and in vivo. Conclusion: Our findings established a paradigm that highlights the cooperation of anaplastic lymphoma kinase, fibroblast growth factor receptor 2, and ephrin type-A receptor 5 kinases in governing the growth advantage of HCC cells, which might offer a conceptual "combined therapeutic target" for diagnosis and subsequent intervention in a subgroup of HCC patients.
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Affiliation(s)
- Xin Wang
- Division of Anti‐tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina
| | - Minmin Zhang
- Division of Anti‐tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina
| | - Fangfang Ping
- Division of Anti‐tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | - Hongchun Liu
- Division of Anti‐tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina
| | - Jingya Sun
- Division of Anti‐tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina
| | - Yueqin Wang
- Division of Anti‐tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | - Aijun Shen
- Division of Anti‐tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina
| | - Jian Ding
- Division of Anti‐tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina
| | - Meiyu Geng
- Division of Anti‐tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina
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30
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Soomro I, Hong A, Li Z, Duncan JS, Skolnik EY. Discoidin Domain Receptor 1 (DDR1) tyrosine kinase is upregulated in PKD kidneys but does not play a role in the pathogenesis of polycystic kidney disease. PLoS One 2019; 14:e0211670. [PMID: 31260458 PMCID: PMC6602183 DOI: 10.1371/journal.pone.0211670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/03/2019] [Indexed: 01/04/2023] Open
Abstract
Tolvaptan is the only drug approved to slow cyst growth and preserve kidney function in patients with autosomal dominant polycystic kidney disease (ADPKD). However, its limited efficacy combined with significant side effects underscores the need to identify new and safe therapeutic drug targets to slow progression to end stage kidney disease. We identified Discoidin Domain Receptor 1 (DDR1) as receptor tyrosine kinase upregulated in vivo in 3 mouse models of ADPKD using a novel mass spectrometry approach to identify kinases upregulated in ADPKD. Previous studies demonstrating critical roles for DDR1 to cancer progression, its potential role in the pathogenesis of a variety of other kidney disease, along with the possibility that DDR1 could provide new insight into how extracellular matrix impacts cyst growth led us to study the role of DDR1 in ADPKD pathogenesis. However, genetic deletion of DDR1 using CRISPR/Cas9 failed to slow cyst growth or preserve kidney function in both a rapid and slow mouse model of ADPKD demonstrating that DDR1 does not play a role in PKD pathogenesis and is thus a not viable drug target. In spite of the negative results, our studies will be of interest to the nephrology community as it will prevent others from potentially conducting similar experiments on DDR1 and reinforces the potential of performing unbiased screens coupled with in vivo gene editing using CRISPR/Cas9 to rapidly identify and confirm new potential drug targets for ADPKD.
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Affiliation(s)
- Irfana Soomro
- Division of Nephrology, New York University Langone Medical Center, New York, New York, United States of America
| | - Aram Hong
- Departments of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, New York, United States of America
| | - Zhai Li
- Departments of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, New York, United States of America
| | - James S. Duncan
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Edward Y. Skolnik
- Division of Nephrology, New York University Langone Medical Center, New York, New York, United States of America
- Departments of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, New York, United States of America
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute for Biomolecular Medicine, New York University Langone Medical Center, New York, New York, United States of America
- * E-mail:
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31
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An S, Fu L. Small-molecule PROTACs: An emerging and promising approach for the development of targeted therapy drugs. EBioMedicine 2018; 36:553-562. [PMID: 30224312 PMCID: PMC6197674 DOI: 10.1016/j.ebiom.2018.09.005] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 08/27/2018] [Accepted: 09/05/2018] [Indexed: 12/29/2022] Open
Abstract
There are several challenges towards the development and clinical use of small molecule inhibitors, which are currently the main type of targeted therapies towards intracellular proteins. PROteolysis-TArgeting Chimeras (PROTACs) exploit the intracellular ubiquitin-proteasome system to selectively degrade target proteins. Recently, small-molecule PROTACs with high potency have been frequently reported. In this review, we summarize the emerging characteristics of small-molecule PROTACs, such as inducing a rapid, profound and sustained degradation, inducing a robust inhibition of downstream signals, displaying enhanced target selectivity, and overcoming resistance to small molecule inhibitors. In tumor xenografts, small-molecule PROTACs can significantly attenuate tumor progression. In addition, we also introduce recent developments of the PROTAC technology such as homo-PROTACs. The outstanding advantages over traditional small-molecule drugs and the promising preclinical data suggest that small-molecule PROTAC technology has the potential to greatly promote the development of targeted therapy drugs.
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Affiliation(s)
- Sainan An
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Liwu Fu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China.
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32
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33
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Naser R, Aldehaiman A, Díaz-Galicia E, Arold ST. Endogenous Control Mechanisms of FAK and PYK2 and Their Relevance to Cancer Development. Cancers (Basel) 2018; 10:E196. [PMID: 29891810 PMCID: PMC6025627 DOI: 10.3390/cancers10060196] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 05/31/2018] [Accepted: 06/06/2018] [Indexed: 02/07/2023] Open
Abstract
Focal adhesion kinase (FAK) and its close paralogue, proline-rich tyrosine kinase 2 (PYK2), are key regulators of aggressive spreading and metastasis of cancer cells. While targeted small-molecule inhibitors of FAK and PYK2 have been found to have promising antitumor activity, their clinical long-term efficacy may be undermined by the strong capacity of cancer cells to evade anti-kinase drugs. In healthy cells, the expression and/or function of FAK and PYK2 is tightly controlled via modulation of gene expression, competing alternatively spliced forms, non-coding RNAs, and proteins that directly or indirectly affect kinase activation or protein stability. The molecular factors involved in this control are frequently deregulated in cancer cells. Here, we review the endogenous mechanisms controlling FAK and PYK2, and with particular focus on how these mechanisms could inspire or improve anticancer therapies.
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Affiliation(s)
- Rayan Naser
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.
| | - Abdullah Aldehaiman
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.
| | - Escarlet Díaz-Galicia
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.
| | - Stefan T Arold
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.
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Kleczko EK, Heasley LE. Mechanisms of rapid cancer cell reprogramming initiated by targeted receptor tyrosine kinase inhibitors and inherent therapeutic vulnerabilities. Mol Cancer 2018; 17:60. [PMID: 29458371 PMCID: PMC5817864 DOI: 10.1186/s12943-018-0816-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/13/2018] [Indexed: 01/06/2023] Open
Abstract
Receptor tyrosine kinase (RTK) pathways serve as frequent oncogene drivers in solid cancers and small molecule and antibody-based inhibitors have been developed as targeted therapeutics for many of these oncogenic RTKs. In general, these drugs, when delivered as single agents in a manner consistent with the principles of precision medicine, induce tumor shrinkage but rarely complete tumor elimination. Moreover, acquired resistance of treated tumors is nearly invariant such that monotherapy strategies with targeted RTK drugs fail to provide long-term control or cures. The mechanisms mediating acquired resistance in tumors at progression treated with RTK inhibitors are relatively well defined compared to the molecular and cellular understanding of the cancer cells that persist early on therapy. We and others propose that these persisting cancer cells, termed "residual disease", provide the reservoir from which acquired resistance eventually emerges. Herein, we will review the literature that describes rapid reprogramming induced upon inhibition of oncogenic RTKs in cancer cells as a mechanism by which cancer cells persist to yield residual disease and consider strategies for disrupting these intrinsic responses for future therapeutic gain.
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Affiliation(s)
- Emily K. Kleczko
- Division of Renal Diseases and Hypertension, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Lynn E. Heasley
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
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Wiegmans AP, Miranda M, Wen SW, Al-Ejeh F, Möller A. RAD51 inhibition in triple negative breast cancer cells is challenged by compensatory survival signaling and requires rational combination therapy. Oncotarget 2018; 7:60087-60100. [PMID: 27507046 PMCID: PMC5312370 DOI: 10.18632/oncotarget.11065] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 07/18/2016] [Indexed: 02/07/2023] Open
Abstract
The molecular rationale to induce synthetic lethality, by targeting defective homologous recombination repair in triple negative breast cancer (TNBC), has proven to have several shortcomings. Not meeting the expected minimal outcomes in clinical trials has highlighted common clinical resistance mechanisms including; increased expression of the target gene PARP1, increased expression or reversion mutation of BRCA1, or up-regulation of the compensatory homologous recombination protein RAD51. Indeed, RAD51 has been demonstrated to be an alternative synthetic lethal target in BRCA1-mutated cancers. To overcome selective pressure on DNA repair pathways, we examined new potential targets within TNBC that demonstrate synthetic lethality in association with RAD51 depletion. We confirmed complementary targets of PARP1/2 and DNA-PK as well as a new synthetic lethality combination with p38. p38 is considered a relevant target in breast cancer, as it has been implicated in resistance to chemotherapy, including tamoxifen. We show that the combination of targeting RAD51 and p38 inhibits cell proliferation both in vitro and in vivo, which was further enhanced by targeting of PARP1. Analysis of the molecular mechanisms revealed that depletion of RAD51 increased ERK1/2 and p38 signaling. Our results highlight a potential compensatory mechanism via p38 that limits DNA targeted therapy.
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Affiliation(s)
- Adrian P Wiegmans
- Tumor Microenvironment Laboratory, QIMR Berghofer, Herston Rd, Herston QLD 4006, Australia
| | - Mariska Miranda
- Personalized Medicine Laboratory, QIMR Berghofer, Herston Rd, Herston QLD 4006, Australia
| | - Shu Wen Wen
- Tumor Microenvironment Laboratory, QIMR Berghofer, Herston Rd, Herston QLD 4006, Australia
| | - Fares Al-Ejeh
- Personalized Medicine Laboratory, QIMR Berghofer, Herston Rd, Herston QLD 4006, Australia
| | - Andreas Möller
- Tumor Microenvironment Laboratory, QIMR Berghofer, Herston Rd, Herston QLD 4006, Australia.,School of Medicine, University of Queensland, Brisbane, QLD 4072, Australia
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Burslem GM, Smith BE, Lai AC, Jaime-Figueroa S, McQuaid DC, Bondeson DP, Toure M, Dong H, Qian Y, Wang J, Crew AP, Hines J, Crews CM. The Advantages of Targeted Protein Degradation Over Inhibition: An RTK Case Study. Cell Chem Biol 2018; 25:67-77.e3. [PMID: 29129716 PMCID: PMC5831399 DOI: 10.1016/j.chembiol.2017.09.009] [Citation(s) in RCA: 412] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/07/2017] [Accepted: 09/27/2017] [Indexed: 01/05/2023]
Abstract
Proteolysis targeting chimera (PROTAC) technology has emerged over the last two decades as a powerful tool for targeted degradation of endogenous proteins. Herein we describe the development of PROTACs for receptor tyrosine kinases, a protein family yet to be targeted for induced protein degradation. The use of VHL-recruiting PROTACs against this protein family reveals several advantages of degradation over inhibition alone: direct comparisons of fully functional, target-degrading PROTACs with target-inhibiting variants that contain an inactivated E3 ligase-recruiting ligand show that degradation leads to more potent inhibition of cell proliferation and a more durable and sustained downstream signaling response, and thus addresses the kinome rewiring challenge seen with many receptor tyrosine kinase inhibitors. Combined, these findings demonstrate the ability to target receptor tyrosine kinases for degradation using the PROTAC technology and outline the advantages of this degradation-based approach.
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Affiliation(s)
- George M Burslem
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, USA
| | - Blake E Smith
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, USA
| | - Ashton C Lai
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, USA
| | - Saul Jaime-Figueroa
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, USA
| | - Daniel C McQuaid
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, USA
| | - Daniel P Bondeson
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, USA
| | - Momar Toure
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, USA
| | - Hanqing Dong
- Arvinas, LLC, 5 Science Park, New Haven, CT, USA
| | - Yimin Qian
- Arvinas, LLC, 5 Science Park, New Haven, CT, USA
| | - Jing Wang
- Arvinas, LLC, 5 Science Park, New Haven, CT, USA
| | | | - John Hines
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, USA
| | - Craig M Crews
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, USA; Departments of Chemistry and Pharmacology, Yale University, New Haven, CT, USA.
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Comprehensive Analysis of Cancer-Proteogenome to Identify Biomarkers for the Early Diagnosis and Prognosis of Cancer. Proteomes 2017; 5:proteomes5040028. [PMID: 29068423 PMCID: PMC5748563 DOI: 10.3390/proteomes5040028] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 02/07/2023] Open
Abstract
During the past century, our understanding of cancer diagnosis and treatment has been based on a monogenic approach, and as a consequence our knowledge of the clinical genetic underpinnings of cancer is incomplete. Since the completion of the human genome in 2003, it has steered us into therapeutic target discovery, enabling us to mine the genome using cutting edge proteogenomics tools. A number of novel and promising cancer targets have emerged from the genome project for diagnostics, therapeutics, and prognostic markers, which are being used to monitor response to cancer treatment. The heterogeneous nature of cancer has hindered progress in understanding the underlying mechanisms that lead to abnormal cellular growth. Since, the start of The Cancer Genome Atlas (TCGA), and the International Genome consortium projects, there has been tremendous progress in genome sequencing and immense numbers of cancer genomes have been completed, and this approach has transformed our understanding of the diagnosis and treatment of different types of cancers. By employing Genomics and proteomics technologies, an immense amount of genomic data is being generated on clinical tumors, which has transformed the cancer landscape and has the potential to transform cancer diagnosis and prognosis. A complete molecular view of the cancer landscape is necessary for understanding the underlying mechanisms of cancer initiation to improve diagnosis and prognosis, which ultimately will lead to personalized treatment. Interestingly, cancer proteome analysis has also allowed us to identify biomarkers to monitor drug and radiation resistance in patients undergoing cancer treatment. Further, TCGA-funded studies have allowed for the genomic and transcriptomic characterization of targeted cancers, this analysis aiding the development of targeted therapies for highly lethal malignancy. High-throughput technologies, such as complete proteome, epigenome, protein-protein interaction, and pharmacogenomics data, are indispensable to glean into the cancer genome and proteome and these approaches have generated multidimensional universal studies of genes and proteins (OMICS) data which has the potential to facilitate precision medicine. However, due to slow progress in computational technologies, the translation of big omics data into their clinical aspects have been slow. In this review, attempts have been made to describe the role of high-throughput genomic and proteomic technologies in identifying a panel of biomarkers which could be used for the early diagnosis and prognosis of cancer.
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Stuhlmiller TJ, Zawistowski JS, Chen X, Sciaky N, Angus SP, Hicks ST, Parry TL, Huang W, Beak JY, Willis MS, Johnson GL, Jensen BC. Kinome and Transcriptome Profiling Reveal Broad and Distinct Activities of Erlotinib, Sunitinib, and Sorafenib in the Mouse Heart and Suggest Cardiotoxicity From Combined Signal Transducer and Activator of Transcription and Epidermal Growth Factor Receptor Inhibition. J Am Heart Assoc 2017; 6:e006635. [PMID: 29051215 PMCID: PMC5721866 DOI: 10.1161/jaha.117.006635] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/11/2017] [Indexed: 01/22/2023]
Abstract
BACKGROUND Most novel cancer therapeutics target kinases that are essential to tumor survival. Some of these kinase inhibitors are associated with cardiotoxicity, whereas others appear to be cardiosafe. The basis for this distinction is unclear, as are the molecular effects of kinase inhibitors in the heart. METHODS AND RESULTS We administered clinically relevant doses of sorafenib, sunitinib (cardiotoxic multitargeted kinase inhibitors), or erlotinib (a cardiosafe epidermal growth factor receptor inhibitor) to mice daily for 2 weeks. We then compared the effects of these 3 kinase inhibitors on the cardiac transcriptome using RNAseq and the cardiac kinome using multiplexed inhibitor beads coupled with mass spectrometry. We found unexpectedly broad molecular effects of all 3 kinase inhibitors, suggesting that target kinase selectivity does not define either the molecular response or the potential for cardiotoxicity. Using in vivo drug administration and primary cardiomyocyte culture, we also show that the cardiosafety of erlotinib treatment may result from upregulation of the cardioprotective signal transducer and activator of transcription 3 pathway, as co-treatment with erlotinib and a signal transducer and activator of transcription inhibitor decreases cardiac contractile function and cardiomyocyte fatty acid oxidation. CONCLUSIONS Collectively our findings indicate that preclinical kinome and transcriptome profiling may predict the cardiotoxicity of novel kinase inhibitors, and suggest caution for the proposed therapeutic strategy of combined signal transducer and activator of transcription/epidermal growth factor receptor inhibition for cancer treatment.
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Affiliation(s)
- Timothy J Stuhlmiller
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Jon S Zawistowski
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Xin Chen
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Noah Sciaky
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Steven P Angus
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Sean T Hicks
- University of North Carolina McAllister Heart Institute, Chapel Hill, NC
| | - Traci L Parry
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC
- University of North Carolina McAllister Heart Institute, Chapel Hill, NC
| | - Wei Huang
- University of North Carolina McAllister Heart Institute, Chapel Hill, NC
| | - Ju Youn Beak
- University of North Carolina McAllister Heart Institute, Chapel Hill, NC
| | - Monte S Willis
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC
- University of North Carolina McAllister Heart Institute, Chapel Hill, NC
| | - Gary L Johnson
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Brian C Jensen
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC
- Division of Cardiology, University of North Carolina School of Medicine, Chapel Hill, NC
- University of North Carolina McAllister Heart Institute, Chapel Hill, NC
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Abstract
Protein and lipid kinases are deregulated in most, if not all, cancers and are among the most valuable therapeutic targets in these diseases. Despite the introduction of dozens of effective kinase inhibitors into clinical practice, the development of drug resistance remains a major barrier to treatment because of adaption of cellular signaling pathways to bypass targeted kinases. So that the basal and adaptive responses of kinases in cancer can be better understood, new methods have emerged that allow simultaneous and unbiased measurement of the activation state of a substantial fraction of the entire kinome. Here, we discuss such kinome-profiling methodologies, emphasizing the relative strengths and weaknesses of each approach.
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Affiliation(s)
- Maria Radu
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111-2497, USA
| | - Jonathan Chernoff
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111-2497, USA
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Cann ML, McDonald IM, East MP, Johnson GL, Graves LM. Measuring Kinase Activity-A Global Challenge. J Cell Biochem 2017; 118:3595-3606. [PMID: 28464261 DOI: 10.1002/jcb.26103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 12/22/2022]
Abstract
The kinase enzymes within a cell, known collectively as the kinome, play crucial roles in many signaling pathways, including survival, motility, differentiation, stress response, and many more. Aberrant signaling through kinase pathways is often linked to cancer, among other diseases. A major area of scientific research involves understanding the relationships between kinases, their targets, and how the kinome adapts to perturbations of the cellular system. This review will discuss many of the current and developing methods for studying kinase activity, and evaluate their applications, advantages, and disadvantages. J. Cell. Biochem. 118: 3595-3606, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Marissa L Cann
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Ian M McDonald
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Michael P East
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Gary L Johnson
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Lee M Graves
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
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41
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Arend KC, Lenarcic EM, Vincent HA, Rashid N, Lazear E, McDonald IM, Gilbert TSK, East MP, Herring LE, Johnson GL, Graves LM, Moorman NJ. Kinome Profiling Identifies Druggable Targets for Novel Human Cytomegalovirus (HCMV) Antivirals. Mol Cell Proteomics 2017; 16:S263-S276. [PMID: 28237943 PMCID: PMC5393402 DOI: 10.1074/mcp.m116.065375] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/23/2017] [Indexed: 11/06/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a significant cause of disease in immune-compromised adults and immune naïve newborns. No vaccine exists to prevent HCMV infection, and current antiviral therapies have toxic side effects that limit the duration and intensity of their use. There is thus an urgent need for new strategies to treat HCMV infection. Repurposing existing drugs as antivirals is an attractive approach to limit the time and cost of new antiviral drug development. Virus-induced changes in infected cells are often driven by changes in cellular kinase activity, which led us to hypothesize that defining the complement of kinases (the kinome), whose abundance or expression is altered during infection would identify existing kinase inhibitors that could be repurposed as new antivirals. To this end, we applied a kinase capture technique, multiplexed kinase inhibitor bead-mass spectrometry (MIB-MS) kinome, to quantitatively measure perturbations in >240 cellular kinases simultaneously in cells infected with a laboratory-adapted (AD169) or clinical (TB40E) HCMV strain. MIB-MS profiling identified time-dependent increases and decreases in MIB binding of multiple kinases including cell cycle kinases, receptor tyrosine kinases, and mitotic kinases. Based on the kinome data, we tested the antiviral effects of kinase inhibitors and other compounds, several of which are in clinical use or development. Using a novel flow cytometry-based assay and a fluorescent reporter virus we identified three compounds that inhibited HCMV replication with IC50 values of <1 μm, and at doses that were not toxic to uninfected cells. The most potent inhibitor of HCMV replication was OTSSP167 (IC50 <1.2 nm), a MELK inhibitor, blocked HCMV early gene expression and viral DNA accumulation, resulting in a >3 log decrease in virus replication. These results show the utility of MIB-MS kinome profiling for identifying existing kinase inhibitors that can potentially be repurposed as novel antiviral drugs.
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Affiliation(s)
- Kyle C Arend
- From the ‡Department of Microbiology & Immunology
- ¶Lineberger Comprehensive Cancer Center
| | - Erik M Lenarcic
- From the ‡Department of Microbiology & Immunology
- ¶Lineberger Comprehensive Cancer Center
| | - Heather A Vincent
- From the ‡Department of Microbiology & Immunology
- ¶Lineberger Comprehensive Cancer Center
| | - Naim Rashid
- ¶Lineberger Comprehensive Cancer Center
- ‖Department of Biostatistics
| | - Eric Lazear
- From the ‡Department of Microbiology & Immunology
- ¶Lineberger Comprehensive Cancer Center
| | | | | | | | - Laura E Herring
- §Department of Pharmacology
- **UNC Michael Hooker Proteomics Core Facility University of North Carolina, Chapel Hill, 27599 North Carolina
| | | | - Lee M Graves
- §Department of Pharmacology
- **UNC Michael Hooker Proteomics Core Facility University of North Carolina, Chapel Hill, 27599 North Carolina
| | - Nathaniel J Moorman
- From the ‡Department of Microbiology & Immunology,
- ¶Lineberger Comprehensive Cancer Center
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Werth EG, McConnell EW, Gilbert TSK, Couso Lianez I, Perez CA, Manley CK, Graves LM, Umen JG, Hicks LM. Probing the global kinome and phosphoproteome in Chlamydomonas reinhardtii via sequential enrichment and quantitative proteomics. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:416-426. [PMID: 27671103 DOI: 10.1111/tpj.13384] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 06/06/2023]
Abstract
The identification of dynamic protein phosphorylation events is critical for understanding kinase/phosphatase-regulated signaling pathways. To date, protein phosphorylation and kinase expression have been examined independently in photosynthetic organisms. Here we present a method to study the global kinome and phosphoproteome in tandem in a model photosynthetic organism, the alga Chlamydomonas reinhardtii (Chlamydomonas), using mass spectrometry-based label-free proteomics. A dual enrichment strategy targets intact protein kinases via capture on immobilized multiplexed inhibitor beads with subsequent proteolytic digestion of unbound proteins and peptide-based phosphorylation enrichment. To increase depth of coverage, both data-dependent and data-independent (via SWATH, Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra) mass spectrometric acquisitions were performed to obtain a more than 50% increase in coverage of the enriched Chlamydomonas kinome over coverage found with no enrichment. The quantitative phosphoproteomic dataset yielded 2250 phosphopeptides and 1314 localized phosphosites with excellent reproducibility across biological replicates (90% of quantified sites with coefficient of variation below 11%). This approach enables simultaneous investigation of kinases and phosphorylation events at the global level to facilitate understanding of kinase networks and their influence in cell signaling events.
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Affiliation(s)
- Emily G Werth
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road, CB#3290, Chapel Hill, NC, 2759934, USA
| | - Evan W McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road, CB#3290, Chapel Hill, NC, 2759934, USA
| | - Thomas S Karim Gilbert
- The Department of Pharmacology, The University of North Carolina at Chapel Hill, NC 27599, USA
| | | | - Carlos A Perez
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road, CB#3290, Chapel Hill, NC, 2759934, USA
| | - Cherrel K Manley
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road, CB#3290, Chapel Hill, NC, 2759934, USA
| | - Lee M Graves
- The Department of Pharmacology, The University of North Carolina at Chapel Hill, NC 27599, USA
| | - James G Umen
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, 125 South Road, CB#3290, Chapel Hill, NC, 2759934, USA
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Predicting and Overcoming Chemotherapeutic Resistance in Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1026:59-104. [PMID: 29282680 DOI: 10.1007/978-981-10-6020-5_4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Our understanding of breast cancer and its therapeutic approach has improved greatly due to the advancement of molecular biology in recent years. Clinically, breast cancers are characterized into three basic types based on their immunohistochemical properties. They are triple-negative breast cancer, estrogen receptor (ER) and progesterone receptor (PR)-positive-HR positive breast cancer, and human epidermal growth factor receptor 2 (HER2)-positive breast cancer. Even though these subtypes have been characterized, assessment of a breast cancer's receptor status is still widely used to determine whether or not a targeted therapy could be applied. Moreover, drug resistance is common in all breast cancer types despite the different treatment modalities applied. The development of resistance to different therapeutics is not mutually exclusive. It seems that tumor could be resistant to multiple treatment strategies, such as being both chemoresistant and monoclonal antibody resistant. However, the underlying mechanisms are complicated and need further investigation. In this chapter, we aim to provide a brief review of the different types of breast cancer and their respective treatment strategies. We also review the possible mechanisms of potential drug resistance associated with each treatment type. We believe that a better understanding of the drug resistance mechanisms can lead to a more effective and efficient therapeutic success.
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44
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Abe Y, Nagano M, Tada A, Adachi J, Tomonaga T. Deep Phosphotyrosine Proteomics by Optimization of Phosphotyrosine Enrichment and MS/MS Parameters. J Proteome Res 2016; 16:1077-1086. [PMID: 28152594 DOI: 10.1021/acs.jproteome.6b00576] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphorylation is a major post-translational modification that regulates protein function, with phosphotyrosine (pY) modifications being implicated in oncogenesis. However, global profiling of pY statuses without treatment with a tyrosine phosphatase inhibitor such as pervanadate is still challenging due to the low occupancy of pY sites. In this study, we greatly improved the identification of pY sites by liquid chromatography-tandem mass spectrometry (LC-MS/MS) by optimization of both the pY-immunoprecipitation (pY-IP) protocol and the LC-MS/MS parameters. Our highly sensitive method reproducibly identified more than 1000 pY sites from 8 mg of protein lysate without the need for tyrosine phosphatase inhibitor treatment. Furthermore, >30% of the identified pY sites were not assigned in the PhosphositePlus database. We further applied our method to the comparison of pY status between PC3 cells with and without treatment using the epidermal growth factor receptor (EGFR) inhibitor Erlotinib. Under Erlotinib treatment, we observed not only a decrease in well-known modes of EGFR downstream signaling but also modulations of kinases that are not relevant to the EGFR cascade, such as PTK6 and MAPK13. Our newly developed method for pY proteomics has the potential to reveal unknown pY signaling modes and to identify novel kinase anticancer targets.
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Affiliation(s)
- Yuichi Abe
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition , Ibaraki Osaka 567-0085, Japan
| | - Maiko Nagano
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition , Ibaraki Osaka 567-0085, Japan
| | - Asa Tada
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition , Ibaraki Osaka 567-0085, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition , Ibaraki Osaka 567-0085, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition , Ibaraki Osaka 567-0085, Japan
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Kathiriya JJ, Pathak RR, Bezginov A, Xue B, Uversky VN, Tillier ERM, Davé V. Structural pliability adjacent to the kinase domain highlights contribution of FAK1 IDRs to cytoskeletal remodeling. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:43-54. [PMID: 27718363 DOI: 10.1016/j.bbapap.2016.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/27/2016] [Accepted: 10/03/2016] [Indexed: 12/24/2022]
Abstract
Therapeutic protein kinase inhibitors are designed on the basis of kinase structures. Here, we define intrinsically disordered regions (IDRs) in structurally hybrid kinases. We reveal that 65% of kinases have an IDR adjacent to their kinase domain (KD). These IDRs are evolutionarily more conserved than IDRs distant to KDs. Strikingly, 36 kinases have adjacent IDRs extending into their KDs, defining a unique structural and functional subset of the kinome. Functional network analysis of this subset of the kinome uncovered FAK1 as topologically the most connected hub kinase. We identify that KD-flanking IDR of FAK1 is more conserved and undergoes more post-translational modifications than other IDRs. It preferentially interacts with proteins regulating scaffolding and kinase activity, which contribute to cytoskeletal remodeling. In summary, spatially and evolutionarily conserved IDRs in kinases may influence their functions, which can be exploited for targeted therapies in diseases including those that involve aberrant cytoskeletal remodeling.
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Affiliation(s)
- Jaymin J Kathiriya
- Morsani College of Medicine, Department of Pathology and Cell Biology, University of South Florida, Tampa, FL 33612, United States
| | - Ravi Ramesh Pathak
- Morsani College of Medicine, Department of Pathology and Cell Biology, University of South Florida, Tampa, FL 33612, United States
| | - Alexandr Bezginov
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; USF Health Byrd Alzheimer's Research Institute, University of South Florida, Tampa, FL 33612, United States; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | | | - Vrushank Davé
- Morsani College of Medicine, Department of Pathology and Cell Biology, University of South Florida, Tampa, FL 33612, United States; Department of Cancer Biology and Evolution, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, United States.
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Yuan LL, Wauson E, Duric V. Kinase-mediated signaling cascades in mood disorders and antidepressant treatment. J Neurogenet 2016; 30:178-184. [PMID: 27785950 PMCID: PMC5590647 DOI: 10.1080/01677063.2016.1245303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/29/2016] [Accepted: 10/03/2016] [Indexed: 10/20/2022]
Abstract
Kinase-mediated signaling cascades regulate a number of different molecular mechanisms involved in cellular homeostasis, and are viewed as one of the most common intracellular processes that are robustly dysregulated in the pathophysiology of mood disorders such as depression. Newly emerged, rapid acting antidepressants are able to achieve therapeutic improvement, possibly in part, through stimulating activity of kinase-dependent signaling pathways. Thus, advancements in our understanding of how kinases may contribute to development and treatment of depression seem crucial. However, current investigations are limited to a single or small number of kinases and are unable to detect novel kinases. Here, we review fast developing kinome profiling approaches that allow identification of multiple kinases and kinase network connections simultaneously, analyze technical limitation and challenges, and discuss their future applications to mood disorders and antidepressant treatment.
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Affiliation(s)
- Li-Lian Yuan
- Department of Physiology and Pharmacology, Des Moines University, Des Moines, IA 50312, USA
| | - Eric Wauson
- Department of Physiology and Pharmacology, Des Moines University, Des Moines, IA 50312, USA
| | - Vanja Duric
- Department of Physiology and Pharmacology, Des Moines University, Des Moines, IA 50312, USA
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Lemmon MA, Freed DM, Schlessinger J, Kiyatkin A. The Dark Side of Cell Signaling: Positive Roles for Negative Regulators. Cell 2016; 164:1172-1184. [PMID: 26967284 DOI: 10.1016/j.cell.2016.02.047] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Indexed: 12/12/2022]
Abstract
Cell signaling is dominated by analyzing positive responses to stimuli. Signal activation is balanced by negative regulators that are generally considered to terminate signaling. Rather than exerting only negative effects, however, many such regulators play important roles in enhancing cell-signaling control. Considering responses downstream of selected cell-surface receptors, we discuss how receptor internalization affects signaling specificity and how rapid kinase/phosphatase and GTP/GDP cycles increase responsiveness and allow kinetic proofreading in receptor signaling. We highlight the blurring of distinctions between positive and negative signals, recasting signal termination as the response to a switch-like transition into a new cellular state.
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Affiliation(s)
- Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, West Haven, CT 06516, USA.
| | - Daniel M Freed
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, West Haven, CT 06516, USA
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, West Haven, CT 06516, USA
| | - Anatoly Kiyatkin
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, West Haven, CT 06516, USA
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48
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Day EK, Sosale NG, Lazzara MJ. Cell signaling regulation by protein phosphorylation: a multivariate, heterogeneous, and context-dependent process. Curr Opin Biotechnol 2016; 40:185-192. [PMID: 27393828 PMCID: PMC4975652 DOI: 10.1016/j.copbio.2016.06.005] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/21/2016] [Accepted: 06/21/2016] [Indexed: 02/08/2023]
Abstract
Proper spatiotemporal regulation of protein phosphorylation in cells and tissues is required for normal development and homeostasis, but aberrant protein phosphorylation regulation leads to various diseases. The study of signaling regulation by protein phosphorylation is complicated in part by the sheer scope of the kinome and phosphoproteome, dependence of signaling protein functionality on cellular localization, and the complex multivariate relationships that exist between protein phosphorylation dynamics and the cellular phenotypes they control. Additional complexities arise from the ability of microenvironmental factors to influence phosphorylation-dependent signaling and from the tendency for some signaling processes to occur heterogeneously among cells. These considerations should be taken into account when measuring cell signaling regulation by protein phosphorylation.
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Affiliation(s)
- Evan K Day
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Nisha G Sosale
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Matthew J Lazzara
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, United States; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States.
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49
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Ferguson MJ, Rhodes SD, Jiang L, Li X, Yuan J, Yang X, Zhang S, Vakili ST, Territo P, Hutchins G, Yang FC, Ingram DA, Clapp DW, Chen S. Preclinical Evidence for the Use of Sunitinib Malate in the Treatment of Plexiform Neurofibromas. Pediatr Blood Cancer 2016; 63:206-13. [PMID: 26375012 PMCID: PMC4862309 DOI: 10.1002/pbc.25763] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/31/2015] [Indexed: 01/16/2023]
Abstract
PURPOSE Plexiform neurofibromas (pNF) are pathognomonic nerve and soft tissue tumors of neurofibromatosis type I (NF1), which are highly resistant to conventional chemotherapy and associated with significant morbidity/mortality. Disruption of aberrant SCF/c-Kit signaling emanating from the pNF microenvironment induced the first ever objective therapeutic responses in a recent phase 2 trial. Sunitinib malate is a potent, highly selective RTK inhibitor with activity against c-Kit, PDGFR, and VEGFR, which have also been implicated in the pathogenesis of these lesions. Here, we evaluate the efficacy of sunitinib malate in a preclinical Krox20;Nf1(flox/-) pNF murine model. EXPERIMENTAL DESIGN Proliferation, β-hexosaminidase release (degranulation), and Erk1/2 phosphorylation were assessed in sunitinib treated Nf1(+/-) mast cells and fibroblasts, respectively. Krox20;Nf1(flox/-) mice with established pNF were treated sunitinib or PBS-vehicle control for a duration of 12 weeks. pNF metabolic activity was monitored by serial [(18)F]DG-PET/CT imaging. RESULTS Sunitinib suppressed multiple in vitro gain-in-functions of Nf1(+/-) mast cells and fibroblasts and attenuated Erk1/2 phosphorylation. Sunitinib treated Krox20;Nf1(flox/-) mice exhibited significant reductions in pNF size, tumor number, and FDG uptake compared to control mice. Histopathology revealed reduced tumor cellularity and infiltrating mast cells, markedly diminished collagen deposition, and increased cellular apoptosis in sunitinib treated pNF. CONCLUSIONS Collectively, these results demonstrate the efficacy of sunitinib in reducing tumor burden in Krox20;Nf1(flox/-) mice. These preclinical findings demonstrate the utility of inhibiting multiple RTKs in pNF and provide insights into the design of future clinical trials.
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Affiliation(s)
- Michael J. Ferguson
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202,Correspondence should be addressed to: Michael J. Ferguson, M.D., M.S., Assistant Professor, Indiana University School of Medicine, Children’s Clinical Research Center, 705 Riley Hospital Drive, RI 2630, Indianapolis, IN 46202, Phone: (317) 278-3153, Fax: (317) 948-0616,
| | - Steven D. Rhodes
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202,Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Li Jiang
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202,Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Xiaohong Li
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202,Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Jin Yuan
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202,Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Xianlin Yang
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202,Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Shaobo Zhang
- Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Saeed T. Vakili
- Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Paul Territo
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Gary Hutchins
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Feng-Chun Yang
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202,Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202,Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - David A. Ingram
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202,Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202
| | - D. Wade Clapp
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202,Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202,Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Shi Chen
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202,Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202
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Roller DG, Capaldo B, Bekiranov S, Mackey AJ, Conaway MR, Petricoin EF, Gioeli D, Weber MJ. Combinatorial drug screening and molecular profiling reveal diverse mechanisms of intrinsic and adaptive resistance to BRAF inhibition in V600E BRAF mutant melanomas. Oncotarget 2016; 7:2734-53. [PMID: 26673621 PMCID: PMC4823068 DOI: 10.18632/oncotarget.6548] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/21/2015] [Indexed: 12/28/2022] Open
Abstract
Over half of BRAFV600E melanomas display intrinsic resistance to BRAF inhibitors, in part due to adaptive signaling responses. In this communication we ask whether BRAFV600E melanomas share common adaptive responses to BRAF inhibition that can provide clinically relevant targets for drug combinations. We screened a panel of 12 treatment-naïve BRAFV600E melanoma cell lines with MAP Kinase pathway inhibitors in pairwise combination with 58 signaling inhibitors, assaying for synergistic cytotoxicity. We found enormous diversity in the drug combinations that showed synergy, with no two cell lines having an identical profile. Although the 6 lines most resistant to BRAF inhibition showed synergistic benefit from combination with lapatinib, the signaling mechanisms by which this combination generated synergistic cytotoxicity differed between the cell lines. We conclude that adaptive responses to inhibition of the primary oncogenic driver (BRAFV600E) are determined not only by the primary oncogenic driver but also by diverse secondary genetic and epigenetic changes ("back-seat drivers") and hence optimal drug combinations will be variable. Because upregulation of receptor tyrosine kinases is a major source of drug resistance arising from diverse adaptive responses, we propose that inhibitors of these receptors may have substantial clinical utility in combination with inhibitors of the MAP Kinase pathway.
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Affiliation(s)
- Devin G. Roller
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, 22908 USA
| | - Brian Capaldo
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908 USA
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908 USA
| | - Aaron J. Mackey
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908 USA
| | - Mark R. Conaway
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908 USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, College of Science, George Mason University, Manassas, VA 20110, USA
| | - Daniel Gioeli
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, 22908 USA
| | - Michael J. Weber
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, 22908 USA
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