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Hou Z, Liu H. Mapping the Protein Kinome: Current Strategy and Future Direction. Cells 2023; 12:cells12060925. [PMID: 36980266 PMCID: PMC10047437 DOI: 10.3390/cells12060925] [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: 01/20/2023] [Revised: 02/23/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular kinome in the physiological environment is essential to understand biological processes, disease development, and to target therapy. Currently, a number of strategies for kinome analysis have been developed, which are based on monitoring the phosphorylation of kinases or substrates. They have enabled researchers to tackle increasingly complex biological problems and pathological processes, and have promoted the development of kinase inhibitors. Additionally, with the increasing interest in how kinases participate in biological processes at spatial scales, it has become urgent to develop tools to estimate spatial kinome activity. With multidisciplinary efforts, a growing number of novel approaches have the potential to be applied to spatial kinome analysis. In this paper, we review the widely used methods used for kinome analysis and the challenges encountered in their applications. Meanwhile, potential approaches that may be of benefit to spatial kinome study are explored.
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Affiliation(s)
- Zhanwu Hou
- Center for Mitochondrial Biology and Medicine, Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Huadong Liu
- School of Health and Life Science, University of Health and Rehabilitation Sciences, Qingdao 266071, China
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Lyon A, Tripathi R, Meeks C, He D, Wu Y, Liu J, Wang C, Chen J, Zhu H, Mukherjee S, Ganguly S, Plattner R. ABL1/2 and DDR1 Drive MEKi Resistance in NRAS-Mutant Melanomas by Stabilizing RAF/MYC/ETS1 and Promoting RAF Homodimerization. Cancers (Basel) 2023; 15:954. [PMID: 36765910 PMCID: PMC9913232 DOI: 10.3390/cancers15030954] [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: 10/11/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
Melanomas harboring NRAS mutations are a particularly aggressive and deadly subtype. If patients cannot tolerate or the melanomas are insensitive to immune checkpoint blockade, there are no effective 2nd-line treatment options. Drugs targeting the RAF/MEK/ERK pathway, which are used for BRAF-mutant melanomas, do little to increase progression-free survival (PFS). Here, using both loss-of-function and gain-of-function approaches, we show that ABL1/2 and DDR1 are critical nodes during NRAS-mutant melanoma intrinsic and acquired MEK inhibitor (MEKi) resistance. In some acquired resistance cells, ABL1/2 and DDR1 cooperate to stabilize RAF proteins, activate ERK cytoplasmic and nuclear signaling, repress p27/KIP1 expression, and drive RAF homodimerization. In contrast, other acquired resistance cells depend solely on ABL1/2 for their survival, and are sensitive to highly specific allosteric ABL1/2 inhibitors, which prevent β-catenin nuclear localization and destabilize MYC and ETS1 in an ERK-independent manner. Significantly, targeting ABL1/2 and DDR1 with an FDA-approved anti-leukemic drug, reverses intrinsic MEKi resistance, delays acquisition of acquired resistance, and doubles the survival time in a NRAS-mutant mouse model. These data indicate that repurposing FDA-approved drugs targeting ABL1/2 and DDR1 may be a novel and effective strategy for treating patients with treatment-refractory NRAS-driven melanomas.
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Affiliation(s)
- Anastasia Lyon
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Rakshamani Tripathi
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Christina Meeks
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Daheng He
- Biostatistics and Bioinformatics Shared Resource Facility, College of Medicine, Markey Cancer Center, University of Kentucky, Lexington, KY 40508, USA
| | - Yuanyuan Wu
- Biostatistics and Bioinformatics Shared Resource Facility, College of Medicine, Markey Cancer Center, University of Kentucky, Lexington, KY 40508, USA
| | - Jinpeng Liu
- Biostatistics and Bioinformatics Shared Resource Facility, College of Medicine, Markey Cancer Center, University of Kentucky, Lexington, KY 40508, USA
| | - Chi Wang
- Biostatistics and Bioinformatics Shared Resource Facility, College of Medicine, Markey Cancer Center, University of Kentucky, Lexington, KY 40508, USA
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Sujata Mukherjee
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Saptadwipa Ganguly
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Rina Plattner
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
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Zhang C, Zhou X, Huang X, Ding X, Wang Y, Zhang R. Genomic characterization of intracranial teratomas using whole genome sequencing. Front Oncol 2022; 12:1013722. [DOI: 10.3389/fonc.2022.1013722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
BackgroundIntracranial teratoma is a rare neoplasm of the central nervous system, often classified into mature and immature types and occurs mainly in children and adolescents. To date, there has been no comprehensive genomic characterization analysis of teratoma due to its rarity of the cases.MethodsForty-six patients with intracranial teratomas were collected and 22 of them underwent whole-exome sequencing, including 8 mature teratomas and 14 immature teratomas. A comprehensive analysis was performed to analyze somatic mutations, copy number variants (CNVs), mutational signatures, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway in our cohort.ResultsThe most common somatic mutated gene in intracranial teratomas was CARD11 (18%) and IRS1 (18%), followed by PSMD11, RELN, RRAS2, SMC1A, SYNE1 and ZFHX3, with mutation rates of 14% for the latter six genes. Copy number variation was dominated by amplification, among which ARAF (50%), ATP2B3 (41%), GATA1 (41%), ATP6AP1 (36%), CCND2 (36%) and ZMYM3 (36%) were the most frequently amplified genes. Copy number deletion of SETDB2 and IL2 only appeared in immature teratoma (43% and 36%, respectively), but not in mature teratoma (p = 0.051 and 0.115, respectively). Prognostic analysis showed that TP53 mutations might be associated with poor prognosis of intracranial teratomas patients.ConclusionsOur study revealed the genetic characteristics of intracranial teratoma which might be valuable for guiding future targeted therapies.
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Riegel K, Vijayarangakannan P, Kechagioglou P, Bogucka K, Rajalingam K. Recent advances in targeting protein kinases and pseudokinases in cancer biology. Front Cell Dev Biol 2022; 10:942500. [PMID: 35938171 PMCID: PMC9354965 DOI: 10.3389/fcell.2022.942500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022] Open
Abstract
Kinases still remain the most favorable members of the druggable genome, and there are an increasing number of kinase inhibitors approved by the FDA to treat a variety of cancers. Here, we summarize recent developments in targeting kinases and pseudokinases with some examples. Targeting the cell cycle machinery garnered significant clinical success, however, a large section of the kinome remains understudied. We also review recent developments in the understanding of pseudokinases and discuss approaches on how to effectively target in cancer.
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Affiliation(s)
- Kristina Riegel
- Cell Biology Unit, University Medical Center Mainz, JGU-Mainz, Mainz, Germany
| | | | - Petros Kechagioglou
- Cell Biology Unit, University Medical Center Mainz, JGU-Mainz, Mainz, Germany
| | - Katarzyna Bogucka
- Cell Biology Unit, University Medical Center Mainz, JGU-Mainz, Mainz, Germany
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center Mainz, JGU-Mainz, Mainz, Germany
- *Correspondence: Krishnaraj Rajalingam,
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