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Cabral G, Moss WJ, Brown KM. Proteomic approaches for protein kinase substrate identification in Apicomplexa. Mol Biochem Parasitol 2024; 259:111633. [PMID: 38821187 PMCID: PMC11194964 DOI: 10.1016/j.molbiopara.2024.111633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/10/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Apicomplexa is a phylum of protist parasites, notable for causing life-threatening diseases including malaria, toxoplasmosis, cryptosporidiosis, and babesiosis. Apicomplexan pathogenesis is generally a function of lytic replication, dissemination, persistence, host cell modification, and immune subversion. Decades of research have revealed essential roles for apicomplexan protein kinases in establishing infections and promoting pathogenesis. Protein kinases modify their substrates by phosphorylating serine, threonine, tyrosine, or other residues, resulting in rapid functional changes in the target protein. Post-translational modification by phosphorylation can activate or inhibit a substrate, alter its localization, or promote interactions with other proteins or ligands. Deciphering direct kinase substrates is crucial to understand mechanisms of kinase signaling, yet can be challenging due to the transient nature of kinase phosphorylation and potential for downstream indirect phosphorylation events. However, with recent advances in proteomic approaches, our understanding of kinase function in Apicomplexa has improved dramatically. Here, we discuss methods that have been used to identify kinase substrates in apicomplexan parasites, classifying them into three main categories: i) kinase interactome, ii) indirect phosphoproteomics and iii) direct labeling. We briefly discuss each approach, including their advantages and limitations, and highlight representative examples from the Apicomplexa literature. Finally, we conclude each main category by introducing prospective approaches from other fields that would benefit kinase substrate identification in Apicomplexa.
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Affiliation(s)
- Gabriel Cabral
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - William J Moss
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kevin M Brown
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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2
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Gybeľ T, Čada Š, Klementová D, Schwalm MP, Berger BT, Šebesta M, Knapp S, Bryja V. Splice variants of CK1α and CK1α-like: Comparative analysis of subcellular localization, kinase activity, and function in the Wnt signaling pathway. J Biol Chem 2024; 300:107407. [PMID: 38796065 DOI: 10.1016/j.jbc.2024.107407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/19/2024] [Accepted: 05/07/2024] [Indexed: 05/28/2024] Open
Abstract
Members of the casein kinase 1 (CK1) family are important regulators of multiple signaling pathways. CK1α is a well-known negative regulator of the Wnt/β-catenin pathway, which promotes the degradation of β-catenin via its phosphorylation of Ser45. In contrast, the closest paralog of CK1α, CK1α-like, is a poorly characterized kinase of unknown function. In this study, we show that the deletion of CK1α, but not CK1α-like, resulted in a strong activation of the Wnt/β-catenin pathway. Wnt-3a treatment further enhanced the activation, which suggests there are at least two modes, a CK1α-dependent and Wnt-dependent, of β-catenin regulation. Rescue experiments showed that only two out of ten naturally occurring splice CK1α/α-like variants were able to rescue the augmented Wnt/β-catenin signaling caused by CK1α deficiency in cells. Importantly, the ability to phosphorylate β-catenin on Ser45 in the in vitro kinase assay was required but not sufficient for such rescue. Our compound CK1α and GSK3α/β KO models suggest that the additional nonredundant function of CK1α in the Wnt pathway beyond Ser45-β-catenin phosphorylation includes Axin phosphorylation. Finally, we established NanoBRET assays for the three most common CK1α splice variants as well as CK1α-like. Target engagement data revealed comparable potency of known CK1α inhibitors for all CK1α variants but not for CK1α-like. In summary, our work brings important novel insights into the biology of CK1α, including evidence for the lack of redundancy with other CK1 kinases in the negative regulation of the Wnt/β-catenin pathway at the level of β-catenin and Axin.
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Affiliation(s)
- Tomáš Gybeľ
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Štěpán Čada
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Darja Klementová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Martin P Schwalm
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; Structural Genomics Consortium, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK Site Frankfurt-Mainz, Heidelberg, Germany
| | - Benedict-Tilman Berger
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; Structural Genomics Consortium, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Marek Šebesta
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; Structural Genomics Consortium, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK Site Frankfurt-Mainz, Heidelberg, Germany
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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Karolak A, Urbaniak K, Monastyrskyi A, Duckett DR, Branciamore S, Stewart PA. Structure-independent machine-learning predictions of the CDK12 interactome. Biophys J 2024:S0006-3495(24)00344-8. [PMID: 38762754 DOI: 10.1016/j.bpj.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/24/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) is a critical regulatory protein involved in transcription and DNA repair processes. Dysregulation of CDK12 has been implicated in various diseases, including cancer. Understanding the CDK12 interactome is pivotal for elucidating its functional roles and potential therapeutic targets. Traditional methods for interactome prediction often rely on protein structure information, limiting applicability to CDK12 characterized by partly disordered terminal C region. In this study, we present a structure-independent machine-learning model that utilizes proteins' sequence and functional data to predict the CDK12 interactome. This approach is motivated by the disordered character of the CDK12 C-terminal region mitigating a structure-driven search for binding partners. Our approach incorporates multiple data sources, including protein-protein interaction networks, functional annotations, and sequence-based features, to construct a comprehensive CDK12 interactome prediction model. The ability to predict CDK12 interactions without relying on structural information is a significant advancement, as many potential interaction partners may lack crystallographic data. In conclusion, our structure-independent machine-learning model presents a powerful tool for predicting the CDK12 interactome and holds promise in advancing our understanding of CDK12 biology, identifying potential therapeutic targets, and facilitating precision-medicine approaches for CDK12-associated diseases.
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Affiliation(s)
| | - Konstancja Urbaniak
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, California
| | | | - Derek R Duckett
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida
| | - Sergio Branciamore
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, California
| | - Paul A Stewart
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
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Ding M, Wang C, Hu J, She J, Shi R, Liu Y, Sun Q, Xu H, Zhou G, Wu W, Xia H. PLOD3 facilitated T cell activation in the colorectal tumor microenvironment and liver metastasis by the TNF-α/ NF-κB pathway. J Transl Med 2024; 22:30. [PMID: 38184566 PMCID: PMC10771005 DOI: 10.1186/s12967-023-04809-w] [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: 07/16/2023] [Accepted: 12/16/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) has been the third most prevalent cancer worldwide. Liver metastasis is the critical factor for the poor prognosis of CRC. Here, we investigated the expression and role of PLOD3 in CRC. METHODS Different liver metastasis models were established by injecting PLOD3 stable knockdown or overexpression CT26 or MC38 mouse CRC cells into the spleen of mice to verify the tumorigenicity and metastasis ability in vivo. RESULTS We identified PLOD3 is significantly overexpressed in liver metastasis samples of CRC. High expression of PLOD3 was significantly associated with poor survival of CRC patients. The knockdown of PLOD3 exhibited remarkable inhibition of proliferation, migration, and invasion in CRC cells, while the opposite results could be found in different PLOD3-overexpressed CRC cells. Stable knockdown of PLOD3 also significantly inhibited liver metastasis of CRC cells in different xenografts models, while stable overexpression of PLOD3 promotes liver metastasis and tumor progression. Further studies showed that PLOD3 facilitated the T cell activation in the tumor microenvironment and affected the TNF-α/ NF-κB pathway. CONCLUSIONS This study revealed the essential biological functions of PLOD3 in colon cancer progression and metastasis, suggesting that PLOD3 is a promising translational medicine target and bioengineering targeting PLOD3 overcomes CRC liver metastasis.
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Affiliation(s)
- Min Ding
- Department of Pathology & Nanjing Drum Tower Hospital Clinical College & Key Laboratory of Antibody Technique of National Health Commission && Jiangsu Antibody Drug Engineering Research Center, Nanjing Medical University, Nanjing, 211166, China
- Zhongda Hospital, School of Medicine, Advanced Institute for Life and Health, Southeast University, Nanjing, 210009, China
- Department of General Surgery & High Talent & Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
- Department of Pathology, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Cheng Wang
- Department of Pathology & Nanjing Drum Tower Hospital Clinical College & Key Laboratory of Antibody Technique of National Health Commission && Jiangsu Antibody Drug Engineering Research Center, Nanjing Medical University, Nanjing, 211166, China
| | - Junhong Hu
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, China
| | - Junjun She
- Department of General Surgery & High Talent & Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Ruoyu Shi
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, 169856, Singapore
| | - Yixuan Liu
- Department of Pathology & Nanjing Drum Tower Hospital Clinical College & Key Laboratory of Antibody Technique of National Health Commission && Jiangsu Antibody Drug Engineering Research Center, Nanjing Medical University, Nanjing, 211166, China
| | - Qi Sun
- Department of Pathology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
| | - Haojun Xu
- Department of Pathology & Nanjing Drum Tower Hospital Clinical College & Key Laboratory of Antibody Technique of National Health Commission && Jiangsu Antibody Drug Engineering Research Center, Nanjing Medical University, Nanjing, 211166, China
| | - Guoren Zhou
- Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, 210009, China.
| | - Wenlan Wu
- Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, 210009, China.
| | - Hongping Xia
- Department of Pathology & Nanjing Drum Tower Hospital Clinical College & Key Laboratory of Antibody Technique of National Health Commission && Jiangsu Antibody Drug Engineering Research Center, Nanjing Medical University, Nanjing, 211166, China.
- Zhongda Hospital, School of Medicine, Advanced Institute for Life and Health, Southeast University, Nanjing, 210009, China.
- Department of General Surgery & High Talent & Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
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Kraszewska I, Sarad K, Andrysiak K, Kopacz A, Schmidt L, Krüger M, Dulak J, Jaźwa-Kusior A. Casein kinase 2 activity is a host restriction factor for AAV transduction. Mol Ther 2024; 32:84-102. [PMID: 37952087 PMCID: PMC10787142 DOI: 10.1016/j.ymthe.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 09/29/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
So far, the mechanisms that impede AAV transduction, especially in the human heart, are poorly understood, hampering the introduction of new, effective gene therapy strategies. Therefore, the aim of this study was to identify and overcome the main cellular barriers to successful transduction in the heart, using induced pluripotent stem cell (iPSC)-derived cardiomyocytes (iPSC-CMs), iPSC-derived cardiac fibroblasts (iPSC-CFs), and primary endothelial cells to model vector-host interactions. Through phosphoproteome analysis we established that casein kinase 2 (CK2) signaling is one of the most significantly affected pathways upon AAV exposure. Transient inhibition of CK2 activity substantially enhanced the transduction rate of AAV2, AAV6, and AAV9 in all tested cell types. In particular, CK2 inhibition improved the trafficking of AAVs through the cytoplasm, impaired DNA damage response through destabilization of MRE11, and altered the RNA processing pathways, which were also highly responsive to AAV transduction. Also, it augmented transgene expression in already transduced iPSC-CFs, which retain AAV genomes in a functional, but probably silent form. In summary, the present study provides new insights into the current understanding of the host-AAV vector interaction, identifying CK2 activity as a key barrier to efficient transduction and transgene expression, which may translate to improving the outcome of AAV-based therapies in the future.
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Affiliation(s)
- Izabela Kraszewska
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Katarzyna Sarad
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Kalina Andrysiak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Aleksandra Kopacz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Luisa Schmidt
- CECAD Research Center, Institute for Genetics, University of Cologne, Cologne, Germany
| | - Marcus Krüger
- CECAD Research Center, Institute for Genetics, University of Cologne, Cologne, Germany
| | - Józef Dulak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agnieszka Jaźwa-Kusior
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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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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Yuan YH, Mao ND, Duan JL, Zhang H, Garrido C, Lirussi F, Gao Y, Xie T, Ye XY. Recent progress in discovery of novel AAK1 inhibitors: from pain therapy to potential anti-viral agents. J Enzyme Inhib Med Chem 2023; 38:2279906. [PMID: 37955299 PMCID: PMC10653628 DOI: 10.1080/14756366.2023.2279906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023] Open
Abstract
Adaptor associated kinase 1 (AAK1), a member of the Ark1/Prk1 family of Ser/Thr kinases, is a specific key kinase regulating Thr156 phosphorylation at the μ2 subunit of the adapter complex-2 (AP-2) protein. Due to their important biological functions, AAK1 systems have been validated in clinics for neuropathic pain therapy, and are being explored as potential therapeutic targets for diseases caused by various viruses such as Hepatitis C (HCV), Dengue, Ebola, and COVID-19 viruses and for amyotrophic lateral sclerosis (ALS). Centreing on the advances of drug discovery programs in this field up to 2023, AAK1 inhibitors are discussed from the aspects of the structure-based rational molecular design, pharmacology, toxicology and synthetic routes for the compounds of interest in this review. The aim is to provide the medicinal chemistry community with up-to-date information and to accelerate the drug discovery programs in the field of AAK1 small molecule inhibitors.
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Affiliation(s)
- Ying-Hui Yuan
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Nian-Dong Mao
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Ji-Long Duan
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Hang Zhang
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
- School of Basic Medical Science, Hangzhou Normal University, Hangzhou, China
| | - Carmen Garrido
- INSERM UMR 1231, Labex LipSTIC, University of Bourgogne, Dijon, France
- Cancer Center George François Leclerc, Dijon, France
- University of Bourgogne Franche-Comté, Besançon, France
| | - Frédéric Lirussi
- INSERM UMR 1231, Labex LipSTIC, University of Bourgogne, Dijon, France
- University of Franche-Comté & University Hospital of Besançon, Besancon, France
| | - Yuan Gao
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Xiang-Yang Ye
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
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