1
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Bashore F, Min SM, Chen X, Howell S, Rinderle CH, Morel G, Silvaroli JA, Wells CI, Bunnell BA, Drewry DH, Pabla NS, Ultanir SK, Bullock AN, Axtman AD. Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2. ACS Med Chem Lett 2024; 15:1325-1333. [PMID: 39140040 PMCID: PMC11318004 DOI: 10.1021/acsmedchemlett.4c00219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 08/15/2024] Open
Abstract
Acylaminoindazole-based inhibitors of CDKL2 were identified via analyses of cell-free binding and selectivity data. Compound 9 was selected as a CDKL2 chemical probe based on its potent inhibition of CDKL2 enzymatic activity, engagement of CDKL2 in cells, and excellent kinome-wide selectivity, especially when used in cells. Compound 16 was designed as a negative control to be used alongside compound 9 in experiments to interrogate CDKL2-mediated biology. A solved cocrystal structure of compound 9 bound to CDKL2 highlighted key interactions it makes within its ATP-binding site. Inhibition of downstream phosphorylation of EB2, a CDKL2 substrate, in rat primary neurons provided evidence that engagement of CDKL2 by compound 9 in cells resulted in inhibition of its activity. When used at relevant concentrations, compound 9 does not impact the viability of rat primary neurons or certain breast cancer cells nor elicit consistent changes in the expression of proteins involved in epithelial-mesenchymal transition.
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Affiliation(s)
- Frances
M. Bashore
- Structural
Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sophia M. Min
- Structural
Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xiangrong Chen
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.
| | - Stefanie Howell
- Structural
Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Caroline H. Rinderle
- Department
of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Gabriel Morel
- Kinases
and Brain Development Laboratory, The Francis
Crick Institute, London NW1 1AT, U.K.
| | - Josie A. Silvaroli
- Division
of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive
Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Carrow I. Wells
- Structural
Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Bruce A. Bunnell
- Department
of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - David H. Drewry
- Structural
Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC
Lineberger
Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Navjot S. Pabla
- Division
of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive
Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sila K. Ultanir
- Kinases
and Brain Development Laboratory, The Francis
Crick Institute, London NW1 1AT, U.K.
| | - Alex N. Bullock
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.
| | - Alison D. Axtman
- Structural
Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Zhang H, Lin J, Zheng S, Ma L, Pang Z, Yin H, Meng C, Wang Y, Han Q, Zhang X, Li Z, Cao L, Liu L, Fei T, Gao D, Yang L, Peng X, Ding C, Wang S, Sheng R. CDKL3 is a targetable regulator of cell cycle progression in cancers. J Clin Invest 2024; 134:e178428. [PMID: 38963708 PMCID: PMC11324297 DOI: 10.1172/jci178428] [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: 12/12/2023] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
Cell cycle regulation is largely abnormal in cancers. Molecular understanding and therapeutic targeting of the aberrant cell cycle are essential. Here, we identified that an underappreciated serine/threonine kinase, cyclin-dependent kinase-like 3 (CDKL3), crucially drives rapid cell cycle progression and cell growth in cancers. With regard to mechanism, CDKL3 localizes in the nucleus and associates with specific cyclin to directly phosphorylate retinoblastoma (Rb) for quiescence exit. In parallel, CDKL3 prevents the ubiquitin-proteasomal degradation of cyclin-dependent kinase 4 (CDK4) by direct phosphorylation on T172 to sustain G1 phase advancement. The crucial function of CDKL3 in cancers was demonstrated both in vitro and in vivo. We also designed, synthesized, and characterized a first-in-class CDKL3-specific inhibitor, HZ1. HZ1 exhibits greater potency than CDK4/6 inhibitor in pan-cancer treatment by causing cell cycle arrest and overcomes acquired resistance to CDK4/6 inhibitor. In particular, CDKL3 has significant clinical relevance in colon cancer, and the effectiveness of HZ1 was demonstrated by murine and patient-derived cancer models. Collectively, this work presents an integrated paradigm of cancer cell cycle regulation and suggests CDKL3 targeting as a feasible approach in cancer treatment.
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Affiliation(s)
- Haijiao Zhang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Jiahui Lin
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Shaoqin Zheng
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Lanjing Ma
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Zhongqiu Pang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Hongyi Yin
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Chengcheng Meng
- Department of Pathology, the Fourth People’s Hospital of Shenyang, Shenyang, China
| | - Yinuo Wang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Qing Han
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Xi Zhang
- College of Sciences, Northeastern University, Shenyang, China
| | - Zexu Li
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Liu Cao
- College of Basic Medical Science, China Medical University, Shenyang, China
| | - Lijun Liu
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Teng Fei
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Daming Gao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Liang Yang
- Department of General Surgery, the Fourth Affiliated Hospital, China Medical University, Shenyang, China
| | - Xueqiang Peng
- Department of General Surgery, the Fourth Affiliated Hospital, China Medical University, Shenyang, China
| | - Chen Ding
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Shixue Wang
- CAS Key Laboratory of High-Performance Synthetic Rubber and its Composite Materials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Ren Sheng
- College of Life and Health Sciences, Northeastern University, Shenyang, China
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3
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Li C, Liu Y, Luo S, Yang M, Li L, Sun L. A review of CDKL: An underestimated protein kinase family. Int J Biol Macromol 2024:133604. [PMID: 38964683 DOI: 10.1016/j.ijbiomac.2024.133604] [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: 06/25/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
Cyclin-dependent kinase-like (CDKL) family proteins are serine/threonine protein kinases and is a specific branch of CMGC (including CDK, MAPK, GSK). Its name is due to the sequence similarity with CDK and it consists of 5 members. Their function in protein phosphorylation underpins their important role in cellular activities, including cell cycle, apoptosis, autophagy and microtubule dynamics. CDKL proteins have been demonstrated to regulate the length of primary cilium, which is a dynamic and diverse signaling hub and closely associated with multiple diseases. Furthermore, CDKL proteins have been shown to be involved in the development and progression of several diseases, including cancer, neurodegenerative diseases and kidney disease. In this review, we summarize the structural characteristics and discovered functions of CDKL proteins and their role in diseases, which might be helpful for the development of innovative therapeutic strategies for disease.
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Affiliation(s)
- Chenrui Li
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Yan Liu
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Shilu Luo
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Ming Yang
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Li Li
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China.
| | - Lin Sun
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China.
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4
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Karimbayli J, Pellarin I, Belletti B, Baldassarre G. Insights into the structural and functional activities of forgotten Kinases: PCTAIREs CDKs. Mol Cancer 2024; 23:135. [PMID: 38951876 PMCID: PMC11218289 DOI: 10.1186/s12943-024-02043-6] [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: 02/21/2024] [Accepted: 06/12/2024] [Indexed: 07/03/2024] Open
Abstract
In cells, signal transduction heavily relies on the intricate regulation of protein kinases, which provide the fundamental framework for modulating most signaling pathways. Dysregulation of kinase activity has been implicated in numerous pathological conditions, particularly in cancer. The druggable nature of most kinases positions them into a focal point during the process of drug development. However, a significant challenge persists, as the role and biological function of nearly one third of human kinases remains largely unknown.Within this diverse landscape, cyclin-dependent kinases (CDKs) emerge as an intriguing molecular subgroup. In human, this kinase family encompasses 21 members, involved in several key biological processes. Remarkably, 13 of these CDKs belong to the category of understudied kinases, and only 5 having undergone broad investigation to date. This knowledge gap underscores the pressing need to delve into the study of these kinases, starting with a comprehensive review of the less-explored ones.Here, we will focus on the PCTAIRE subfamily of CDKs, which includes CDK16, CDK17, and CDK18, arguably among the most understudied CDKs members. To contextualize PCTAIREs within the spectrum of human pathophysiology, we conducted an exhaustive review of the existing literature and examined available databases. This approach resulted in an articulate depiction of these PCTAIREs, encompassing their expression patterns, 3D configurations, mechanisms of activation, and potential functions in normal tissues and in cancer.We propose that this effort offers the possibility of identifying promising areas of future research that extend from basic research to potential clinical and therapeutic applications.
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Affiliation(s)
- Javad Karimbayli
- Division of Molecular Oncology, Centro di Riferimento Oncologico (CRO) of Aviano, IRCCS, National Cancer Institute, Via Franco Gallini, Aviano, 33081, Italy
| | - Ilenia Pellarin
- Division of Molecular Oncology, Centro di Riferimento Oncologico (CRO) of Aviano, IRCCS, National Cancer Institute, Via Franco Gallini, Aviano, 33081, Italy
| | - Barbara Belletti
- Division of Molecular Oncology, Centro di Riferimento Oncologico (CRO) of Aviano, IRCCS, National Cancer Institute, Via Franco Gallini, Aviano, 33081, Italy
| | - Gustavo Baldassarre
- Division of Molecular Oncology, Centro di Riferimento Oncologico (CRO) of Aviano, IRCCS, National Cancer Institute, Via Franco Gallini, Aviano, 33081, Italy.
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5
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Wu Q, Lu M, Ouyang H, Zhou T, Lei J, Wang P, Wang W. CDKL3 is a promising biomarker for diagnosis and prognosis prediction in patients with hepatocellular carcinoma. Exp Biol Med (Maywood) 2024; 249:10106. [PMID: 38993199 PMCID: PMC11237920 DOI: 10.3389/ebm.2024.10106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/02/2023] [Indexed: 07/13/2024] Open
Abstract
Cyclin-dependent kinase-like 3 (CDKL3) has been identified as an oncogene in certain types of tumors. Nonetheless, its function in hepatocellular carcinoma (HCC) is poorly understood. In this study, we conducted a comprehensive analysis of CDKL3 based on data from the HCC cohort of The Cancer Genome Atlas (TCGA). Our analysis included gene expression, diagnosis, prognosis, functional enrichment, tumor microenvironment and metabolic characteristics, tumor burden, mRNA expression-based stemness, alternative splicing, and prediction of therapy response. Additionally, we performed a cell counting kit-8 assay, TdT-mediated dUTP nick-end Labeling staining, migration assay, wound healing assay, colony formation assay, and nude mouse experiments to confirm the functional relevance of CDKL3 in HCC. Our findings showed that CDKL3 was significantly upregulated in HCC patients compared to controls. Various bioinformatic analyses suggested that CDKL3 could serve as a potential marker for HCC diagnosis and prognosis. Furthermore, CDKL3 was found to be involved in various mechanisms linked to the development of HCC, including copy number variation, tumor burden, genomic heterogeneity, cancer stemness, and alternative splicing of CDKL3. Notably, CDKL3 was also closely correlated with tumor immune cell infiltration and the expression of immune checkpoint markers. Additionally, CDKL3 was shown to independently function as a risk predictor for overall survival in HCC patients by multivariate Cox regression analysis. Furthermore, the knockdown of CDKL3 significantly inhibited cell proliferation in vitro and in vivo, indicating its role as an oncogene in HCC. Taken together, our findings suggest that CDKL3 shows promise as a biomarker for the detection and treatment outcome prediction of HCC patients.
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Affiliation(s)
- Qingsi Wu
- Department of Blood Transfusion, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Microbiology and Parasitology, Hefei, Anhui, China
| | - Mengran Lu
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Huijuan Ouyang
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Tingting Zhou
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Jingyuan Lei
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Panpan Wang
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Wei Wang
- Department of Gastroenterology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
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Bashore FM, Min SM, Chen X, Howell S, Rinderle CH, Morel G, Silvaroli JA, Wells CI, Bunnell BA, Drewry DH, Pabla NS, Ultanir SK, Bullock AN, Axtman AD. Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593776. [PMID: 38798634 PMCID: PMC11118373 DOI: 10.1101/2024.05.12.593776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Acylaminoindazole-based inhibitors of CDKL2 were identified via analyses of cell-free binding and selectivity data. Compound 9 was selected as a CDKL2 chemical probe based on its potent inhibition of CDKL2 enzymatic activity, engagement of CDKL2 in cells, and excellent kinome-wide selectivity, especially when used in cells. Compound 16 was designed as a negative control to be used alongside compound 9 in experiments to interrogate CDKL2-mediated biology. A solved co-crystal structure of compound 9 bound to CDKL2 highlighted key interactions it makes within its ATP-binding site. Inhibition of downstream phosphorylation of EB2, a CDKL2 substrate, in rat primary neurons provided evidence that engagement of CDKL2 by compound 9 in cells resulted in inhibition of its activity. When used at relevant concentrations, compound 9 does not impact the viability of rat primary neurons or certain breast cancer cells nor elicit consistent changes in the expression of proteins involved in epithelial-mesenchymal transition.
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Affiliation(s)
- Frances M. Bashore
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sophia M. Min
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xiangrong Chen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Stefanie Howell
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Caroline H. Rinderle
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Gabriel Morel
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Josie A. Silvaroli
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210, United States of America
| | - Carrow I. Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bruce A. Bunnell
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Navjot S. Pabla
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210, United States of America
| | - Sila K. Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Alex N. Bullock
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Alison D. Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Li Z, Xue H, Li J, Zheng Z, Liu Z, Dong X, Wang H, Chen J, Xu S. CDKL1 potentiates the antitumor efficacy of radioimmunotherapy by binding to transcription factor YBX1 and blocking PD-L1 expression in lung cancer. J Exp Clin Cancer Res 2024; 43:89. [PMID: 38520004 PMCID: PMC10958935 DOI: 10.1186/s13046-024-03007-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: 12/14/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND The evasion of the immune response by tumor cells through programmed death-ligand 1 (PD-L1) has been identified as a factor contributing to resistance to radioimmunotherapy in lung cancer patients. However, the precise molecular mechanisms underlying the regulation of PD-L1 remain incompletely understood. This study aimed to investigate the role of cyclin-dependent kinase-like 1 (CDKL1) in the modulation of PD-L1 expression and the response to radioimmunotherapy in lung cancer. METHODS The tumorigenic roles of CDKL1 were assessed via cell growth, colony formation, and EdU assays and an in vivo nude mouse xenograft model. The in vitro radiosensitization effect of CDKL1 was evaluated using a neutral comet assay, γH2AX foci formation analysis, and a clonogenic cell survival assay. The protein‒protein interactions were confirmed via coimmunoprecipitation and GST pulldown assays. The regulation of PD-L1 by CDKL1 was evaluated via chromatin immunoprecipitation (ChIP), real-time quantitative PCR, and flow cytometry analysis. An in vitro conditioned culture model and an in vivo C57BL/6J mouse xenograft model were developed to detect the activation markers of CD8+ T cells and evaluate the efficacy of CDKL1 overexpression combined with radiotherapy (RT) and an anti-PD-L1 antibody in treating lung cancer. RESULTS CDKL1 was downregulated and suppressed the growth and proliferation of lung cancer cells and increased radiosensitivity in vitro and in vivo. Mechanistically, CDKL1 interacted with the transcription factor YBX1 and decreased the binding affinity of YBX1 for the PD-L1 gene promoter, which consequently inhibits the expression of PD-L1, ultimately leading to the activation of CD8+ T cells and the inhibition of immune evasion in lung cancer. Moreover, the combination of CDKL1 overexpression, RT, and anti-PD-L1 antibody therapy exhibited the most potent antitumor efficacy against lung cancer. CONCLUSIONS Our findings demonstrate that CDKL1 plays a crucial role in regulating PD-L1 expression, thereby enhancing the antitumor effects of radioimmunotherapy. These results suggest that CDKL1 may be a promising therapeutic target for the treatment of lung cancer.
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Affiliation(s)
- Zixuan Li
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Wuhan, 430022, China
| | - Huichan Xue
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Wuhan, 430022, China
| | - Jinsong Li
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zhikun Zheng
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zhiwei Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Wuhan, 430022, China
| | - Xiaorong Dong
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Wuhan, 430022, China
| | - Hongbo Wang
- Clinical Research Center of Cancer Immunotherapy, Wuhan, 430022, China
| | - Jing Chen
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Key Laboratory of Precision Radiation Oncology, Wuhan, 430022, China.
| | - Shuangbing Xu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Key Laboratory of Precision Radiation Oncology, Wuhan, 430022, China.
- Clinical Research Center of Cancer Immunotherapy, Wuhan, 430022, China.
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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8
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Bi Y, Liu J, Qin S, Ji F, Zhou C, Yang H, Zhou S. CDKL3 shapes immunosuppressive tumor microenvironment and initiates autophagy in esophageal cancer. Front Immunol 2024; 15:1295011. [PMID: 38562942 PMCID: PMC10982402 DOI: 10.3389/fimmu.2024.1295011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Background CDKL3 has been associated with the prognosis of several tumors. However, the potential role of CDKL3 in immunotherapy and the tumor microenvironment (TME) in esophageal carcinoma (ESCA) remains unclear. Methods In this study, Cox regression analysis was used to assess the predictive value of CDKL3 for ESCA outcomes. We systematically correlated CDKL3 with immunological features in the TME. The role of CDKL3 in predicting the efficacy of immunotherapy was also analyzed. Correlation analysis, Cox analysis and LASSO Cox regression were used to construct the CDKL3-related autophagy (CrA) risk score model. The relationship between CDKL3 expression and postoperative pathological complete response (pCR) rate in esophageal squamous cell carcinoma (ESCC) patients undergoing neoadjuvant chemoradiotherapy (nCRT) was evaluated using Immunohistochemical staining (IHC). The relationship between CDKL3 expression and autophagy induction was confirmed by immunofluorescence staining and western blot, and the effect of CDKL3 expression on macrophage polarization was verified by flow cytometry. Results High expression of CDKL3 was found in ESCA and was associated with poor prognosis in ESCA. Moreover, CDKL3 expression was negatively correlated with tumor-infiltrating immune cells (TIICs), the integrality of the cancer immunity cycles, and anti-tumor signatures, while CDKL3 expression was positively correlated with suppressive TME-related chemokines and receptors, immune hyperprogressive genes, and suppressive immune checkpoint, resulting in immunosuppressive TME formation in ESCA. An analysis of immunotherapy cohorts of the ESCA and pan-cancer showed a better response to immunotherapy in tumor patients with lower CDKL3 levels. The CrA risk score model was constructed and validated to accurately predict the prognosis of ESCA. Notably, the CrA risk score of ESCA patients was significantly positively correlated with M2 macrophages. Furthermore, knockdown CDKL3 in KYSE150 cells could inhibit autophagy induction and M2 macrophage polarization. And, radiation could downregulate CDKL3 expression and autophagy induction, while ESCC patients with high CDKL3 expression had a significantly lower response rate after nCRT than those with low CDKL3 expression. Conclusion CDKL3 may play an important role in anti-tumor immunity by regulating autophagy to promote the formation of immunosuppressive TME, thus playing a critical role in the prognosis of ESCA.
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Affiliation(s)
- Yanping Bi
- Department of Radiation Oncology, Xi’an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi’an, Shaanxi, China
| | - Jie Liu
- Department of Medical Research Center, Xi’an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi’an, Shaanxi, China
| | - Songbing Qin
- Department of Radiation Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Fuqing Ji
- Department of Thyroid Breast Surgery, Xi’an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi’an, Shaanxi, China
| | - Chao Zhou
- Department of Radiation Oncology, Taizhou Hospital Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Haihua Yang
- Department of Radiation Oncology, Taizhou Hospital Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou, Zhejiang, China
| | - Suna Zhou
- Department of Radiation Oncology, Taizhou Hospital Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou, Zhejiang, China
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9
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Flax RG, Rosston P, Rocha C, Anderson B, Capener JL, Durcan TM, Drewry DH, Prinos P, Axtman AD. Illumination of understudied ciliary kinases. Front Mol Biosci 2024; 11:1352781. [PMID: 38523660 PMCID: PMC10958382 DOI: 10.3389/fmolb.2024.1352781] [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: 12/08/2023] [Accepted: 01/29/2024] [Indexed: 03/26/2024] Open
Abstract
Cilia are cellular signaling hubs. Given that human kinases are central regulators of signaling, it is not surprising that kinases are key players in cilia biology. In fact, many kinases modulate ciliogenesis, which is the generation of cilia, and distinct ciliary pathways. Several of these kinases are understudied with few publications dedicated to the interrogation of their function. Recent efforts to develop chemical probes for members of the cyclin-dependent kinase like (CDKL), never in mitosis gene A (NIMA) related kinase (NEK), and tau tubulin kinase (TTBK) families either have delivered or are working toward delivery of high-quality chemical tools to characterize the roles that specific kinases play in ciliary processes. A better understanding of ciliary kinases may shed light on whether modulation of these targets will slow or halt disease onset or progression. For example, both understudied human kinases and some that are more well-studied play important ciliary roles in neurons and have been implicated in neurodevelopmental, neurodegenerative, and other neurological diseases. Similarly, subsets of human ciliary kinases are associated with cancer and oncological pathways. Finally, a group of genetic disorders characterized by defects in cilia called ciliopathies have associated gene mutations that impact kinase activity and function. This review highlights both progress related to the understanding of ciliary kinases as well as in chemical inhibitor development for a subset of these kinases. We emphasize known roles of ciliary kinases in diseases of the brain and malignancies and focus on a subset of poorly characterized kinases that regulate ciliary biology.
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Affiliation(s)
- Raymond G. Flax
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Peter Rosston
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Cecilia Rocha
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC, Canada
| | - Brian Anderson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jacob L. Capener
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Thomas M. Durcan
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC, Canada
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Panagiotis Prinos
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Alison D. Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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10
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Silvestre M, Dempster K, Mihaylov SR, Claxton S, Ultanir SK. Cell type-specific expression, regulation and compensation of CDKL5 activity in mouse brain. Mol Psychiatry 2024:10.1038/s41380-024-02434-7. [PMID: 38326557 DOI: 10.1038/s41380-024-02434-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/04/2024] [Accepted: 01/15/2024] [Indexed: 02/09/2024]
Abstract
CDKL5 is a brain-enriched serine/threonine kinase, associated with a profound developmental and epileptic encephalopathy called CDKL5 deficiency disorder (CDD). To design targeted therapies for CDD, it is essential to determine where CDKL5 is expressed and is active in the brain and test if compensatory mechanisms exist at cellular level. We generated conditional Cdkl5 knockout mice in excitatory neurons, inhibitory neurons and astrocytes. To assess CDKL5 activity, we utilized a phosphospecific antibody for phosphorylated EB2, a well-known substrate of CDKL5. We found that CDKL5 and EB2 pS222 were prominent in excitatory and inhibitory neurons but were not detected in astrocytes. We observed that approximately 15-20% of EB2 pS222 remained in Cdkl5 knockout brains and primary neurons. Surprisingly, the remaining phosphorylation was modulated by NMDA and PP1/PP2A in neuronal CDKL5 knockout cultures, indicating the presence of a compensating kinase. Using a screen of candidate kinases with highest homology to the CDKL5 kinase domain, we found that CDKL2 and ICK can phosphorylate EB2 S222 in HEK293T cells and in primary neurons. We then generated Cdkl5/Cdkl2 dual knockout mice to directly test if CDKL2 phosphorylates EB2 in vivo and found that CDKL2 phosphorylates CDKL5 substrates in the brain. This study is the first indication that CDKL2 could potentially replace CDKL5 functions in the brain, alluding to novel therapeutic possibilities.
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Affiliation(s)
- Margaux Silvestre
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
| | - Kelvin Dempster
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
| | - Simeon R Mihaylov
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
| | - Suzanne Claxton
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK.
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11
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Lindberg MF, Deau E, Miege F, Greverie M, Roche D, George N, George P, Merlet L, Gavard J, Brugman SJT, Aret E, Tinnemans P, de Gelder R, Sadownik J, Verhofstad E, Sleegers D, Santangelo S, Dairou J, Fernandez-Blanco Á, Dierssen M, Krämer A, Knapp S, Meijer L. Chemical, Biochemical, Cellular, and Physiological Characterization of Leucettinib-21, a Down Syndrome and Alzheimer's Disease Drug Candidate. J Med Chem 2023; 66:15648-15670. [PMID: 38051674 DOI: 10.1021/acs.jmedchem.3c01888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Leucettinibs are substituted 2-aminoimidazolin-4-ones (inspired by the marine sponge natural product Leucettamine B) developed as pharmacological inhibitors of DYRK1A (dual-specificity, tyrosine phosphorylation-regulated kinase 1A), a therapeutic target for indications such as Down syndrome and Alzheimer's disease. Leucettinib-21 was selected as a drug candidate following extensive structure/activity studies and multiparametric evaluations. We here report its physicochemical properties (X-ray powder diffraction, differential scanning calorimetry, stability, solubility, crystal structure) and drug-like profile. Leucettinib-21's selectivity (analyzed by radiometric, fluorescence, interaction, thermal shift, residence time assays) reveals DYRK1A as the first target but also some "off-targets" which may contribute to the drug's biological effects. Leucettinib-21 was cocrystallized with CLK1 and modeled in the DYRK1A structure. Leucettinib-21 inhibits DYRK1A in cells (demonstrated by direct catalytic activity and phosphorylation levels of Thr286-cyclin D1 or Thr212-Tau). Leucettinib-21 corrects memory disorders in the Down syndrome mouse model Ts65Dn and is now entering safety/tolerance phase 1 clinical trials.
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Affiliation(s)
- Mattias F Lindberg
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
| | - Emmanuel Deau
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
| | - Frédéric Miege
- Edelris, Bâtiment Bioserra 1, 60 Avenue Rockefeller, 69008 Lyon, France
| | - Marie Greverie
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
| | - Didier Roche
- Edelris, Bâtiment Bioserra 1, 60 Avenue Rockefeller, 69008 Lyon, France
| | - Nicolas George
- Oncodesign, 25-27 Avenue du Québec, 91140 Villebon-sur-Yvette, France
| | - Pascal George
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
| | - Laura Merlet
- Team SOAP, CRCI2NA, Nantes Université, Inserm, CNRS, Université d'Angers, 8 Quai Moncousu, 44007 Nantes Cedex 1, France
- Equipe Labellisée Ligue Contre le Cancer, 75013 Paris, France
| | - Julie Gavard
- Team SOAP, CRCI2NA, Nantes Université, Inserm, CNRS, Université d'Angers, 8 Quai Moncousu, 44007 Nantes Cedex 1, France
- Equipe Labellisée Ligue Contre le Cancer, 75013 Paris, France
- Institut de Cancérologie de l'Ouest (ICO), Boulevard Professeur Jacques Monod, 44800 Saint-Herblain, France
| | | | - Edwin Aret
- Symeres, Peelterbaan 2, 6002 NK Weert, The Netherlands
| | - Paul Tinnemans
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - René de Gelder
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jan Sadownik
- Symeres, Peelterbaan 2, 6002 NK Weert, The Netherlands
| | | | | | | | - Julien Dairou
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS, 45 rue des Saints Pères, 75006 Paris, France
| | - Álvaro Fernandez-Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08036, Spain
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08036, Spain
| | - Andreas Krämer
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von Laue Strasse 15, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von Laue Strasse 15, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Laurent Meijer
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
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12
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Castano A, Silvestre M, Wells CI, Sanderson JL, Ferrer CA, Ong HW, Lang Y, Richardson W, Silvaroli JA, Bashore FM, Smith JL, Genereux IM, Dempster K, Drewry DH, Pabla NS, Bullock AN, Benke TA, Ultanir SK, Axtman AD. Discovery and characterization of a specific inhibitor of serine-threonine kinase cyclin-dependent kinase-like 5 (CDKL5) demonstrates role in hippocampal CA1 physiology. eLife 2023; 12:e88206. [PMID: 37490324 PMCID: PMC10406435 DOI: 10.7554/elife.88206] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/24/2023] [Indexed: 07/26/2023] Open
Abstract
Pathological loss-of-function mutations in cyclin-dependent kinase-like 5 (CDKL5) cause CDKL5 deficiency disorder (CDD), a rare and severe neurodevelopmental disorder associated with severe and medically refractory early-life epilepsy, motor, cognitive, visual, and autonomic disturbances in the absence of any structural brain pathology. Analysis of genetic variants in CDD has indicated that CDKL5 kinase function is central to disease pathology. CDKL5 encodes a serine-threonine kinase with significant homology to GSK3β, which has also been linked to synaptic function. Further, Cdkl5 knock-out rodents have increased GSK3β activity and often increased long-term potentiation (LTP). Thus, development of a specific CDKL5 inhibitor must be careful to exclude cross-talk with GSK3β activity. We synthesized and characterized specific, high-affinity inhibitors of CDKL5 that do not have detectable activity for GSK3β. These compounds are very soluble in water but blood-brain barrier penetration is low. In rat hippocampal brain slices, acute inhibition of CDKL5 selectively reduces postsynaptic function of AMPA-type glutamate receptors in a dose-dependent manner. Acute inhibition of CDKL5 reduces hippocampal LTP. These studies provide new tools and insights into the role of CDKL5 as a newly appreciated key kinase necessary for synaptic plasticity. Comparisons to rodent knock-out studies suggest that compensatory changes have limited the understanding of the roles of CDKL5 in synaptic physiology, plasticity, and human neuropathology.
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Affiliation(s)
- Anna Castano
- Department of Pharmacology, University of Colorado School of MedicineAuroraUnited States
| | - Margaux Silvestre
- Kinases and Brain Development Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Jennifer L Sanderson
- Department of Pharmacology, University of Colorado School of MedicineAuroraUnited States
| | - Carla A Ferrer
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Han Wee Ong
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Yi Lang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - William Richardson
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Josie A Silvaroli
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State UniversityColumbusUnited States
| | - Frances M Bashore
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Jeffery L Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Isabelle M Genereux
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Kelvin Dempster
- Kinases and Brain Development Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel HillChapel HillUnited States
| | - Navlot S Pabla
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State UniversityColumbusUnited States
| | - Alex N Bullock
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Tim A Benke
- Departments of Pediatrics, Pharmacology, Neurology and Otolaryngology, University of Colorado School of MedicineAuroraUnited States
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
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13
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Castano A, Silvestre M, Wells CI, Sanderson JL, Ferrer CA, Ong HW, Liang Y, Richardson W, Silvaroli JA, Bashore FM, Smith JL, Genereux IM, Dempster K, Drewry DH, Pabla NS, Bullock AN, Benke TA, Ultanir SK, Axtman AD. Discovery and characterization of a specific inhibitor of serine-threonine kinase cyclin dependent kinase-like 5 (CDKL5) demonstrates role in hippocampal CA1 physiology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538049. [PMID: 37162893 PMCID: PMC10168277 DOI: 10.1101/2023.04.24.538049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Pathological loss-of-function mutations in cyclin-dependent kinase-like 5 ( CDKL5 ) cause CDKL5 deficiency disorder (CDD), a rare and severe neurodevelopmental disorder associated with severe and medically refractory early-life epilepsy, motor, cognitive, visual and autonomic disturbances in the absence of any structural brain pathology. Analysis of genetic variants in CDD have indicated that CDKL5 kinase function is central to disease pathology. CDKL5 encodes a serine-threonine kinase with significant homology to GSK3β, which has also been linked to synaptic function. Further, Cdkl5 knock-out rodents have increased GSK3β activity and often increased long-term potentiation (LTP). Thus, development of a specific CDKL5 inhibitor must be careful to exclude cross-talk with GSK3β activity. We synthesized and characterized specific, high-affinity inhibitors of CDKL5 that do not have detectable activity for GSK3β. These compounds are very soluble in water but blood-brain barrier penetration is low. In rat hippocampal brain slices, acute inhibition of CDKL5 selectively reduces post-synaptic function of AMPA-type glutamate receptors in a dose-dependent manner. Acute inhibition of CDKL5 reduces hippocampal LTP. These studies provide new tools and insights into the role of CDKL5 as a newly appreciated, key kinase necessary for synaptic plasticity. Comparisons to rodent knock-out studies suggest that compensatory changes have limited the understanding of the roles of CDKL5 in synaptic physiology, plasticity and human neuropathology.
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14
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Ong HW, Liang Y, Richardson W, Lowry ER, Wells CI, Chen X, Silvestre M, Dempster K, Silvaroli JA, Smith JL, Wichterle H, Pabla NS, Ultanir SK, Bullock AN, Drewry DH, Axtman AD. Discovery of a Potent and Selective CDKL5/GSK3 Chemical Probe That Is Neuroprotective. ACS Chem Neurosci 2023; 14:1672-1685. [PMID: 37084253 PMCID: PMC10161233 DOI: 10.1021/acschemneuro.3c00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Despite mediating several essential processes in the brain, including during development, cyclin-dependent kinase-like 5 (CDKL5) remains a poorly characterized human protein kinase. Accordingly, its substrates, functions, and regulatory mechanisms have not been fully described. We realized that availability of a potent and selective small molecule probe targeting CDKL5 could enable illumination of its roles in normal development as well as in diseases where it has become aberrant due to mutation. We prepared analogs of AT-7519, a compound that has advanced to phase II clinical trials and is a known inhibitor of several cyclin-dependent kinases (CDKs) and cyclin-dependent kinase-like kinases (CDKLs). We identified analog 2 as a highly potent and cell-active chemical probe for CDKL5/GSK3 (glycogen synthase kinase 3). Evaluation of its kinome-wide selectivity confirmed that analog 2 demonstrates excellent selectivity and only retains GSK3α/β affinity. We next demonstrated the inhibition of downstream CDKL5 and GSK3α/β signaling and solved a co-crystal structure of analog 2 bound to human CDKL5. A structurally similar analog (4) proved to lack CDKL5 affinity and maintain potent and selective inhibition of GSK3α/β, making it a suitable negative control. Finally, we used our chemical probe pair (2 and 4) to demonstrate that inhibition of CDKL5 and/or GSK3α/β promotes the survival of human motor neurons exposed to endoplasmic reticulum stress. We have demonstrated a neuroprotective phenotype elicited by our chemical probe pair and exemplified the utility of our compounds to characterize the role of CDKL5/GSK3 in neurons and beyond.
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Affiliation(s)
- Han Wee Ong
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yi Liang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - William Richardson
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Emily R Lowry
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032, United States
- The Project ALS Therapeutics Core, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xiangrong Chen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Margaux Silvestre
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Kelvin Dempster
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Josie A Silvaroli
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jeffery L Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Hynek Wichterle
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032, United States
- The Project ALS Therapeutics Core, Columbia University Irving Medical Center, New York, New York 10032, United States
- Departments of Neurology, Neuroscience, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, New York 10032, United States
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Navjot S Pabla
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Alex N Bullock
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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15
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Ong HW, Liang Y, Richardson W, Lowry ER, Wells CI, Chen X, Silvestre M, Dempster K, Silvaroli JA, Smith JL, Wichterle H, Pabla NS, Ultanir SK, Bullock AN, Drewry DH, Axtman AD. A Potent and Selective CDKL5/GSK3 Chemical Probe is Neuroprotective. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527935. [PMID: 36798313 PMCID: PMC9934649 DOI: 10.1101/2023.02.09.527935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Despite mediating several essential processes in the brain, including during development, cyclin-dependent kinase-like 5 (CDKL5) remains a poorly characterized human protein kinase. Accordingly, its substrates, functions, and regulatory mechanisms have not been fully described. We realized that availability of a potent and selective small molecule probe targeting CDKL5 could enable illumination of its roles in normal development as well as in diseases where it has become aberrant due to mutation. We prepared analogs of AT-7519, a known inhibitor of several cyclin dependent and cyclin-dependent kinase-like kinases that has been advanced into Phase II clinical trials. We identified analog 2 as a highly potent and cell-active chemical probe for CDKL5/GSK3 (glycogen synthase kinase 3). Evaluation of its kinome-wide selectivity confirmed that analog 2 demonstrates excellent selectivity and only retains GSK3α/β affinity. As confirmation that our chemical probe is a high-quality tool to use in directed biological studies, we demonstrated inhibition of downstream CDKL5 and GSK3α/β signaling and solved a co-crystal structure of analog 2 bound to CDKL5. A structurally similar analog ( 4 ) proved to lack CDKL5 affinity and maintain potent and selective inhibition of GSK3α/β. Finally, we used our chemical probe pair ( 2 and 4 ) to demonstrate that inhibition of CDKL5 and/or GSK3α/β promotes the survival of human motor neurons exposed to endoplasmic reticulum (ER) stress. We have demonstrated a neuroprotective phenotype elicited by our chemical probe pair and exemplified the utility of our compounds to characterize the role of CDKL5/GSK3 in neurons and beyond.
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Affiliation(s)
- Han Wee Ong
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
| | - Yi Liang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
| | - William Richardson
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Emily R. Lowry
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, 10032, United States of America; The Project ALS Therapeutics Core, Columbia University Irving Medical Center, New York, New York, 10032, United States of America
| | - Carrow I. Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
| | - Xiangrong Chen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Margaux Silvestre
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Kelvin Dempster
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Josie A. Silvaroli
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210, United States of America
| | - Jeffery L. Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
| | - Hynek Wichterle
- Departments of Pathology and Cell Biology, Neurology, Neuroscience, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, New York, New York, 10032, United States of America; Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, New York, 10032, United States of America; Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, New York, 10032, United States of America; The Project ALS Therapeutics Core, Columbia University Irving Medical Center, New York, New York, 10032, United States of America
| | - Navjot S. Pabla
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210, United States of America
| | - Sila K. Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Alex N. Bullock
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America; UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
| | - Alison D. Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
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16
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Karalis V, Donovan KE, Sahin M. Primary Cilia Dysfunction in Neurodevelopmental Disorders beyond Ciliopathies. J Dev Biol 2022; 10:54. [PMID: 36547476 PMCID: PMC9782889 DOI: 10.3390/jdb10040054] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Primary cilia are specialized, microtubule-based structures projecting from the surface of most mammalian cells. These organelles are thought to primarily act as signaling hubs and sensors, receiving and integrating extracellular cues. Several important signaling pathways are regulated through the primary cilium including Sonic Hedgehog (Shh) and Wnt signaling. Therefore, it is no surprise that mutated genes encoding defective proteins that affect primary cilia function or structure are responsible for a group of disorders collectively termed ciliopathies. The severe neurologic abnormalities observed in several ciliopathies have prompted examination of primary cilia structure and function in other brain disorders. Recently, neuronal primary cilia defects were observed in monogenic neurodevelopmental disorders that were not traditionally considered ciliopathies. The molecular mechanisms of how these genetic mutations cause primary cilia defects and how these defects contribute to the neurologic manifestations of these disorders remain poorly understood. In this review we will discuss monogenic neurodevelopmental disorders that exhibit cilia deficits and summarize findings from studies exploring the role of primary cilia in the brain to shed light into how these deficits could contribute to neurologic abnormalities.
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Affiliation(s)
- Vasiliki Karalis
- The Rosamund Stone Zander Translational Neuroscience Center, Department of Neurology Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- FM Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Kathleen E. Donovan
- The Rosamund Stone Zander Translational Neuroscience Center, Department of Neurology Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- FM Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Mustafa Sahin
- The Rosamund Stone Zander Translational Neuroscience Center, Department of Neurology Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- FM Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA 02115, USA
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17
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Park K, Leroux MR. Composition, organization and mechanisms of the transition zone, a gate for the cilium. EMBO Rep 2022; 23:e55420. [PMID: 36408840 PMCID: PMC9724682 DOI: 10.15252/embr.202255420] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/08/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
The cilium evolved to provide the ancestral eukaryote with the ability to move and sense its environment. Acquiring these functions required the compartmentalization of a dynein-based motility apparatus and signaling proteins within a discrete subcellular organelle contiguous with the cytosol. Here, we explore the potential molecular mechanisms for how the proximal-most region of the cilium, termed transition zone (TZ), acts as a diffusion barrier for both membrane and soluble proteins and helps to ensure ciliary autonomy and homeostasis. These include a unique complement and spatial organization of proteins that span from the microtubule-based axoneme to the ciliary membrane; a protein picket fence; a specialized lipid microdomain; differential membrane curvature and thickness; and lastly, a size-selective molecular sieve. In addition, the TZ must be permissive for, and functionally integrates with, ciliary trafficking systems (including intraflagellar transport) that cross the barrier and make the ciliary compartment dynamic. The quest to understand the TZ continues and promises to not only illuminate essential aspects of human cell signaling, physiology, and development, but also to unravel how TZ dysfunction contributes to ciliopathies that affect multiple organ systems, including eyes, kidney, and brain.
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Affiliation(s)
- Kwangjin Park
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
- Present address:
Terry Fox LaboratoryBC CancerVancouverBCCanada
- Present address:
Department of Medical GeneticsUniversity of British ColumbiaVancouverBCCanada
| | - Michel R Leroux
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
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18
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Colarusso A, Lauro C, Calvanese M, Parrilli E, Tutino ML. Active human full-length CDKL5 produced in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Microb Cell Fact 2022; 21:211. [PMID: 36242022 PMCID: PMC9563788 DOI: 10.1186/s12934-022-01939-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/24/2022] [Indexed: 11/24/2022] Open
Abstract
Background A significant fraction of the human proteome is still inaccessible to in vitro studies since the recombinant production of several proteins failed in conventional cell factories. Eukaryotic protein kinases are difficult-to-express in heterologous hosts due to folding issues both related to their catalytic and regulatory domains. Human CDKL5 belongs to this category. It is a serine/threonine protein kinase whose mutations are involved in CDKL5 Deficiency Disorder (CDD), a severe neurodevelopmental pathology still lacking a therapeutic intervention. The lack of successful CDKL5 manufacture hampered the exploitation of the otherwise highly promising enzyme replacement therapy. As almost two-thirds of the enzyme sequence is predicted to be intrinsically disordered, the recombinant product is either subjected to a massive proteolytic attack by host-encoded proteases or tends to form aggregates. Therefore, the use of an unconventional expression system can constitute a valid alternative to solve these issues. Results Using a multiparametric approach we managed to optimize the transcription of the CDKL5 gene and the synthesis of the recombinant protein in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 applying a bicistronic expression strategy, whose generalization for recombinant expression in the cold has been here confirmed with the use of a fluorescent reporter. The recombinant protein largely accumulated as a full-length product in the soluble cell lysate. We also demonstrated for the first time that full-length CDKL5 produced in Antarctic bacteria is catalytically active by using two independent assays, making feasible its recovery in native conditions from bacterial lysates as an active product, a result unmet in other bacteria so far. Finally, the setup of an in cellulo kinase assay allowed us to measure the impact of several CDD missense mutations on the kinase activity, providing new information towards a better understanding of CDD pathophysiology. Conclusions Collectively, our data indicate that P. haloplanktis TAC125 can be a valuable platform for both the preparation of soluble active human CDKL5 and the study of structural–functional relationships in wild type and mutant CDKL5 forms. Furthermore, this paper further confirms the more general potentialities of exploitation of Antarctic bacteria to produce “intractable” proteins, especially those containing large intrinsically disordered regions. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01939-6.
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Affiliation(s)
- Andrea Colarusso
- Department of Chemical Sciences, "Federico II" University of Naples, Complesso Universitario Monte S. Angelo-Via Cintia, 80126, Naples, Italy.,Istituto Nazionale Biostrutture e Biosistemi-I.N.B.B., Viale Medaglie d'Oro, 305-00136, Rome, Italy
| | - Concetta Lauro
- Department of Chemical Sciences, "Federico II" University of Naples, Complesso Universitario Monte S. Angelo-Via Cintia, 80126, Naples, Italy.,Istituto Nazionale Biostrutture e Biosistemi-I.N.B.B., Viale Medaglie d'Oro, 305-00136, Rome, Italy
| | - Marzia Calvanese
- Department of Chemical Sciences, "Federico II" University of Naples, Complesso Universitario Monte S. Angelo-Via Cintia, 80126, Naples, Italy
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, "Federico II" University of Naples, Complesso Universitario Monte S. Angelo-Via Cintia, 80126, Naples, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, "Federico II" University of Naples, Complesso Universitario Monte S. Angelo-Via Cintia, 80126, Naples, Italy.
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19
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Faubel RJ, Santos Canellas VS, Gaesser J, Beluk NH, Feinstein TN, Wang Y, Yankova M, Karunakaran KB, King SM, Ganapathiraju MK, Lo CW. Flow blockage disrupts cilia-driven fluid transport in the epileptic brain. Acta Neuropathol 2022; 144:691-706. [PMID: 35980457 DOI: 10.1007/s00401-022-02463-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 01/28/2023]
Abstract
A carpet of ependymal motile cilia lines the brain ventricular system, forming a network of flow channels and barriers that pattern cerebrospinal fluid (CSF) flow at the surface. This CSF transport system is evolutionary conserved, but its physiological function remains unknown. Here we investigated its potential role in epilepsy with studies focused on CDKL5 deficiency disorder (CDD), a neurodevelopmental disorder with early-onset epilepsy refractory to seizure medications and the most common cause of infant epilepsy. CDKL5 is a highly conserved X-linked gene suggesting its function in regulating cilia length and motion in the green alga Chlamydomonas might have implication in the etiology of CDD. Examination of the structure and function of airway motile cilia revealed both the CDD patients and the Cdkl5 knockout mice exhibit cilia lengthening and abnormal cilia motion. Similar defects were observed for brain ventricular cilia in the Cdkl5 knockout mice. Mapping ependymal cilia generated flow in the ventral third ventricle (v3V), a brain region with important physiological functions showed altered patterning of flow. Tracing of cilia-mediated inflow into v3V with fluorescent dye revealed the appearance of a flow barrier at the inlet of v3V in Cdkl5 knockout mice. Analysis of mice with a mutation in another epilepsy-associated kinase, Yes1, showed the same disturbance of cilia motion and flow patterning. The flow barrier was also observed in the Foxj1± and FOXJ1CreERT:Cdkl5y/fl mice, confirming the contribution of ventricular cilia to the flow disturbances. Importantly, mice exhibiting altered cilia-driven flow also showed increased susceptibility to anesthesia-induced seizure-like activity. The cilia-driven flow disturbance arises from altered cilia beating orientation with the disrupted polarity of the cilia anchoring rootlet meshwork. Together these findings indicate motile cilia disturbances have an essential role in CDD-associated seizures and beyond, suggesting cilia regulating kinases may be a therapeutic target for medication-resistant epilepsy.
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Affiliation(s)
- Regina J Faubel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201, USA
| | - Veronica S Santos Canellas
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201, USA
| | - Jenna Gaesser
- Division of Child Neurology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201, USA
| | - Nancy H Beluk
- Division of Radiology, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Tim N Feinstein
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201, USA
| | - Yong Wang
- Laboratory for Fluid Physics, Pattern Formation and Biocomplexity, Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077, Göttingen, Germany
| | - Maya Yankova
- Department of Molecular Biology and Biophysics, And Electron Microscopy Facility, University of Connecticut Health Center, Farmington, CT, 06030-3305, USA
| | - Kalyani B Karunakaran
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | - Stephen M King
- Department of Molecular Biology and Biophysics, And Electron Microscopy Facility, University of Connecticut Health Center, Farmington, CT, 06030-3305, USA
| | - Madhavi K Ganapathiraju
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201, USA
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201, USA.
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20
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Mechanisms of Regulation in Intraflagellar Transport. Cells 2022; 11:cells11172737. [PMID: 36078145 PMCID: PMC9454703 DOI: 10.3390/cells11172737] [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: 08/16/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022] Open
Abstract
Cilia are eukaryotic organelles essential for movement, signaling or sensing. Primary cilia act as antennae to sense a cell’s environment and are involved in a wide range of signaling pathways essential for development. Motile cilia drive cell locomotion or liquid flow around the cell. Proper functioning of both types of cilia requires a highly orchestrated bi-directional transport system, intraflagellar transport (IFT), which is driven by motor proteins, kinesin-2 and IFT dynein. In this review, we explore how IFT is regulated in cilia, focusing from three different perspectives on the issue. First, we reflect on how the motor track, the microtubule-based axoneme, affects IFT. Second, we focus on the motor proteins, considering the role motor action, cooperation and motor-train interaction plays in the regulation of IFT. Third, we discuss the role of kinases in the regulation of the motor proteins. Our goal is to provide mechanistic insights in IFT regulation in cilia and to suggest directions of future research.
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21
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CDKL5 deficiency disorder: molecular insights and mechanisms of pathogenicity to fast-track therapeutic development. Biochem Soc Trans 2022; 50:1207-1224. [PMID: 35997111 PMCID: PMC9444073 DOI: 10.1042/bst20220791] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022]
Abstract
CDKL5 deficiency disorder (CDD) is an X-linked brain disorder of young children and is caused by pathogenic variants in the cyclin-dependent kinase-like 5 (CDKL5) gene. Individuals with CDD suffer infantile onset, drug-resistant seizures, severe neurodevelopmental impairment and profound lifelong disability. The CDKL5 protein is a kinase that regulates key phosphorylation events vital to the development of the complex neuronal network of the brain. Pathogenic variants identified in patients may either result in loss of CDKL5 catalytic activity or are hypomorphic leading to partial loss of function. Whilst the progressive nature of CDD provides an excellent opportunity for disease intervention, we cannot develop effective therapeutics without in-depth knowledge of CDKL5 function in human neurons. In this mini review, we summarize new findings on the function of CDKL5. These include CDKL5 phosphorylation targets and the consequence of disruptions on signaling pathways in the human brain. This new knowledge of CDKL5 biology may be leveraged to advance targeted drug discovery and rapid development of treatments for CDD. Continued development of effective humanized models will further propel our understanding of CDD biology and may permit the development and testing of therapies that will significantly alter CDD disease trajectory in young children.
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22
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Maurya AK, Sengupta P. The DYF-5 RCK and CDKL-1 CDKL5 kinases contribute differentially to shape distinct sensory neuron cilia morphologies in C. elegans. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000619. [PMID: 35996689 PMCID: PMC9391949 DOI: 10.17912/micropub.biology.000619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/03/2022] [Accepted: 08/03/2022] [Indexed: 12/03/2022]
Abstract
The conserved CCRK, RCK, and CDKL5 kinases regulate cilia length in diverse organisms. In C. elegans , DYF-18 CCRK regulates DYF-5 RCK to shape both simple and complex cilia morphologies. The CDKL5 ortholog CDKL-1 has also been suggested to act downstream of DYF-18 but independently of DYF-5 to regulate lengths of simple rod-like cilia. Here we show that CDKL-1 is largely dispensable for regulation of complex cilia structures. Using genetic epistasis experiments, we confirm that CDKL-1 and DYF-5 act independently to control cilia architecture. Our results indicate that multiple kinases act via distinct pathways to regulate unique cilia ultrastructures.
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Affiliation(s)
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, MA, USA
,
Correspondence to: Piali Sengupta (
)
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23
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Napoli G, Panzironi N, Traversa A, Catalanotto C, Pace V, Petrizzelli F, Giovannetti A, Lazzari S, Cogoni C, Tartaglia M, Carella M, Mazza T, Pizzuti A, Parisi C, Caputo V. Potassium Channel KCNH1 Activating Variants Cause Altered Functional and Morphological Ciliogenesis. Mol Neurobiol 2022; 59:4825-4838. [PMID: 35639255 PMCID: PMC9363390 DOI: 10.1007/s12035-022-02886-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/17/2022] [Indexed: 12/18/2022]
Abstract
The primary cilium is a non-motile sensory organelle that extends from the surface of most vertebrate cells and transduces signals regulating proliferation, differentiation, and migration. Primary cilia dysfunctions have been observed in cancer and in a group of heterogeneous disorders called ciliopathies, characterized by renal and liver cysts, skeleton and limb abnormalities, retinal degeneration, intellectual disability, ataxia, and heart disease and, recently, in autism spectrum disorder, schizophrenia, and epilepsy. The potassium voltage-gated channel subfamily H member 1 (KCNH1) gene encodes a member of the EAG (ether-à-go-go) family, which controls potassium flux regulating resting membrane potential in both excitable and non-excitable cells and is involved in intracellular signaling, cell proliferation, and tumorigenesis. KCNH1 missense variants have been associated with syndromic neurodevelopmental disorders, including Zimmermann-Laband syndrome 1 (ZLS1, MIM #135500), Temple-Baraitser syndrome (TMBTS, MIM #611816), and, recently, with milder phenotypes as epilepsy. In this work, we provide evidence that KCNH1 localizes at the base of the cilium in pre-ciliary vesicles and ciliary pocket of human dermal fibroblasts and retinal pigment epithelial (hTERT RPE1) cells and that the pathogenic missense variants (L352V and R330Q; NP_002229.1) perturb cilia morphology, assembly/disassembly, and Sonic Hedgehog signaling, disclosing a multifaceted role of the protein. The study of KCNH1 localization, its functions related to primary cilia, and the alterations introduced by mutations in ciliogenesis, cell cycle coordination, cilium morphology, and cilia signaling pathways could help elucidate the molecular mechanisms underlying neurological phenotypes and neurodevelopmental disorders not considered as classical ciliopathies but for which a significant role of primary cilia is emerging.
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Affiliation(s)
- Giulia Napoli
- Institute of Biochemistry and Cell Biology, CNR-National Research Council, Monterotondo Scalo, Rome, Italy
| | - Noemi Panzironi
- Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Alice Traversa
- Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo (FG), Italy
| | | | - Valentina Pace
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Francesco Petrizzelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Agnese Giovannetti
- Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Sara Lazzari
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Carlo Cogoni
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Massimo Carella
- Research Unit of Medical Genetics, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Tommaso Mazza
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Chiara Parisi
- Institute of Biochemistry and Cell Biology, CNR-National Research Council, Monterotondo Scalo, Rome, Italy.
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.
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24
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Altered genome-wide hippocampal gene expression profiles following early life lead exposure and their potential for reversal by environmental enrichment. Sci Rep 2022; 12:11937. [PMID: 35879375 PMCID: PMC9314447 DOI: 10.1038/s41598-022-15861-9] [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: 08/05/2021] [Accepted: 06/30/2022] [Indexed: 12/02/2022] Open
Abstract
Early life lead (Pb) exposure is detrimental to neurobehavioral development. The quality of the environment can modify negative influences from Pb exposure, impacting the developmental trajectory following Pb exposure. Little is known about the molecular underpinnings in the brain of the interaction between Pb and the quality of the environment. We examined relationships between early life Pb exposure and living in an enriched versus a non-enriched postnatal environment on genome-wide transcription profiles in hippocampus CA1. RNA-seq identified differences in the transcriptome of enriched vs. non-enriched Pb-exposed animals. Most of the gene expression changes associated with Pb exposure were reversed by enrichment. This was also true for changes in upstream regulators, splicing events and long noncoding RNAs. Non-enriched rats also had memory impairments; enriched rats had no deficits. The results demonstrate that an enriched environment has a profound impact on behavior and the Pb-modified CA1 transcriptome. These findings show the potential for interactions between Pb exposure and the environment to result in significant transcriptional changes in the brain and, to the extent that this may occur in Pb-exposed children, could influence neuropsychological/educational outcomes, underscoring the importance for early intervention and environmental enrichment for Pb-exposed children.
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25
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Schembs L, Willems A, Hasenpusch-Theil K, Cooper JD, Whiting K, Burr K, Bøstrand SMK, Selvaraj BT, Chandran S, Theil T. The ciliary gene INPP5E confers dorsal telencephalic identity to human cortical organoids by negatively regulating Sonic hedgehog signaling. Cell Rep 2022; 39:110811. [PMID: 35584663 PMCID: PMC9620745 DOI: 10.1016/j.celrep.2022.110811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 02/07/2022] [Accepted: 04/20/2022] [Indexed: 12/02/2022] Open
Abstract
Defects in primary cilia, cellular antennas that control multiple intracellular signaling pathways, underlie several neurodevelopmental disorders, but it remains unknown how cilia control essential steps in human brain formation. Here, we show that cilia are present on the apical surface of radial glial cells in human fetal forebrain. Interfering with cilia signaling in human organoids by mutating the INPP5E gene leads to the formation of ventral telencephalic cell types instead of cortical progenitors and neurons. INPP5E mutant organoids also show increased Sonic hedgehog (SHH) signaling, and cyclopamine treatment partially rescues this ventralization. In addition, ciliary expression of SMO, GLI2, GPR161, and several intraflagellar transport (IFT) proteins is increased. Overall, these findings establish the importance of primary cilia for dorsal and ventral patterning in human corticogenesis, indicate a tissue-specific role of INPP5E as a negative regulator of SHH signaling, and have implications for the emerging roles of cilia in the pathogenesis of neurodevelopmental disorders.
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Affiliation(s)
- Leah Schembs
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Ariane Willems
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh EH16 4SB, UK; Simons Initiative for the Developing Brain, University of Edinburgh, Hugh Robson Building, Edinburgh EH8 9XD, UK
| | - Kerstin Hasenpusch-Theil
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK; Simons Initiative for the Developing Brain, University of Edinburgh, Hugh Robson Building, Edinburgh EH8 9XD, UK
| | - James D Cooper
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Katie Whiting
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Karen Burr
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Sunniva M K Bøstrand
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Bhuvaneish T Selvaraj
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh EH16 4SB, UK; Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Siddharthan Chandran
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh EH16 4SB, UK; Simons Initiative for the Developing Brain, University of Edinburgh, Hugh Robson Building, Edinburgh EH8 9XD, UK; Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Thomas Theil
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK; Simons Initiative for the Developing Brain, University of Edinburgh, Hugh Robson Building, Edinburgh EH8 9XD, UK.
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26
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Di Nardo A, Rühmkorf A, Award P, Brennecke A, Fagiolini M, Sahin M. Phenotypic characterization of Cdkl5-knockdown neurons establishes elongated cilia as a functional assay for CDKL5 Deficiency Disorder. Neurosci Res 2022; 176:73-78. [PMID: 34624412 PMCID: PMC8960319 DOI: 10.1016/j.neures.2021.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/14/2021] [Accepted: 10/04/2021] [Indexed: 11/28/2022]
Abstract
CDKL5 Deficiency Disorder (CDD) is a severe encephalopathy characterized by intractable epilepsy, infantile spasms, and cognitive disabilities. The detrimental CNS manifestations and lack of therapeutic interventions represent unmet needs, necessitating identification of CDD-dependent phenotypes for in vitro disease modeling and therapeutic testing. Here, we optimized a high-content assay to quantify cilia in CDKL5-deficient neurons. Our work shows that Cdkl5-knockdown neurons have elongated cilia and uncovers cilium lengthening in hippocampi of Cdkl5 knockout mice. Collectively, our findings identify cilia length alterations under CDKL5 activity loss in vitro and in vivo and reveal elongated cilia as a robust functional phenotype for CDD.
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Affiliation(s)
- Alessia Di Nardo
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA 02115, USA; Genetic and Developmental Disorders Research Unit, Biogen 115 Broadway, Cambridge, MA 02142, USA(1)
| | - Alina Rühmkorf
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Patricia Award
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ashton Brennecke
- Genetic and Developmental Disorders Research Unit, Biogen 115 Broadway, Cambridge, MA 02142, USA(1)
| | - Michela Fagiolini
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Hock E. Tan and K. Lisa Yang Center for Autism Research at Harvard University, Boston, MA 02115, USA
| | - Mustafa Sahin
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA 02115, USA.
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27
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Chen Z, Lv Y, He L, Wu S, Wu Z. Decreased CDKL2 Expression in Clear Cell Renal Cell Carcinoma Predicts Worse Overall Survival. Front Mol Biosci 2022; 8:657672. [PMID: 35096961 PMCID: PMC8793634 DOI: 10.3389/fmolb.2021.657672] [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: 07/27/2021] [Accepted: 12/24/2021] [Indexed: 11/26/2022] Open
Abstract
Background: Clear cell renal cell carcinoma (ccRCC) is the most frequent and lethal type of kidney cancer. Although differential expression of cyclin-dependent kinase-like 2 (CDKL2) has been reported to be associated with tumor progression in other cancers, its prognostic value, and potential mechanism in patients with ccRCC still remain unknown. Methods: Gene expression analysis was conducted using The Cancer Genome Atlas (TCGA), Gene Expression Omnibus, and International Cancer Genome Consortium databases. Further, clinicopathologic analysis; Kaplan–Meier survival analysis; weighted gene co-expression network analysis; gene set enrichment analysis; gene ontology enrichment; methylation; and immune infiltration analyses were performed using TCGA-kidney renal clear cell carcinoma profiles. CDKL2 translational levels were analyzed using The Human Protein Atlas database. Results:CDKL2 expression was decreased in ccRCC samples retrieved from the four databases. Gender, survival status, histologic grade, clinical stage, TNM classification, and tumor status were closely related to CDKL2 expression. In addition, CDKL2 downregulation was an independent prognostic factor for poor prognosis in multivariate analysis. Enrichment analyses using multiple tests revealed that CDKL2 is not just closely related to immune response but this association is highly correlated as well. Further, we found that CDKL2 expression was significantly correlated with the infiltration levels of T cell CD4 memory resting; monocytes; macrophages M0, M1, and M2; dendritic cells resting; mast cells resting; plasma cells; T cell CD8; and T cell regulatory. Conclusion: This is the first report to study the expression of CDKL2 in ccRCC, wherein we suggest that decreased CDKL2 expression is closely correlated with poor prognosis in ccRCC. We consider that CDKL2 is a novel and potential prognostic biomarker associated with immune infiltrates in ccRCC.
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East MP, Johnson GL. Adaptive chromatin remodeling and transcriptional changes of the functional kinome in tumor cells in response to targeted kinase inhibition. J Biol Chem 2021; 298:101525. [PMID: 34958800 PMCID: PMC8888345 DOI: 10.1016/j.jbc.2021.101525] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Pharmacological inhibition of protein kinases induces adaptive reprogramming of tumor cell regulatory networks by altering expression of genes that regulate signaling, including protein kinases. Adaptive responses are dependent on transcriptional changes resulting from remodeling of enhancer and promoter landscapes. Enhancer and promoter remodeling in response to targeted kinase inhibition is controlled by changes in open chromatin state and by activity of specific transcription factors, such as c-MYC. This review focuses on the dynamic plasticity of protein kinase expression of the tumor cell kinome and the resulting adaptive resistance to targeted kinase inhibition. Plasticity of the functional kinome has been shown in patient window trials where triple-negative and human epidermal growth factor receptor 2–positive breast cancer patient tumors were characterized by RNAseq after biopsies before and after 1 week of therapy. The expressed kinome changed dramatically during drug treatment, and these changes in kinase expression were shown in cell lines and xenografts in mice to be correlated with adaptive tumor cell drug resistance. The dynamic transcriptional nature of the kinome also differs for inhibitors targeting different kinase signaling pathways (e.g., BRAF-MEK-ERK versus PI3K-AKT) that are commonly activated in cancers. Heterogeneity arising from differences in gene regulation and mutations represents a challenge to therapeutic durability and prevention of clinical drug resistance with drug-tolerant tumor cell populations developing and persisting through treatment. We conclude that understanding the heterogeneity of kinase expression at baseline and in response to therapy is imperative for development of combinations and timing intervals of therapies making interventions durable.
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Affiliation(s)
- Michael P East
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Gary L Johnson
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.
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Cui Y, Yang Z, Wang H, Yan Y, Huang Q, Gong Z, Hong F, Zhang X, Li W, Chen J, Xu T. Identification of CDKL3 as a critical regulator in development of glioma through regulating RRM2 and the JNK signaling pathway. Cancer Sci 2021; 112:3150-3162. [PMID: 34097336 PMCID: PMC8353949 DOI: 10.1111/cas.15010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022] Open
Abstract
Glioma is one of the most commonly diagnosed intracranial malignancies. The molecular mechanism underlying the development of glioma is still largely unknown. In this study, we present the first report concerning the function and mechanism of cyclin‐dependent kinase‐like 3 (CDKL3) in the development and prognosis of glioma. It is shown that CDKL3 was upregulated in glioma tissues and could independently predict poor prognosis of patients. Silencing CDKL3 in glioma cells could inhibit cell proliferation and migration and induce cell apoptosis and cell cycle arrest, whereas the overexpression of CDKL3 promoted cell proliferation. The in vivo experiments also indicated that knockdown of CDKL3 significantly suppressed tumor growth of glioma. Gene expression profiling of CDKL3 knockdown U87 cells identified RRM2 as a potential target of CDKL3, which was proved to have direct interaction with CDKL3. Given similar effects on glioma development with CDKL3, knockdown of RRM2 could rescue the effects of CDKL3 overexpression on glioma cells. Moreover, knockdown of CDKL3 or RRM2 suppressed the activity of JNK signaling, whereas CDKL3 overexpression produced the opposite effect. In conclusion, our results identified CDKL3 as a promotor for glioma, probably through the regulation of RRM2 and activation of the JNK signalling pathway, highlighting the significance of CDKL3 as a promising therapeutic target of glioma.
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Affiliation(s)
- Yong Cui
- Department of Neurosurgery, Third Affiliated Hospital, Naval Medical University, Shanghai, China
| | - Zhigang Yang
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hongxiang Wang
- Department of Neurosurgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yong Yan
- Department of Neurosurgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Qilin Huang
- Department of Neurosurgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Zhenyu Gong
- Department of Neurosurgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Fan Hong
- Department of Neurosurgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xu Zhang
- Department of Neurosurgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Weiqing Li
- Department of Pathology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Juxiang Chen
- Department of Neurosurgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Tao Xu
- Department of Neurosurgery, Changzheng Hospital, Naval Medical University, Shanghai, China
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Nita A, Abraham SP, Krejci P, Bosakova M. Oncogenic FGFR Fusions Produce Centrosome and Cilia Defects by Ectopic Signaling. Cells 2021; 10:1445. [PMID: 34207779 PMCID: PMC8227969 DOI: 10.3390/cells10061445] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/27/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
A single primary cilium projects from most vertebrate cells to guide cell fate decisions. A growing list of signaling molecules is found to function through cilia and control ciliogenesis, including the fibroblast growth factor receptors (FGFR). Aberrant FGFR activity produces abnormal cilia with deregulated signaling, which contributes to pathogenesis of the FGFR-mediated genetic disorders. FGFR lesions are also found in cancer, raising a possibility of cilia involvement in the neoplastic transformation and tumor progression. Here, we focus on FGFR gene fusions, and discuss the possible mechanisms by which they function as oncogenic drivers. We show that a substantial portion of the FGFR fusion partners are proteins associated with the centrosome cycle, including organization of the mitotic spindle and ciliogenesis. The functions of centrosome proteins are often lost with the gene fusion, leading to haploinsufficiency that induces cilia loss and deregulated cell division. We speculate that this complements the ectopic FGFR activity and drives the FGFR fusion cancers.
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Affiliation(s)
- Alexandru Nita
- Department of Biology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic; (A.N.); (S.P.A.); (P.K.)
| | - Sara P. Abraham
- Department of Biology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic; (A.N.); (S.P.A.); (P.K.)
| | - Pavel Krejci
- Department of Biology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic; (A.N.); (S.P.A.); (P.K.)
- Institute of Animal Physiology and Genetics of the CAS, 60200 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, 65691 Brno, Czech Republic
| | - Michaela Bosakova
- Department of Biology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic; (A.N.); (S.P.A.); (P.K.)
- Institute of Animal Physiology and Genetics of the CAS, 60200 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, 65691 Brno, Czech Republic
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Van Bergen NJ, Massey S, Stait T, Ellery M, Reljić B, Formosa LE, Quigley A, Dottori M, Thorburn D, Stroud DA, Christodoulou J. Abnormalities of mitochondrial dynamics and bioenergetics in neuronal cells from CDKL5 deficiency disorder. Neurobiol Dis 2021; 155:105370. [PMID: 33905871 DOI: 10.1016/j.nbd.2021.105370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/01/2021] [Accepted: 04/20/2021] [Indexed: 01/29/2023] Open
Abstract
CDKL5 deficiency disorder (CDD) is a rare neurodevelopmental disorder caused by pathogenic variants in the Cyclin-dependent kinase-like 5 (CDKL5) gene, resulting in dysfunctional CDKL5 protein. It predominantly affects females and causes seizures in the first few months of life, ultimately resulting in severe intellectual disability. In the absence of targeted therapies, treatment is currently only symptomatic. CDKL5 is a serine/threonine kinase that is highly expressed in the brain, with a critical role in neuronal development. Evidence of mitochondrial dysfunction in CDD is gathering, but has not been studied extensively. We used human patient-derived induced pluripotent stem cells with a pathogenic truncating mutation (p.Arg59*) and CRISPR/Cas9 gene-corrected isogenic controls, differentiated into neurons, to investigate the impact of CDKL5 mutation on cellular function. Quantitative proteomics indicated mitochondrial defects in CDKL5 p.Arg59* neurons, and mitochondrial bioenergetics analysis confirmed decreased activity of mitochondrial respiratory chain complexes. Additionally, mitochondrial trafficking velocity was significantly impaired, and there was a higher percentage of stationary mitochondria. We propose mitochondrial dysfunction is contributing to CDD pathology, and should be a focus for development of targeted treatments for CDD.
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Affiliation(s)
- Nicole J Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Tegan Stait
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Molly Ellery
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Boris Reljić
- Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Anita Quigley
- Electrical and Biomedical Engineering, College of Science, Engineering and Health, RMIT University, Melbourne, Victoria 3000, Australia; Department of Medicine, University of Melbourne, St Vincent's Hospital Melbourne, Fitzroy, Victoria 3065, Australia; BioFab3D@ACMD, St Vincent's Hospital Melbourne, Fitzroy, Victoria 3065, Australia
| | - Mirella Dottori
- Centre for Neural Engineering, The University of Melbourne, Carlton, VIC 3010, Australia; Illawarra Health and Medical Research Institute, Centre for Molecular and Medical Bioscience, University of Wollongong, Wollongong, New South Wales 2500, Australia
| | - David Thorburn
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David A Stroud
- Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia; Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia.
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Park K, Li C, Tsiropoulou S, Gonçalves J, Kondratev C, Pelletier L, Blacque OE, Leroux MR. CDKL kinase regulates the length of the ciliary proximal segment. Curr Biol 2021; 31:2359-2373.e7. [PMID: 33857430 DOI: 10.1016/j.cub.2021.03.068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/25/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022]
Abstract
Cilia are organelles found throughout most unicellular eukaryotes and different metazoan cell types. To accomplish their essential roles in cell motility, fluid flow, and signaling, cilia are divided into subcompartments with variable structures, compositions, and functions. How these specific subcompartments are built remains almost completely unexplored. Here, we show that C. elegans CDKL-1, related to the human CDKL kinase family (CDKL1/CDKL2/CDKL3/CDKL4/CDKL5), specifically controls the length of the proximal segment, a ciliary subdomain conserved in evolution from Tetrahymena motile cilia to C. elegans chemosensory, mammalian olfactory, and photoreceptor non-motile cilia. CDKL-1 associates with intraflagellar transport (IFT), influences the distribution of the IFT anterograde motors heterotrimeric kinesin-II and homodimeric OSM-3-kinesin/KIF17 in the proximal segment, and shifts the boundary between the proximal and distal segments (PS/DS boundary). CDKL-1 appears to function independently from several factors that influence cilium length, namely the kinases DYF-5 (mammalian CILK1/MAK) and NEKL-1 (NEK9), as well as the depolymerizing kinesins KLP-13 (KIF19) and KLP-7 (KIF2). However, a different kinase, DYF-18 (CCRK), is needed for the correct localization and function of CDKL-1 and similarly influences the length of the proximal segment. Loss of CDKL-1, which affects proximal segment length without impairing overall ciliary microtubule structural integrity, also impairs cilium-dependent processes, namely cGMP-signaling-dependent body length control and CO2 avoidance. Collectively, our findings suggest that cilium length is regulated by various pathways and that the IFT-associated kinase CDKL-1 is essential for the construction of a specific ciliary compartment and contributes to development and sensory physiology.
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Affiliation(s)
- Kwangjin Park
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada; Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Chunmei Li
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada; Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Sofia Tsiropoulou
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - João Gonçalves
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Christine Kondratev
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada; Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada; Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.
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Liu S, Trupiano MX, Simon J, Guo J, Anton ES. The essential role of primary cilia in cerebral cortical development and disorders. Curr Top Dev Biol 2021; 142:99-146. [PMID: 33706927 DOI: 10.1016/bs.ctdb.2020.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Primary cilium, first described in the 19th century in different cell types and organisms by Alexander Ecker, Albert Kolliker, Aleksandr Kowalevsky, Paul Langerhans, and Karl Zimmermann (Ecker, 1844; Kolliker, 1854; Kowalevsky, 1867; Langerhans, 1876; Zimmermann, 1898), play an essential modulatory role in diverse aspects of nervous system development and function. The primary cilium, sometimes referred to as the cell's 'antennae', can receive wide ranging inputs from cellular milieu, including morphogens, growth factors, neuromodulators, and neurotransmitters. Its unique structural and functional organization bequeaths it the capacity to hyper-concentrate signaling machinery in a restricted cellular domain approximately one-thousandth the volume of cell soma. Thus enabling it to act as a signaling hub that integrates diverse developmental and homestatic information from cellular milieu to regulate the development and function of neural cells. Dysfunction of primary cilia contributes to the pathophysiology of several brain malformations, intellectual disabilities, epilepsy, and psychiatric disorders. This review focuses on the most essential contributions of primary cilia to cerebral cortical development and function, in the context of neurodevelopmental disorders and malformations. It highlights the recent progress made in identifying the mechanisms underlying primary cilia's role in cortical progenitors, neurons and glia, in health and disease. A future challenge will be to translate these insights and advances into effective clinical treatments for ciliopathies.
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Affiliation(s)
- Siling Liu
- UNC Neuroscience Center and the Department of Cell and Molecular Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Mia X Trupiano
- UNC Neuroscience Center and the Department of Cell and Molecular Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Jeremy Simon
- UNC Neuroscience Center and the Department of Cell and Molecular Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Jiami Guo
- Hotchkiss Brain Institute, Alberta Children's Hospital Research Institute, and the Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
| | - E S Anton
- UNC Neuroscience Center and the Department of Cell and Molecular Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, United States.
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CDKL2 Is Associated with HER2 Status and Overall Survival in Gastric Cancer: Comparative Analysis of CDKL2 Protein Expression and Gene Copy Number. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1712723. [PMID: 33178818 PMCID: PMC7648667 DOI: 10.1155/2020/1712723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/27/2020] [Accepted: 10/08/2020] [Indexed: 01/01/2023]
Abstract
Background Cyclin-dependent kinase-like 2 (CDKL2) is a member of the CDKL family and recognized as a novel regulator of epithelial-mesenchymal transition of breast cancer cells, but its role has not been explored in gastric cancer (GC). This study was to characterize the CDKL2 protein expression and gene copy number in relation to human epidermal growth factor receptor 2 (HER2) status, clinicopathological features, and overall survival (OS) in GC. Methods This study detected the CDKL2 protein expression and gene copy number by immunochemistry (IHC) and fluorescent in situ hybridization (FISH), respectively, in 334 GC samples. HER2 status was determined according to established criteria. Associations of the CDKL2 protein expression and gene copy number with OS in GC were evaluated, and the association between CDKL2 mRNA expression and OS in GC was also analyzed using TCGA data. Results The detection results suggested that 34.1% cases showed high CDKL2 protein expression; 11.4% cases had ≥5 copies of CDKL2 gene or a ratio of CDKL2 to chromosome of ≥2. The CDKL2 protein expression was markedly correlated with its gene copy number. High protein expression and high gene copy number were both significantly associated with positive HER2 status, and they both could predicted a shorter OS, although not as independent markers suggested by the multivariate Cox proportional hazard regression analysis. The TCGA data indicated that higher CDKL2 mRNA level also predicted a shorter OS in GC. Conclusions The combined detection of the CDKL2 protein level and gene copy number could be of important value in predicting HER2 status and prognosis of patients with GC.
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Kim JY, Bai Y, Jayne LA, Cianciolo RE, Bajwa A, Pabla NS. Involvement of the CDKL5-SOX9 signaling axis in rhabdomyolysis-associated acute kidney injury. Am J Physiol Renal Physiol 2020; 319:F920-F929. [PMID: 33044867 DOI: 10.1152/ajprenal.00429.2020] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Acute kidney injury (AKI) is a common clinical syndrome associated with adverse short- and long-term sequelae. Renal tubular epithelial cell (RTEC) dysfunction and cell death are among the key pathological features of AKI. Diverse systemic and localized stress conditions such as sepsis, rhabdomyolysis, cardiac surgery, and nephrotoxic drugs can trigger RTEC dysfunction. Through an unbiased RNA inhibition screen, we recently identified cyclin-dependent kinase-like 5 (Cdkl5), also known as serine/threonine kinase-9, as a critical regulator of RTEC dysfunction associated with nephrotoxic and ischemia-associated AKI. In the present study, we examined the role of Cdkl5 in rhabdomyolysis-associated AKI. Using activation-specific antibodies and kinase assays, we found that Cdkl5 is activated in RTECs early during the development of rhabdomyolysis-associated AKI. Furthermore, we found that RTEC-specific Cdkl5 gene ablation mitigates rhabdomyolysis-associated renal impairment. In addition, the small-molecule kinase inhibitor AST-487 alleviated rhabdomyolysis-associated AKI in a Cdkl5-dependent manner. Mechanistically, we demonstrated that Cdkl5 phosphorylates the transcriptional regulator sex-determining region Y box 9 (Sox9) and suppresses its protective function under stress conditions. On the basis of these results, we propose that, by suppressing the protective Sox9-directed transcriptional program, Cdkl5 contributes to rhabdomyolysis-associated renal impairment. All together, the present study identified Cdkl5 as a critical stress-induced kinase that drives RTEC dysfunction and kidney injury linked with distinct etiologies.
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Affiliation(s)
- Ji Young Kim
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Yuntao Bai
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Laura A Jayne
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Rachel E Cianciolo
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio
| | - Amandeep Bajwa
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, College of Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Navjot Singh Pabla
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
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Uzquiano A, Cifuentes-Diaz C, Jabali A, Romero DM, Houllier A, Dingli F, Maillard C, Boland A, Deleuze JF, Loew D, Mancini GMS, Bahi-Buisson N, Ladewig J, Francis F. Mutations in the Heterotopia Gene Eml1/EML1 Severely Disrupt the Formation of Primary Cilia. Cell Rep 2020; 28:1596-1611.e10. [PMID: 31390572 DOI: 10.1016/j.celrep.2019.06.096] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/31/2019] [Accepted: 06/27/2019] [Indexed: 02/06/2023] Open
Abstract
Apical radial glia (aRGs) are predominant progenitors during corticogenesis. Perturbing their function leads to cortical malformations, including subcortical heterotopia (SH), characterized by the presence of neurons below the cortex. EML1/Eml1 mutations lead to SH in patients, as well as to heterotopic cortex (HeCo) mutant mice. In HeCo mice, some aRGs are abnormally positioned away from the ventricular zone (VZ). Thus, unraveling EML1/Eml1 function will clarify mechanisms maintaining aRGs in the VZ. We pinpoint an unknown EML1/Eml1 function in primary cilium formation. In HeCo aRGs, cilia are shorter, less numerous, and often found aberrantly oriented within vesicles. Patient fibroblasts and human cortical progenitors show similar defects. EML1 interacts with RPGRIP1L, a ciliary protein, and RPGRIP1L mutations were revealed in a heterotopia patient. We also identify Golgi apparatus abnormalities in EML1/Eml1 mutant cells, potentially upstream of the cilia phenotype. We thus reveal primary cilia mechanisms impacting aRG dynamics in physiological and pathological conditions.
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Affiliation(s)
- Ana Uzquiano
- INSERM U 1270, Paris, France; Sorbonne University, UMR-S 1270, 75005 Paris, France; Institut du Fer à Moulin, Paris, France
| | - Carmen Cifuentes-Diaz
- INSERM U 1270, Paris, France; Sorbonne University, UMR-S 1270, 75005 Paris, France; Institut du Fer à Moulin, Paris, France
| | - Ammar Jabali
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; HITBR Hector Institute for Translational Brain Research gGmbH, Mannheim, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Delfina M Romero
- INSERM U 1270, Paris, France; Sorbonne University, UMR-S 1270, 75005 Paris, France; Institut du Fer à Moulin, Paris, France
| | - Anne Houllier
- INSERM U 1270, Paris, France; Sorbonne University, UMR-S 1270, 75005 Paris, France; Institut du Fer à Moulin, Paris, France
| | - Florent Dingli
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Paris, France
| | - Camille Maillard
- Laboratory of Genetics and Development of the Cerebral Cortex, INSERM UMR1163 Imagine Institute, Paris, France; Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, 91057 Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, 91057 Evry, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Paris, France
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015CN Rotterdam, the Netherlands
| | - Nadia Bahi-Buisson
- Laboratory of Genetics and Development of the Cerebral Cortex, INSERM UMR1163 Imagine Institute, Paris, France; Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France; Pediatric Neurology APHP-Necker Enfants Malades University Hospital, Paris, France; Centre de Référence, Déficiences Intellectuelles de Causes Rares, APHP-Necker Enfants Malades University Hospital, Paris, France
| | - Julia Ladewig
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; HITBR Hector Institute for Translational Brain Research gGmbH, Mannheim, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Fiona Francis
- INSERM U 1270, Paris, France; Sorbonne University, UMR-S 1270, 75005 Paris, France; Institut du Fer à Moulin, Paris, France.
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Cyclin-Dependent Kinase-Like 5 (CDKL5): Possible Cellular Signalling Targets and Involvement in CDKL5 Deficiency Disorder. Neural Plast 2020; 2020:6970190. [PMID: 32587608 PMCID: PMC7293752 DOI: 10.1155/2020/6970190] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/29/2022] Open
Abstract
Cyclin-dependent kinase-like 5 (CDKL5, also known as STK9) is a serine/threonine protein kinase originally identified in 1998 during a transcriptional mapping project of the human X chromosome. Thereafter, a mutation in CDKL5 was reported in individuals with the atypical Rett syndrome, a neurodevelopmental disorder, suggesting that CDKL5 plays an important regulatory role in neuronal function. The disease associated with CDKL5 mutation has recently been recognised as CDKL5 deficiency disorder (CDD) and has been distinguished from the Rett syndrome owing to its symptomatic manifestation. Because CDKL5 mutations identified in patients with CDD cause enzymatic loss of function, CDKL5 catalytic activity is likely strongly associated with the disease. Consequently, the exploration of CDKL5 substrate characteristics and regulatory mechanisms of its catalytic activity are important for identifying therapeutic target molecules and developing new treatment. In this review, we summarise recent findings on the phosphorylation of CDKL5 substrates and the mechanisms of CDKL5 phosphorylation and dephosphorylation. We also discuss the relationship between changes in the phosphorylation signalling pathways and the Cdkl5 knockout mouse phenotype and consider future prospects for the treatment of mental and neurological disease associated with CDKL5 mutations.
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38
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Kim JY, Bai Y, Jayne LA, Hector RD, Persaud AK, Ong SS, Rojesh S, Raj R, Feng MJHH, Chung S, Cianciolo RE, Christman JW, Campbell MJ, Gardner DS, Baker SD, Sparreboom A, Govindarajan R, Singh H, Chen T, Poi M, Susztak K, Cobb SR, Pabla NS. A kinome-wide screen identifies a CDKL5-SOX9 regulatory axis in epithelial cell death and kidney injury. Nat Commun 2020; 11:1924. [PMID: 32317630 PMCID: PMC7174303 DOI: 10.1038/s41467-020-15638-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 03/21/2020] [Indexed: 12/18/2022] Open
Abstract
Renal tubular epithelial cells (RTECs) perform the essential function of maintaining the constancy of body fluid composition and volume. Toxic, inflammatory, or hypoxic-insults to RTECs can cause systemic fluid imbalance, electrolyte abnormalities and metabolic waste accumulation- manifesting as acute kidney injury (AKI), a common disorder associated with adverse long-term sequelae and high mortality. Here we report the results of a kinome-wide RNAi screen for cellular pathways involved in AKI-associated RTEC-dysfunction and cell death. Our screen and validation studies reveal an essential role of Cdkl5-kinase in RTEC cell death. In mouse models, genetic or pharmacological Cdkl5 inhibition mitigates nephrotoxic and ischemia-associated AKI. We propose that Cdkl5 is a stress-responsive kinase that promotes renal injury in part through phosphorylation-dependent suppression of pro-survival transcription regulator Sox9. These findings reveal a surprising non-neuronal function of Cdkl5, identify a pathogenic Cdkl5-Sox9 axis in epithelial cell-death, and support CDKL5 antagonism as a therapeutic approach for AKI. Protein kinases have emerged as critical regulators of disease pathogenesis. Here, the authors have utilized kinome-wide screening approaches to reveal a pathogenic role of CDKL5 kinase in acute kidney injury, which is dependent on suppression of a SOX9-associated transcriptional network.
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Affiliation(s)
- Ji Young Kim
- Division of Pharmaceutics & Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Yuntao Bai
- Division of Pharmaceutics & Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Laura A Jayne
- Division of Pharmaceutics & Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Ralph D Hector
- Simons Initiative for the Developing Brain & Patrick Wild Centre, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Avinash K Persaud
- Division of Pharmaceutics & Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Pharmacy Practice and Science, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Su Sien Ong
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shreshtha Rojesh
- Renal Electrolyte and Hypertension Division, Department of Medicine and Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Radhika Raj
- Division of Pharmaceutics & Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Mei Ji He Ho Feng
- Division of Pharmaceutics & Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Sangwoon Chung
- Pulmonary, Sleep and Critical Care Medicine, Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, USA
| | - Rachel E Cianciolo
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - John W Christman
- Pulmonary, Sleep and Critical Care Medicine, Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, USA
| | - Moray J Campbell
- Division of Pharmaceutics & Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - David S Gardner
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, UK
| | - Sharyn D Baker
- Division of Pharmaceutics & Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alex Sparreboom
- Division of Pharmaceutics & Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Rajgopal Govindarajan
- Division of Pharmaceutics & Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Harpreet Singh
- Department of Physiology and Cell Biology and Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Taosheng Chen
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ming Poi
- Division of Pharmaceutics & Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Pharmacy Practice and Science, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, Department of Medicine and Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Stuart R Cobb
- Simons Initiative for the Developing Brain & Patrick Wild Centre, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Navjot Singh Pabla
- Division of Pharmaceutics & Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
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39
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Liu X, Chen W, Li W, Priest JR, Fu Y, Pang K, Ma B, Han B, Liu X, Hu S, Zhou Z. Exome-Based Case-Control Analysis Highlights the Pathogenic Role of Ciliary Genes in Transposition of the Great Arteries. Circ Res 2020; 126:811-821. [PMID: 32078439 DOI: 10.1161/circresaha.119.315821] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE Transposition of the great arteries (TGA) is one of the most severe types of congenital heart diseases. Understanding the clinical characteristics and pathogenesis of TGA is, therefore, urgently needed for patient management of this severe disease. However, the clinical characteristics and genetic cause underlying TGA remain largely unexplored. OBJECTIVE We sought to systematically examine the clinical characteristics and genetic cause for isolated nonsyndromic TGA. METHODS AND RESULTS We recruited 249 patients with TGA (66 family trios) and performed whole-exome sequencing. The incidence of patent ductus arteriosus in dextro-TGA (52.7%) and dextrocardia/mesocardia in congenitally corrected TGA (32.8%) were significantly higher than that in other subtypes. A high prevalence of bicuspid pulmonic valve (9.6%) was observed in patients with TGA. Similar results were observed in a replication group of TGA (n=132). Through a series of bioinformatics filtering steps, we obtained 82 candidate genes harboring potentially damaging de novo, loss of function, compound heterozygous, or X-linked recessive variants. Established congenital heart disease-causing genes, such as FOXH1, were found among the list of candidate genes. A total of 19 ciliary genes harboring rare potentially damaging variants were also found; for example, DYNC2LI1 with a de novo putatively damaging variant. The enrichment of ciliary genes supports the roles of cilia in the pathogenesis of TGA. In total, 33% of the TGA probands had >1 candidate gene hit by putatively deleterious variants, suggesting that a portion of the TGA cases were probably affected by oligogenic or polygenic inheritance. CONCLUSIONS The findings of clinical characteristic analyses have important implications for TGA patient stratification. The results of genetic analyses highlight the pathogenic role of ciliary genes and a complex genetic architecture underlying TGA.
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Affiliation(s)
- Xuanyu Liu
- From the State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (Xuanyu Liu, W.C., W.L., Y.F., B.M., B.H., Xuewen Liu, S.H., Z.Z.).,Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, China (Xuanyu Liu, W.C., W.L., Y.F., Z.Z.)
| | - Wen Chen
- From the State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (Xuanyu Liu, W.C., W.L., Y.F., B.M., B.H., Xuewen Liu, S.H., Z.Z.).,Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, China (Xuanyu Liu, W.C., W.L., Y.F., Z.Z.)
| | - Wenke Li
- Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, China (Xuanyu Liu, W.C., W.L., Y.F., Z.Z.)
| | - James R Priest
- Department of Pediatrics, Stanford University School of Medicine, CA (J.R.P.)
| | - Yuanyuan Fu
- From the State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (Xuanyu Liu, W.C., W.L., Y.F., B.M., B.H., Xuewen Liu, S.H., Z.Z.).,Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, China (Xuanyu Liu, W.C., W.L., Y.F., Z.Z.)
| | - Kunjing Pang
- Department of Echocardiography, Fuwai Hospital, Beijing, China (K.P.)
| | - Baihui Ma
- From the State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (Xuanyu Liu, W.C., W.L., Y.F., B.M., B.H., Xuewen Liu, S.H., Z.Z.)
| | - Bianmei Han
- From the State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (Xuanyu Liu, W.C., W.L., Y.F., B.M., B.H., Xuewen Liu, S.H., Z.Z.)
| | - Xuewen Liu
- From the State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (Xuanyu Liu, W.C., W.L., Y.F., B.M., B.H., Xuewen Liu, S.H., Z.Z.)
| | - Shengshou Hu
- From the State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (Xuanyu Liu, W.C., W.L., Y.F., B.M., B.H., Xuewen Liu, S.H., Z.Z.)
| | - Zhou Zhou
- From the State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (Xuanyu Liu, W.C., W.L., Y.F., B.M., B.H., Xuewen Liu, S.H., Z.Z.).,Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, China (Xuanyu Liu, W.C., W.L., Y.F., Z.Z.)
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40
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Fahmi M, Yasui G, Seki K, Katayama S, Kaneko-Kawano T, Inazu T, Kubota Y, Ito M. In Silico Study of Rett Syndrome Treatment-Related Genes, MECP2, CDKL5, and FOXG1, by Evolutionary Classification and Disordered Region Assessment. Int J Mol Sci 2019; 20:ijms20225593. [PMID: 31717404 PMCID: PMC6888432 DOI: 10.3390/ijms20225593] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 12/28/2022] Open
Abstract
Rett syndrome (RTT), a neurodevelopmental disorder, is mainly caused by mutations in methyl CpG-binding protein 2 (MECP2), which has multiple functions such as binding to methylated DNA or interacting with a transcriptional co-repressor complex. It has been established that alterations in cyclin-dependent kinase-like 5 (CDKL5) or forkhead box protein G1 (FOXG1) correspond to distinct neurodevelopmental disorders, given that a series of studies have indicated that RTT is also caused by alterations in either one of these genes. We investigated the evolution and molecular features of MeCP2, CDKL5, and FOXG1 and their binding partners using phylogenetic profiling to gain a better understanding of their similarities. We also predicted the structural order-disorder propensity and assessed the evolutionary rates per site of MeCP2, CDKL5, and FOXG1 to investigate the relationships between disordered structure and other related properties with RTT. Here, we provide insight to the structural characteristics, evolution and interaction landscapes of those three proteins. We also uncovered the disordered structure properties and evolution of those proteins which may provide valuable information for the development of therapeutic strategies of RTT.
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Affiliation(s)
- Muhamad Fahmi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; (M.F.); (G.Y.); (K.S.)
| | - Gen Yasui
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; (M.F.); (G.Y.); (K.S.)
| | - Kaito Seki
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; (M.F.); (G.Y.); (K.S.)
| | - Syouichi Katayama
- Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; (S.K.); (T.K.-K.); (T.I.)
| | - Takako Kaneko-Kawano
- Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; (S.K.); (T.K.-K.); (T.I.)
| | - Tetsuya Inazu
- Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; (S.K.); (T.K.-K.); (T.I.)
| | - Yukihiko Kubota
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan;
| | - Masahiro Ito
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; (M.F.); (G.Y.); (K.S.)
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan;
- Correspondence:
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41
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Dickson DW, Baker MC, Jackson JL, DeJesus-Hernandez M, Finch NA, Tian S, Heckman MG, Pottier C, Gendron TF, Murray ME, Ren Y, Reddy JS, Graff-Radford NR, Boeve BF, Petersen RC, Knopman DS, Josephs KA, Petrucelli L, Oskarsson B, Sheppard JW, Asmann YW, Rademakers R, van Blitterswijk M. Extensive transcriptomic study emphasizes importance of vesicular transport in C9orf72 expansion carriers. Acta Neuropathol Commun 2019; 7:150. [PMID: 31594549 PMCID: PMC6781370 DOI: 10.1186/s40478-019-0797-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 08/24/2019] [Indexed: 12/12/2022] Open
Abstract
The majority of the clinico-pathological variability observed in patients harboring a repeat expansion in the C9orf72-SMCR8 complex subunit (C9orf72) remains unexplained. This expansion, which represents the most common genetic cause of frontotemporal lobar degeneration (FTLD) and motor neuron disease (MND), results in a loss of C9orf72 expression and the generation of RNA foci and dipeptide repeat (DPR) proteins. The C9orf72 protein itself plays a role in vesicular transport, serving as a guanine nucleotide exchange factor that regulates GTPases. To further elucidate the mechanisms underlying C9orf72-related diseases and to identify potential disease modifiers, we performed an extensive RNA sequencing study. We included individuals for whom frontal cortex tissue was available: FTLD and FTLD/MND patients with (n = 34) or without (n = 44) an expanded C9orf72 repeat as well as control subjects (n = 24). In total, 6706 genes were differentially expressed between these groups (false discovery rate [FDR] < 0.05). The top gene was C9orf72 (FDR = 1.41E-14), which was roughly two-fold lower in C9orf72 expansion carriers than in (disease) controls. Co-expression analysis revealed groups of correlated genes (modules) that were enriched for processes such as protein folding, RNA splicing, synaptic signaling, metabolism, and Golgi vesicle transport. Within our cohort of C9orf72 expansion carriers, machine learning uncovered interesting candidates associated with clinico-pathological features, including age at onset (vascular endothelial growth factor A [VEGFA]), C9orf72 expansion size (cyclin dependent kinase like 1 [CDKL1]), DPR protein levels (eukaryotic elongation factor 2 kinase [EEF2K]), and survival after onset (small G protein signaling modulator 3 [SGSM3]). Given the fact that we detected a module involved in vesicular transport in addition to a GTPase activator (SGSM3) as a potential modifier, our findings seem to suggest that the presence of a C9orf72 repeat expansion might hamper vesicular transport and that genes affecting this process may modify the phenotype of C9orf72-linked diseases.
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Affiliation(s)
- Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Matthew C. Baker
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Jazmyne L. Jackson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | | | - NiCole A. Finch
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Shulan Tian
- Department of Health Sciences Research, Mayo Clinic, 200 1st St SW, Rochester, MN 55905 USA
| | - Michael G. Heckman
- Division of Biomedical Statistics and Informatics, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Cyril Pottier
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Tania F. Gendron
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Melissa E. Murray
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Yingxue Ren
- Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Joseph S. Reddy
- Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | | | - Bradley F. Boeve
- Department of Neurology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905 USA
| | - Ronald C. Petersen
- Department of Neurology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905 USA
| | - David S. Knopman
- Department of Neurology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905 USA
| | - Keith A. Josephs
- Department of Neurology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905 USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Björn Oskarsson
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - John W. Sheppard
- Gianforte School of Computing, Montana State University, 357 Barnard Hall, Bozeman, MT 59717 USA
| | - Yan W. Asmann
- Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Marka van Blitterswijk
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
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42
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Barbiero I, De Rosa R, Kilstrup-Nielsen C. Microtubules: A Key to Understand and Correct Neuronal Defects in CDKL5 Deficiency Disorder? Int J Mol Sci 2019; 20:E4075. [PMID: 31438497 PMCID: PMC6747382 DOI: 10.3390/ijms20174075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 02/06/2023] Open
Abstract
CDKL5 deficiency disorder (CDD) is a severe neurodevelopmental encephalopathy caused by mutations in the X-linked CDKL5 gene that encodes a serine/threonine kinase. CDD is characterised by the early onset of seizures and impaired cognitive and motor skills. Loss of CDKL5 in vitro and in vivo affects neuronal morphology at early and late stages of maturation, suggesting a link between CDKL5 and the neuronal cytoskeleton. Recently, various microtubule (MT)-binding proteins have been identified as interactors of CDKL5, indicating that its roles converge on regulating MT functioning. MTs are dynamic structures that are important for neuronal morphology, migration and polarity. The delicate control of MT dynamics is fundamental for proper neuronal functions, as evidenced by the fact that aberrant MT dynamics are involved in various neurological disorders. In this review, we highlight the link between CDKL5 and MTs, discussing how CDKL5 deficiency may lead to deranged neuronal functions through aberrant MT dynamics. Finally, we discuss whether the regulation of MT dynamics through microtubule-targeting agents may represent a novel strategy for future pharmacological approaches in the CDD field.
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Affiliation(s)
- Isabella Barbiero
- Department of Biotechnology and Life Sciences, (DBSV), University of Insubria, Via Manara 7, 21052 Busto Arsizio (VA), Italy
| | - Roberta De Rosa
- Department of Biotechnology and Life Sciences, (DBSV), University of Insubria, Via Manara 7, 21052 Busto Arsizio (VA), Italy
| | - Charlotte Kilstrup-Nielsen
- Department of Biotechnology and Life Sciences, (DBSV), University of Insubria, Via Manara 7, 21052 Busto Arsizio (VA), Italy.
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43
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Graham SE, Nielsen JB, Zawistowski M, Zhou W, Fritsche LG, Gabrielsen ME, Skogholt AH, Surakka I, Hornsby WE, Fermin D, Larach DB, Kheterpal S, Brummett CM, Lee S, Kang HM, Abecasis GR, Romundstad S, Hallan S, Sampson MG, Hveem K, Willer CJ. Sex-specific and pleiotropic effects underlying kidney function identified from GWAS meta-analysis. Nat Commun 2019; 10:1847. [PMID: 31015462 PMCID: PMC6478837 DOI: 10.1038/s41467-019-09861-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 04/03/2019] [Indexed: 12/19/2022] Open
Abstract
Chronic kidney disease (CKD) is a growing health burden currently affecting 10–15% of adults worldwide. Estimated glomerular filtration rate (eGFR) as a marker of kidney function is commonly used to diagnose CKD. We analyze eGFR data from the Nord-Trøndelag Health Study and Michigan Genomics Initiative and perform a GWAS meta-analysis with public summary statistics, more than doubling the sample size of previous meta-analyses. We identify 147 loci (53 novel) associated with eGFR, including genes involved in transcriptional regulation, kidney development, cellular signaling, metabolism, and solute transport. Additionally, sex-stratified analysis identifies one locus with more significant effects in women than men. Using genetic risk scores constructed from these eGFR meta-analysis results, we show that associated variants are generally predictive of CKD with only modest improvements in detection compared with other known clinical risk factors. Collectively, these results yield additional insight into the genetic factors underlying kidney function and progression to CKD. Estimated glomerular filtration rate (eGFR) is a measure of kidney function and used to characterize chronic kidney disease. Here, Graham et al. identify 53 novel loci for eGFR in a GWAS meta-analysis, a subset of which are associated with other common diseases, such as diabetes and hypertension, based on PheWAS.
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Affiliation(s)
- Sarah E Graham
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Jonas B Nielsen
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Matthew Zawistowski
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Lars G Fritsche
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | - Anne Heidi Skogholt
- K.G. Jebsen Center for Genetic Epidemiology, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | - Ida Surakka
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Whitney E Hornsby
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Damian Fermin
- Department of Pediatrics: Pediatric Nephrology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Daniel B Larach
- Department of Anesthesiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Sachin Kheterpal
- Department of Anesthesiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Chad M Brummett
- Department of Anesthesiology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Seunggeun Lee
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Hyun Min Kang
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Goncalo R Abecasis
- Department of Biostatistics: Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Solfrid Romundstad
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Internal Medicine, Levanger Hospital, Health Trust Nord-Trøndelag, Levanger, 7600, Norway
| | - Stein Hallan
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway.,Department of Nephrology, St Olav Hospital, Trondheim, 7491, Norway
| | - Matthew G Sampson
- Department of Pediatrics: Pediatric Nephrology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway. .,Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491, Norway. .,HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, 7600, Norway.
| | - Cristen J Willer
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, 48109, MI, USA. .,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, MI, USA. .,Department of Human Genetics, University of Michigan, Ann Arbor, 48109, MI, USA.
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44
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Li W, Cao J, Liu J, Chu W, Zhang C, Chen S, Kang Z. Downregulation of CDKL1 suppresses neuroblastoma cell proliferation, migration and invasion. Cell Mol Biol Lett 2019; 24:19. [PMID: 30891073 PMCID: PMC6407201 DOI: 10.1186/s11658-019-0139-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 02/11/2019] [Indexed: 01/28/2023] Open
Abstract
Background Cyclin-dependent kinase-like 1 (CDKL1) is a member of the cell division control protein 2-related serine–threonine protein kinase family. It is known to occur in various malignant tumors, but its role in neuroblastoma (NB) remains unclear. Methods We constructed a CDKL1-silenced NB cell strain (SH-SY5Y) and used real-time PCR and western blotting to confirm the silencing. Functional analyses were performed using the MTT, colony-formation, FACS, wound-healing and transwell invasion assays. Results The expression of CDKL1 was significantly upregulated in NB tissue as compared to the adjacent normal tissue. CDKL1 knockdown significantly suppressed cell viability and colony formation ability. It also induced cell cycle G0/G1 phase arrest and apoptosis, and suppressed the migration and invasion ability of SH-SY5Y cells. CDKL1 knockdown decreased the CDK4, cyclin D1 and vimentin expression levels, and increased the caspase-3, PARP and E-cadherin expression levels in SH-SY5Y cells. Conclusions Our findings suggest that CDKL1 plays an important role in NB cell proliferation, migration and invasion. It might serve as a potential target for NB therapy.
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Affiliation(s)
- Weiyi Li
- 1Eye Hospital, China Academy of Chinese Medical Sciences, No 33 Lugu Road, Shijingshan district, Beijing, 100040 China
| | - Jing Cao
- Yinan Branch of Qilu Hospital of Shandong University, Linyi, Shandong China
| | - Jian Liu
- 1Eye Hospital, China Academy of Chinese Medical Sciences, No 33 Lugu Road, Shijingshan district, Beijing, 100040 China
| | - Wenli Chu
- 1Eye Hospital, China Academy of Chinese Medical Sciences, No 33 Lugu Road, Shijingshan district, Beijing, 100040 China
| | - Congqing Zhang
- 1Eye Hospital, China Academy of Chinese Medical Sciences, No 33 Lugu Road, Shijingshan district, Beijing, 100040 China
| | - Shuiling Chen
- 1Eye Hospital, China Academy of Chinese Medical Sciences, No 33 Lugu Road, Shijingshan district, Beijing, 100040 China
| | - Zefeng Kang
- 1Eye Hospital, China Academy of Chinese Medical Sciences, No 33 Lugu Road, Shijingshan district, Beijing, 100040 China
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45
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Cilia Distal Domain: Diversity in Evolutionarily Conserved Structures. Cells 2019; 8:cells8020160. [PMID: 30769894 PMCID: PMC6406257 DOI: 10.3390/cells8020160] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/25/2019] [Accepted: 02/13/2019] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic cilia are microtubule-based organelles that protrude from the cell surface to fulfill sensory and motility functions. Their basic structure consists of an axoneme templated by a centriole/basal body. Striking differences in ciliary ultra-structures can be found at the ciliary base, the axoneme and the tip, not only throughout the eukaryotic tree of life, but within a single organism. Defects in cilia biogenesis and function are at the origin of human ciliopathies. This structural/functional diversity and its relationship with the etiology of these diseases is poorly understood. Some of the important events in cilia function occur at their distal domain, including cilia assembly/disassembly, IFT (intraflagellar transport) complexes' remodeling, and signal detection/transduction. How axonemal microtubules end at this domain varies with distinct cilia types, originating different tip architectures. Additionally, they show a high degree of dynamic behavior and are able to respond to different stimuli. The existence of microtubule-capping structures (caps) in certain types of cilia contributes to this diversity. It has been proposed that caps play a role in axoneme length control and stabilization, but their roles are still poorly understood. Here, we review the current knowledge on cilia structure diversity with a focus on the cilia distal domain and caps and discuss how they affect cilia structure and function.
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46
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McDiarmid TA, Au V, Loewen AD, Liang J, Mizumoto K, Moerman DG, Rankin CH. CRISPR-Cas9 human gene replacement and phenomic characterization in Caenorhabditis elegans to understand the functional conservation of human genes and decipher variants of uncertain significance. Dis Model Mech 2018; 11:dmm.036517. [PMID: 30361258 PMCID: PMC6307914 DOI: 10.1242/dmm.036517] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/19/2018] [Indexed: 12/13/2022] Open
Abstract
Our ability to sequence genomes has vastly surpassed our ability to interpret the genetic variation we discover. This presents a major challenge in the clinical setting, where the recent application of whole-exome and whole-genome sequencing has uncovered thousands of genetic variants of uncertain significance. Here, we present a strategy for targeted human gene replacement and phenomic characterization, based on CRISPR-Cas9 genome engineering in the genetic model organism Caenorhabditis elegans, that will facilitate assessment of the functional conservation of human genes and structure-function analysis of disease-associated variants with unprecedented precision. We validate our strategy by demonstrating that direct single-copy replacement of the C. elegans ortholog (daf-18) with the critical human disease-associated gene phosphatase and tensin homolog (PTEN) is sufficient to rescue multiple phenotypic abnormalities caused by complete deletion of daf-18, including complex chemosensory and mechanosensory impairments. In addition, we used our strategy to generate animals harboring a single copy of the known pathogenic lipid phosphatase inactive PTEN variant (PTEN-G129E), and showed that our automated in vivo phenotypic assays could accurately and efficiently classify this missense variant as loss of function. The integrated nature of the human transgenes allows for analysis of both homozygous and heterozygous variants and greatly facilitates high-throughput precision medicine drug screens. By combining genome engineering with rapid and automated phenotypic characterization, our strategy streamlines the identification of novel conserved gene functions in complex sensory and learning phenotypes that can be used as in vivo functional assays to decipher variants of uncertain significance.
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Affiliation(s)
- Troy A McDiarmid
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Vinci Au
- Department of Zoology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z4, Canada
| | - Aaron D Loewen
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Joseph Liang
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Kota Mizumoto
- Department of Zoology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z4, Canada
| | - Donald G Moerman
- Department of Zoology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z4, Canada
| | - Catharine H Rankin
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada .,Department of Psychology, University of British Columbia, 2136 West Mall, Vancouver, BC V6T 1Z4, Canada
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47
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Abstract
Mutation or inactivation of CDKL5 kinase is associated with a human neurodevelopmental condition commonly referred to as CDKL5 deficiency disorder.§ Two recent phosphoproteomics studies identify the first physiological substrates of mammalian CDKL5 and evaluate functional consequences of their phosphorylation and its loss in cells lacking functional CDKL5, highlighting potential roles for this kinase in regulating neuronal microtubule dynamics.
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Affiliation(s)
- Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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48
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Muñoz IM, Morgan ME, Peltier J, Weiland F, Gregorczyk M, Brown FC, Macartney T, Toth R, Trost M, Rouse J. Phosphoproteomic screening identifies physiological substrates of the CDKL5 kinase. EMBO J 2018; 37:embj.201899559. [PMID: 30266825 PMCID: PMC6293279 DOI: 10.15252/embj.201899559] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 08/14/2018] [Accepted: 09/10/2018] [Indexed: 12/21/2022] Open
Abstract
Mutations in the gene encoding the protein kinase CDKL5 cause a debilitating neurodevelopmental disease termed CDKL5 disorder. The impact of these mutations on CDKL5 function is poorly understood because the substrates and cellular processes controlled by CDKL5 are unclear. Here, we describe a quantitative phosphoproteomic screening which identified MAP1S, CEP131 and DLG5—regulators of microtubule and centrosome function—as cellular substrates of CDKL5. Antibodies against MAP1S phospho‐Ser900 and CEP131 phospho‐Ser35 confirmed CDKL5‐dependent phosphorylation of these targets in human cells. The phospho‐acceptor serine residues in MAP1S, CEP131 and DLG5 lie in the motif RPXSA, although CDKL5 can tolerate residues other than Ala immediately C‐terminal to the phospho‐acceptor serine. We provide insight into the control of CDKL5 activity and show that pathogenic mutations in CDKL5 cause a major reduction in CDKL5 activity in vitro and in cells. These data reveal the first cellular substrates of CDKL5, which may represent important biomarkers in the diagnosis and treatment of CDKL5 disorder, and illuminate the functions of this poorly characterized kinase.
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Affiliation(s)
- Ivan M Muñoz
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Michael E Morgan
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Julien Peltier
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK.,Faculty of Medical Sciences, Institute for Cell and Molecular Biosciences, Newcastle upon Tyne, UK
| | - Florian Weiland
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Mateusz Gregorczyk
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Fiona Cm Brown
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Thomas Macartney
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK .,Faculty of Medical Sciences, Institute for Cell and Molecular Biosciences, Newcastle upon Tyne, UK
| | - John Rouse
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
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49
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Yi P, Xie C, Ou G. The kinases male germ cell-associated kinase and cell cycle-related kinase regulate kinesin-2 motility inCaenorhabditis elegansneuronal cilia. Traffic 2018; 19:522-535. [DOI: 10.1111/tra.12572] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Peishan Yi
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences and MOE Key Laboratory for Protein Science; Tsinghua University; Beijing China
| | - Chao Xie
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences and MOE Key Laboratory for Protein Science; Tsinghua University; Beijing China
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences and MOE Key Laboratory for Protein Science; Tsinghua University; Beijing China
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