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Roy AS, Feroz T, Islam MK, Munim MA, Supti DA, Antora NJ, Al Reza H, Gosh S, Bahadur NM, Alam MR, Hossain MS. A computational approach for structural and functional analyses of disease-associated mutations in the human CYLD gene. Genomics Inform 2024; 22:4. [PMID: 38907316 PMCID: PMC11184958 DOI: 10.1186/s44342-024-00007-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 12/26/2023] [Indexed: 06/23/2024] Open
Abstract
Tumor suppressor cylindromatosis protein (CYLD) regulates NF-κB and JNK signaling pathways by cleaving K63-linked poly-ubiquitin chain from its substrate molecules and thus preventing the progression of tumorigenesis and metastasis of the cancer cells. Mutations in CYLD can cause aberrant structure and abnormal functionality leading to tumor formation. In this study, we utilized several computational tools such as PANTHER, PROVEAN, PredictSNP, PolyPhen-2, PhD-SNP, PON-P2, and SIFT to find out deleterious nsSNPs. We also highlighted the damaging impact of those deleterious nsSNPs on the structure and function of the CYLD utilizing ConSurf, I-Mutant, SDM, Phyre2, HOPE, Swiss-PdbViewer, and Mutation 3D. We shortlisted 18 high-risk nsSNPs from a total of 446 nsSNPs recorded in the NCBI database. Based on the conservation profile, stability status, and structural impact analysis, we finalized 13 nsSNPs. Molecular docking analysis and molecular dynamic simulation concluded the study with the findings of two significant nsSNPs (R830K, H827R) which have a remarkable impact on binding affinity, RMSD, RMSF, radius of gyration, and hydrogen bond formation during CYLD-ubiquitin interaction. The principal component analysis compared native and two mutants R830K and H827R of CYLD that signify structural and energy profile fluctuations during molecular dynamic (MD) simulation. Finally, the protein-protein interaction network showed CYLD interacts with 20 proteins involved in several biological pathways that mutations can impair. Considering all these in silico analyses, our study recommended conducting large-scale association studies of nsSNPs of CYLD with cancer as well as designing precise medications against diseases associated with these polymorphisms.
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Affiliation(s)
- Arpita Singha Roy
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Tasmiah Feroz
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Md Kobirul Islam
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Md Adnan Munim
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Dilara Akhter Supti
- Department of Food Technology & Nutrition Sciences, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Nusrat Jahan Antora
- Department of Genetic Engineering and Biotechnology, East West University, Dhaka, 1212, Bangladesh
| | - Hasan Al Reza
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Supriya Gosh
- Department of Food Technology & Nutrition Sciences, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Mohammad Rahanur Alam
- Department of Food Technology & Nutrition Sciences, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh.
| | - Md Shahadat Hossain
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh.
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Role of K63-linked ubiquitination in cancer. Cell Death Dis 2022; 8:410. [PMID: 36202787 PMCID: PMC9537175 DOI: 10.1038/s41420-022-01204-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/16/2022] [Accepted: 09/26/2022] [Indexed: 11/08/2022]
Abstract
Ubiquitination is a critical type of post-translational modifications, of which K63-linked ubiquitination regulates interaction, translocation, and activation of proteins. In recent years, emerging evidence suggest involvement of K63-linked ubiquitination in multiple signaling pathways and various human diseases including cancer. Increasing number of studies indicated that K63-linked ubiquitination controls initiation, development, invasion, metastasis, and therapy of diverse cancers. Here, we summarized molecular mechanisms of K63-linked ubiquitination dictating different biological activities of tumor and highlighted novel opportunities for future therapy targeting certain regulation of K63-linked ubiquitination in tumor.
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Pirooznia SK, Wang H, Panicker N, Kumar M, Neifert S, Dar MA, Lau E, Kang BG, Redding-Ochoa J, Troncoso JC, Dawson VL, Dawson TM. Deubiquitinase CYLD acts as a negative regulator of dopamine neuron survival in Parkinson's disease. SCIENCE ADVANCES 2022; 8:eabh1824. [PMID: 35363524 PMCID: PMC10938605 DOI: 10.1126/sciadv.abh1824] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Mutations in PINK1 and parkin highlight the mitochondrial axis of Parkinson's disease (PD) pathogenesis. PINK1/parkin regulation of the transcriptional repressor PARIS bears direct relevance to dopamine neuron survival through augmentation of PGC-1α-dependent mitochondrial biogenesis. Notably, knockout of PARIS attenuates dopaminergic neurodegeneration in mouse models, indicating that interventions that prevent dopaminergic accumulation of PARIS could have therapeutic potential in PD. To this end, we have identified the deubiquitinase cylindromatosis (CYLD) to be a regulator of PARIS protein stability and proteasomal degradation via the PINK1/parkin pathway. Knockdown of CYLD in multiple models of PINK1 or parkin inactivation attenuates PARIS accumulation by modulating its ubiquitination levels and relieving its repressive effect on PGC-1α to promote mitochondrial biogenesis. Together, our studies identify CYLD as a negative regulator of dopamine neuron survival, and inhibition of CYLD may potentially be beneficial in PD by lowering PARIS levels and promoting mitochondrial biogenesis.
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Affiliation(s)
- Sheila K. Pirooznia
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hu Wang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nikhil Panicker
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Manoj Kumar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stewart Neifert
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mohamad Aasif Dar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Evan Lau
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bong Gu Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Javier Redding-Ochoa
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Juan C. Troncoso
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Valina L. Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Ted M. Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Departments of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Umemura S, Zhu J, Chahine JJ, Kallakury B, Chen V, Kim IK, Zhang YW, Goto K, He Y, Giaccone G. Downregulation of CYLD promotes IFN-γ mediated PD-L1 expression in thymic epithelial tumors. Lung Cancer 2020; 147:221-228. [PMID: 32738418 DOI: 10.1016/j.lungcan.2020.07.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/09/2020] [Accepted: 07/16/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Recent genomic studies suggest the biological significance of the cylindromatosis (CYLD) gene in thymic epithelial tumors (TETs). CYLD is a crucial regulator of immune response, and we previously reported that CYLD mutation is associated with high PD-L1 expression in thymic carcinoma. Therefore, we wanted to explore the role and mechanism of CYLD in regulating PD-L1 expression in TETs. MATERIALS AND METHODS The role of CYLD in PD-L1 expression was assessed by knockdown of CYLD in TET cells upon stimulation with interferon gamma (IFN-γ), tumor necrosis factor-α (TNF-α) or polyinosinic-polycytidylic acid (poly I:C). The molecular mechanism was investigated through analysis of downstream molecules in the STAT1/IRF1 pathway. Moreover, the clinical correlation between low CYLD and high PD-L1 expression, and the clinical impact of CYLD expression were evaluated in tissue microarrays of 105 TET cases. RESULTS CYLD knockdown significantly enhanced the expression of PD-L1 in presence of IFN-γ stimulation in most TET cell lines. However, this phenomenon was not observed in presence of TNF-α stimulation. CYLD knockdown upregulated IFN-γ mediated activation of the STAT1/IRF1 axis, which in turn induced PD-L1 expression. Interestingly, we found a significant association between low CYLD expression and ≥ 50 % PD-L1 expression (p = 0.001). In addition, the average proportion of tumor cells exhibiting PD-L1 staining was significantly higher in the low CYLD expression group (24.7 %) than in the high CYLD expression group (5.2 %) (p = 0.005). There was no correlation between CYLD expression and the frequency of pre-existing paraneoplastic auto-immune diseases. In advanced stages (III/IV), the low CYLD expressing group had numerically worse survival than the high CYLD group (log-rank p = 0.089). CONCLUSIONS Our findings provide insight into the mechanism of regulation of PD-L1 expression by CYLD in TET cells. Tumors with low CYLD expression could be potential targets for PD-1/PD-L1 inhibitors.
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Affiliation(s)
- Shigeki Umemura
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA; Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Jianquan Zhu
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA; Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Lung Cancer Center, Tianjin Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, People's Republic of China
| | - Joeffrey J Chahine
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Bhaskar Kallakury
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Vincent Chen
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - In-Kyu Kim
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Yu-Wen Zhang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA; Department of Cell Biology, University of Virginia, VA, USA
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Yongfeng He
- Meyer Cancer Center, Weill Cornel Medicine, NY, USA
| | - Giuseppe Giaccone
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA; Meyer Cancer Center, Weill Cornel Medicine, NY, USA.
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