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Kamal MM, Teeya ST, Rahman MM, Talukder MEK, Sarmin S, Wani TA, Hasan MM. Prediction and assessment of deleterious and disease causing nonsynonymous single nucleotide polymorphisms (nsSNPs) in human FOXP4 gene: An in - silico study. Heliyon 2024; 10:e32791. [PMID: 38994097 PMCID: PMC11237951 DOI: 10.1016/j.heliyon.2024.e32791] [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: 05/01/2024] [Accepted: 06/10/2024] [Indexed: 07/13/2024] Open
Abstract
In humans, FOXP gene family is involved in embryonic development and cancer progression. The FOXP4 (Forkhead box protein P4) gene belongs to this FOXP gene family. FOXP4 gene plays a crucial role in oncogenesis. Single nucleotide polymorphisms are biological markers and common determinants of human diseases. Mutations can largely affect the function of the corresponding protein. Therefore, the molecular mechanism of nsSNPs in the FOXP4 gene needs to be elucidated. Initially, the SNPs of the FOXP4 gene were extracted from the dbSNP database and a total of 23124 SNPs was found, where 555 nonsynonymous, 20525 intronic, 1114 noncoding transcript, 334 synonymous were obtained and the rest were unspecified. Then, a series of bioinformatics tools (SIFT, PolyPhen2, SNAP2, PhD SNP, PANTHER, I-Mutant2.0, MUpro, GOR IV, ConSurf, NetSurfP 2.0, HOPE, DynaMut2, GeneMANIA, STRING and Schrodinger) were used to explore the effect of nsSNPs on FOXP4 protein function and structural stability. First, 555 nsSNPs were analyzed using SIFT, of which 57 were found as deleterious. Following, PolyPhen2, SNAP2, PhD SNP and PANTHER analyses, 10 nsSNPs (rs372762294, rs141899153, rs142575732, rs376938850, rs367607523, rs112517943, rs140387832, rs373949416, rs373949416 and rs376160648) were common and observed as deleterious, damaging and diseases associated. Following that, using I-Mutant2.0 and MUpro servers, 7 nsSNPs were found to be the most unstable. GOR IV predicted that these seven nsSNPs affect protein structure by altering the protein contents of alpha helixes, extended strands, and random coils. Following DynaMut2, 5 nsSNPs showed a decrease in the ΔΔG value compared with the wild-type and were found to be responsible for destabilizing the corresponding protein. GeneMANIA and STRING network revealed interaction of FOXP4 with other genes. Finally, molecular dynamics simulation analysis revealed consistent fluctuation in RMSD and RMSF values, Rg and hydrogen bonds in the mutant proteins compared with WT, which might alter the functional and structural stability of the corresponding protein. As a result, the aforementioned integrated comprehensive bioinformatic analyses provide insight into how various nsSNPs of the FOXP4 gene change the structural and functional properties of the corresponding protein, potentially proceeding with the pathophysiology of human diseases.
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Affiliation(s)
- Md. Mostafa Kamal
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- Laboratory of Computational Biology, Biological Solution Centre, Jashore, 7408, Bangladesh
| | - Shamiha Tabassum Teeya
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md. Mahfuzur Rahman
- Department of Genetic Engineering & Biotechnology, Bangabandhu Sheikh Mujibur Rahman Maritime University, Dhaka, 1216, Bangladesh
| | - Md. Enamul Kabir Talukder
- Department of Genetic Engineering & Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- Laboratory of Computational Biology, Biological Solution Centre, Jashore, 7408, Bangladesh
| | - Sonia Sarmin
- BIRTAN-Bangladesh Institute of Research and Training on Applied Nutrition, Jhenaidah, 7300, Bangladesh
| | - Tanveer A. Wani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Md. Mahmudul Hasan
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
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Zhong Q, Xiao X, Qiu Y, Xu Z, Chen C, Chong B, Zhao X, Hai S, Li S, An Z, Dai L. Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications. MedComm (Beijing) 2023; 4:e261. [PMID: 37143582 PMCID: PMC10152985 DOI: 10.1002/mco2.261] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Protein posttranslational modifications (PTMs) refer to the breaking or generation of covalent bonds on the backbones or amino acid side chains of proteins and expand the diversity of proteins, which provides the basis for the emergence of organismal complexity. To date, more than 650 types of protein modifications, such as the most well-known phosphorylation, ubiquitination, glycosylation, methylation, SUMOylation, short-chain and long-chain acylation modifications, redox modifications, and irreversible modifications, have been described, and the inventory is still increasing. By changing the protein conformation, localization, activity, stability, charges, and interactions with other biomolecules, PTMs ultimately alter the phenotypes and biological processes of cells. The homeostasis of protein modifications is important to human health. Abnormal PTMs may cause changes in protein properties and loss of protein functions, which are closely related to the occurrence and development of various diseases. In this review, we systematically introduce the characteristics, regulatory mechanisms, and functions of various PTMs in health and diseases. In addition, the therapeutic prospects in various diseases by targeting PTMs and associated regulatory enzymes are also summarized. This work will deepen the understanding of protein modifications in health and diseases and promote the discovery of diagnostic and prognostic markers and drug targets for diseases.
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Affiliation(s)
- Qian Zhong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xina Xiao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Yijie Qiu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhiqiang Xu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Chunyu Chen
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Baochen Chong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xinjun Zhao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shan Hai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shuangqing Li
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhenmei An
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Lunzhi Dai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
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Zhao C, Yu H, Fan X, Niu W, Fan J, Sun S, Gong M, Zhao B, Fang Z, Chen X. GSK3β palmitoylation mediated by ZDHHC4 promotes tumorigenicity of glioblastoma stem cells in temozolomide-resistant glioblastoma through the EZH2-STAT3 axis. Oncogenesis 2022; 11:28. [PMID: 35606353 PMCID: PMC9126914 DOI: 10.1038/s41389-022-00402-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Glioblastoma stem cells (GSCs) are a highly tumorigenic cell subgroup of glioblastoma (GBM). Glycogen synthase kinase 3β (GSK3β) is considered a key hub for promoting malignant phenotypes in GBM. However, the functional relationships between GSK3β and GSCs in GBM are unclear. Here, we found that GSK3β was noted as a substrate for ZDHHC4-mediated palmitoylation at the Cys14 residue, which enhanced GBM temozolomide (TMZ) resistance and GSC self-renewal. Clinically, the expression level of ZDHHC4 was upregulated in GBM, which significantly correlated with tumor grade and poor prognosis. The above phenotypes were based on decreasing p-Ser9 and increasing p-Tyr216 by GSK3β palmitoylation, which further activated the enhancer of the zeste homolog 2 (EZH2)-STAT3 pathway. Notably, STAT3 silencing also inhibited ZDHHC4 expression. This study revealed that GSK3β palmitoylation mediated by ZDHHC4 improved the stemness of TMZ-resistant GBM by activating the EZH2-STAT3 signaling axis, providing a new theoretical basis for further understanding the mechanism of TMZ resistance and recurrence after treatment.
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Affiliation(s)
- Chenggang Zhao
- Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China.,Science Island Branch, Graduate School of University of Science and Technology of China, No. 96, Jin Zhai Road, 230026, Hefei, Anhui, China.,Department of Laboratory Medicine, Hefei Cancer Hospital, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China.,MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, No. 96, Jin Zhai Road, 230027, Hefei, Anhui, China
| | - Huihan Yu
- Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China.,MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, No. 96, Jin Zhai Road, 230027, Hefei, Anhui, China
| | - Xiaoqing Fan
- Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China.,Science Island Branch, Graduate School of University of Science and Technology of China, No. 96, Jin Zhai Road, 230026, Hefei, Anhui, China.,Department of Laboratory Medicine, Hefei Cancer Hospital, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China.,MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, No. 96, Jin Zhai Road, 230027, Hefei, Anhui, China.,Department of Anesthesiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), No. 17, Lu Jiang Road, 230001, Hefei, Anhui, China
| | - Wanxiang Niu
- Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China.,Science Island Branch, Graduate School of University of Science and Technology of China, No. 96, Jin Zhai Road, 230026, Hefei, Anhui, China.,Department of Laboratory Medicine, Hefei Cancer Hospital, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China.,MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, No. 96, Jin Zhai Road, 230027, Hefei, Anhui, China
| | - Junqi Fan
- Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China.,Science Island Branch, Graduate School of University of Science and Technology of China, No. 96, Jin Zhai Road, 230026, Hefei, Anhui, China.,Department of Laboratory Medicine, Hefei Cancer Hospital, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China.,MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, No. 96, Jin Zhai Road, 230027, Hefei, Anhui, China
| | - Suling Sun
- Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China.,Science Island Branch, Graduate School of University of Science and Technology of China, No. 96, Jin Zhai Road, 230026, Hefei, Anhui, China.,Department of Laboratory Medicine, Hefei Cancer Hospital, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China.,MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, No. 96, Jin Zhai Road, 230027, Hefei, Anhui, China
| | - Meiting Gong
- Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China.,MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, No. 96, Jin Zhai Road, 230027, Hefei, Anhui, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, No. 678, Fu Rong Road, 230601, Hefei, Anhui, China.
| | - Zhiyou Fang
- Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China. .,Science Island Branch, Graduate School of University of Science and Technology of China, No. 96, Jin Zhai Road, 230026, Hefei, Anhui, China. .,Department of Laboratory Medicine, Hefei Cancer Hospital, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China. .,MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, No. 96, Jin Zhai Road, 230027, Hefei, Anhui, China.
| | - Xueran Chen
- Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China. .,Science Island Branch, Graduate School of University of Science and Technology of China, No. 96, Jin Zhai Road, 230026, Hefei, Anhui, China. .,Department of Laboratory Medicine, Hefei Cancer Hospital, Chinese Academy of Sciences, No. 350, Shushan Hu Road, 230031, Hefei, Anhui, China. .,MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, No. 96, Jin Zhai Road, 230027, Hefei, Anhui, China.
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