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Sun H, Han L, Guo Y, An H, Wang B, Zhang X, Li J, Jiang Y, Wang Y, Sun G, Zhu S, Tang S, Ge J, Chen M, Guo X, Wang Q. The global phosphorylation landscape of mouse oocytes during meiotic maturation. EMBO J 2024:10.1038/s44318-024-00222-1. [PMID: 39256562 DOI: 10.1038/s44318-024-00222-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 08/10/2024] [Accepted: 08/13/2024] [Indexed: 09/12/2024] Open
Abstract
Phosphorylation is a key post-translational modification regulating protein function and biological outcomes. However, the phosphorylation dynamics orchestrating mammalian oocyte development remains poorly understood. In the present study, we apply high-resolution mass spectrometry-based phosphoproteomics to obtain the first global in vivo quantification of mouse oocyte phosphorylation. Of more than 8000 phosphosites, 75% significantly oscillate and 64% exhibit marked upregulation during meiotic maturation, indicative of the dominant regulatory role. Moreover, we identify numerous novel phosphosites on oocyte proteins and a few highly conserved phosphosites in oocytes from different species. Through functional perturbations, we demonstrate that phosphorylation status of specific sites participates in modulating critical events including metabolism, translation, and RNA processing during meiosis. Finally, we combine inhibitor screening and enzyme-substrate network prediction to discover previously unexplored kinases and phosphatases that are essential for oocyte maturation. In sum, our data define landscape of the oocyte phosphoproteome, enabling in-depth mechanistic insights into developmental control of germ cells.
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Affiliation(s)
- Hongzheng Sun
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China
| | - Longsen Han
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China
| | - Huiqing An
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China
| | - Bing Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China
| | - Xiangzheng Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China
| | - Jiashuo Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China
| | - Yingtong Jiang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China
| | - Yue Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China
| | - Guangyi Sun
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China
| | - Shuai Zhu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China
| | - Shoubin Tang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China
| | - Juan Ge
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China
| | - Minjian Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China.
- Department of Histology and Embryology, Nanjing Medical University, 211166, Nanjing, China.
| | - Qiang Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 211166, Nanjing, China.
- Center for Global Health, School of Public Health, Nanjing Medical University, 211166, Nanjing, China.
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2
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Qin J, Huang X, Gou S, Zhang S, Gou Y, Zhang Q, Chen H, Sun L, Chen M, Liu D, Han C, Tang M, Feng Z, Niu S, Zhao L, Tu Y, Liu Z, Xuan W, Dai L, Jia D, Xue Y. Ketogenic diet reshapes cancer metabolism through lysine β-hydroxybutyrylation. Nat Metab 2024; 6:1505-1528. [PMID: 39134903 DOI: 10.1038/s42255-024-01093-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 07/02/2024] [Indexed: 08/29/2024]
Abstract
Lysine β-hydroxybutyrylation (Kbhb) is a post-translational modification induced by the ketogenic diet (KD), a diet showing therapeutic effects on multiple human diseases. Little is known how cellular processes are regulated by Kbhb. Here we show that protein Kbhb is strongly affected by the KD through a multi-omics analysis of mouse livers. Using a small training dataset with known functions, we developed a bioinformatics method for the prediction of functionally important lysine modification sites (pFunK), which revealed functionally relevant Kbhb sites on various proteins, including aldolase B (ALDOB) Lys108. KD consumption or β-hydroxybutyrate supplementation in hepatocellular carcinoma cells increases ALDOB Lys108bhb and inhibits the enzymatic activity of ALDOB. A Kbhb-mimicking mutation (p.Lys108Gln) attenuates ALDOB activity and its binding to substrate fructose-1,6-bisphosphate, inhibits mammalian target of rapamycin signalling and glycolysis, and markedly suppresses cancer cell proliferation. Our study reveals a critical role of Kbhb in regulating cancer cell metabolism and provides a generally applicable algorithm for predicting functionally important lysine modification sites.
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Affiliation(s)
- Junhong Qin
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Xinhe Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Shengsong Gou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Sitao Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Yujie Gou
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Hongyu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Lin Sun
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Miaomiao Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Dan Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Cheng Han
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Min Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Zihao Feng
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Shenghui Niu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Lin Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Yingfeng Tu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Zexian Liu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Weimin Xuan
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China.
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, China.
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3
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Barman SK, Nesarajah AN, Zaman MS, Malladi CS, Mahns DA, Wu MJ. Distinctive expression and cellular localisation of zinc homeostasis-related proteins in breast and prostate cancer cells. J Trace Elem Med Biol 2024; 86:127500. [PMID: 39047373 DOI: 10.1016/j.jtemb.2024.127500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/25/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Zinc transport proteins (ZIP and ZnT), metallothioneins (MT) and protein kinase CK2 are involved in dysregulation of zinc homeostasis in breast and prostate cancer cells. Following up our previous research, we targeted ZIP12, ZnT1, MT2A and CK2 in this study by investigating their expression levels and protein localisation. METHODS Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and immunofluorescence confocal microscopy were employed to quantify the expression of ZIP12, ZnT1, MT2A and CK2 subunits in a panel of breast and prostate cell lines without or with extracellular zinc exposure. The cellular localisations of these target proteins were also examined by immunofluorescence confocal microscopy. RESULTS In response to the extracellular zinc exposure, the gene expression was elevated for SLC39A12 (ZIP12), SLC30A1 (ZnT1) and MT2A (MT2A) in normal prostate epithelial cells (RWPE-1) in contrast to their cancerous counterparts (PC3 and DU145), whilst the gene expression was higher for SLC39A12 (ZIP12) and SLC30A1 (ZnT1) in both normal (MCF10A) and basal breast cancer cells (MDA-MB-231) compared to luminal breast cancer cells (MCF-7). At the protein level, the expression for both ZIP12 and ZnT1 was trending lower in the time course for the breast cancer cells whilst their expression was remained constant in the normal breast epithelial cells. The expression of ZIP12 in prostate cancer cells was higher than the normal prostate cells. The protein expression for CK2 α/αꞌ and CK2β was markedly higher in prostate cancer cells than the normal prostate cells. Upon extracellular zinc exposure, ZIP12 was, for the first time, conspicuously localised in the plasma membrane of breast cancer cells but not in normal breast epithelial cells and prostate cells. ZnT1 is only localised in the plasma membrane of breast cancer cells. MT2A is distinctively seen close to the plasma membrane in breast cancer cells. CK2 is also for the first time shown to be localised in proximity to the plasma membrane of breast cancer cells. CONCLUSION The findings, particularly the localisation of ZIP12 and CK2, are novel and significant for our understanding of zinc homeostasis in breast and prostate cancer cells.
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Affiliation(s)
- Shital K Barman
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Abinaya N Nesarajah
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Mohammad S Zaman
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Chandra S Malladi
- Proteomics and Lipidomics Lab, School of Medicine, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - David A Mahns
- School of Medicine, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Ming J Wu
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
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4
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Wang A, Shi S, Ma Y, Li S, Gui W. Insights into the role of FoxL2 in tebuconazole-induced male- biased sex differentiation of zebrafish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174543. [PMID: 38977095 DOI: 10.1016/j.scitotenv.2024.174543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/30/2024] [Accepted: 07/04/2024] [Indexed: 07/10/2024]
Abstract
Tebuconazole (TEB) is a commonly used fungicide that inhibits the aromatase Cyp19A and downregulates the transcription factor forkhead box L2 (FoxL2), leading to male-biased sex differentiation in zebrafish larvae. However, the specific mechanism by which FoxL2 functions following TEB exposure remains unclear. In this study, the phosphorylation sites and kinase-specific residues in zebrafish FoxL2 protein (zFoxL2) were predicted. Subsequently, recombinant zFoxL2 was prepared via prokaryotic expression, and a polyclonal rabbit-anti-zFoxL2 antibody was generated. Zebrafish fibroblast (ZF4) cells were exposed to 100-μM TEB alone for 8 h, after which changes in the expression of genes involved in the foxl2 regulatory pathway (akt1, pi3k, cyp19a1b, c/ebpb and sox9a) were detected. When co-exposed to 1-μM estradiol and 100-μM TEB, the expression of these key genes tended to be restored. Interestingly, TEB did not affect the expression of the foxl2 gene or protein but it significantly suppressed the phosphorylation of FoxL2 (pFoxL2) at serine 238 (decreased by 43.64 %, p = 0.009). Co-immunoprecipitation assays showed that, following exposure to 100-μM TEB, the total precipitated proteins in ZF4 cells decreased by 17.02 % (p = 0.029) and 31.39 % (p = 0.027) in the anti-zFoxL2 antibody group and anti-pFoxL2 (ser238) antibody group, respectively, indicating that TEB suppressed the capacity of the FoxL2 protein to bind to other proteins via repression of its own phosphorylation. The pull-down assay confirmed this conclusion. This study preliminarily elucidated that the foxl2 gene functions via post-translational regulation through hypophosphorylation of its encoded protein during TEB-induced male-biased sex differentiation.
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Affiliation(s)
- Aoxue Wang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Shiyao Shi
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Yongfang Ma
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Shuying Li
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China; Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, PR China; Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, PR China.
| | - Wenjun Gui
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China; Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, PR China; Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, PR China
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5
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Yadav AK, Murthy TPK, Divyashri G, Prasad N D, Prakash S, Vaishnavi V V, Shukla R, Singh TR. Computational screening of pathogenic missense nsSNPs in heme oxygenase 1 (HMOX1) gene and their structural and functional consequences. J Biomol Struct Dyn 2024; 42:5072-5091. [PMID: 37434323 DOI: 10.1080/07391102.2023.2231553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/07/2023] [Indexed: 07/13/2023]
Abstract
Heme Oxygenase 1 (HMOX1) is a cytoprotective enzyme, exhibiting the highest activity in the spleen, catalyzing the heme ring breakdown into products of biological significance- biliverdin, CO, and Fe2+. In vascular cells, HMOX1 possesses strong anti-apoptotic, antioxidant, anti-proliferative, anti-inflammatory, and immunomodulatory actions. The majority of these activities are crucial for the prevention of atherogenesis. Single amino acid substitutions in proteins generated by missense non-synonymous single nucleotide polymorphism (nsSNPs) in the protein-encoding regions of genes are potent enough to cause significant medical challenges due to the alteration of protein structure and function. The current study aimed at characterizing and analyzing high-risk nsSNPs associated with the human HMOX1 gene. Preliminary screening of the total available 288 missense SNPs was performed through the lens of deleteriousness and stability prediction tools. Finally, a total of seven nsSNPs (Y58D, A131T, Y134H, F166S, F167S, R183S and M186V) were found to be most deleterious by all tools that are present at highly conserved positions. Molecular dynamics simulations (MDS) analysis explained the mutational effects on the dynamic action of the wild-type and mutant proteins. In a nutshell, R183S (rs749644285) was identified as a highly detrimental mutation that could significantly render the enzymatic activity of HMOX1. The finding of this computational analysis might help subject the experimental confirmatory analysis to characterize the role of nsSNPs in HMOX1.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arvind Kumar Yadav
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - T P Krishna Murthy
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Gangaraju Divyashri
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Durga Prasad N
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Sriraksha Prakash
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Vijaya Vaishnavi V
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
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6
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Vijayakumar S, DiGuiseppi JA, Dabestani PJ, Ryan WG, Quevedo RV, Li Y, Diers J, Tu S, Fleegel J, Nguyen C, Rhoda LM, Imami AS, Hamoud ARA, Lovas S, McCullumsmith RE, Zallocchi M, Zuo J. In silico transcriptome screens identify epidermal growth factor receptor inhibitors as therapeutics for noise-induced hearing loss. SCIENCE ADVANCES 2024; 10:eadk2299. [PMID: 38896614 PMCID: PMC11186505 DOI: 10.1126/sciadv.adk2299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
Noise-induced hearing loss (NIHL) is a common sensorineural hearing impairment that lacks U.S. Food and Drug Administration-approved drugs. To fill the gap in effective screening models, we used an in silico transcriptome-based drug screening approach, identifying 22 biological pathways and 64 potential small molecule treatments for NIHL. Two of these, afatinib and zorifertinib [epidermal growth factor receptor (EGFR) inhibitors], showed efficacy in zebrafish and mouse models. Further tests with EGFR knockout mice and EGF-morpholino zebrafish confirmed their protective role against NIHL. Molecular studies in mice highlighted EGFR's crucial involvement in NIHL and the protective effect of zorifertinib. When given orally, zorifertinib was found in the perilymph with favorable pharmacokinetics. In addition, zorifertinib combined with AZD5438 (a cyclin-dependent kinase 2 inhibitor) synergistically prevented NIHL in zebrafish. Our results underscore the potential for in silico transcriptome-based drug screening in diseases lacking efficient models and suggest EGFR inhibitors as potential treatments for NIHL, meriting clinical trials.
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Affiliation(s)
- Sarath Vijayakumar
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Joseph A. DiGuiseppi
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Parinaz Jila Dabestani
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - William G. Ryan
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA.
| | - Rene Vielman Quevedo
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Yuju Li
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Jack Diers
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Shu Tu
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Jonathan Fleegel
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Cassidy Nguyen
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Lauren M. Rhoda
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Ali Sajid Imami
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA.
| | | | - Sándor Lovas
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Robert E. McCullumsmith
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA.
- Neurosciences Institute, ProMedica, Toledo, OH 43606, USA
| | - Marisa Zallocchi
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Jian Zuo
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
- Ting Therapeutics, University of California San Diego, 9310 Athena Circle, San Diego, CA 92037, USA
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7
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Packer J, Gubieda AG, Brooks A, Deutz LN, Squires I, Ellison S, Schneider C, Naganathan SR, Wollman AJ, Dickinson DJ, Rodriguez J. Atypical Protein Kinase C Promotes its own Asymmetric Localisation by Phosphorylating Cdc42 in the C. elegans zygote. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.27.563985. [PMID: 38009101 PMCID: PMC10675845 DOI: 10.1101/2023.10.27.563985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
Atypical protein kinase C (aPKC) is a major regulator of cell polarity. Acting in conjunction with Par6, Par3 and the small GTPase Cdc42, aPKC becomes asymmetrically localised and drives the polarisation of cells. aPKC activity is crucial for its own asymmetric localisation, suggesting a hitherto unknown feedback mechanism contributing to polarisation. Here we show in the C. elegans zygote that the feedback relies on aPKC phosphorylation of Cdc42 at serine 71. The turnover of CDC-42 phosphorylation ensures optimal aPKC asymmetry and activity throughout polarisation by tuning Par6/aPKC association with Par3 and Cdc42. Moreover, turnover of Cdc42 phosphorylation regulates actomyosin cortex dynamics that are known to drive aPKC asymmetry. Given the widespread role of aPKC and Cdc42 in cell polarity, this form of self-regulation of aPKC may be vital for the robust control of polarisation in many cell types.
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Affiliation(s)
- John Packer
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- These authors contributed equally
| | - Alicia G. Gubieda
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- These authors contributed equally
| | - Aaron Brooks
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- These authors contributed equally
| | - Lars N. Deutz
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- These authors contributed equally
| | - Iolo Squires
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- These authors contributed equally
| | | | | | - Sundar Ram Naganathan
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Adam J.M. Wollman
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Daniel J. Dickinson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Josana Rodriguez
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Lead contact
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8
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Solís KH, Romero-Ávila MT, Rincón-Heredia R, García-Sáinz JA. Lysophosphatidic Acid Receptor 3 (LPA3): Signaling and Phosphorylation Sites. Int J Mol Sci 2024; 25:6491. [PMID: 38928196 PMCID: PMC11203643 DOI: 10.3390/ijms25126491] [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: 04/05/2024] [Revised: 06/03/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
LPA3 receptors were expressed in TREx HEK 293 cells, and their signaling and phosphorylation were studied. The agonist, lysophosphatidic acid (LPA), increased intracellular calcium and ERK phosphorylation through pertussis toxin-insensitive processes. Phorbol myristate acetate, but not LPA, desensitizes LPA3-mediated calcium signaling, the agonists, and the phorbol ester-induced LPA3 internalization. Pitstop 2 (clathrin heavy chain inhibitor) markedly reduced LPA-induced receptor internalization; in contrast, phorbol ester-induced internalization was only delayed. LPA induced rapid β-arrestin-LPA3 receptor association. The agonist and the phorbol ester-induced marked LPA3 receptor phosphorylation, and phosphorylation sites were detected using mass spectrometry. Phosphorylated residues were detected in the intracellular loop 3 (S221, T224, S225, and S229) and in the carboxyl terminus (S321, S325, S331, T333, S335, Y337, and S343). Interestingly, phosphorylation sites are within sequences predicted to constitute β-arrestin binding sites. These data provide insight into LPA3 receptor signaling and regulation.
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Affiliation(s)
- K. Helivier Solís
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ap. Postal 70-600, Ciudad de México 04510, Mexico; (K.H.S.); (M.T.R.-Á.)
| | - M. Teresa Romero-Ávila
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ap. Postal 70-600, Ciudad de México 04510, Mexico; (K.H.S.); (M.T.R.-Á.)
| | - Ruth Rincón-Heredia
- Unidad de Imagenología, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ap. Postal 70-600, Ciudad de México 04510, Mexico;
| | - J. Adolfo García-Sáinz
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ap. Postal 70-600, Ciudad de México 04510, Mexico; (K.H.S.); (M.T.R.-Á.)
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9
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Mahur P, Sharma A, Jahan G, S G A, Kumar Singh A, Muthukumaran J, Jain M. Understanding Genetic Risks: Computational Exploration of Human β-Synuclein nsSNPs and their Potential Impact on Structural Alteration. Neurosci Lett 2024; 833:137826. [PMID: 38768940 DOI: 10.1016/j.neulet.2024.137826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Synucleins are pivotal in neurodegenerative conditions. Beta-synuclein (β-synuclein) is part of the synuclein protein family alongside alpha-synuclein (α-synuclein) and gamma-synuclein (γ-synuclein). These proteins, found mainly in brain tissue and cancers, are soluble and unstructured. β-synuclein shares significant similarity with α-synuclein, especially in their N-terminus, with a 90% match. However, their aggregation tendencies differ significantly. While α-synuclein aggregation is believed to be counteracted by β-synuclein, which occurs in conditions like Parkinson's disease, β-synuclein may counteract α-synuclein's toxic effects on the nervous system, offering potential treatment for neurodegenerative diseases. Under normal circumstances, β-synuclein may guard against disease by interacting with α-synuclein. Yet, in pathological environments with heightened levels or toxic substances, it might contribute to disease. Our research aims to explore potential harmful mutations in the β-synuclein using computational tools to predict their destabilizing impact on protein structure. Consensus analysis revealed rs1207608813 (A63P), rs1340051870 (S72F), and rs1581178262 (G36C) as deleterious. These findings highlight the intricate relationship between nsSNPs and protein function, shedding light on their potential implications in disease pathways. Understanding the structural consequences of nsSNPs is crucial for elucidating their role in pathogenesis and developing targeted therapeutic interventions. Our results offer a robust computational framework for identifying neurodegenerative disorder-related mutations from SNP datasets, potentially reducing the costs associated with experimental characterization.
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Affiliation(s)
- Pragati Mahur
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Abhishek Sharma
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Gulnaz Jahan
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Adithya S G
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Amit Kumar Singh
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India.
| | - Monika Jain
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India.
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10
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Wang D, Pourmirzaei M, Abbas UL, Zeng S, Manshour N, Esmaili F, Poudel B, Jiang Y, Shao Q, Chen J, Xu D. S-PLM: Structure-aware Protein Language Model via Contrastive Learning between Sequence and Structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.06.552203. [PMID: 37609352 PMCID: PMC10441326 DOI: 10.1101/2023.08.06.552203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Proteins play an essential role in various biological and engineering processes. Large protein language models (PLMs) present excellent potential to reshape protein research by accelerating the determination of protein function and the design of proteins with the desired functions. The prediction and design capacity of PLMs relies on the representation gained from the protein sequences. However, the lack of crucial 3D structure information in most PLMs restricts the prediction capacity of PLMs in various applications, especially those heavily dependent on 3D structures. To address this issue, we introduce S-PLM, a 3D structure-aware PLM that utilizes multi-view contrastive learning to align the sequence and 3D structure of a protein in a coordinated latent space. S-PLM applies Swin-Transformer on AlphaFold-predicted protein structures to embed the structural information and fuses it into sequence-based embedding from ESM2. Additionally, we provide a library of lightweight tuning tools to adapt S-PLM for diverse protein property prediction tasks. Our results demonstrate S-PLM's superior performance over sequence-only PLMs on all protein clustering and classification tasks, achieving competitiveness comparable to state-of-the-art methods requiring both sequence and structure inputs. S-PLM and its lightweight tuning tools are available at https://github.com/duolinwang/S-PLM/ .
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11
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Cai YD, Chow GK, Hidalgo S, Liu X, Jackson KC, Vasquez CD, Gao ZY, Lam VH, Tabuloc CA, Zheng H, Zhao C, Chiu JC. Alternative splicing of clock transcript mediates the response of circadian clocks to temperature changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593646. [PMID: 38766142 PMCID: PMC11100826 DOI: 10.1101/2024.05.10.593646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Circadian clocks respond to temperature changes over the calendar year, allowing organisms to adjust their daily biological rhythms to optimize health and fitness. In Drosophila, seasonal adaptations and temperature compensation are regulated by temperature-sensitive alternative splicing (AS) of period (per) and timeless (tim) genes that encode key transcriptional repressors of clock gene expression. Although clock (clk) gene encodes the critical activator of clock gene expression, AS of its transcripts and its potential role in temperature regulation of clock function have not been explored. We therefore sought to investigate whether clk exhibits AS in response to temperature and the functional changes of the differentially spliced transcripts. We observed that clk transcripts indeed undergo temperature-sensitive AS. Specifically, cold temperature leads to the production of an alternative clk transcript, hereinafter termed clk-cold, which encodes a CLK isoform with an in-frame deletion of four amino acids proximal to the DNA binding domain. Notably, serine 13 (S13), which we found to be a CK1α-dependent phosphorylation site, is among the four amino acids deleted in CLK-cold protein. Using a combination of transgenic fly, tissue culture, and in vitro experiments, we demonstrated that upon phosphorylation at CLK(S13), CLK-DNA interaction is reduced, thus decreasing CLK occupancy at clock gene promoters. This is in agreement with our findings that CLK occupancy at clock genes and transcriptional output are elevated at cold temperature, which can be explained by the higher amounts of CLK-cold isoforms that lack S13 residue. This study provides new insights into the complex collaboration between AS and phospho-regulation in shaping temperature responses of the circadian clock.
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Affiliation(s)
- Yao D. Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Gary K. Chow
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Sergio Hidalgo
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Kiya C. Jackson
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Cameron D. Vasquez
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Zita Y. Gao
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Vu H. Lam
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Christine A. Tabuloc
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Caifeng Zhao
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
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12
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Zhang Y, Yao L, Chung CR, Huang Y, Li S, Zhang W, Pang Y, Lee TY. KinPred-RNA-kinase activity inference and cancer type classification using machine learning on RNA-seq data. iScience 2024; 27:109333. [PMID: 38523792 PMCID: PMC10959666 DOI: 10.1016/j.isci.2024.109333] [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: 08/26/2023] [Revised: 12/07/2023] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Kinases as important enzymes can transfer phosphate groups from high-energy and phosphate-donating molecules to specific substrates and play essential roles in various cellular processes. Existing algorithms for kinase activity from phosphorylated proteomics data are often costly, requiring valuable samples. Moreover, methods to extract kinase activities from bulk RNA sequencing data remain undeveloped. In this study, we propose a computational framework KinPred-RNA to derive kinase activities from bulk RNA-sequencing data in cancer samples. KinPred-RNA framework, using the extreme gradient boosting (XGBoost) regression model, outperforms random forest regression, multiple linear regression, and support vector machine regression models in predicting kinase activities from cancer-related RNA sequencing data. Efficient gene signatures from the LINCS-L1000 dataset were used as inputs for KinPred-RNA. The results highlight its potential to be related to biological function. In conclusion, KinPred RNA constitutes a significant advance in cancer research by potentially facilitating the identification of cancer.
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Affiliation(s)
- Yuntian Zhang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Lantian Yao
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Chia-Ru Chung
- Department of Computer Science and Information Engineering, National Central University, Taoyuan 320953, Taiwan
| | - Yixian Huang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Shangfu Li
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Wenyang Zhang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Yuxuan Pang
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Tzong-Yi Lee
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
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13
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Jorge GL, Kim D, Xu C, Cho SH, Su L, Xu D, Bartley LE, Stacey G, Thelen JJ. Unveiling orphan receptor-like kinases in plants: novel client discovery using high-confidence library predictions in the Kinase-Client (KiC) assay. FRONTIERS IN PLANT SCIENCE 2024; 15:1372361. [PMID: 38633461 PMCID: PMC11021772 DOI: 10.3389/fpls.2024.1372361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024]
Abstract
Plants are remarkable in their ability to adapt to changing environments, with receptor-like kinases (RLKs) playing a pivotal role in perceiving and transmitting environmental cues into cellular responses. Despite extensive research on RLKs from the plant kingdom, the function and activity of many kinases, i.e., their substrates or "clients", remain uncharted. To validate a novel client prediction workflow and learn more about an important RLK, this study focuses on P2K1 (DORN1), which acts as a receptor for extracellular ATP (eATP), playing a crucial role in plant stress resistance and immunity. We designed a Kinase-Client (KiC) assay library of 225 synthetic peptides, incorporating previously identified P2K phosphorylated peptides and novel predictions from a deep-learning phosphorylation site prediction model (MUsite) and a trained hidden Markov model (HMM) based tool, HMMER. Screening the library against purified P2K1 cytosolic domain (CD), we identified 46 putative substrates, including 34 novel clients, 27 of which may be novel peptides, not previously identified experimentally. Gene Ontology (GO) analysis among phosphopeptide candidates revealed proteins associated with important biological processes in metabolism, structure development, and response to stress, as well as molecular functions of kinase activity, catalytic activity, and transferase activity. We offer selection criteria for efficient further in vivo experiments to confirm these discoveries. This approach not only expands our knowledge of P2K1's substrates and functions but also highlights effective prediction algorithms for identifying additional potential substrates. Overall, the results support use of the KiC assay as a valuable tool in unraveling the complexities of plant phosphorylation and provide a foundation for predicting the phosphorylation landscape of plant species based on peptide library results.
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Affiliation(s)
- Gabriel Lemes Jorge
- Division of Biochemistry, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Daewon Kim
- Division of Plant Science & Technology, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Chunhui Xu
- Institute for Data Science and Informatics, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Sung-Hwan Cho
- Division of Plant Science & Technology, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Lingtao Su
- Department of Electrical Engineering and Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Shandong University of Science and Technology, Qingdao, Shandong, China
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Laura E. Bartley
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Gary Stacey
- Division of Plant Science & Technology, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Jay J. Thelen
- Division of Biochemistry, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
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14
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Meitinger F, Belal H, Davis RL, Martinez MB, Shiau AK, Oegema K, Desai A. Control of cell proliferation by memories of mitosis. Science 2024; 383:1441-1448. [PMID: 38547292 DOI: 10.1126/science.add9528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 02/04/2024] [Indexed: 04/02/2024]
Abstract
Mitotic duration is tightly constrained, and extended mitosis is characteristic of problematic cells prone to chromosome missegregation and genomic instability. We show here that mitotic extension leads to the formation of p53-binding protein 1 (53BP1)-ubiquitin-specific protease 28 (USP28)-p53 protein complexes that are transmitted to, and stably retained by, daughter cells. Complexes assembled through a Polo-like kinase 1-dependent mechanism during extended mitosis and elicited a p53 response in G1 that prevented the proliferation of the progeny of cells that experienced an approximately threefold extended mitosis or successive less extended mitoses. The ability to monitor mitotic extension was lost in p53-mutant cancers and some p53-wild-type (p53-WT) cancers, consistent with classification of TP53BP1 and USP28 as tumor suppressors. Cancers retaining the ability to monitor mitotic extension exhibited sensitivity to antimitotic agents.
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Affiliation(s)
- Franz Meitinger
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Hazrat Belal
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Robert L Davis
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Mallory B Martinez
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Andrew K Shiau
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Karen Oegema
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Arshad Desai
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
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15
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Sun J, Qu J, Zhao C, Zhang X, Liu X, Wang J, Wei C, Liu X, Wang M, Zeng P, Tang X, Ling X, Qing L, Jiang S, Chen J, Chen TSR, Kuang Y, Gao J, Zeng X, Huang D, Yuan Y, Fan L, Yu H, Ding J. Precise prediction of phase-separation key residues by machine learning. Nat Commun 2024; 15:2662. [PMID: 38531854 DOI: 10.1038/s41467-024-46901-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
Understanding intracellular phase separation is crucial for deciphering transcriptional control, cell fate transitions, and disease mechanisms. However, the key residues, which impact phase separation the most for protein phase separation function have remained elusive. We develop PSPHunter, which can precisely predict these key residues based on machine learning scheme. In vivo and in vitro validations demonstrate that truncating just 6 key residues in GATA3 disrupts phase separation, enhancing tumor cell migration and inhibiting growth. Glycine and its motifs are enriched in spacer and key residues, as revealed by our comprehensive analysis. PSPHunter identifies nearly 80% of disease-associated phase-separating proteins, with frequent mutated pathological residues like glycine and proline often residing in these key residues. PSPHunter thus emerges as a crucial tool to uncover key residues, facilitating insights into phase separation mechanisms governing transcriptional control, cell fate transitions, and disease development.
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Affiliation(s)
- Jun Sun
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiale Qu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Cai Zhao
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyao Zhang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyu Liu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jia Wang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Chao Wei
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyi Liu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Mulan Wang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Pengguihang Zeng
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiuxiao Tang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaoru Ling
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Li Qing
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shaoshuai Jiang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiahao Chen
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tara S R Chen
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Yalan Kuang
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Jinhang Gao
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Xiaoxi Zeng
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Dongfeng Huang
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Yong Yuan
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
| | - Lili Fan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong, China.
| | - Haopeng Yu
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
| | - Junjun Ding
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China.
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16
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Zahiri Z, Mehrshad N, Mehrshad M. DF-Phos: Prediction of Protein Phosphorylation Sites by Deep Forest. J Biochem 2024; 175:447-456. [PMID: 38153271 DOI: 10.1093/jb/mvad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/29/2023] Open
Abstract
Phosphorylation is the most important and studied post-translational modification (PTM), which plays a crucial role in protein function studies and experimental design. Many significant studies have been performed to predict phosphorylation sites using various machine-learning methods. Recently, several studies have claimed that deep learning-based methods are the best way to predict the phosphorylation sites because deep learning as an advanced machine learning method can automatically detect complex representations of phosphorylation patterns from raw sequences and thus offers a powerful tool to improve phosphorylation site prediction. In this study, we report DF-Phos, a new phosphosite predictor based on the Deep Forest to predict phosphorylation sites. In DF-Phos, the feature vector taken from the CkSAApair method is as input for a Deep Forest framework for predicting phosphorylation sites. The results of 10-fold cross-validation show that the Deep Forest method has the highest performance among other available methods. We implemented a Python program of DF-Phos, which is freely available for non-commercial use at https://github.com/zahiriz/DF-Phos Moreover, users can use it for various PTM predictions.
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Affiliation(s)
- Zeynab Zahiri
- Faculty of Electrical and Computer Engineering, University of Birjand, Birjand, Iran
| | - Nasser Mehrshad
- Faculty of Electrical and Computer Engineering, University of Birjand, Birjand, Iran
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, 750 07 Sweden
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17
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Kac PR, González-Ortiz F, Emeršič A, Dulewicz M, Koutarapu S, Turton M, An Y, Smirnov D, Kulczyńska-Przybik A, Varma VR, Ashton NJ, Montoliu-Gaya L, Camporesi E, Winkel I, Paradowski B, Moghekar A, Troncoso JC, Lashley T, Brinkmalm G, Resnick SM, Mroczko B, Kvartsberg H, Gregorič Kramberger M, Hanrieder J, Čučnik S, Harrison P, Zetterberg H, Lewczuk P, Thambisetty M, Rot U, Galasko D, Blennow K, Karikari TK. Plasma p-tau212 antemortem diagnostic performance and prediction of autopsy verification of Alzheimer's disease neuropathology. Nat Commun 2024; 15:2615. [PMID: 38521766 PMCID: PMC10960791 DOI: 10.1038/s41467-024-46876-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 03/04/2024] [Indexed: 03/25/2024] Open
Abstract
Blood phosphorylated tau (p-tau) biomarkers, including p-tau217, show high associations with Alzheimer's disease (AD) neuropathologic change and clinical stage. Certain plasma p-tau217 assays recognize tau forms phosphorylated additionally at threonine-212, but the contribution of p-tau212 alone to AD is unknown. We developed a blood-based immunoassay that is specific to p-tau212 without cross-reactivity to p-tau217. Here, we examined the diagnostic utility of plasma p-tau212. In five cohorts (n = 388 participants), plasma p-tau212 showed high performances for AD diagnosis and for the detection of both amyloid and tau pathology, including at autopsy as well as in memory clinic populations. The diagnostic accuracy and fold changes of plasma p-tau212 were similar to those for p-tau217 but higher than p-tau181 and p-tau231. Immunofluorescent staining of brain tissue slices showed prominent p-tau212 reactivity in neurofibrillary tangles that co-localized with p-tau217 and p-tau202/205. These findings support plasma p-tau212 as a peripherally accessible biomarker of AD pathophysiology.
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Grants
- R01 AG075336 NIA NIH HHS
- R01 AG078796 NIA NIH HHS
- R01 AG083874 NIA NIH HHS
- R01 AG072641 NIA NIH HHS
- R01 AG068398 NIA NIH HHS
- R21 AG078538 NIA NIH HHS
- R01 MH108509 NIMH NIH HHS
- RF1 AG025516 NIA NIH HHS
- P30 AG066468 NIA NIH HHS
- R01 AG073267 NIA NIH HHS
- P01 AG025204 NIA NIH HHS
- #AARF-21-850325 Alzheimer's Association
- R01 MH121619 NIMH NIH HHS
- R37 AG023651 NIA NIH HHS
- R21 AG080705 NIA NIH HHS
- U24 AG082930 NIA NIH HHS
- RF1 AG052525 NIA NIH HHS
- R01 AG053952 NIA NIH HHS
- Demensförbundet (Dementia Association)
- Anna Lisa and Brother Björnsson’s Foundation
- BrightFocus Foundation (BrightFocus)
- Alzheimerfonden
- the Swedish Dementia Foundation, Gun and Bertil Stohnes Foundation, Åhlén-stifelsen, and Gamla Tjänarinnor Foundation.
- Vetenskapsrådet (Swedish Research Council)
- Alzheimer’s Drug Discovery Foundation (ADDF)
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- EU Joint Programme – Neurodegenerative Disease Research (Programi i Përbashkët i BE-së për Kërkimet mbi Sëmundjet Neuro-degjeneruese)
- Swedish State Support for Clinical Research (#ALFGBG-71320), the AD Strategic Fund and the Alzheimer’s Association (#ADSF-21-831376-C, #ADSF-21-831381-C, and #ADSF-21-831377-C) the Bluefield Project, the Olav Thon Foundation, the Erling-Persson Family Foundation, Hjärnfonden, Sweden (#FO2022-0270), the National Institute for Health and Care Research University College London Hospitals Biomedical Research Centre, and the UK Dementia Research Institute at UCL (UKDRI-1003)
- the Swedish Alzheimer Foundation (#AF-930351, #AF-939721 and #AF-968270), Hjärnfonden, Sweden (#FO2017-0243 and #ALZ2022-0006), the Swedish state under the agreement between the Swedish government and the County Councils, the ALF-agreement (#ALFGBG-715986 and #ALFGBG-965240), the National Institute of Health (NIH), USA, (grant #1R01AG068398-01) the Alzheimer’s Association 2021 Zenith Award (ZEN-21-848495).
- Alzheimer’s Association
- National Institute of Health (NIH) - (R01 AG083874-01, U24 AG082930-01 1 RF1 AG052525-01A1, 5 P30 AG066468-04, 5 R01 AG053952-05, 3 R01 MH121619-04S1, 5 R37 AG023651-18, 2 RF1 AG025516-12A1, 5 R01 AG073267-02, 2 R01 MH108509-06, 5 R01 AG075336-02, 5 R01 AG072641-02, 2 P01 AG025204-16) the Swedish Alzheimer Foundation (Alzheimerfonden), the Aina (Ann) Wallströms and Mary-Ann Sjöbloms stiftelsen, and the Emil och Wera Cornells stiftelsen.
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Affiliation(s)
- Przemysław R Kac
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden.
| | - Fernando González-Ortiz
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 431 80, Sweden
| | - Andreja Emeršič
- Department of Neurology, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Maciej Dulewicz
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | - Srinivas Koutarapu
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | | | - Yang An
- Brain Aging and Behavior Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Denis Smirnov
- Department of Neurosciences, University of California, San Diego, CA, 92161, USA
| | | | - Vijay R Varma
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Nicholas J Ashton
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Department of Old Age Psychiatry, King's College London, London, SE5 8AF, UK
- Centre for Age-Related Medicine, Stavanger University Hospital, 4011, Stavanger, Norway
- South London & Maudsley NHS Foundation, NIHR Biomedical Research Centre for Mental Health & Biomedical Research Unit for Dementia, SE5 8AF, London, UK
| | - Laia Montoliu-Gaya
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | - Elena Camporesi
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | - Izabela Winkel
- Dementia Disorders Center, Medical University of Wrocław, 59-330, Ścinawa, Poland
| | - Bogusław Paradowski
- Department of Neurology, Medical University of Wrocław, 50-556, Wrocław, Poland
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Juan C Troncoso
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Pathology, John Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Tammaryn Lashley
- Department of Neurodegenerative diseases, UCL Queen Square Institute of Neurology, WC1N 1PJ, London, UK
| | - Gunnar Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Barbara Mroczko
- Department of Neurodegeneration Diagnostics, Medical University of Białystok, Białystok, 15-269, Poland
| | - Hlin Kvartsberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 431 80, Sweden
| | - Milica Gregorič Kramberger
- Department of Neurology, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Karolinska Institutet, Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics, 141 52, Huddinge, Sweden
| | - Jörg Hanrieder
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Department of Neurodegenerative Disease, Dementia Research Centre, UCL Institute of Neurology, Queen Square, London, WC1E 6BT, UK
| | - Saša Čučnik
- Department of Neurology, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
- Department of Rheumatology, University Medical Center Ljubljana, Ljubljana, Slovenia
| | | | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 431 80, Sweden
- Department of Neurodegenerative Disease, Dementia Research Centre, UCL Institute of Neurology, Queen Square, London, WC1E 6BT, UK
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK
- Hong Kong Center for Neurodegenerative Diseases, HKCeND, Hong Kong, 1512-1518, China
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - Piotr Lewczuk
- Department of Neurodegeneration Diagnostics, Medical University of Białystok, Białystok, 15-269, Poland
- Department of Psychiatry and Psychotherapy, Universitätsklinikum Erlangen, and Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Uroš Rot
- Department of Neurology, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Douglas Galasko
- Department of Neurosciences, University of California, San Diego, CA, 92161, USA
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 431 80, Sweden
| | - Thomas K Karikari
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
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18
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Jiang W, Jaehnig EJ, Liao Y, Yaron-Barir TM, Johnson JL, Cantley LC, Zhang B. Illuminating the Dark Cancer Phosphoproteome Through a Machine-Learned Co-Regulation Map of 26,280 Phosphosites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585786. [PMID: 38562798 PMCID: PMC10983930 DOI: 10.1101/2024.03.19.585786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Mass spectrometry-based phosphoproteomics offers a comprehensive view of protein phosphorylation, but limited knowledge about the regulation and function of most phosphosites restricts our ability to extract meaningful biological insights from phosphoproteomics data. To address this, we combine machine learning and phosphoproteomic data from 1,195 tumor specimens spanning 11 cancer types to construct CoPheeMap, a network mapping the co-regulation of 26,280 phosphosites. Integrating network features from CoPheeMap into a machine learning model, CoPheeKSA, we achieve superior performance in predicting kinase-substrate associations. CoPheeKSA reveals 24,015 associations between 9,399 phosphosites and 104 serine/threonine kinases, including many unannotated phosphosites and under-studied kinases. We validate the accuracy of these predictions using experimentally determined kinase-substrate specificities. By applying CoPheeMap and CoPheeKSA to phosphosites with high computationally predicted functional significance and cancer-associated phosphosites, we demonstrate the effectiveness of these tools in systematically illuminating phosphosites of interest, revealing dysregulated signaling processes in human cancer, and identifying under-studied kinases as putative therapeutic targets.
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19
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Chen Z, Lin B, Yao X, Weng J, Liu J, He Q, Song K, Zhou C, Zuo Z, Huang X, Liu Z, Huang Q, Xu Q, Guo X. Endothelial β-catenin upregulation and Y142 phosphorylation drive diabetic angiogenesis via upregulating KDR/HDAC9. Cell Commun Signal 2024; 22:182. [PMID: 38491522 PMCID: PMC10941375 DOI: 10.1186/s12964-024-01566-1] [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: 11/07/2023] [Accepted: 03/09/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Diabetic angiogenesis is closely associated with disabilities and death caused by diabetic microvascular complications. Advanced glycation end products (AGEs) are abnormally accumulated in diabetic patients and are a key pathogenic factor for diabetic angiogenesis. The present study focuses on understanding the mechanisms underlying diabetic angiogenesis and identifying therapeutic targets based on these mechanisms. METHODS In this study, AGE-induced angiogenesis serves as a model to investigate the mechanisms underlying diabetic angiogensis. Mouse aortic rings, matrigel plugs, and HUVECs or 293T cells were employed as research objects to explore this pathological process by using transcriptomics, gene promoter reporter assays, virtual screening and so on. RESULTS Here, we found that AGEs activated Wnt/β-catenin signaling pathway and enhanced the β-catenin protein level by affecting the expression of β-catenin degradation-related genes, such as FZDs (Frizzled receptors), LRPs (LDL Receptor Related Proteins), and AXIN1. AGEs could also mediate β-catenin Y142 phosphorylation through VEGFR1 isoform5. These dual effects of AGEs elevated the nuclear translocation of β-catenin and sequentially induced the expression of KDR (Kinase Insert Domain Receptor) and HDAC9 (Histone Deacetylase 9) by POU5F1 and NANOG, respectively, thus mediating angiogenesis. Finally, through virtual screening, Bioymifi, an inhibitor that blocks VEGFR1 isoform5-β-catenin complex interaction and alleviates AGE-induced angiogenesis, was identified. CONCLUSION Collectively, this study offers insight into the pathophysiological functions of β-catenin in diabetic angiogenesis.
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Affiliation(s)
- Zhenfeng Chen
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Bingqi Lin
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaodan Yao
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jie Weng
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jinlian Liu
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Qi He
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Ke Song
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Chuyu Zhou
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zirui Zuo
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoxia Huang
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zhuanhua Liu
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Qiaobing Huang
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Qiulin Xu
- Department of Intensive Care Unit, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Southern Medical University, Guangzhou, 510515, China.
| | - Xiaohua Guo
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
- National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
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20
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Sánchez Milán JA, Fernández‐Rhodes M, Guo X, Mulet M, Ngan SC, Iyappan R, Katoueezadeh M, Sze SK, Serra A, Gallart‐Palau X. Trioxidized cysteine in the aging proteome mimics the structural dynamics and interactome of phosphorylated serine. Aging Cell 2024; 23:e14062. [PMID: 38111315 PMCID: PMC10928580 DOI: 10.1111/acel.14062] [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: 08/03/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/20/2023] Open
Abstract
Aging is the primary risk factor for the development of numerous human chronic diseases. On a molecular level, it significantly impacts the regulation of protein modifications, leading to the accumulation of degenerative protein modifications (DPMs) such as aberrant serine phosphorylation (p-Ser) and trioxidized cysteine (t-Cys) within the proteome. The altered p-Ser is linked to abnormal cell signaling, while the accumulation of t-Cys is associated with chronic diseases induced by oxidative stress. Despite this, the potential cross-effects and functional interplay between these two critical molecular factors of aging remain undisclosed. This study analyzes the aging proteome of wild-type C57BL/6NTac mice over 2 years using advanced proteomics and bioinformatics. Our objective is to provide a comprehensive analysis of how t-Cys affects cell signaling and protein structure in the aging process. The results obtained indicate that t-Cys residues accumulate in the aging proteome, interact with p-Ser interacting enzymes, as validated in vitro, and alter their structures similarly to p-Ser. These findings have significant implications for understanding the interplay of oxidative stress and phosphorylation in the aging process. Additionally, they open new venues for further research on the role(s) of these protein modifications in various human chronic diseases and aging, wherein exacerbated oxidation and aberrant phosphorylation are implicated.
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Affiliation(s)
- Jose Antonio Sánchez Milán
- Biomedical Research Institute of Lleida (IRBLLEIDA) ‐ +Pec Proteomics Research Group (+PPRG) ‐ Neuroscience AreaUniversity Hospital Arnau de Vilanova (HUAV)LleidaSpain
- Department of Basic Medical Sciences, Biomedical Research Institute of Lleida (IRB Lleida) ‐ +Pec Proteomics Research Group (+PPRG) ‐ Neuroscience AreaUniversity of Lleida (UdL)LleidaSpain
| | - María Fernández‐Rhodes
- Biomedical Research Institute of Lleida (IRBLLEIDA) ‐ +Pec Proteomics Research Group (+PPRG) ‐ Neuroscience AreaUniversity Hospital Arnau de Vilanova (HUAV)LleidaSpain
- Department of Basic Medical Sciences, Biomedical Research Institute of Lleida (IRB Lleida) ‐ +Pec Proteomics Research Group (+PPRG) ‐ Neuroscience AreaUniversity of Lleida (UdL)LleidaSpain
| | - Xue Guo
- Institute of Molecular and Cell Biology (IMCB)SingaporeSingapore
| | - María Mulet
- Biomedical Research Institute of Lleida (IRBLLEIDA) ‐ +Pec Proteomics Research Group (+PPRG) ‐ Neuroscience AreaUniversity Hospital Arnau de Vilanova (HUAV)LleidaSpain
- Department of Basic Medical Sciences, Biomedical Research Institute of Lleida (IRB Lleida) ‐ +Pec Proteomics Research Group (+PPRG) ‐ Neuroscience AreaUniversity of Lleida (UdL)LleidaSpain
| | - SoFong Cam Ngan
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesOntarioCanada
| | - Ranjith Iyappan
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesOntarioCanada
| | - Maryam Katoueezadeh
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesOntarioCanada
| | - Siu Kwan Sze
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesOntarioCanada
| | - Aida Serra
- Department of Basic Medical Sciences, Biomedical Research Institute of Lleida (IRB Lleida) ‐ +Pec Proteomics Research Group (+PPRG) ‐ Neuroscience AreaUniversity of Lleida (UdL)LleidaSpain
| | - Xavier Gallart‐Palau
- Biomedical Research Institute of Lleida (IRBLLEIDA) ‐ +Pec Proteomics Research Group (+PPRG) ‐ Neuroscience AreaUniversity Hospital Arnau de Vilanova (HUAV)LleidaSpain
- Department of PsychologyUniversity of Lleida (UdL)LleidaSpain
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21
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Locke AJ, Abou Farraj R, Tran C, Zeinali E, Mashayekhi F, Ali JYH, Glover JNM, Ismail IH. The role of RNF138 in DNA end resection is regulated by ubiquitylation and CDK phosphorylation. J Biol Chem 2024; 300:105709. [PMID: 38309501 PMCID: PMC10910129 DOI: 10.1016/j.jbc.2024.105709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 01/02/2024] [Accepted: 01/18/2024] [Indexed: 02/05/2024] Open
Abstract
Double-strand breaks (DSBs) are DNA lesions that pose a significant threat to genomic stability. The repair of DSBs by the homologous recombination (HR) pathway is preceded by DNA end resection, the 5' to 3' nucleolytic degradation of DNA away from the DSB. We and others previously identified a role for RNF138, a really interesting new gene finger E3 ubiquitin ligase, in stimulating DNA end resection and HR. Yet, little is known about how RNF138's function is regulated in the context of DSB repair. Here, we show that RNF138 is phosphorylated at residue T27 by cyclin-dependent kinase (CDK) activity during the S and G2 phases of the cell cycle. We also observe that RNF138 is ubiquitylated constitutively, with ubiquitylation occurring in part on residue K158 and rising during the S/G2 phases. Interestingly, RNF138 ubiquitylation decreases upon genotoxic stress. By mutating RNF138 at residues T27, K158, and the previously identified S124 ataxia telangiectasia mutated phosphorylation site (Han et al., 2016, ref. 22), we find that post-translational modifications at all three positions mediate DSB repair. Cells expressing the T27A, K158R, and S124A variants of RNF138 are impaired in DNA end resection, HR activity, and are more sensitive to ionizing radiation compared to those expressing wildtype RNF138. Our findings shed more light on how RNF138 activity is controlled by the cell during HR.
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Affiliation(s)
- Andrew J Locke
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Rabih Abou Farraj
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Caroline Tran
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Elham Zeinali
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Fatemeh Mashayekhi
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Jana Yasser Hafez Ali
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - J N Mark Glover
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Ismail Hassan Ismail
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada; Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt.
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22
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Yang N, Ren J, Dai S, Wang K, Leung M, Lu Y, An Y, Burlingame A, Xu S, Wang Z, Yu W, Li N. The Quantitative Biotinylproteomics Studies Reveal a WInd-Related Kinase 1 (Raf-Like Kinase 36) Functioning as an Early Signaling Component in Wind-Induced Thigmomorphogenesis and Gravitropism. Mol Cell Proteomics 2024; 23:100738. [PMID: 38364992 PMCID: PMC10951710 DOI: 10.1016/j.mcpro.2024.100738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
Wind is one of the most prevalent environmental forces entraining plants to develop various mechano-responses, collectively called thigmomorphogenesis. Largely unknown is how plants transduce these versatile wind force signals downstream to nuclear events and to the development of thigmomorphogenic phenotype or anemotropic response. To identify molecular components at the early steps of the wind force signaling, two mechanical signaling-related phosphoproteins, identified from our previous phosphoproteomic study of Arabidopsis touch response, mitogen-activated protein kinase kinase 1 (MKK1) and 2 (MKK2), were selected for performing in planta TurboID (ID)-based quantitative proximity-labeling (PL) proteomics. This quantitative biotinylproteomics was separately performed on MKK1-ID and MKK2-ID transgenic plants, respectively, using the genetically engineered TurboID biotin ligase expression transgenics as a universal control. This unique PTM proteomics successfully identified 11 and 71 MKK1 and MKK2 putative interactors, respectively. Biotin occupancy ratio (BOR) was found to be an alternative parameter to measure the extent of proximity and specificity between the proximal target proteins and the bait fusion protein. Bioinformatics analysis of these biotinylprotein data also found that TurboID biotin ligase favorably labels the loop region of target proteins. A WInd-Related Kinase 1 (WIRK1), previously known as rapidly accelerated fibrosarcoma (Raf)-like kinase 36 (RAF36), was found to be a putative common interactor for both MKK1 and MKK2 and preferentially interacts with MKK2. Further molecular biology studies of the Arabidopsis RAF36 kinase found that it plays a role in wind regulation of the touch-responsive TCH3 and CML38 gene expression and the phosphorylation of a touch-regulated PATL3 phosphoprotein. Measurement of leaf morphology and shoot gravitropic response of wirk1 (raf36) mutant revealed that the WIRK1 gene is involved in both wind-triggered rosette thigmomorphogenesis and gravitropism of Arabidopsis stems, suggesting that the WIRK1 (RAF36) protein probably functioning upstream of both MKK1 and MKK2 and that it may serve as the crosstalk point among multiple mechano-signal transduction pathways mediating both wind mechano-response and gravitropism.
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Affiliation(s)
- Nan Yang
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Jia Ren
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Shuaijian Dai
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Kai Wang
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Manhin Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Yinglin Lu
- Institute of Nanfan and Seed Industry, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Yuxing An
- Institute of Nanfan and Seed Industry, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Al Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Shouling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
| | - Zhiyong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
| | - Weichuan Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
| | - Ning Li
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China; Shenzhen Research Institute, The Hong Kong University of Science and Technology, Shenzhen, Guangdong, China.
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23
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Jain G, Das G, Malhotra R, Ramchandran S, Phani NM, Appaswamy G, Sridharan U, Dwivedi A. Hypomagnesemia with Secondary Hypoparathyroidism and Hypocalcemia due to Novel Variants in the Transient Receptor Potential Cation Channel Subfamily M Member 6 ( TRPM6 ) Gene. J Pediatr Genet 2024; 13:35-42. [PMID: 38567178 PMCID: PMC10984712 DOI: 10.1055/s-0041-1733949] [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: 12/28/2020] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
HOMG1 (hypomagnesemia 1, intestinal) or hypomagnesemia with secondary hypocalcemia is a rare autosomal recessive disorder of magnesium metabolism, characterized by impaired magnesium absorption. This disorder may mimic other conditions presenting with neonatal seizures. Here, we report an infant diagnosed to have hypomagnesemia with secondary hypocalcemia due to novel variants in TRPM6 gene.
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Affiliation(s)
| | - Gourab Das
- Army Hospital (Research and Referral), New Delhi, India
| | - Rakhi Malhotra
- Department of Endocrinology, Army Hospital (Research and Referral), New Delhi, Delhi, India
| | - Sateesh Ramchandran
- Department of Endocrinology, Army Hospital (Research and Referral), New Delhi, Delhi, India
| | - Nagaraja M. Phani
- Department of Molecular Genetics, Life cell Diagnostics Pvt. Ltd., India
| | | | | | - Aradhana Dwivedi
- Department of Pediatrics, Division of Clinical Genetics, Army Hospital (Research and Referral), New Delhi, India
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24
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Alonso N, Menao S, Lastra R, Arruebo M, Bueso MP, Pérez E, Murillo ML, Álvarez M, Alonso A, Rebollar S, Cruellas M, Arribas D, Ramos M, Isla D, Galano-Frutos JJ, García-Cebollada H, Sancho J, Andrés R. Association between missense variants of uncertain significance in the CHEK2 gene and hereditary breast cancer: a cosegregation and bioinformatics analysis. Front Genet 2024; 14:1274108. [PMID: 38476463 PMCID: PMC10927753 DOI: 10.3389/fgene.2023.1274108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/06/2023] [Indexed: 03/14/2024] Open
Abstract
Inherited mutations in the CHEK2 gene have been associated with an increased lifetime risk of developing breast cancer (BC). We aim to identify in the study population the prevalence of mutations in the CHEK2 gene in diagnosed BC patients, evaluate the phenotypic characteristics of the tumor and family history, and predict the deleteriousness of the variants of uncertain significance (VUS). A genetic study was performed, from May 2016 to April 2020, in 396 patients diagnosed with BC at the University Hospital Lozano Blesa of Zaragoza, Spain. Patients with a genetic variant in the CHEK2 gene were selected for the study. We performed a descriptive analysis of the clinical variables, a bibliographic review of the variants, and a cosegregation study when possible. Moreover, an in-depth bioinformatics analysis of CHEK2 VUS was carried out. We identified nine genetic variants in the CHEK2 gene in 10 patients (two pathogenic variants and seven VUS). This supposes a prevalence of 0.75% and 1.77%, respectively. In all cases, there was a family history of BC in first- and/or second-degree relatives. We carried out a cosegregation study in two families, being positive in one of them. The bioinformatics analyses predicted the pathogenicity of six of the VUS. In conclusion, CHEK2 mutations have been associated with an increased risk for BC. This risk is well-established for foundation variants. However, the risk assessment for other variants is unclear. The incorporation of bioinformatics analysis provided supporting evidence of the pathogenicity of VUS.
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Affiliation(s)
- Natalia Alonso
- Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
- Medical Oncology Department, Hospital San Pedro, Logroño, Spain
| | - Sebastián Menao
- Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
- Biochemistry Department, University Hospital Lozano Blesa, Zaragoza, Spain
| | - Rodrigo Lastra
- Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
- Medical Oncology Department, University Hospital Lozano Blesa, Zaragoza, Spain
| | - María Arruebo
- Biochemistry Department, University Hospital Lozano Blesa, Zaragoza, Spain
| | - María P. Bueso
- Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
- Medical Oncology Department, University Hospital Lozano Blesa, Zaragoza, Spain
| | - Esther Pérez
- Breast Unit, University Hospital Lozano Blesa, Zaragoza, Spain
| | - M. Laura Murillo
- Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
- Medical Oncology Department, University Hospital Lozano Blesa, Zaragoza, Spain
| | - María Álvarez
- Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
- Medical Oncology Department, University Hospital Lozano Blesa, Zaragoza, Spain
| | - Alba Alonso
- Biochemistry Department, University Hospital Arnau de Vilanova, Lleida, Spain
| | - Soraya Rebollar
- Biochemistry Department, University Hospital Lozano Blesa, Zaragoza, Spain
| | - Mara Cruellas
- Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
- Medical Oncology Department, University Hospital of Valld’Hebron, and Valld’Hebron Institute of Oncology, Barcelona, Spain
| | - Dolores Arribas
- General Surgery Department, University Hospital Lozano Blesa, Zaragoza, Spain
| | - Mónica Ramos
- Biochemistry Department, University Hospital Lozano Blesa, Zaragoza, Spain
| | - Dolores Isla
- Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
- Medical Oncology Department, University Hospital Lozano Blesa, Zaragoza, Spain
| | - Juan José Galano-Frutos
- Department of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, Zaragoza, Spain
- Biocomputation and Complex Systems Physics Institute (BIFI), Joint Units BIFI-IQFR (CSIC) and GBs-CSIC, University of Zaragoza, Zaragoza, Spain
| | - Helena García-Cebollada
- Department of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, Zaragoza, Spain
- Biocomputation and Complex Systems Physics Institute (BIFI), Joint Units BIFI-IQFR (CSIC) and GBs-CSIC, University of Zaragoza, Zaragoza, Spain
| | - Javier Sancho
- Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
- Department of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, Zaragoza, Spain
- Biocomputation and Complex Systems Physics Institute (BIFI), Joint Units BIFI-IQFR (CSIC) and GBs-CSIC, University of Zaragoza, Zaragoza, Spain
| | - Raquel Andrés
- Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
- Medical Oncology Department, University Hospital Lozano Blesa, Zaragoza, Spain
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25
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Thalwieser Z, Fonódi M, Király N, Csortos C, Boratkó A. PP2A Affects Angiogenesis via Its Interaction with a Novel Phosphorylation Site of TSP1. Int J Mol Sci 2024; 25:1844. [PMID: 38339122 PMCID: PMC10855381 DOI: 10.3390/ijms25031844] [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: 01/13/2024] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Alterations in angiogenic properties play a pivotal role in the manifestation and onset of various pathologies, including vascular diseases and cancer. Thrombospondin-1 (TSP1) protein is one of the master regulators of angiogenesis. This study unveils a novel aspect of TSP1 regulation through reversible phosphorylation. The silencing of the B55α regulatory subunit of protein phosphatase 2A (PP2A) in endothelial cells led to a significant decrease in TSP1 expression. Direct interaction between TSP1 and PP2A-B55α was confirmed via various methods. Truncated TSP1 constructs were employed to identify the phosphorylation site and the responsible kinase, ultimately pinpointing PKC as the enzyme phosphorylating TSP1 on Ser93. The biological effects of B55α-TSP1 interaction were also analyzed. B55α silencing not only counteracted the increase in TSP1 expression during wound closure but also prolonged wound closure time. Although B55α silenced cells initiated tube-like structures earlier than control cells, their spheroid formation was disrupted, leading to disintegration. Cells transfected with phosphomimic TSP1 S93D exhibited smaller spheroids and reduced effectiveness in tube formation, revealing insights into the effects of TSP1 phosphorylation on angiogenic properties. In this paper, we introduce a new regulatory mechanism of angiogenesis by reversible phosphorylation on TSP1 S93 by PKC and PP2A B55α.
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Affiliation(s)
| | | | | | | | - Anita Boratkó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Z.T.); (M.F.); (C.C.)
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26
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Yi X, Wen B, Ji S, Saltzman AB, Jaehnig EJ, Lei JT, Gao Q, Zhang B. Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification. Mol Cell Proteomics 2024; 23:100707. [PMID: 38154692 PMCID: PMC10831110 DOI: 10.1016/j.mcpro.2023.100707] [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: 01/10/2023] [Revised: 11/06/2023] [Accepted: 12/23/2023] [Indexed: 12/30/2023] Open
Abstract
Shotgun phosphoproteomics enables high-throughput analysis of phosphopeptides in biological samples. One of the primary challenges associated with this technology is the relatively low rate of phosphopeptide identification during data analysis. This limitation hampers the full realization of the potential offered by shotgun phosphoproteomics. Here we present DeepRescore2, a computational workflow that leverages deep learning-based retention time and fragment ion intensity predictions to improve phosphopeptide identification and phosphosite localization. Using a state-of-the-art computational workflow as a benchmark, DeepRescore2 increases the number of correctly identified peptide-spectrum matches by 17% in a synthetic dataset and identifies 19% to 46% more phosphopeptides in biological datasets. In a liver cancer dataset, 30% of the significantly altered phosphosites between tumor and normal tissues and 60% of the prognosis-associated phosphosites identified from DeepRescore2-processed data could not be identified based on the state-of-the-art workflow. Notably, DeepRescore2-processed data uniquely identifies EGFR hyperactivation as a new target in poor-prognosis liver cancer, which is validated experimentally. Integration of deep learning prediction in DeepRescore2 improves phosphopeptide identification and facilitates biological discoveries.
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Affiliation(s)
- Xinpei Yi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Shuyi Ji
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital and Key Laboratory of Carcinogenesis and Cancer Invasion of the Ministry of China, Fudan University, Shanghai, China
| | - Alexander B Saltzman
- Mass Spectrometry Proteomics Core, Advanced Technology Cores, Baylor College of Medicine, Houston, Texas, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital and Key Laboratory of Carcinogenesis and Cancer Invasion of the Ministry of China, Fudan University, Shanghai, China
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
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27
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Ruperti F, Becher I, Stokkermans A, Wang L, Marschlich N, Potel C, Maus E, Stein F, Drotleff B, Schippers KJ, Nickel M, Prevedel R, Musser JM, Savitski MM, Arendt D. Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response. Curr Biol 2024; 34:361-375.e9. [PMID: 38181793 DOI: 10.1016/j.cub.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/03/2023] [Accepted: 12/07/2023] [Indexed: 01/07/2024]
Abstract
A hallmark of animals is the coordination of whole-body movement. Neurons and muscles are central to this, yet coordinated movements also exist in sponges that lack these cell types. Sponges are sessile animals with a complex canal system for filter-feeding. They undergo whole-body movements resembling "contractions" that lead to canal closure and water expulsion. Here, we combine live 3D optical coherence microscopy, pharmacology, and functional proteomics to elucidate the sequence and detail of shape changes, the tissues and molecular physiology involved, and the control of these movements. Morphometric analysis and targeted perturbation suggest that the movement is driven by the relaxation of actomyosin stress fibers in epithelial canal cells, which leads to whole-body deflation via collapse of the incurrent and expansion of the excurrent canal system. Thermal proteome profiling and quantitative phosphoproteomics confirm the control of cellular relaxation by an Akt/NO/PKG/PKA pathway. Agitation-induced deflation leads to differential phosphorylation of proteins forming epithelial cell junctions, implying their mechanosensitive role. Unexpectedly, untargeted metabolomics detect a concomitant decrease in antioxidant molecules during deflation, reflecting an increase in reactive oxygen species. Together with the secretion of proteinases, cytokines, and granulin, this indicates an inflammation-like state of the deflating sponge reminiscent of vascular endothelial cells experiencing oscillatory shear stress. These results suggest the conservation of an ancient relaxant-inflammatory response of perturbed fluid-carrying systems in animals and offer a possible mechanism for whole-body coordination through diffusible paracrine signals and mechanotransduction.
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Affiliation(s)
- Fabian Ruperti
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Collaboration for joint Ph.D. degree between EMBL and Heidelberg University, Faculty of Biosciences 69117 Heidelberg, Germany
| | - Isabelle Becher
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Ling Wang
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Nick Marschlich
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
| | - Clement Potel
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Emanuel Maus
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Bernhard Drotleff
- Metabolomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Klaske J Schippers
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Michael Nickel
- Bionic consulting Dr. Michael Nickel, 71686 Remseck am Neckar, Germany
| | - Robert Prevedel
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jacob M Musser
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Proteomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany.
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28
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Kumar SB, Girish A, Sutar S, Premanand SA, Garg V, Yadav AK, Shukla R, Murthy TPK, Singh TR. A computational study on structural and functional consequences of nsSNPs in human dopa decarboxylase. J Biomol Struct Dyn 2024:1-15. [PMID: 38193892 DOI: 10.1080/07391102.2023.2301517] [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: 07/28/2023] [Accepted: 11/04/2023] [Indexed: 01/10/2024]
Abstract
The Dopa Decarboxylase (DDC) gene plays an important role in the synthesis of biogenic amines such as dopamine, serotonin, and histamine. Non-synonymous single nucleotide polymorphisms (nsSNPs) in the DDC gene have been linked with various neurodegenerative disorders. In this study, a comprehensive in silico analysis of nsSNPs in the DDC gene was conducted to assess their potential functional consequences and associations with disease outcomes. Using publicly available databases, a complete list of nsSNPs in the DDC gene was obtained. 29 computational tools and algorithms were used to characterise the effects of these nsSNPs on protein structure, function, and stability. In addition, the population-based association studies were performed to investigate possible associations between specific nsSNPs and arthritis. Our research identified four novel DDC gene nsSNPs that have a major impact on the structure and function of proteins. Through molecular dynamics simulations (MDS), we observed changes in the stability of the DDC protein induced by specific nsSNPs. Furthermore, population-based association studies have revealed potential associations between certain DDC nsSNPs and various neurological disorders, including Parkinson's disease and dementia. The in silico approach used in this study offers insightful information about the functional effects of nsSNPs in the DDC gene. These discoveries provide insight into the cellular processes that underlie cognitive disorders. Furthermore, the detection of disease-associated nsSNPs in the DDC gene may facilitate the development of tailored and targeted therapy approaches.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Birendra Kumar
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, India
| | - Aishwarya Girish
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, India
| | - Samruddhi Sutar
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, India
| | | | - Vrinda Garg
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, India
| | - Arvind Kumar Yadav
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, India
| | - Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, India
| | - T P Krishna Murthy
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, India
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29
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Salyer LG, Salhi HE, Brundage EA, Shettigar V, Sturgill SL, Zanella H, Templeton B, Abay E, Emmer KM, Lowe J, Rafael-Fortney JA, Parinandi N, Foster DB, McKinsey TA, Woulfe KC, Ziolo MT, Biesiadecki BJ. Troponin I Tyrosine Phosphorylation Beneficially Accelerates Diastolic Function. Circ Res 2024; 134:33-45. [PMID: 38095088 PMCID: PMC10872382 DOI: 10.1161/circresaha.123.323132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND A healthy heart is able to modify its function and increase relaxation through post-translational modifications of myofilament proteins. While there are known examples of serine/threonine kinases directly phosphorylating myofilament proteins to modify heart function, the roles of tyrosine (Y) phosphorylation to directly modify heart function have not been demonstrated. The myofilament protein TnI (troponin I) is the inhibitory subunit of the troponin complex and is a key regulator of cardiac contraction and relaxation. We previously demonstrated that TnI-Y26 phosphorylation decreases calcium-sensitive force development and accelerates calcium dissociation, suggesting a novel role for tyrosine kinase-mediated TnI-Y26 phosphorylation to regulate cardiac relaxation. Therefore, we hypothesize that increasing TnI-Y26 phosphorylation will increase cardiac relaxation in vivo and be beneficial during pathological diastolic dysfunction. METHODS The signaling pathway involved in TnI-Y26 phosphorylation was predicted in silico and validated by tyrosine kinase activation and inhibition in primary adult murine cardiomyocytes. To investigate how TnI-Y26 phosphorylation affects cardiac muscle, structure, and function in vivo, we developed a novel TnI-Y26 phosphorylation-mimetic mouse that was subjected to echocardiography, pressure-volume loop hemodynamics, and myofibril mechanical studies. TnI-Y26 phosphorylation-mimetic mice were further subjected to the nephrectomy/DOCA (deoxycorticosterone acetate) model of diastolic dysfunction to investigate the effects of increased TnI-Y26 phosphorylation in disease. RESULTS Src tyrosine kinase is sufficient to phosphorylate TnI-Y26 in cardiomyocytes. TnI-Y26 phosphorylation accelerates in vivo relaxation without detrimental structural or systolic impairment. In a mouse model of diastolic dysfunction, TnI-Y26 phosphorylation is beneficial and protects against the development of disease. CONCLUSIONS We have demonstrated that tyrosine kinase phosphorylation of TnI is a novel mechanism to directly and beneficially accelerate myocardial relaxation in vivo.
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Affiliation(s)
- Lorien G Salyer
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute (L.G.S., H.E.S., E.A.B., V.S., S.L.S., H.Z., B.T., E.A., J.L., J.A.R.-F., M.T.Z., B.J.B.), Ohio State University, Columbus
| | - Hussam E Salhi
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute (L.G.S., H.E.S., E.A.B., V.S., S.L.S., H.Z., B.T., E.A., J.L., J.A.R.-F., M.T.Z., B.J.B.), Ohio State University, Columbus
| | - Elizabeth A Brundage
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute (L.G.S., H.E.S., E.A.B., V.S., S.L.S., H.Z., B.T., E.A., J.L., J.A.R.-F., M.T.Z., B.J.B.), Ohio State University, Columbus
| | - Vikram Shettigar
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute (L.G.S., H.E.S., E.A.B., V.S., S.L.S., H.Z., B.T., E.A., J.L., J.A.R.-F., M.T.Z., B.J.B.), Ohio State University, Columbus
| | - Sarah L Sturgill
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute (L.G.S., H.E.S., E.A.B., V.S., S.L.S., H.Z., B.T., E.A., J.L., J.A.R.-F., M.T.Z., B.J.B.), Ohio State University, Columbus
| | - Helena Zanella
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute (L.G.S., H.E.S., E.A.B., V.S., S.L.S., H.Z., B.T., E.A., J.L., J.A.R.-F., M.T.Z., B.J.B.), Ohio State University, Columbus
| | - Benjamin Templeton
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute (L.G.S., H.E.S., E.A.B., V.S., S.L.S., H.Z., B.T., E.A., J.L., J.A.R.-F., M.T.Z., B.J.B.), Ohio State University, Columbus
| | - Eaman Abay
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute (L.G.S., H.E.S., E.A.B., V.S., S.L.S., H.Z., B.T., E.A., J.L., J.A.R.-F., M.T.Z., B.J.B.), Ohio State University, Columbus
| | - Kathryn M Emmer
- University Laboratory Animal Resources (K.M.E.), Ohio State University, Columbus
| | - Jeovanna Lowe
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute (L.G.S., H.E.S., E.A.B., V.S., S.L.S., H.Z., B.T., E.A., J.L., J.A.R.-F., M.T.Z., B.J.B.), Ohio State University, Columbus
| | - Jill A Rafael-Fortney
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute (L.G.S., H.E.S., E.A.B., V.S., S.L.S., H.Z., B.T., E.A., J.L., J.A.R.-F., M.T.Z., B.J.B.), Ohio State University, Columbus
| | - Narasimham Parinandi
- Division of Pulmonary, Critical Care and Sleep Medicine (N.P.), Ohio State University, Columbus
| | - D Brian Foster
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD (D.B.F.)
| | - Timothy A McKinsey
- Department of Medicine, Division of Cardiology (T.A.M., K.C.W.), University of Colorado Anschutz Medical Campus, Aurora
- Consortium for Fibrosis Research and Translation (T.A.M.), University of Colorado Anschutz Medical Campus, Aurora
| | - Kathleen C Woulfe
- Department of Medicine, Division of Cardiology (T.A.M., K.C.W.), University of Colorado Anschutz Medical Campus, Aurora
| | - Mark T Ziolo
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute (L.G.S., H.E.S., E.A.B., V.S., S.L.S., H.Z., B.T., E.A., J.L., J.A.R.-F., M.T.Z., B.J.B.), Ohio State University, Columbus
| | - Brandon J Biesiadecki
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute (L.G.S., H.E.S., E.A.B., V.S., S.L.S., H.Z., B.T., E.A., J.L., J.A.R.-F., M.T.Z., B.J.B.), Ohio State University, Columbus
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30
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Chatterjee S, Zaia J. Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples. MASS SPECTROMETRY REVIEWS 2024; 43:193-229. [PMID: 36177493 PMCID: PMC9538640 DOI: 10.1002/mas.21813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host-pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.
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Affiliation(s)
- Sayantani Chatterjee
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA
- Bioinformatics Program, Boston University School of Medicine, Boston, Massachusetts, USA
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31
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Wang T, Wang H, Lian Q, Jia Q, You C, Copenhaver GP, Wang C, Wang Y. HEI10 is subject to phase separation and mediates RPA1a degradation during meiotic interference-sensitive crossover formation. Proc Natl Acad Sci U S A 2023; 120:e2310542120. [PMID: 38134200 PMCID: PMC10756261 DOI: 10.1073/pnas.2310542120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/27/2023] [Indexed: 12/24/2023] Open
Abstract
Reciprocal exchanges of DNA between homologous chromosomes during meiosis, or crossovers (COs), shuffle genetic information in gametes and progeny. In many eukaryotes, the majority of COs (class I COs) are sensitive to a phenomenon called interference, which influences the occurrence of closely spaced double COs. Class I COs depend on a group of factors called ZMM (Zip, Msh, Mer) proteins including HEI10 (Human Enhancer of Invasion-10). However, how these proteins are recruited to class I CO sites is unclear. Here, we show that HEI10 forms foci on chromatin via a liquid-liquid phase separation (LLPS) mechanism that relies on residue Ser70. A HEI10S70F allele results in LLPS failure and a defect in class I CO formation. We further used immunoprecipitation-mass spectrometry to identify RPA1a (Replication Protein A 1) as a HEI10 interacting protein. Surprisingly, we find that RPA1a also undergoes phase separation and its ubiquitination and degradation are directly regulated by HEI10. We also show that HEI10 is required for the condensation of other class I CO factors. Thus, our results provide mechanistic insight into how meiotic class I CO formation is controlled by HEI10 coupling LLPS and ubiquitination.
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Affiliation(s)
- Tianyi Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai200438, China
| | - Hongkuan Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai200438, China
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI49503
| | - Qichao Lian
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai200438, China
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Qian Jia
- College of Life Sciences, South China Agricultural University, Guangzhou510642, China
| | - Chenjiang You
- College of Life Sciences, South China Agricultural University, Guangzhou510642, China
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC27599-3280
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC27599-3280
| | - Cong Wang
- College of Life Sciences, South China Agricultural University, Guangzhou510642, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai200438, China
- College of Life Sciences, South China Agricultural University, Guangzhou510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou510642, China
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32
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Kac PR, González-Ortiz F, Emeršič A, Dulewicz M, Koutarapu S, Turton M, An Y, Smirnov D, Kulczyńska-Przybik A, Varma V, Ashton NJ, Montoliu-Gaya L, Camporesi E, Winkel I, Paradowski B, Moghekar A, Troncoso JC, Brinkmalm G, Resnick SM, Mroczko B, Kvartsberg H, Kramberger MG, Hanrieder J, Čučnik S, Harrison P, Zetterberg H, Lewczuk P, Thambisetty M, Rot U, Galasko D, Blennow K, Karikari TK. Plasma p-tau212: antemortem diagnostic performance and prediction of autopsy verification of Alzheimer's disease neuropathology. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.11.23299806. [PMID: 38168323 PMCID: PMC10760276 DOI: 10.1101/2023.12.11.23299806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Blood phosphorylated tau (p-tau) biomarkers, including p-tau217, show high associations with Alzheimer's disease (AD) neuropathologic change and clinical stage. Certain plasma p-tau217 assays recognize tau forms phosphorylated additionally at threonine-212, but the contribution of p-tau212 alone to AD is unknown. We developed a blood-based immunoassay that is specific to p-tau212 without cross-reactivity to p-tau217. Thereafter, we examined the diagnostic utility of plasma p-tau212. In five cohorts (n=388 participants), plasma p-tau212 showed high performances for AD diagnosis and for the detection of both amyloid and tau pathology, including at autopsy as well as in memory clinic populations. The diagnostic accuracy and fold changes of plasma p-tau212 were similar to those for p-tau217 but higher than p-tau181 and p-tau231. Immunofluorescent staining of brain tissue slices showed prominent p-tau212 reactivity in neurofibrillary tangles that co-localized with p-tau217 and p-tau202/205. These findings support plasma p-tau212 as a novel peripherally accessible biomarker of AD pathophysiology.
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Affiliation(s)
- Przemysław R Kac
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | - Fernando González-Ortiz
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 431 80, Sweden
| | - Andreja Emeršič
- Department of Neurology, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Maciej Dulewicz
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | - Srinivas Koutarapu
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | | | - Yang An
- Brain Aging and Behavior Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States of America
| | - Denis Smirnov
- Department of Neurosciences, University of California, San Diego, CA 92161 United States of America
| | | | - Vijay Varma
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States of America
| | - Nicholas J Ashton
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Department of Old Age Psychiatry, King's College London, London SE5 8AF, United Kingdom
- Centre for Age-Related Medicine, Stavanger University Hospital, 4011 Stavanger, Norway
- South London & Maudsley NHS Foundation, NIHR Biomedical Research Centre for Mental Health & Biomedical Research Unit for Dementia, SE5 8AF London, United Kingdom
| | - Laia Montoliu-Gaya
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | - Elena Camporesi
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | - Izabela Winkel
- Dementia Disorders Center, Medical University of Wrocław, 59-330 Scinawa, Poland
| | - Bogusław Paradowski
- Department of Neurology, Medical University of Wrocław, 50-556 Wroclaw, Poland
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States of America
| | - Juan C Troncoso
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States of America
- Department of Pathology, John Hopkins University School of Medicine, Baltimore, MD 21287, United States of America
| | - Gunnar Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States of America
| | - Barbara Mroczko
- Department of Neurodegeneration Diagnostics, Medical University of Białystok, Białystok 15-269, Poland
| | - Hlin Kvartsberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 431 80, Sweden
| | - Milica Gregorič Kramberger
- Department of Neurology, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Karolinska Institutet, Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics, 141 52 Huddinge, Sweden
| | - Jörg Hanrieder
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Department of Neurodegenerative Disease, Dementia Research Centre, UCL Institute of Neurology, Queen Square, London, WC1E 6BT, United Kingdom
| | - Saša Čučnik
- Department of Neurology, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
- Department of Rheumatology, University Medical Center Ljubljana, Ljubljana, Slovenia
| | | | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 431 80, Sweden
- Department of Neurodegenerative Disease, Dementia Research Centre, UCL Institute of Neurology, Queen Square, London, WC1E 6BT, United Kingdom
- UK Dementia Research Institute, University College London, London, WC1E 6BT, United Kingdom
- Hong Kong Center for Neurodegenerative Diseases, HKCeND, Hong Kong, 1512-1518, China
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Piotr Lewczuk
- Department of Psychiatry and Psychotherapy, Universitätsklinikum Erlangen, and Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
- Department of Biochemical Diagnostics, University Hospital of Białystok, Białystok, 15-269, Poland
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States of America
| | - Uroš Rot
- Department of Neurology, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Douglas Galasko
- Department of Neurosciences, University of California, San Diego, CA 92161 United States of America
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 431 80, Sweden
| | - Thomas K Karikari
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States of America
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33
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Lv D, Zhong C, Dixit D, Yang K, Wu Q, Godugu B, Prager BC, Zhao G, Wang X, Xie Q, Bao S, He C, Heiland DH, Rosenfeld MG, Rich JN. EGFR promotes ALKBH5 nuclear retention to attenuate N6-methyladenosine and protect against ferroptosis in glioblastoma. Mol Cell 2023; 83:4334-4351.e7. [PMID: 37979586 PMCID: PMC10842222 DOI: 10.1016/j.molcel.2023.10.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 08/01/2023] [Accepted: 10/18/2023] [Indexed: 11/20/2023]
Abstract
Growth factor receptors rank among the most important oncogenic pathways, but pharmacologic inhibitors often demonstrate limited benefit as monotherapy. Here, we show that epidermal growth factor receptor (EGFR) signaling repressed N6-methyladenosine (m6A) levels in glioblastoma stem cells (GSCs), whereas genetic or pharmacologic EGFR targeting elevated m6A levels. Activated EGFR induced non-receptor tyrosine kinase SRC to phosphorylate the m6A demethylase, AlkB homolog 5 (ALKBH5), thereby inhibiting chromosomal maintenance 1 (CRM1)-mediated nuclear export of ALKBH5 to permit sustained mRNA m6A demethylation in the nucleus. ALKBH5 critically regulated ferroptosis through m6A modulation and YTH N6-methyladenosine RNA binding protein (YTHDF2)-mediated decay of the glutamate-cysteine ligase modifier subunit (GCLM). Pharmacologic targeting of ALKBH5 augmented the anti-tumor efficacy of EGFR and GCLM inhibitors, supporting an EGFR-ALKBH5-GCLM oncogenic axis. Collectively, EGFR reprograms the epitranscriptomic landscape through nuclear retention of the ALKBH5 demethylase to protect against ferroptosis, offering therapeutic paradigms for the treatment of lethal cancers.
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Affiliation(s)
- Deguan Lv
- UPMC Hillman Cancer Center and Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Cuiqing Zhong
- UPMC Hillman Cancer Center and Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Deobrat Dixit
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Qiulian Wu
- UPMC Hillman Cancer Center and Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Bhaskar Godugu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Briana C Prager
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Guofeng Zhao
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xiuxing Wang
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Qi Xie
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Shideng Bao
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Dieter Henrik Heiland
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeremy N Rich
- UPMC Hillman Cancer Center and Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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34
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Xiao D, Lin M, Liu C, Geddes TA, Burchfield J, Parker B, Humphrey SJ, Yang P. SnapKin: a snapshot deep learning ensemble for kinase-substrate prediction from phosphoproteomics data. NAR Genom Bioinform 2023; 5:lqad099. [PMID: 37954574 PMCID: PMC10632189 DOI: 10.1093/nargab/lqad099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/18/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
A major challenge in mass spectrometry-based phosphoproteomics lies in identifying the substrates of kinases, as currently only a small fraction of substrates identified can be confidently linked with a known kinase. Machine learning techniques are promising approaches for leveraging large-scale phosphoproteomics data to computationally predict substrates of kinases. However, the small number of experimentally validated kinase substrates (true positive) and the high data noise in many phosphoproteomics datasets together limit their applicability and utility. Here, we aim to develop advanced kinase-substrate prediction methods to address these challenges. Using a collection of seven large phosphoproteomics datasets, and both traditional and deep learning models, we first demonstrate that a 'pseudo-positive' learning strategy for alleviating small sample size is effective at improving model predictive performance. We next show that a data resampling-based ensemble learning strategy is useful for improving model stability while further enhancing prediction. Lastly, we introduce an ensemble deep learning model ('SnapKin') by incorporating the above two learning strategies into a 'snapshot' ensemble learning algorithm. We propose SnapKin, an ensemble deep learning method, for predicting substrates of kinases from large-scale phosphoproteomics data. We demonstrate that SnapKin consistently outperforms existing methods in kinase-substrate prediction. SnapKin is freely available at https://github.com/PYangLab/SnapKin.
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Affiliation(s)
- Di Xiao
- Computational Systems Biology Group, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Michael Lin
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chunlei Liu
- Computational Systems Biology Group, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Thomas A Geddes
- Computational Systems Biology Group, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Environmental and Life Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - James G Burchfield
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Environmental and Life Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin L Parker
- Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, Melbourne, VIC 3010, Australia
| | - Sean J Humphrey
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Environmental and Life Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Melbourne, VIC, 3052, Australia
| | - Pengyi Yang
- Computational Systems Biology Group, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
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35
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Murthy TPK, Shukla R, Durga Prasad N, Swetha P, Shreyas S, Singh TR, Pattabiraman R, Nair SS, Mathew BB, Kumar KM. Comprehensive analysis of non-synonymous missense SNPs of human galactose mutarotase (GALM) gene: an integrated computational approach. J Biomol Struct Dyn 2023; 41:11178-11192. [PMID: 36591702 DOI: 10.1080/07391102.2022.2160813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/15/2022] [Indexed: 01/03/2023]
Abstract
Missense Non-synonymous single nucleotide polymorphisms (nsSNPs) of Galactose Mutarotase (GALM) are associated with the Novel type of Galactosemia (Galactosemia type 4) together with symptoms such as high blood galactose levels and eye cataracts. The objective of the present study was to identify deleterious nsSNPs of GALM recorded on the dbSNP database through comprehensive insilico analysis. Among the 319 missense nsSNPs reported, various insilco tools predicted R78S, R82G, A163E, P210S, Y281C, E307G and F339C as the most deleterious mutations. Structural analysis, PTM analysis and molecular dynamics simulations (MDS) were carried out to understand the effect of these mutations on the structural and physicochemical properties of the GALM protein. The residues R82G and E307G were found to be part of the binding site that resulted in decreased surface accessibility. Replacing the charged wild-type residue with a neutral mutant type affected its substrate binding. All 7 mutations were found to increase the rigidity of the protein structure, which is unfavorable during ligand binding. The mutation F339E made the protein structure more rigid than all the other mutations. Y281 is a phosphorylated site, and therefore, less significant structural changes were observed when compared to other mutations; however, it may have significant differences in the usual functioning of the protein. In summary, the structural and functional analysis of missense SNPs of GALM is important to reduce the number of potential mutations to be evaluated in vitro to understand the association with some genetic diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- T P Krishna Murthy
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - N Durga Prasad
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Praveen Swetha
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - S Shreyas
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - Ramya Pattabiraman
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Shishira S Nair
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Blessy B Mathew
- Department of Biotechnology, Dayananda Sagar College of Engineering, Bengaluru, Karnataka, Inida
| | - K M Kumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
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Wu Y, Song L, Kong J, Wen Q, Jiao J, Wang X, Li G, Xu X, Zhan L. Scribble promotes fibrosis-dependent mechanisms of hepatocarcinogenesis by p53/PUMA-mediated glycolysis. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166823. [PMID: 37632981 DOI: 10.1016/j.bbadis.2023.166823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 07/02/2023] [Accepted: 07/24/2023] [Indexed: 08/28/2023]
Abstract
BACKGROUNDS AND AIMS Liver cancer is the sixth most common type of cancer and the fifth leading cause of cancer mortality worldwide. Scribble has been shown to function as a neoplastic tumor suppressor gene in most tumors. Our previous studies reported that down-regulation or mislocalization of Scribble was sufficient to initiate mammary tumorigenesis and NSCLC. Recently, it was reported that Scribble was highly expressed in hepatocellular carcinoma (HCC). We aim to study how it was up-regulated and the contradictory role of Scribble in HCC. METHODS AND RESULTS Using a mouse model of carbon tetrachloride (CCl4)-induced liver fibrosis system, we showed that Scribble was over-expressed and which may protect the mice against hepatic fibrosis. Unexpectedly, we found out the potential for Scribble to act as a tumor driver at the advanced stage of N-nitrosodiethylamine (DEN) plus CCl4 induced HCC mice model in vivo. In addition, we observed even higher expression of Scribble in HCC tumors harboring elevated levels of wild-type p53. Most importantly, nuclear translocated Scribble could interact with p53, which lead to enhanced stability and transcriptional activity of p53. Mechanistically, our data suggested that Scribble might drive HCC progression by promoting metabolic regulation of p53 through p53-upregulated modulator of apoptosis (PUMA)-mediated Warburg effect. CONCLUSIONS Our data identified the molecular basis of hepatic fibrosis-specific gene expression of polarity gene, such as Scribble. Interestingly, with the progression from fibrosis to cirrhosis to HCC, its nuclear translocation promoted a wild-type p53-mediated cancer metabolic switch and tumor progression in HCC. Taken together, we demonstrated that Scribble was up-regulated and served a protective role in liver fibrosis, while also apparently acting as a tumor driver in fibrosis-dependent hepatocarcinogenesis.
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Affiliation(s)
- Yanjun Wu
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Shanghai 200031, China
| | - Lele Song
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Shanghai 200031, China
| | - Jingwen Kong
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Shanghai 200031, China
| | - Qian Wen
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Shanghai 200031, China
| | - Jiazheng Jiao
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Shanghai 200031, China
| | - Xinyu Wang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Shanghai 200031, China
| | - Gang Li
- Department of Hepatopancreatobiliary Surgery, First Affiliated Hospital, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Xiao Xu
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China.
| | - Lixing Zhan
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Shanghai 200031, China; Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China.
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37
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Zhang Y, Chen XN, Zhang H, Wen JK, Gao HT, Shi B, Wang DD, Han ZW, Gu JF, Zhao CM, Xue WY, Zhang YP, Qu CB, Yang Z. CDK13 promotes lipid deposition and prostate cancer progression by stimulating NSUN5-mediated m5C modification of ACC1 mRNA. Cell Death Differ 2023; 30:2462-2476. [PMID: 37845385 PMCID: PMC10733287 DOI: 10.1038/s41418-023-01223-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 09/05/2023] [Indexed: 10/18/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) regulate cell cycle progression and the transcription of a number of genes, including lipid metabolism-related genes, and aberrant lipid metabolism is involved in prostate carcinogenesis. Previous studies have shown that CDK13 expression is upregulated and fatty acid synthesis is increased in prostate cancer (PCa). However, the molecular mechanisms linking CDK13 upregulation and aberrant lipid metabolism in PCa cells remain largely unknown. Here, we showed that upregulation of CDK13 in PCa cells increases the fatty acyl chains and lipid classes, leading to lipid deposition in the cells, which is positively correlated with the expression of acetyl-CoA carboxylase (ACC1), the first rate-limiting enzyme in fatty acid synthesis. Gain- and loss-of-function studies showed that ACC1 mediates CDK13-induced lipid accumulation and PCa progression by enhancing lipid synthesis. Mechanistically, CDK13 interacts with RNA-methyltransferase NSUN5 to promote its phosphorylation at Ser327. In turn, phosphorylated NSUN5 catalyzes the m5C modification of ACC1 mRNA, and then the m5C-modified ACC1 mRNA binds to ALYREF to enhance its stability and nuclear export, thereby contributing to an increase in ACC1 expression and lipid deposition in PCa cells. Overall, our results disclose a novel function of CDK13 in regulating the ACC1 expression and identify a previously unrecognized CDK13/NSUN5/ACC1 pathway that mediates fatty acid synthesis and lipid accumulation in PCa cells, and targeting this newly identified pathway may be a novel therapeutic option for the treatment of PCa.
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Affiliation(s)
- Yong Zhang
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
| | - Xiao-Nan Chen
- Department of Urology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Shenyang, 110004, P R China
| | - Hong Zhang
- Department of Biochemistry and Molecular Biology, Ministry of Education of China, Hebei Medical University, No. 361 Zhongshan E Rd, Shijiazhuang, 050017, China
| | - Jin-Kun Wen
- Department of Biochemistry and Molecular Biology, Ministry of Education of China, Hebei Medical University, No. 361 Zhongshan E Rd, Shijiazhuang, 050017, China
| | - Hai-Tao Gao
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Bei Shi
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Dan-Dan Wang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Zhen-Wei Han
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Jun-Fei Gu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Chen-Ming Zhao
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Wen-Yong Xue
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Yan-Ping Zhang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Chang-Bao Qu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China.
| | - Zhan Yang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China.
- Center of Tumor Immunology and Cytotherapy, Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China.
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38
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Esmaili F, Pourmirzaei M, Ramazi S, Shojaeilangari S, Yavari E. A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1266-1285. [PMID: 37863385 PMCID: PMC11082408 DOI: 10.1016/j.gpb.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 01/16/2023] [Accepted: 03/23/2023] [Indexed: 10/22/2023]
Abstract
Post-translational modifications (PTMs) have key roles in extending the functional diversity of proteins and, as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a vital PTM that occurs in most proteins and plays a significant role in many biological processes. Disorders in the phosphorylation process lead to multiple diseases, including neurological disorders and cancers. The purpose of this review is to organize this body of knowledge associated with phosphorylation site (p-site) prediction to facilitate future research in this field. At first, we comprehensively review all related databases and introduce all steps regarding dataset creation, data preprocessing, and method evaluation in p-site prediction. Next, we investigate p-site prediction methods, which are divided into two computational groups: algorithmic and machine learning (ML). Additionally, it is shown that there are basically two main approaches for p-site prediction by ML: conventional and end-to-end deep learning methods, both of which are given an overview. Moreover, this review introduces the most important feature extraction techniques, which have mostly been used in p-site prediction. Finally, we create three test sets from new proteins related to the released version of the database of protein post-translational modifications (dbPTM) in 2022 based on general and human species. Evaluating online p-site prediction tools on newly added proteins introduced in the dbPTM 2022 release, distinct from those in the dbPTM 2019 release, reveals their limitations. In other words, the actual performance of these online p-site prediction tools on unseen proteins is notably lower than the results reported in their respective research papers.
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Affiliation(s)
- Farzaneh Esmaili
- Department of Information Technology, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Mahdi Pourmirzaei
- Department of Information Technology, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Shahin Ramazi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-111, Iran.
| | - Seyedehsamaneh Shojaeilangari
- Biomedical Engineering Group, Department of Electrical Engineering and Information Technology, Iranian Research Organization for Science and Technology (IROST), Tehran 33535-111, Iran
| | - Elham Yavari
- Department of Information Technology, Tarbiat Modares University, Tehran 14115-111, Iran
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Xie J, Quan L, Wang X, Wu H, Jin Z, Pan D, Chen T, Wu T, Lyu Q. DeepMPSF: A Deep Learning Network for Predicting General Protein Phosphorylation Sites Based on Multiple Protein Sequence Features. J Chem Inf Model 2023; 63:7258-7271. [PMID: 37931253 DOI: 10.1021/acs.jcim.3c00996] [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: 11/08/2023]
Abstract
Phosphorylation, as one of the most important post-translational modifications, plays a key role in various cellular physiological processes and disease occurrences. In recent years, computer technology has been gradually applied to the prediction of protein phosphorylation sites. However, most existing methods rely on simple protein sequence features that provide limited contextual information. To overcome this limitation, we propose DeepMPSF, a phosphorylation site prediction model based on multiple protein sequence features. There are two types of features: sequence semantic features, which comprise protein residue type information and relative position information within protein sequence, and protein background biophysical features, which include global semantic information containing more comprehensive protein background information obtained from pretrained models. To extract these features, DeepMPSF employs two separate subnetworks: the S71SFE module and the BBFE module, which automatically extract high-level semantic features. Our model incorporates a learning strategy for handling imbalanced datasets through ensemble learning during training and prediction. DeepMPSF is trained and evaluated on a well-established dataset of human proteins. Comparing the analysis with other benchmark methods reveals that DeepMPSF outperforms in predicting both S/T residues and Y residues. In particular, DeepMPSF showed excellent generalization performance in cross-species blind test performance, with an average improvement of 5.63%/5.72%, 22.28%/25.94%, 20.11%/17.49%, and 26.40%/28.33% for Mus musculus/Rattus norvegicus test sets in area under curves (AUCs) of ROC curve, AUC of the PR curve, F1-score, and MCC metrics, respectively. Furthermore, it also shows excellent performance in the latest updated case of natural proteins with functional phosphorylation sites. Through an ablation study and visual analysis, we uncover that the design of different feature modules significantly contributes to the accurate classification of DeepMPSF, which provides valuable insights for predicting phosphorylation sites and offers effective support for future downstream research.
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Affiliation(s)
- Jingxin Xie
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Lijun Quan
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
- Province Key Lab for Information Processing Technologies, Soochow University, Suzhou 215006, China
- Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
| | - Xuejiao Wang
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Hongjie Wu
- Suzhou University of Science and Technology, Suzhou 215006, China
| | - Zhi Jin
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Deng Pan
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Taoning Chen
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Tingfang Wu
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
- Province Key Lab for Information Processing Technologies, Soochow University, Suzhou 215006, China
- Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
| | - Qiang Lyu
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
- Province Key Lab for Information Processing Technologies, Soochow University, Suzhou 215006, China
- Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
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40
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Bartolomé RA, Martín-Regalado Á, Pintado-Berninches L, Robles J, Ramírez-González MÁ, Boukich I, Sanchez-Gómez P, Balyasnikova IV, Casal JI. Schnurri-3 drives tumor growth and invasion in cancer cells expressing interleukin-13 receptor alpha 2. Cell Death Dis 2023; 14:742. [PMID: 37963919 PMCID: PMC10645886 DOI: 10.1038/s41419-023-06255-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Interleukin 13 receptor alpha 2 (IL13Rα2) is a relevant therapeutic target in glioblastoma (GBM) and other tumors associated with tumor growth and invasion. In a previous study, we demonstrated that protein tyrosine phosphatase 1B (PTP1B) is a key mediator of the IL-13/IL13Rα2 signaling pathway. PTP1B regulates cancer cell invasion through Src activation. However, PTP1B/Src downstream signaling mechanisms that modulate the invasion process remain unclear. In the present research, we have characterized the PTP1B interactome and the PTP1B-associated phosphoproteome after IL-13 treatment, in different cellular contexts, using proteomic strategies. PTP1B was associated with proteins involved in signal transduction, vesicle transport, and with multiple proteins from the NF-κB signaling pathway, including Tenascin-C (TNC). PTP1B participated with NF-κB in TNC-mediated proliferation and invasion. Analysis of the phosphorylation patterns obtained after PTP1B activation with IL-13 showed increased phosphorylation of the transcription factor Schnurri-3 (SHN3), a reported competitor of NF-κB. SHN3 silencing caused a potent inhibition in cell invasion and proliferation, associated with a down-regulation of the Wnt/β-catenin pathway, an extensive decline of MMP9 expression and the subsequent inhibition of tumor growth and metastasis in mouse models. Regarding clinical value, high expression of SHN3 was associated with poor survival in GBM, showing a significant correlation with the classical and mesenchymal subtypes. In CRC, SHN3 expression showed a preferential association with the mesenchymal subtypes CMS4 and CRIS-B. Moreover, SHN3 expression strongly correlated with IL13Rα2 and MMP9-associated poor prognosis in different cancers. In conclusion, we have uncovered the participation of SNH3 in the IL-13/IL13Rα2/PTP1B pathway to promote tumor growth and invasion. These findings support a potential therapeutic value for SHN3.
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Affiliation(s)
- Rubén A Bartolomé
- Department of Molecular Biomedicine, Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
| | - Ángela Martín-Regalado
- Department of Molecular Biomedicine, Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Laura Pintado-Berninches
- Department of Molecular Biomedicine, Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
- Universidad Autónoma de Madrid. Cantoblanco, Madrid, Spain
| | - Javier Robles
- Department of Molecular Biomedicine, Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
- Protein Alternatives SL. Tres Cantos, Madrid, Spain
| | | | - Issam Boukich
- Department of Molecular Biomedicine, Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
- Protein Alternatives SL. Tres Cantos, Madrid, Spain
| | - Pilar Sanchez-Gómez
- Unidad Funcional de Investigación en Enfermedades Crónicas. Instituto de Salud Carlos III, Madrid, Spain
| | - Irina V Balyasnikova
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - J Ignacio Casal
- Department of Molecular Biomedicine, Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
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41
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Kumari S, Gupta R, Ambasta RK, Kumar P. Emerging trends in post-translational modification: Shedding light on Glioblastoma multiforme. Biochim Biophys Acta Rev Cancer 2023; 1878:188999. [PMID: 37858622 DOI: 10.1016/j.bbcan.2023.188999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023]
Abstract
Recent multi-omics studies, including proteomics, transcriptomics, genomics, and metabolomics have revealed the critical role of post-translational modifications (PTMs) in the progression and pathogenesis of Glioblastoma multiforme (GBM). Further, PTMs alter the oncogenic signaling events and offer a novel avenue in GBM therapeutics research through PTM enzymes as potential biomarkers for drug targeting. In addition, PTMs are critical regulators of chromatin architecture, gene expression, and tumor microenvironment (TME), that play a crucial function in tumorigenesis. Moreover, the implementation of artificial intelligence and machine learning algorithms enhances GBM therapeutics research through the identification of novel PTM enzymes and residues. Herein, we briefly explain the mechanism of protein modifications in GBM etiology, and in altering the biologics of GBM cells through chromatin remodeling, modulation of the TME, and signaling pathways. In addition, we highlighted the importance of PTM enzymes as therapeutic biomarkers and the role of artificial intelligence and machine learning in protein PTM prediction.
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Affiliation(s)
- Smita Kumari
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological, University, India
| | - Rohan Gupta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological, University, India; School of Medicine, University of South Carolina, Columbia, SC, United States of America
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological, University, India; Department of Biotechnology and Microbiology, SRM University, Sonepat, Haryana, India.
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological, University, India.
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42
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Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, Hüttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell 2023; 186:4597-4614.e26. [PMID: 37738970 PMCID: PMC10604369 DOI: 10.1016/j.cell.2023.08.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/22/2023] [Accepted: 08/22/2023] [Indexed: 09/24/2023]
Abstract
SARS-CoV-2 variants of concern (VOCs) emerged during the COVID-19 pandemic. Here, we used unbiased systems approaches to study the host-selective forces driving VOC evolution. We discovered that VOCs evolved convergent strategies to remodel the host by modulating viral RNA and protein levels, altering viral and host protein phosphorylation, and rewiring virus-host protein-protein interactions. Integrative computational analyses revealed that although Alpha, Beta, Gamma, and Delta ultimately converged to suppress interferon-stimulated genes (ISGs), Omicron BA.1 did not. ISG suppression correlated with the expression of viral innate immune antagonist proteins, including Orf6, N, and Orf9b, which we mapped to specific mutations. Later Omicron subvariants BA.4 and BA.5 more potently suppressed innate immunity than early subvariant BA.1, which correlated with Orf6 levels, although muted in BA.4 by a mutation that disrupts the Orf6-nuclear pore interaction. Our findings suggest that SARS-CoV-2 convergent evolution overcame human adaptive and innate immune barriers, laying the groundwork to tackle future pandemics.
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Affiliation(s)
- Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ann-Kathrin Reuschl
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK
| | - Benjamin J Polacco
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Lucy G Thorne
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK
| | - Manisha R Ummadi
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Chengjin Ye
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Romel Rosales
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adrian Pelin
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jyoti Batra
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Gwendolyn M Jang
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jiewei Xu
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jack M Moen
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Alicia L Richards
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Yuan Zhou
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Bhavya Harjai
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Erica Stevenson
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Ajda Rojc
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Roberta Ragazzini
- Division of Infection and Immunity, University College London, London, UK; Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, London, UK
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Abdullah M Syed
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Ciling
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Noa Deutsch
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Daniel Pirak
- School of Electrical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Giulia Dowgier
- COVID Surveillance Unit, The Francis Crick Institute, London, UK
| | - Dejan Mesner
- Division of Infection and Immunity, University College London, London, UK
| | - Jane L Turner
- Division of Infection and Immunity, University College London, London, UK
| | - Briana L McGovern
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Luis Rodriguez
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rocio Leiva-Rebollo
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alistair S Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Saffron Walden, UK
| | - Xiaofang Zhong
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Andrea Fossati
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Nicholas F Liotta
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA
| | - Thomas Kehrer
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anastasija Cupic
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magdalena Rutkowska
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ignacio Mena
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sadaf Aslam
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alyssa Hoffert
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Helene Foussard
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Charles Ochieng' Olwal
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Weiqing Huang
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Zwaka
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John Pham
- Synthego Corporation, Redwood City, CA, USA
| | | | | | | | | | | | | | | | | | | | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Margaret Soucheray
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Ruth Hüttenhain
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ignacia Echeverria
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Kliment Verba
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Paola Bonfanti
- Division of Infection and Immunity, University College London, London, UK; Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Pedro Beltrao
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK; Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zurich, Switzerland
| | - Roded Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Jennifer A Doudna
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Luis Martinez-Sobrido
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Lisa Miorin
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kris White
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Adolfo Garcia-Sastre
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Clare Jolly
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK.
| | - Lorena Zuliani-Alvarez
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA.
| | - Greg J Towers
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK.
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA.
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Fisch D, Pfleiderer MM, Anastasakou E, Mackie GM, Wendt F, Liu X, Clough B, Lara-Reyna S, Encheva V, Snijders AP, Bando H, Yamamoto M, Beggs AD, Mercer J, Shenoy AR, Wollscheid B, Maslowski KM, Galej WP, Frickel EM. PIM1 controls GBP1 activity to limit self-damage and to guard against pathogen infection. Science 2023; 382:eadg2253. [PMID: 37797010 PMCID: PMC7615196 DOI: 10.1126/science.adg2253] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 08/23/2023] [Indexed: 10/07/2023]
Abstract
Disruption of cellular activities by pathogen virulence factors can trigger innate immune responses. Interferon-γ (IFN-γ)-inducible antimicrobial factors, such as the guanylate binding proteins (GBPs), promote cell-intrinsic defense by attacking intracellular pathogens and by inducing programmed cell death. Working in human macrophages, we discovered that GBP1 expression in the absence of IFN-γ killed the cells and induced Golgi fragmentation. IFN-γ exposure improved macrophage survival through the activity of the kinase PIM1. PIM1 phosphorylated GBP1, leading to its sequestration by 14-3-3σ, which thereby prevented GBP1 membrane association. During Toxoplasma gondii infection, the virulence protein TgIST interfered with IFN-γ signaling and depleted PIM1, thereby increasing GBP1 activity. Although infected cells can restrain pathogens in a GBP1-dependent manner, this mechanism can protect uninfected bystander cells. Thus, PIM1 can provide a bait for pathogen virulence factors, guarding the integrity of IFN-γ signaling.
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Affiliation(s)
- Daniel Fisch
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, London, UK
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, UK
| | - Moritz M Pfleiderer
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
| | - Eleni Anastasakou
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
| | - Gillian M Mackie
- Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, UK
| | - Fabian Wendt
- Department of Health Sciences and Technology (D-HEST), ETH Zurich, Institute of Translational Medicine (ITM), Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Xiangyang Liu
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
| | - Barbara Clough
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, UK
| | - Samuel Lara-Reyna
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, UK
| | - Vesela Encheva
- Mass Spectrometry and Proteomics Platform, The Francis Crick Institute, London, UK
| | - Ambrosius P Snijders
- Mass Spectrometry and Proteomics Platform, The Francis Crick Institute, London, UK
- Bruker Nederland BV
| | - Hironori Bando
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Masahiro Yamamoto
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Andrew D Beggs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, UK
| | - Jason Mercer
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, UK
| | - Avinash R Shenoy
- MRC Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Bernd Wollscheid
- Department of Health Sciences and Technology (D-HEST), ETH Zurich, Institute of Translational Medicine (ITM), Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Kendle M Maslowski
- Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, UK
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Wojtek P Galej
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
| | - Eva-Maria Frickel
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, London, UK
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, UK
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44
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Yao J, Wang ZN, Liu H, Jin H, Zhang Y. Survey of Acetylation for Thermoanaerobacter tengcongensis. Appl Biochem Biotechnol 2023; 195:6081-6097. [PMID: 36809429 DOI: 10.1007/s12010-023-04361-9] [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] [Accepted: 01/10/2023] [Indexed: 02/23/2023]
Abstract
Non-histone protein acetylation is involved in key cellular processes both in eukaryotes and prokaryotes. Acetylation in bacteria is used to modify proteins involved in metabolism and allow the bacteria to adapt to their environment. TTE (Thermoanaerobacter tengcongensis) is an anaerobic, thermophilic saccharolytic bacterium that grows at extreme temperature range between 50 and 80 ℃. The annotated TTE proteome contains less than 3000 proteins. We analyzed the proteome and acetylome of TTE using 2DLC-MS/MS (2-dimensional liquid chromatography mass spectrum). We evaluated the ability of mass spectrometry technology to cover a relatively small proteome as much as possible. And we also observed wide spread of acetylation in TTE, which changed under different temperatures. A total of 2082 proteins were identified, which accounts for about 82% of the database. A total of 2050 (~ 98%) proteins were quantified in at least one culture condition and 1818 proteins were quantified in all 4 conditions. The result also consisted 3457 acetylation sites corresponding to 827 distinct proteins, which covered 40% of the proteins identified. Bioinformatics analysis reported that proteins related to replication, recombination, repair, and extracellular structure cell wall biogenesis had more than half members acetylated, while energy production, carbohydrate transport, and metabolism related proteins were least acetylated. Our result suggested that acetylation affects the ATP-related energy metabolism and energy-dependent biosynthesis process. Comparing the enzymes related with lysine acetylation and acetyl-CoA (acetyl-coenzyme A) metabolism, we suggested that the acetylation of TTE took a non-enzymatic mechanism and affected by abundance of acetyl-CoA.
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Affiliation(s)
- Jun Yao
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Ze-Ning Wang
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Hang Liu
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Jin
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
| | - Yang Zhang
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
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45
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Jacobsen NL, Bloch M, Millard PS, Ruidiaz SF, Elsborg JD, Boomsma W, Hendus‐Altenburger R, Hartmann‐Petersen R, Kragelund BB. Phosphorylation of Schizosaccharomyces pombe Dss1 mediates direct binding to the ubiquitin-ligase Dma1 in vitro. Protein Sci 2023; 32:e4733. [PMID: 37463013 PMCID: PMC10443397 DOI: 10.1002/pro.4733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 08/25/2023]
Abstract
Intrinsically disordered proteins (IDPs) are often multifunctional and frequently posttranslationally modified. Deleted in split hand/split foot 1 (Dss1-Sem1 in budding yeast) is a highly multifunctional IDP associated with a range of protein complexes. However, it remains unknown if the different functions relate to different modified states. In this work, we show that Schizosaccharomyces pombe Dss1 is a substrate for casein kinase 2 in vitro, and we identify three phosphorylated threonines in its linker region separating two known disordered ubiquitin-binding motifs. Phosphorylations of the threonines had no effect on ubiquitin-binding but caused a slight destabilization of the C-terminal α-helix and mediated a direct interaction with the forkhead-associated (FHA) domain of the RING-FHA E3-ubiquitin ligase defective in mitosis 1 (Dma1). The phosphorylation sites are not conserved and are absent in human Dss1. Sequence analyses revealed that the Txx(E/D) motif, which is important for phosphorylation and Dma1 binding, is not linked to certain branches of the evolutionary tree. Instead, we find that the motif appears randomly, supporting the mechanism of ex nihilo evolution of novel motifs. In support of this, other threonine-based motifs, although frequent, are nonconserved in the linker, pointing to additional functions connected to this region. We suggest that Dss1 acts as an adaptor protein that docks to Dma1 via the phosphorylated FHA-binding motifs, while the C-terminal α-helix is free to bind mitotic septins, thereby stabilizing the complex. The presence of Txx(D/E) motifs in the disordered regions of certain septin subunits may be of further relevance to the formation and stabilization of these complexes.
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Affiliation(s)
- Nina L. Jacobsen
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Magnus Bloch
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
| | - Peter S. Millard
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Sarah F. Ruidiaz
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
| | - Jonas D. Elsborg
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
| | - Wouter Boomsma
- Department of Computer ScienceUniversity of CopenhagenCopenhagen ØDenmark
| | | | - Rasmus Hartmann‐Petersen
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Birthe B. Kragelund
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
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46
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Wang D, Shang Q, Mao J, Gao C, Wang J, Wang D, Wang H, Jia H, Peng P, Du M, Luo Z, Yang L. Phosphorylation of KRT8 (keratin 8) by excessive mechanical load-activated PKN (protein kinase N) impairs autophagosome initiation and contributes to disc degeneration. Autophagy 2023; 19:2485-2503. [PMID: 36897022 PMCID: PMC10392755 DOI: 10.1080/15548627.2023.2186099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 03/11/2023] Open
Abstract
Excessive mechanical load (overloading) is a well-documented pathogenetic factor for many mechano stress-induced pathologies, i.e. intervertebral disc degeneration (IDD). Under overloading, the balance between anabolism and catabolism within nucleus pulposus (NP) cells are badly thrown off, and NP cells undergo apoptosis. However, little is known about how the overloading is transduced to the NP cells and contributes to disc degeneration. The current study shows that conditional knockout of Krt8 (keratin 8) within NP aggravates load-induced IDD in vivo, and overexpression of Krt8 endows NP cells greater resistance to overloading-induced apoptosis and degeneration in vitro. Discovery-driven experiments shows that phosphorylation of KRT8 on Ser43 by overloading activated RHOA-PKN (protein kinase N) impedes trafficking of Golgi resident small GTPase RAB33B, suppresses the autophagosome initiation and contributes to IDD. Overexpression of Krt8 and knockdown of Pkn1 and Pkn2, at an early stage of IDD, ameliorates disc degeneration; yet only knockdown of Pkn1 and Pkn2, when treated at late stage of IDD, shows a therapeutic effect. This study validates a protective role of Krt8 during overloading-induced IDD and demonstrates that targeting overloading activation of PKNs could be a novel and effective approach to mechano stress-induced pathologies with a wider window of therapeutic opportunity.Abbreviations: AAV: adeno-associated virus; AF: anulus fibrosus; ANOVA: analysis of variance; ATG: autophagy related; BSA: bovine serum albumin; cDNA: complementary deoxyribonucleic acid; CEP: cartilaginous endplates; CHX: cycloheximide; cKO: conditional knockout; Cor: coronal plane; CT: computed tomography; Cy: coccygeal vertebra; D: aspartic acid; DEG: differentially expressed gene; DHI: disc height index; DIBA: dot immunobinding assay; dUTP: 2'-deoxyuridine 5'-triphosphate; ECM: extracellular matrix; EDTA: ethylene diamine tetraacetic acid; ER: endoplasmic reticulum; FBS: fetal bovine serum; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GPS: group-based prediction system; GSEA: gene set enrichment analysis; GTP: guanosine triphosphate; HE: hematoxylin-eosin; HRP: horseradish peroxidase; IDD: intervertebral disc degeneration; IF: immunofluorescence staining; IL1: interleukin 1; IVD: intervertebral disc; KEGG: Kyoto encyclopedia of genes and genomes; KRT8: keratin 8; KD: knockdown; KO: knockout; L: lumbar vertebra; LBP: low back pain; LC/MS: liquid chromatograph mass spectrometer; LSI: mouse lumbar instability model; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MMP3: matrix metallopeptidase 3; MRI: nuclear magnetic resonance imaging; NC: negative control; NP: nucleus pulposus; PBS: phosphate-buffered saline; PE: p-phycoerythrin; PFA: paraformaldehyde; PI: propidium iodide; PKN: protein kinase N; OE: overexpression; PTM: post translational modification; PVDF: polyvinylidene fluoride; qPCR: quantitative reverse-transcriptase polymerase chain reaction; RHOA: ras homolog family member A; RIPA: radio immunoprecipitation assay; RNA: ribonucleic acid; ROS: reactive oxygen species; RT: room temperature; TCM: rat tail compression-induced IDD model; TCS: mouse tail suturing compressive model; S: serine; Sag: sagittal plane; SD rats: Sprague-Dawley rats; shRNA: short hairpin RNA; siRNA: small interfering RNA; SOFG: safranin O-fast green; SQSTM1: sequestosome 1; TUNEL: terminal deoxynucleotidyl transferase dUTP nick end labeling; VG/ml: viral genomes per milliliter; WCL: whole cell lysate.
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Affiliation(s)
- Di Wang
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Qiliang Shang
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Jianxin Mao
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Chu Gao
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, People’s Republic of China
- Medical Research Institute, Northwestern Polytechnical University, Xi’an, People’s Republic of China
| | - Jie Wang
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Dong Wang
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Han Wang
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Haoruo Jia
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Pandi Peng
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, People’s Republic of China
- Medical Research Institute, Northwestern Polytechnical University, Xi’an, People’s Republic of China
| | - Mu Du
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Zhuojing Luo
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, People’s Republic of China
- Medical Research Institute, Northwestern Polytechnical University, Xi’an, People’s Republic of China
| | - Liu Yang
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, People’s Republic of China
- Medical Research Institute, Northwestern Polytechnical University, Xi’an, People’s Republic of China
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47
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Emser SV, Spielvogel CP, Millesi E, Steinborn R. Mitochondrial polymorphism m.3017C>T of SHLP6 relates to heterothermy. Front Physiol 2023; 14:1207620. [PMID: 37675281 PMCID: PMC10478271 DOI: 10.3389/fphys.2023.1207620] [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: 04/17/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023] Open
Abstract
Heterothermic thermoregulation requires intricate regulation of metabolic rate and activation of pro-survival factors. Eliciting these responses and coordinating the necessary energy shifts likely involves retrograde signalling by mitochondrial-derived peptides (MDPs). Members of the group were suggested before to play a role in heterothermic physiology, a key component of hibernation and daily torpor. Here we studied the mitochondrial single-nucleotide polymorphism (SNP) m.3017C>T that resides in the evolutionarily conserved gene MT-SHLP6. The substitution occurring in several mammalian orders causes truncation of SHLP6 peptide size from twenty to nine amino acids. Public mass spectrometric (MS) data of human SHLP6 indicated a canonical size of 20 amino acids, but not the use of alternative translation initiation codons that would expand the peptide. The shorter isoform of SHLP6 was found in heterothermic rodents at higher frequency compared to homeothermic rodents (p < 0.001). In heterothermic mammals it was associated with lower minimal body temperature (T b, p < 0.001). In the thirteen-lined ground squirrel, brown adipose tissue-a key organ required for hibernation, showed dynamic changes of the steady-state transcript level of mt-Shlp6. The level was significantly higher before hibernation and during interbout arousal and lower during torpor and after hibernation. Our finding argues to further explore the mode of action of SHLP6 size isoforms with respect to mammalian thermoregulation and possibly mitochondrial retrograde signalling.
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Affiliation(s)
- Sarah V. Emser
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
| | - Clemens P. Spielvogel
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Vienna, Austria
| | - Eva Millesi
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
- Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
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48
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Mann JR, McKenna ED, Mawrie D, Papakis V, Alessandrini F, Anderson EN, Mayers R, Ball HE, Kaspi E, Lubinski K, Baron DM, Tellez L, Landers JE, Pandey UB, Kiskinis E. Loss of function of the ALS-associated NEK1 kinase disrupts microtubule homeostasis and nuclear import. SCIENCE ADVANCES 2023; 9:eadi5548. [PMID: 37585529 PMCID: PMC10431718 DOI: 10.1126/sciadv.adi5548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
Loss-of-function variants in NIMA-related kinase 1 (NEK1) constitute a major genetic cause of amyotrophic lateral sclerosis (ALS), accounting for 2 to 3% of all cases. However, how NEK1 mutations cause motor neuron (MN) dysfunction is unknown. Using mass spectrometry analyses for NEK1 interactors and NEK1-dependent expression changes, we find functional enrichment for proteins involved in the microtubule cytoskeleton and nucleocytoplasmic transport. We show that α-tubulin and importin-β1, two key proteins involved in these processes, are phosphorylated by NEK1 in vitro. NEK1 is essential for motor control and survival in Drosophila models in vivo, while using several induced pluripotent stem cell (iPSC)-MN models, including NEK1 knockdown, kinase inhibition, and a patient mutation, we find evidence for disruptions in microtubule homeostasis and nuclear import. Notably, stabilizing microtubules with two distinct classes of drugs restored NEK1-dependent deficits in both pathways. The capacity of NEK1 to modulate these processes that are critically involved in ALS pathophysiology renders this kinase a formidable therapeutic candidate.
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Affiliation(s)
- Jacob R. Mann
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Elizabeth D. McKenna
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Darilang Mawrie
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Vasileios Papakis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Francesco Alessandrini
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Eric N. Anderson
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Ryan Mayers
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Hannah E. Ball
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Evan Kaspi
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Katherine Lubinski
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Desiree M. Baron
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Liana Tellez
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Udai B. Pandey
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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49
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Ruperti F, Becher I, Stokkermans A, Wang L, Marschlich N, Potel C, Maus E, Stein F, Drotleff B, Schippers K, Nickel M, Prevedel R, Musser JM, Savitski MM, Arendt D. Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551666. [PMID: 37577507 PMCID: PMC10418225 DOI: 10.1101/2023.08.02.551666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
A hallmark of animals is the coordination of whole-body movement. Neurons and muscles are central to this, yet coordinated movements also exist in sponges that lack these cell types. Sponges are sessile animals with a complex canal system for filter-feeding. They undergo whole-body movements resembling "contractions" that lead to canal closure and water expulsion. Here, we combine 3D optical coherence microscopy, pharmacology, and functional proteomics to elucidate anatomy, molecular physiology, and control of these movements. We find them driven by the relaxation of actomyosin stress fibers in epithelial canal cells, which leads to whole-body deflation via collapse of the incurrent and expansion of the excurrent system, controlled by an Akt/NO/PKG/A pathway. A concomitant increase in reactive oxygen species and secretion of proteinases and cytokines indicate an inflammation-like state reminiscent of vascular endothelial cells experiencing oscillatory shear stress. This suggests an ancient relaxant-inflammatory response of perturbed fluid-carrying systems in animals.
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Affiliation(s)
- Fabian Ruperti
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Collaboration for joint Ph.D. degree between EMBL and Heidelberg University, Faculty of Biosciences 69117 Heidelberg, Germany
| | - Isabelle Becher
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Ling Wang
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Nick Marschlich
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
| | - Clement Potel
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Emanuel Maus
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Bernhard Drotleff
- Metabolomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Klaske Schippers
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Michael Nickel
- Bionic Consulting Dr. Michael Nickel, 71686 Remseck am Neckar, Germany
| | - Robert Prevedel
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jacob M Musser
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Proteomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
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50
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Li C, Allison DB, He D, Mao F, Wang X, Rychahou P, Imam IA, Kong Y, Zhang Q, Zhang Y, Liu J, Wang R, Rao X, Wu S, Shao Q, Wang C, Li Z, Liu X. Phosphorylation of AHR by PLK1 promotes metastasis of LUAD via DIO2-TH signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551298. [PMID: 37577647 PMCID: PMC10418090 DOI: 10.1101/2023.07.31.551298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Metastasis of Lung adenocarcinoma (LUAD) is a major cause of death in patients. Aryl hydrocarbon receptor (AHR) is an important transcription factor involved in the initiation and progression of lung cancer. Polo-like kinase 1 (PLK1), a serine/threonine kinase, is an oncogene that promotes the malignancy of multiple cancer types. Nonetheless, the interaction between these two factors and significance in lung cancer remains to be determined. Here, we demonstrate that PLK1 phosphorylates AHR at S489 in LUAD, which leads to epithelial-mesenchymal transition (EMT) and metastatic events. RNA-seq analyses show that type 2 deiodinase (DIO2) is responsible for EMT and enhanced metastatic potential. DIO2 converts tetraiodothyronine (T4) to triiodothyronine (T3), which then activates thyroid hormone signaling. In vitro and in vivo experiments demonstrate that treatment with T3 or T4 promotes the metastasis of LUAD, whereas depletion of DIO2 or deiodinase inhibitor disrupts this property. Taken together, our results identify the phosphorylation of AHR by PLK1 as a mechanism leading to the progression of LUAD and provide possible therapeutic interventions for this event.
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