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Ke J, Pan J, Lin H, Huang S, Zhang J, Wang C, Chang ACY, Gu J. Targeting Rab7-Rilp Mediated Microlipophagy Alleviates Lipid Toxicity in Diabetic Cardiomyopathy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401676. [PMID: 38837607 DOI: 10.1002/advs.202401676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/25/2024] [Indexed: 06/07/2024]
Abstract
Diabetic cardiomyopathy (DbCM) is characterized by diastolic dysfunction, which progresses into heart failure and aberrant electrophysiology in diabetic patients. Dyslipidemia in type 2 diabetic patients leads to the accumulation of lipid droplets (LDs) in cardiomyocytes and results in lipid toxicity which has been suggested to drive DbCM. It is aimed to explore potential pathways that may boost LDs degradation in DbCM and restore cardiac function. LDs accumulation resulted in an increase in lipid toxicity in DbCM hearts is confirmed. Microlipophagy pathway, rather than traditional macrolipophagy, is activated in DbCM hearts. RNA-Seq data and Rab7-CKO mice implicate that Rab7 is a major modulator of the microlipophagy pathway. Mechanistically, Rab7 is phosphorylated at Tyrosine 183, which allows the recruitment of Rab-interacting lysosome protein (Rilp) to proceed LDs degradation by lysosome. Treating DbCM mice with Rab7 activator ML-098 enhanced Rilp level and rescued the observed cardiac dysfunction. Overall, Rab7-Rilp-mediated microlipophagy may be a promising target in the treatment of lipid toxicity in DbCM is suggested.
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Affiliation(s)
- Jiahan Ke
- Department of Cardiology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200001, China
| | - Jianan Pan
- Department of Cardiology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200001, China
| | - Hao Lin
- Department of Cardiology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200001, China
| | - Shuying Huang
- Department of Cardiology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200001, China
| | - Junfeng Zhang
- Department of Cardiology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200001, China
| | - Changqian Wang
- Department of Cardiology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200001, China
| | - Alex Chia Yu Chang
- Department of Cardiology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200001, China
- Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200120, China
| | - Jun Gu
- Department of Cardiology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200001, China
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2
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Chen C, Lee S, Zyner KG, Fernando M, Nemeruck V, Wong E, Marshall LL, Wark JR, Aryamanesh N, Tam PPL, Graham ME, Gonzalez-Cordero A, Yang P. Trans-omic profiling uncovers molecular controls of early human cerebral organoid formation. Cell Rep 2024; 43:114219. [PMID: 38748874 DOI: 10.1016/j.celrep.2024.114219] [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: 01/03/2024] [Revised: 04/01/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024] Open
Abstract
Defining the molecular networks orchestrating human brain formation is crucial for understanding neurodevelopment and neurological disorders. Challenges in acquiring early brain tissue have incentivized the use of three-dimensional human pluripotent stem cell (hPSC)-derived neural organoids to recapitulate neurodevelopment. To elucidate the molecular programs that drive this highly dynamic process, here, we generate a comprehensive trans-omic map of the phosphoproteome, proteome, and transcriptome of the exit of pluripotency and neural differentiation toward human cerebral organoids (hCOs). These data reveal key phospho-signaling events and their convergence on transcriptional factors to regulate hCO formation. Comparative analysis with developing human and mouse embryos demonstrates the fidelity of our hCOs in modeling embryonic brain development. Finally, we demonstrate that biochemical modulation of AKT signaling can control hCO differentiation. Together, our data provide a comprehensive resource to study molecular controls in human embryonic brain development and provide a guide for the future development of hCO differentiation protocols.
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Affiliation(s)
- Carissa Chen
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Scott Lee
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Katherine G Zyner
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Milan Fernando
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Victoria Nemeruck
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Emilie Wong
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Lee L Marshall
- Bioinformatics Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Jesse R Wark
- Synapse Proteomics, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Nader Aryamanesh
- Bioinformatics Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Patrick P L Tam
- Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Mark E Graham
- Synapse Proteomics, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
| | - Anai Gonzalez-Cordero
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
| | - Pengyi Yang
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia.
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3
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Supplee JG, Affronti HC, Duan R, Brooks RC, Stine ZE, Nguyen PTT, Pinheiro LV, Noji MC, Drummond JM, Huang K, Schultz K, Dang CV, Marmorstein R, Wellen KE. ACLY alternative splicing correlates with cancer phenotypes. J Biol Chem 2024:107418. [PMID: 38815867 DOI: 10.1016/j.jbc.2024.107418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/23/2024] [Accepted: 05/18/2024] [Indexed: 06/01/2024] Open
Abstract
ATP-citrate lyase (ACLY) links carbohydrate and lipid metabolism and provides nucleocytosolic acetyl-CoA necessary for protein acetylation. ACLY has two major splice isoforms: the full-length canonical "long" isoform and an uncharacterized "short" isoform in which exon 14 is spliced out. Exon 14 encodes 10 amino acids within a disordered region of the protein and includes at least 1 site that is dynamically phosphorylated. Both isoforms are expressed in healthy tissues to varying degrees. Analysis of human transcriptomic data revealed that the Percent Spliced In (PSI) of exon 14, i.e., the proportion of long isoform, is increased in several cancers and correlated with poorer overall survival in a pan-cancer analysis, though not in individual tumor types, which prompted us to explore potential biochemical and functional differences between ACLY isoforms. Here, we show that there are no discernible differences in enzymatic activity or stability between isoforms or phosphomutants of ACLY in vitro. Similarly, both isoforms and phosphomutants were able to rescue ACLY functions, including fatty acid synthesis and bulk histone acetylation, when re-expressed in Acly knockout cells. Deletion of Acly exon 14 in mice did not overtly impact development or metabolic physiology, nor did it attenuate tumor burden in a genetic model of intestinal cancer. Notably, expression of epithelial splicing regulatory protein 1 (ESRP1) is highly correlated with ACLY PSI. We report that ACLY splicing is regulated by ESRP1. In turn, both ESRP1 expression and ACLY PSI are correlated with specific immune signatures in tumors. Despite these intriguing patterns of ACLY splicing in healthy and cancer tissues, functional differences between the isoforms remain elusive.
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Affiliation(s)
- Julianna G Supplee
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA
| | - Hayley C Affronti
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA
| | - Richard Duan
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA
| | | | | | - Phuong T T Nguyen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA
| | - Laura V Pinheiro
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA
| | - Michael C Noji
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA
| | - Jack M Drummond
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA
| | - Kevin Huang
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA
| | - Kollin Schultz
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA
| | - Chi V Dang
- Wistar Cancer Institute, Philadelphia, PA; Johns Hopkins University School of Medicine, Baltimore, MD; Ludwig Institute for Cancer Research, New York, NY
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA
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4
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Muscò A, Martini D, Digregorio M, Broccoli V, Andreazzoli M. Shedding a Light on Dark Genes: A Comparative Expression Study of PRR12 Orthologues during Zebrafish Development. Genes (Basel) 2024; 15:492. [PMID: 38674426 PMCID: PMC11050278 DOI: 10.3390/genes15040492] [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: 03/16/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Haploinsufficiency of the PRR12 gene is implicated in a human neuro-ocular syndrome. Although identified as a nuclear protein highly expressed in the embryonic mouse brain, PRR12 molecular function remains elusive. This study explores the spatio-temporal expression of zebrafish PRR12 co-orthologs, prr12a and prr12b, as a first step to elucidate their function. In silico analysis reveals high evolutionary conservation in the DNA-interacting domains for both orthologs, with significant syntenic conservation observed for the prr12b locus. In situ hybridization and RT-qPCR analyses on zebrafish embryos and larvae reveal distinct expression patterns: prr12a is expressed early in zygotic development, mainly in the central nervous system, while prr12b expression initiates during gastrulation, localizing later to dopaminergic telencephalic and diencephalic cell clusters. Both transcripts are enriched in the ganglion cell and inner neural layers of the 72 hpf retina, with prr12b widely distributed in the ciliary marginal zone. In the adult brain, prr12a and prr12b are found in the cerebellum, amygdala and ventral telencephalon, which represent the main areas affected in autistic patients. Overall, this study suggests PRR12's potential involvement in eye and brain development, laying the groundwork for further investigations into PRR12-related neurobehavioral disorders.
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Affiliation(s)
- Alessia Muscò
- Cell and Developmental Biology Unit, University of Pisa, 56126 Pisa, Italy (D.M.)
| | - Davide Martini
- Cell and Developmental Biology Unit, University of Pisa, 56126 Pisa, Italy (D.M.)
| | - Matteo Digregorio
- Cell and Developmental Biology Unit, University of Pisa, 56126 Pisa, Italy (D.M.)
| | - Vania Broccoli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
- CNR Institute of Neuroscience, 20132 Milan, Italy
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5
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Zhang S, Yu Q, Li Z, Zhao Y, Sun Y. Protein neddylation and its role in health and diseases. Signal Transduct Target Ther 2024; 9:85. [PMID: 38575611 PMCID: PMC10995212 DOI: 10.1038/s41392-024-01800-9] [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] [Received: 01/11/2024] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 04/06/2024] Open
Abstract
NEDD8 (Neural precursor cell expressed developmentally downregulated protein 8) is an ubiquitin-like protein that is covalently attached to a lysine residue of a protein substrate through a process known as neddylation, catalyzed by the enzyme cascade, namely NEDD8 activating enzyme (E1), NEDD8 conjugating enzyme (E2), and NEDD8 ligase (E3). The substrates of neddylation are categorized into cullins and non-cullin proteins. Neddylation of cullins activates CRLs (cullin RING ligases), the largest family of E3 ligases, whereas neddylation of non-cullin substrates alters their stability and activity, as well as subcellular localization. Significantly, the neddylation pathway and/or many neddylation substrates are abnormally activated or over-expressed in various human diseases, such as metabolic disorders, liver dysfunction, neurodegenerative disorders, and cancers, among others. Thus, targeting neddylation becomes an attractive strategy for the treatment of these diseases. In this review, we first provide a general introduction on the neddylation cascade, its biochemical process and regulation, and the crystal structures of neddylation enzymes in complex with cullin substrates; then discuss how neddylation governs various key biological processes via the modification of cullins and non-cullin substrates. We further review the literature data on dysregulated neddylation in several human diseases, particularly cancer, followed by an outline of current efforts in the discovery of small molecule inhibitors of neddylation as a promising therapeutic approach. Finally, few perspectives were proposed for extensive future investigations.
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Affiliation(s)
- Shizhen Zhang
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Qing Yu
- Department of Thyroid Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, 310022, China
| | - Zhijian Li
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Yongchao Zhao
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang University Cancer Center, Hangzhou, 310029, China.
| | - Yi Sun
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
- Zhejiang University Cancer Center, Hangzhou, 310029, China.
- Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang, Hangzhou, 310024, China.
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China.
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6
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Tibben BM, Rothbart SB. Mechanisms of DNA Methylation Regulatory Function and Crosstalk with Histone Lysine Methylation. J Mol Biol 2024; 436:168394. [PMID: 38092287 PMCID: PMC10957332 DOI: 10.1016/j.jmb.2023.168394] [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: 09/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
DNA methylation is a well-studied epigenetic modification that has key roles in regulating gene expression, maintaining genome integrity, and determining cell fate. Precisely how DNA methylation patterns are established and maintained in specific cell types at key developmental stages is still being elucidated. However, research over the last two decades has contributed to our understanding of DNA methylation regulation by other epigenetic processes. Specifically, lysine methylation on key residues of histone proteins has been shown to contribute to the allosteric regulation of DNA methyltransferase (DNMT) activities. In this review, we discuss the dynamic interplay between DNA methylation and histone lysine methylation as epigenetic regulators of genome function by synthesizing key recent studies in the field. With a focus on DNMT3 enzymes, we discuss mechanisms of DNA methylation and histone lysine methylation crosstalk in the regulation of gene expression and the maintenance of genome integrity. Further, we discuss how alterations to the balance of various sites of histone lysine methylation and DNA methylation contribute to human developmental disorders and cancers. Finally, we provide perspectives on the current direction of the field and highlight areas for continued research and development.
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Affiliation(s)
- Bailey M Tibben
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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7
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Hermosilla VE, Gyenis L, Rabalski AJ, Armijo ME, Sepúlveda P, Duprat F, Benítez-Riquelme D, Fuentes-Villalobos F, Quiroz A, Hepp MI, Farkas C, Mastel M, González-Chavarría I, Jackstadt R, Litchfield DW, Castro AF, Pincheira R. Casein kinase 2 phosphorylates and induces the SALL2 tumor suppressor degradation in colon cancer cells. Cell Death Dis 2024; 15:223. [PMID: 38493149 PMCID: PMC10944491 DOI: 10.1038/s41419-024-06591-z] [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: 05/04/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
Spalt-like proteins are Zinc finger transcription factors from Caenorhabditis elegans to vertebrates, with critical roles in development. In vertebrates, four paralogues have been identified (SALL1-4), and SALL2 is the family's most dissimilar member. SALL2 is required during brain and eye development. It is downregulated in cancer and acts as a tumor suppressor, promoting cell cycle arrest and cell death. Despite its critical functions, information about SALL2 regulation is scarce. Public data indicate that SALL2 is ubiquitinated and phosphorylated in several residues along the protein, but the mechanisms, biological consequences, and enzymes responsible for these modifications remain unknown. Bioinformatic analyses identified several putative phosphorylation sites for Casein Kinase II (CK2) located within a highly conserved C-terminal PEST degradation motif of SALL2. CK2 is a serine/threonine kinase that promotes cell proliferation and survival and is often hyperactivated in cancer. We demonstrated that CK2 phosphorylates SALL2 residues S763, T778, S802, and S806 and promotes SALL2 degradation by the proteasome. Accordingly, pharmacological inhibition of CK2 with Silmitasertib (CX-4945) restored endogenous SALL2 protein levels in SALL2-deficient breast MDA-MB-231, lung H1299, and colon SW480 cancer cells. Silmitasertib induced a methuosis-like phenotype and cell death in SW480 cells. However, the phenotype was significantly attenuated in CRISPr/Cas9-mediated SALL2 knockout SW480 cells. Similarly, Sall2-deficient tumor organoids were more resistant to Silmitasertib-induced cell death, confirming that SALL2 sensitizes cancer cells to CK2 inhibition. We identified a novel CK2-dependent mechanism for SALL2 regulation and provided new insights into the interplay between these two proteins and their role in cell survival and proliferation.
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Affiliation(s)
- V E Hermosilla
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Dept of Orofacial Sciences and Dept of Anatomy, University of California-San Francisco, San Francisco, CA, USA
| | - L Gyenis
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - A J Rabalski
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
- Odyssey Therapeutics, Boston, MA, USA
| | - M E Armijo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - P Sepúlveda
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - F Duprat
- Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - D Benítez-Riquelme
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - F Fuentes-Villalobos
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Inmunovirología. Departamento de Microbiologia. Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - A Quiroz
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - M I Hepp
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Investigación en Ciencias Biomédicas, Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - C Farkas
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Investigación en Ciencias Biomédicas, Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - M Mastel
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg. Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - I González-Chavarría
- Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - R Jackstadt
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg. Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - D W Litchfield
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - A F Castro
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
| | - R Pincheira
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
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8
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Dong B, Wang X, Song X, Wang J, Liu X, Yu Z, Zhou Y, Deng J, Wu Y. RNF20 contributes to epigenetic immunosuppression through CDK9-dependent LSD1 stabilization. Proc Natl Acad Sci U S A 2024; 121:e2307150121. [PMID: 38315842 PMCID: PMC10873621 DOI: 10.1073/pnas.2307150121] [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: 04/29/2023] [Accepted: 12/28/2023] [Indexed: 02/07/2024] Open
Abstract
Cyclin-dependent kinase 9 (CDK9) plays a critical role in transcription initiation and is essential for maintaining gene silencing at heterochromatic loci. Inhibition of CDK9 increases sensitivity to immunotherapy, but the underlying mechanism remains unclear. We now report that RNF20 stabilizes LSD1 via K29-mediated ubiquitination, which is dependent on CDK9-mediated phosphorylation. This CDK9- and RNF20-dependent LSD1 stabilization is necessary for the demethylation of histone H3K4, then subsequent repression of endogenous retrovirus, and an interferon response, leading to epigenetic immunosuppression. Moreover, we found that loss of RNF20 sensitizes cancer cells to the immune checkpoint inhibitor anti-PD-1 in vivo and that this effect can be rescued by the expression of ectopic LSD1. Our findings are supported by the observation that RNF20 levels correlate with LSD1 levels in human breast cancer specimens. This study sheds light on the role of RNF20 in CDK9-dependent LSD1 stabilization, which is crucial for epigenetic silencing and immunosuppression. Our findings explore the potential importance of targeting the CDK9-RNF20-LSD1 axis in the development of new cancer therapies.
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Affiliation(s)
- Bo Dong
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40508
- Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY40508
| | - Xinzhao Wang
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40508
- Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY40508
- Department of Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong250355, People’s Republic of China
| | - Xiang Song
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40508
- Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY40508
- Department of Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong250355, People’s Republic of China
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong250355, People’s Republic of China
| | - Jianlin Wang
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40508
- Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY40508
| | - Xia Liu
- Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY40508
| | - Zhiyong Yu
- Department of Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong250355, People’s Republic of China
| | - Yongkun Zhou
- Department of Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong250355, People’s Republic of China
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong250355, People’s Republic of China
| | - Jiong Deng
- Medical Research Institute, Binzhou Medical University Hospital, Binzhou256600, People’s Republic of China
| | - Yadi Wu
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY40508
- Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY40508
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9
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Dos Passos PM, Hemamali EH, Mamede LD, Hayes LR, Ayala YM. RNA-mediated ribonucleoprotein assembly controls TDP-43 nuclear retention. PLoS Biol 2024; 22:e3002527. [PMID: 38422113 DOI: 10.1371/journal.pbio.3002527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 03/12/2024] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
TDP-43 is an essential RNA-binding protein strongly implicated in the pathogenesis of neurodegenerative disorders characterized by cytoplasmic aggregates and loss of nuclear TDP-43. The protein shuttles between nucleus and cytoplasm, yet maintaining predominantly nuclear TDP-43 localization is important for TDP-43 function and for inhibiting cytoplasmic aggregation. We previously demonstrated that specific RNA binding mediates TDP-43 self-assembly and biomolecular condensation, requiring multivalent interactions via N- and C-terminal domains. Here, we show that these complexes play a key role in TDP-43 nuclear retention. TDP-43 forms macromolecular complexes with a wide range of size distribution in cells and we find that defects in RNA binding or inter-domain interactions, including phase separation, impair the assembly of the largest species. Our findings suggest that recruitment into these macromolecular complexes prevents cytoplasmic egress of TDP-43 in a size-dependent manner. Our observations uncover fundamental mechanisms controlling TDP-43 cellular homeostasis, whereby regulation of RNA-mediated self-assembly modulates TDP-43 nucleocytoplasmic distribution. Moreover, these findings highlight pathways that may be implicated in TDP-43 proteinopathies and identify potential therapeutic targets.
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Affiliation(s)
- Patricia M Dos Passos
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Erandika H Hemamali
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Lohany D Mamede
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Lindsey R Hayes
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yuna M Ayala
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
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10
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Latchford LP, Perez LS, Conage-Pough JE, Turk R, Cusimano MA, Vargas VI, Arora S, White FM, Thévenin AF. Differential substrate specificity of ERK, JNK, and p38 MAP kinases toward Connexin 43. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.30.573692. [PMID: 38234737 PMCID: PMC10793482 DOI: 10.1101/2023.12.30.573692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Phosphorylation of connexin 43 (Cx43) is an important regulatory mechanism of gap junction (GJ) function. Cx43 is modified by several kinases on over 15 sites within its ∼140 amino acid-long C-terminus (CT). Phosphorylation of Cx43CT on S255, S262, S279, and S282 by ERK has been widely documented in several cell lines, by many investigators. Phosphorylation of these sites by JNK and p38, on the other hand, is not well-established. Indeed, ERK is a kinase activated by growth factors and is upregulated in diseases, such as cancer. JNK and p38, however, have a largely tumor-suppressive function due to their stress-activated and apoptotic role. We investigated substrate specificity of all three MAPKs toward Cx43CT, both in vitro and in two cell lines (MDCK - non-cancerous, epithelial cells and porcine PAECs - pulmonary artery endothelial cells). Cx43 phosphorylation was monitored through gel-shift assays on an SDS-PAGE, immunodetection with phospho-Cx43 antibodies, and LC-MS/MS phosphoproteomic analyses. Our results demonstrate that p38 and JNK specificity differ from each other and from ERK. JNK has a strong preference for S255 and S279, while p38 readily phosphorylates S279 and S282. In addition, while we confirmed that ERK can phosphorylate all four serines (255, 262, 279, and 282), we identified T290 as a novel ERK phosphorylation site. This work underscores the importance of delineating the effects of ERK, JNK, and p38 signaling pathways on Cx43 and GJ function.
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11
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Dos Passos PM, Hemamali EH, Mamede LD, Hayes LR, Ayala YM. RNA-mediated ribonucleoprotein assembly controls TDP-43 nuclear retention. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.06.552215. [PMID: 37609278 PMCID: PMC10441353 DOI: 10.1101/2023.08.06.552215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
TDP-43 is an essential RNA-binding protein strongly implicated in the pathogenesis of neurodegenerative disorders characterized by cytoplasmic aggregates and loss of nuclear TDP-43. The protein shuttles between nucleus and cytoplasm, yet maintaining predominantly nuclear TDP-43 localization is important for TDP-43 function and for inhibiting cytoplasmic aggregation. We previously demonstrated that specific RNA binding mediates TDP-43 self-assembly and biomolecular condensation, requiring multivalent interactions via N- and C-terminal domains. Here, we show that these complexes play a key role in TDP-43 nuclear retention. TDP-43 forms macromolecular complexes with a wide range of size distribution in cells and we find that defects in RNA binding or inter-domain interactions, including phase separation, impair the assembly of the largest species. Our findings suggest that recruitment into these macromolecular complexes prevents cytoplasmic egress of TDP-43 in a size-dependent manner. Our observations uncover fundamental mechanisms controlling TDP-43 cellular homeostasis, whereby regulation of RNA-mediated self-assembly modulates TDP-43 nucleocytoplasmic distribution. Moreover, these findings highlight pathways that may be implicated in TDP-43 proteinopathies and identify potential therapeutic targets.
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12
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Lövfors W, Magnusson R, Jönsson C, Gustafsson M, Olofsson CS, Cedersund G, Nyman E. A comprehensive mechanistic model of adipocyte signaling with layers of confidence. NPJ Syst Biol Appl 2023; 9:24. [PMID: 37286693 DOI: 10.1038/s41540-023-00282-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/17/2023] [Indexed: 06/09/2023] Open
Abstract
Adipocyte signaling, normally and in type 2 diabetes, is far from fully understood. We have earlier developed detailed dynamic mathematical models for several well-studied, partially overlapping, signaling pathways in adipocytes. Still, these models only cover a fraction of the total cellular response. For a broader coverage of the response, large-scale phosphoproteomic data and systems level knowledge on protein interactions are key. However, methods to combine detailed dynamic models with large-scale data, using information about the confidence of included interactions, are lacking. We have developed a method to first establish a core model by connecting existing models of adipocyte cellular signaling for: (1) lipolysis and fatty acid release, (2) glucose uptake, and (3) the release of adiponectin. Next, we use publicly available phosphoproteome data for the insulin response in adipocytes together with prior knowledge on protein interactions, to identify phosphosites downstream of the core model. In a parallel pairwise approach with low computation time, we test whether identified phosphosites can be added to the model. We iteratively collect accepted additions into layers and continue the search for phosphosites downstream of these added layers. For the first 30 layers with the highest confidence (311 added phosphosites), the model predicts independent data well (70-90% correct), and the predictive capability gradually decreases when we add layers of decreasing confidence. In total, 57 layers (3059 phosphosites) can be added to the model with predictive ability kept. Finally, our large-scale, layered model enables dynamic simulations of systems-wide alterations in adipocytes in type 2 diabetes.
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Affiliation(s)
- William Lövfors
- Department of Biomedical Engineering, Linköping University, Linköping, Sweden.
- Department of Mathematics, Linköping University, Linköping, Sweden.
- School of Medical Sciences and Inflammatory Response and Infection Susceptibility Centre (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| | - Rasmus Magnusson
- School of Bioscience, Systems Biology Research Center, University of Skövde, Skövde, Sweden
| | - Cecilia Jönsson
- Department of Biomedical Engineering, Linköping University, Linköping, Sweden
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | - Mika Gustafsson
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Charlotta S Olofsson
- Department of Physiology/Metabolic Physiology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Gunnar Cedersund
- Department of Biomedical Engineering, Linköping University, Linköping, Sweden.
- School of Medical Sciences and Inflammatory Response and Infection Susceptibility Centre (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
- Center for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden.
| | - Elin Nyman
- Department of Biomedical Engineering, Linköping University, Linköping, Sweden.
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13
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Li Y, Zhu J, Yu Z, Li H, Jin X. The role of Lamin B2 in human diseases. Gene 2023; 870:147423. [PMID: 37044185 DOI: 10.1016/j.gene.2023.147423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 04/14/2023]
Abstract
Lamin B2 (LMNB2), on the inner side of the nuclear envelope, constitutes the nuclear skeleton by connecting with other nuclear proteins. LMNB2 is involved in a wide range of nuclear functions, including DNA replication and stability, regulation of chromatin, and nuclear stiffness. Moreover, LMNB2 regulates several cellular processes, such as tissue development, cell cycle, cellular proliferation and apoptosis, chromatin localization and stability, and DNA methylation. Besides, the influence of abnormal expression and mutations of LMNB2 has been gradually discovered in cancers and laminopathies. Therefore, this review summarizes the recent advances of LMNB2-associated biological roles in physiological or pathological conditions, with a particular emphasis on cancers and laminopathies, as well as the potential mechanism of LMNB2 in related cancers.
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Affiliation(s)
- Yuxuan Li
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Zongdong Yu
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Hong Li
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China.
| | - Xiaofeng Jin
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China.
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14
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Huang CJ, Lyu X, Kang J. The molecular characteristics and functional roles of microspherule protein 1 (MCRS1) in gene expression, cell proliferation, and organismic development. Cell Cycle 2023; 22:619-632. [PMID: 36384428 PMCID: PMC9980701 DOI: 10.1080/15384101.2022.2145816] [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: 06/01/2022] [Revised: 09/21/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022] Open
Abstract
Accurate spatial and temporal regulation of cell cycle progression is essential for cell proliferation and organismic development. This review demonstrates the role of microspherule protein 58kD, commonly known as MCRS1, as a key cell cycle regulator of higher eukaryotic organisms. We discuss the isoforms and functional domains of MCRS1 as well as their subcellular localization at specific stages of the cell cycle. These molecular characteristics reveal MCRS1's dynamic regulatory role in gene expression, genome stability, cell proliferation, and organismic development. Furthermore, we discuss the molecular details of its seemingly opposite, tumor-suppressive or tumor-promoting, role in different types of cancer.
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Affiliation(s)
| | - Xiaoai Lyu
- Arts and Science, New York University Shanghai, Shanghai, China
- Graduate School of Arts and Science, New York University, New York, USA
| | - Jungseog Kang
- Arts and Science, New York University Shanghai, Shanghai, China
- NYU-ECNU Center for Computational Chemistry, New York University Shanghai, Shanghai, China
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15
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Baral I, Shirude MB, Jothi DL, Mukherjee A, Dutta D. Characterization of a Distinct State in the Continuum of Pluripotency Facilitated by Inhibition of PKCζ in Mouse Embryonic Stem Cells. Stem Cell Rev Rep 2023; 19:1098-1115. [PMID: 36781773 DOI: 10.1007/s12015-023-10513-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2023] [Indexed: 02/15/2023]
Abstract
Inhibition of PKC (PKCi) signaling maintains pluripotency of embryonic stem cells (ESCs) across different mammalian species. However, the position of PKCi maintained ESCs in the pluripotency continuum is largely unknown. Here we demonstrate that mouse ESCs when cultured continuously, with PKCi, for 75 days are retained in naïve state of pluripotency. Gene expression analysis and proteomics studies demonstrated enhanced naïve character of PKCi maintained ESCs in comparison to classical serum/LIF (S/L) supported ESCs. Molecular analysis revealed that activation of PKCζ isoform associate with primed state of pluripotency, present in epiblast-like stem cells generated in vitro while inhibition of PKCζ phosphorylation associated with naïve state of pluripotency in vitro and in vivo. Phosphoproteomics and chromatin modification enzyme array based studies showed loss in DNA methyl transferase 3B (DNMT3B) and its phosphorylation level upon functional inhibition of PKCζ as one of the crucial components of this regulatory pathway. Unlike ground state of pluripotency maintained by MEK/GSK3 inhibitor in addition to LIF (2i/LIF), loss in DNMT3B is a reversible phenomenon in PKCi maintained ESCs. Absence of phosphorylation of c-MYC, RAF1, SPRY4 while presence of ERF, DUSP6, CIC and YAP1 phosphorylation underlined the phosphoproteomics signature of PKCi mediated maintenance of naïve pluripotency. States of pluripotency represent the developmental continuum and the existence of PKCi mediated mouse ESCs in a distinct state in the continuum of pluripotency (DiSCo) might contribute to the establishment of stages of murine embryonic development that were non-permissible till date.
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Affiliation(s)
- Ishita Baral
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India.,Manipal Academy of Higher Education, Karnataka State, Manipal, 576104, India
| | - Mayur Balkrishna Shirude
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India.,Manipal Academy of Higher Education, Karnataka State, Manipal, 576104, India
| | - Dhana Lakshmi Jothi
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India
| | - Ananda Mukherjee
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India
| | - Debasree Dutta
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India.
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16
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Coordinated transcriptional and post-transcriptional epigenetic regulation during skeletal muscle development and growth in pigs. J Anim Sci Biotechnol 2022; 13:146. [PMID: 36457054 PMCID: PMC9714148 DOI: 10.1186/s40104-022-00791-3] [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: 05/10/2022] [Accepted: 10/06/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) and DNA 5-methylcytosine (5mC) methylation plays crucial roles in diverse biological processes, including skeletal muscle development and growth. Recent studies unveiled a potential link between these two systems, implicating the potential mechanism of coordinated transcriptional and post-transcriptional regulation in porcine prenatal myogenesis and postnatal skeletal muscle growth. METHODS Immunofluorescence and co-IP assays were carried out between the 5mC writers and m6A writers to investigate the molecular basis underneath. Large-scale in-house transcriptomic data were compiled for applying weighted correlation network analysis (WGCNA) to identify the co-expression patterns of m6A and 5mC regulators and their potential role in pig myogenesis. Whole-genome bisulfite sequencing (WGBS) and methylated RNA immunoprecipitation sequencing (MeRIP-seq) were performed on the skeletal muscle samples from Landrace pigs at four postnatal growth stages (days 30, 60, 120 and 180). RESULTS Significantly correlated expression between 5mC writers and m6A writers and co-occurrence of 5mC and m6A modification were revealed from public datasets of C2C12 myoblasts. The protein-protein interactions between the DNA methylase and the m6A methylase were observed in mouse myoblast cells. Further, by analyzing transcriptome data comprising 81 pig skeletal muscle samples across 27 developmental stages, we identified a 5mC/m6A epigenetic module eigengene and decoded its potential functions in pre- or post-transcriptional regulation in postnatal skeletal muscle development and growth of pigs. Following integrative multi-omics analyses on the WGBS methylome data and MeRIP-seq data for both m6A and gene expression profiles revealed a genome/transcriptome-wide correlated dynamics and co-occurrence of 5mC and m6A modifications as a consequence of 5mC/m6A crosstalk in the postnatal myogenesis progress of pigs. Last, we identified a group of myogenesis-related genes collaboratively regulated by both 5mC and m6A modifications in postnatal skeletal muscle growth in pigs. CONCLUSIONS Our study discloses a potential epigenetic mechanism in skeletal muscle development and provides a novel direction for animal breeding and drug development of related human muscle-related diseases.
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17
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Franke K, Kirchner M, Mertins P, Zuberbier T, Babina M. The SCF/KIT axis in human mast cells: Capicua acts as potent KIT repressor and ERK predominates PI3K. Allergy 2022; 77:3337-3349. [PMID: 35652819 DOI: 10.1111/all.15396] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND The SCF/KIT axis regulates nearly all aspects of mast cell (MC) biology. A comprehensive view of SCF-triggered phosphorylation dynamics is lacking. The relationship between signaling modules and SCF-supported functions likewise remains ill-defined. METHODS Mast cells were isolated from human skin; upon stimulation by SCF, global phosphoproteomic changes were analyzed by LC-MS/MS and selectively validated by immunoblotting. MC survival was inspected by YoPro; BrdU incorporation served to monitor proliferation. Gene expression was quantified by RT-qPCR and cytokines by ELISA. Pharmacological inhibitors were supplemented by ERK1 and/or ERK2 knockdown. CIC translocation and degradation were studied in nuclear and cytoplasmic fractions. CIC's impact on KIT signaling and function was assessed following RNA interference. RESULTS ≈5400 out of ≈10,500 phosphosites experienced regulation by SCF. The MEK/ERK cascade was strongly induced surpassing STAT5 > PI3K/Akt > p38 > JNK. Comparison between MEK/ERK's and PI3K's support of basic programs (apoptosis, proliferation) revealed equipotency between modules. In functional outputs (gene expression, cytokines), ERK was the most influential kinase. OSM and LIF production was identified in skin MCs. Strikingly, SCF triggered massive phosphorylation of a protein not associated with KIT previously: CIC. Phosphorylation was followed by CIC's cytoplasmic appearance and degradation, the latter sensitive to protease but not preoteasome inhibition. Both shuttling and degradation were ERK-dependent. Conversely, CIC-siRNA facilitated KIT signaling, functional outputs, and survival. CONCLUSION The SCF/KIT axis shows notable strength in MCs, and MEK/ERK as most prominent module. An inhibitory circuit exists between KIT and CIC. CIC stabilization in MCs may turn out as a therapeutic option to interfere with allergic and MC-driven diseases.
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Affiliation(s)
- Kristin Franke
- Institute of Allergology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, Berlin, Germany
| | - Marieluise Kirchner
- Core Unit Proteomics, Berlin Institute of Health at Charité- Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | - Philipp Mertins
- Core Unit Proteomics, Berlin Institute of Health at Charité- Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | - Torsten Zuberbier
- Institute of Allergology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, Berlin, Germany
| | - Magda Babina
- Institute of Allergology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, Berlin, Germany
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18
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Garay YC, Cejas RB, Lorenz V, Zlocowski N, Parodi P, Ferrero FA, Angeloni G, García VA, Sendra VG, Lardone RD, Irazoqui FJ. Polypeptide N-acetylgalactosamine transferase 3: a post-translational writer on human health. J Mol Med (Berl) 2022; 100:1387-1403. [PMID: 36056254 DOI: 10.1007/s00109-022-02249-5] [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: 04/27/2022] [Revised: 08/10/2022] [Accepted: 08/17/2022] [Indexed: 10/14/2022]
Abstract
Polypeptide N-acetylgalactosamine transferase 3 (ppGalNAc-T3) is an enzyme involved in the initiation of O-GalNAc glycan biosynthesis. Acting as a writer of frequent post-translational modification (PTM) on human proteins, ppGalNAc-T3 has key functions in the homeostasis of human cells and tissues. We review the relevant roles of this molecule in the biosynthesis of O-GalNAc glycans, as well as in biological functions related to human physiological and pathological conditions. With main emphasis in ppGalNAc-T3, we draw attention to the different ways involved in the modulation of ppGalNAc-Ts enzymatic activity. In addition, we take notice on recent reports of ppGalNAc-T3 having different subcellular localizations, highlight critical intrinsic and extrinsic functions in cellular physiology that are exerted by ppGalNAc-T3-synthesized PTMs, and provide an update on several human pathologies associated with dysfunctional ppGalNAc-T3. Finally, we propose biotechnological tools as new therapeutic options for the treatment of pathologies related to altered ppGalNAc-T3. KEY MESSAGES: ppGalNAc-T3 is a key enzyme in the human O-GalNAc glycans biosynthesis. enzyme activity is regulated by PTMs, lectin domain and protein-protein interactions. ppGalNAc-T3 is located in human Golgi apparatus and cell nucleus. ppGalNAc-T3 has a central role in cell physiology as well as in several pathologies. Biotechnological tools for pathological management are proposed.
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Affiliation(s)
- Yohana Camila Garay
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Romina Beatriz Cejas
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Virginia Lorenz
- Facultad de Bioquímica Y Ciencias Biológicas, Instituto de Salud Y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL) - Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Santa Fe, Argentina
| | - Natacha Zlocowski
- Centro de Microscopía Electrónica, Facultad de Ciencias Médicas, Instituto de Investigaciones en Ciencias de La Salud (INICSA-CONICET), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Pedro Parodi
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Franco Alejandro Ferrero
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Genaro Angeloni
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Valentina Alfonso García
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Victor German Sendra
- Center for Translational Ocular Immunology, Department of Ophthalmology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA
| | - Ricardo Dante Lardone
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Fernando José Irazoqui
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.
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19
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Detering NT, Schüning T, Hensel N, Claus P. The phospho-landscape of the survival of motoneuron protein (SMN) protein: relevance for spinal muscular atrophy (SMA). Cell Mol Life Sci 2022; 79:497. [PMID: 36006469 PMCID: PMC11071818 DOI: 10.1007/s00018-022-04522-9] [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] [Received: 03/21/2022] [Revised: 07/27/2022] [Accepted: 08/09/2022] [Indexed: 11/03/2022]
Abstract
Spinal muscular atrophy (SMA) is caused by low levels of the survival of motoneuron (SMN) Protein leading to preferential degeneration of lower motoneurons in the ventral horn of the spinal cord and brain stem. However, the SMN protein is ubiquitously expressed and there is growing evidence of a multisystem phenotype in SMA. Since a loss of SMN function is critical, it is important to decipher the regulatory mechanisms of SMN function starting on the level of the SMN protein itself. Posttranslational modifications (PTMs) of proteins regulate multiple functions and processes, including activity, cellular trafficking, and stability. Several PTM sites have been identified within the SMN sequence. Here, we map the identified SMN PTMs highlighting phosphorylation as a key regulator affecting localization, stability and functions of SMN. Furthermore, we propose SMN phosphorylation as a crucial factor for intracellular interaction and cellular distribution of SMN. We outline the relevance of phosphorylation of the spinal muscular atrophy (SMA) gene product SMN with regard to basic housekeeping functions of SMN impaired in this neurodegenerative disease. Finally, we compare SMA patient mutations with putative and verified phosphorylation sites. Thus, we emphasize the importance of phosphorylation as a cellular modulator in a clinical perspective as a potential additional target for combinatorial SMA treatment strategies.
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Affiliation(s)
- Nora Tula Detering
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Hannover, Germany
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Tobias Schüning
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Hannover, Germany
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Niko Hensel
- Ottawa Hospital Research Institute (OHRI), Ottawa, Canada
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Peter Claus
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Hannover, Germany.
- Center for Systems Neuroscience (ZSN), Hannover, Germany.
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20
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Leite AC, Martins TS, Campos A, Costa V, Pereira C. Phosphoregulation of the ATP synthase beta subunit stimulates mitochondrial activity for G2/M progression. Adv Biol Regul 2022; 85:100905. [PMID: 36030696 DOI: 10.1016/j.jbior.2022.100905] [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: 07/03/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 10/15/2022]
Abstract
Mitochondrial ATP synthase is a multifunctional enzyme complex involved in ATP production. We previously reported that the ATP synthase catalytic beta subunit (Atp2p in yeast) is regulated by the 2A-like protein phosphatase Sit4p, which targets Atp2p at T124/T317 impacting on ATP synthase levels and mitochondrial respiration. Here we report that Atp2-T124/T317 is also potentially regulated by Cdc5p, a polo-like mitotic kinase. Since both Cdc5p and Sit4p have established roles in cell cycle regulation, we investigated whether Atp2-T124/T317 phosphorylation was cell cycle-related. We present evidence that Atp2p levels and phosphorylation vary during cell cycle progression, with an increase at G2/M phase. Atp2-T124/T317 phosphorylation stimulates mitochondrial membrane potential, respiration and ATP levels at G2/M phase, indicating that dynamic Atp2p phosphorylation contributes to mitochondrial activity at this specific cell cycle phase. Preventing Atp2p phosphorylation delays G2/M to G1 transition, suggesting that enhanced bioenergetics at G2/M may help meet the energetic demands of cell cycle progression. However, mimicking constitutive T124/T317 phosphorylation or overexpressing Atp2p leads to mitochondrial DNA instability, indicating that reversible Atp2p phosphorylation is critical for homeostasis. These results indicate that transient phosphorylation of Atp2p, a protein at the core of the ATP production machinery, impacts on mitochondrial bioenergetics and supports cell cycle progression at G2/M.
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Affiliation(s)
- Ana Cláudia Leite
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Telma Silva Martins
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Ana Campos
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal
| | - Vítor Costa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Clara Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal.
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21
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Zhang X, Yang L, Lei W, Hou Q, Huang M, Zhou R, Enver T, Wu S. Single-cell sequencing reveals CD133+CD44−-originating evolution and novel stemness related variants in human colorectal cancer. EBioMedicine 2022; 82:104125. [PMID: 35785618 PMCID: PMC9254347 DOI: 10.1016/j.ebiom.2022.104125] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
Background Tumor heterogeneity of human colorectal cancer (CRC)-initiating cells (CRCICs) in cancer tissues often represents aggressive features of cancer progression. For high-resolution examination of CRCICs, we performed single-cell whole-exome sequencing (scWES) and bulk cell targeted exome sequencing (TES) of CRCICs to investigate stemness-specific somatic alterations or clonal evolution. Methods Single cells of three subpopulations of CRCICs (CD133+CD44+, CD133−CD44+, and CD133+CD44− cells), CRC cells (CRCCs), and control cells from one CRC tissue were sorted for scWES. Then, we set up a mutation panel from scWES data and TES was used to validate mutation distribution and clonal evolution in additional 96 samples (20 patients) those were also sorted into the same three groups of CRCICs and CRCCs. The knock-down experiments were used to analyze stemness-related mutant genes. Neoantigens of these mutant genes and their MHC binding affinity were also analyzed. Findings Clonal evolution analysis of scWES and TES showed that the CD133+CD44− CRCICs were the likely origin of CRC before evolving into other groups of CRCICs/CRCCs. We revealed that AHNAK2, PLIN4, HLA-B, ALK, CCDC92 and ALMS1 genes were specifically mutated in CRCICs followed by the validation of their functions. Furthermore, four predicted neoantigens of AHNAK2 were identified and validated, which might have applications in immunotherapy for CRC patients. Interpretation All the integrative analyses above revealed clonal evolution of CRC and new markers for CRCICs and demonstrate the important roles of CRCICs in tumorigenesis and progression of CRCs. Funding A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.
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Affiliation(s)
- Xiaoyan Zhang
- Department of Radiotherapy, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ling Yang
- Department of Radiotherapy, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wanjun Lei
- Novogene Bioinformatics Institute, Beijing, China
| | - Qiang Hou
- Clinical laboratory, Hangzhou Cancer Hospital, Hangzhou, China
| | - Ming Huang
- Clinical laboratory, Hangzhou Cancer Hospital, Hangzhou, China
| | - Rongjing Zhou
- Department of Pathology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Tariq Enver
- Cancer Institute, University College London, United Kingdom.
| | - Shixiu Wu
- Department of Radiotherapy, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
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22
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Ferreira MJS, Mancini FE, Humphreys PA, Ogene L, Buckley M, Domingos MAN, Kimber SJ. Pluripotent stem cells for skeletal tissue engineering. Crit Rev Biotechnol 2022; 42:774-793. [PMID: 34488516 DOI: 10.1080/07388551.2021.1968785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Here, we review the use of human pluripotent stem cells for skeletal tissue engineering. A number of approaches have been used for generating cartilage and bone from both human embryonic stem cells and induced pluripotent stem cells. These range from protocols relying on intrinsic cell interactions and signals from co-cultured cells to those attempting to recapitulate the series of steps occurring during mammalian skeletal development. The importance of generating authentic tissues rather than just differentiated cells is emphasized and enabling technologies for doing this are reported. We also review the different methods for characterization of skeletal cells and constructs at the tissue and single-cell level, and indicate newer resources not yet fully utilized in this field. There have been many challenges in this research area but the technologies to overcome these are beginning to appear, often adopted from related fields. This makes it more likely that cost-effective and efficacious human pluripotent stem cell-engineered constructs may become available for skeletal repair in the near future.
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Affiliation(s)
- Miguel J S Ferreira
- Department of Mechanical, Aerospace and Civil Engineering, School of Engineering, Faculty of Science and Engineering & Henry Royce Institute, The University of Manchester, Manchester, UK
| | - Fabrizio E Mancini
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Paul A Humphreys
- Department of Mechanical, Aerospace and Civil Engineering, School of Engineering, Faculty of Science and Engineering & Henry Royce Institute, The University of Manchester, Manchester, UK
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Leona Ogene
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Michael Buckley
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Marco A N Domingos
- Department of Mechanical, Aerospace and Civil Engineering, School of Engineering, Faculty of Science and Engineering & Henry Royce Institute, The University of Manchester, Manchester, UK
| | - Susan J Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
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23
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Xie Y, Li H, Luo X, Li H, Gao Q, Zhang L, Teng Y, Zhao Q, Zuo Z, Ren J. IBS 2.0: an upgraded illustrator for the visualization of biological sequences. Nucleic Acids Res 2022; 50:W420-W426. [PMID: 35580044 PMCID: PMC9252815 DOI: 10.1093/nar/gkac373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/23/2022] [Accepted: 04/29/2022] [Indexed: 11/14/2022] Open
Abstract
The visualization of biological sequences with various functional elements is fundamental for the publication of scientific achievements in the field of molecular and cellular biology. However, due to the limitations of the currently used applications, there are still considerable challenges in the preparation of biological schematic diagrams. Here, we present a professional tool called IBS 2.0 for illustrating the organization of both protein and nucleotide sequences. With the abundant graphical elements provided in IBS 2.0, biological sequences can be easily represented in a concise and clear way. Moreover, we implemented a database visualization module in IBS 2.0, enabling batch visualization of biological sequences from the UniProt and the NCBI RefSeq databases. Furthermore, to increase the design efficiency, a resource platform that allows uploading, retrieval, and browsing of existing biological sequence diagrams has been integrated into IBS 2.0. In addition, a lightweight JS library was developed in IBS 2.0 to assist the visualization of biological sequences in customized web services. To obtain the latest version of IBS 2.0, please visit https://ibs.renlab.org.
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Affiliation(s)
- Yubin Xie
- School of Life Sciences, Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Huiqin Li
- School of Life Sciences, Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Xiaotong Luo
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Hongyu Li
- School of Life Sciences, Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Qiuyuan Gao
- School of Life Sciences, Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Luowanyue Zhang
- School of Life Sciences, Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Yuyan Teng
- School of Life Sciences, Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Jian Ren
- School of Life Sciences, Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
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24
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Thompson AF, Blackburn PR, Arons NS, Stevens SN, Babovic-Vuksanovic D, Lian JB, Klee EW, Stumpff J. Pathogenic mutations in the chromokinesin KIF22 disrupt anaphase chromosome segregation. eLife 2022; 11:78653. [PMID: 35730929 PMCID: PMC9302971 DOI: 10.7554/elife.78653] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/21/2022] [Indexed: 11/22/2022] Open
Abstract
The chromokinesin KIF22 generates forces that contribute to mitotic chromosome congression and alignment. Mutations in the α2 helix of the motor domain of KIF22 have been identified in patients with abnormal skeletal development, and we report the identification of a patient with a novel mutation in the KIF22 tail. We demonstrate that pathogenic mutations do not result in a loss of KIF22’s functions in early mitosis. Instead, mutations disrupt chromosome segregation in anaphase, resulting in reduced proliferation, abnormal daughter cell nuclear morphology, and, in a subset of cells, cytokinesis failure. This phenotype could be explained by a failure of KIF22 to inactivate in anaphase. Consistent with this model, constitutive activation of the motor via a known site of phosphoregulation in the tail phenocopied the effects of pathogenic mutations. These results suggest that the motor domain α2 helix may be an important site for regulation of KIF22 activity at the metaphase to anaphase transition. In support of this conclusion, mimicking phosphorylation of α2 helix residue T158 also prevents inactivation of KIF22 in anaphase. These findings demonstrate the importance of both the head and tail of the motor in regulating the activity of KIF22 and offer insight into the cellular consequences of preventing KIF22 inactivation and disrupting force balance in anaphase.
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Affiliation(s)
- Alex F Thompson
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, United States
| | | | - Noah S Arons
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, United States
| | - Sarah N Stevens
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, United States
| | | | - Jane B Lian
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, United States
| | - Eric W Klee
- Biomedical Informatics, Mayo Clinic, Rochester, United States
| | - Jason Stumpff
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, United States
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25
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Ubiquitin specific peptidase 11 as a novel therapeutic target for cancer management. Cell Death Dis 2022; 8:292. [PMID: 35715413 PMCID: PMC9205893 DOI: 10.1038/s41420-022-01083-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/25/2022]
Abstract
Ubiquitination is a critical biological process in post-translational modification of proteins and involves multiple signaling pathways in protein metabolism, apoptosis, DNA damage, cell-cycle progression, and cancer development. Deubiquitinase, a specific enzyme that regulates the ubiquitination process, is also thought to be closely associated with the development and progression of various cancers. In this article, we systematically review the emerging role of the deubiquitinase ubiquitin-specific peptidase 11 (USP11) in many cancer-related pathways. The results show that USP11 promotes or inhibits the progression and chemoresistance of different cancers, including colorectal, breast, ovarian, and hepatocellular carcinomas, via deubiquitinating several critical proteins of cancer-related pathways. We initially summarize the role of USP11 in different cancers and further discuss the possibility of USP11 as a therapeutic strategy.
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26
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Koehler LC, Grese ZR, Bastos ACS, Mamede LD, Heyduk T, Ayala YM. TDP-43 Oligomerization and Phase Separation Properties Are Necessary for Autoregulation. Front Neurosci 2022; 16:818655. [PMID: 35495061 PMCID: PMC9048411 DOI: 10.3389/fnins.2022.818655] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/21/2022] [Indexed: 12/11/2022] Open
Abstract
Loss of TDP-43 protein homeostasis and dysfunction, in particular TDP-43 aggregation, are tied to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). TDP-43 is an RNA binding protein tightly controlling its own expression levels through a negative feedback loop, involving TDP-43 recruitment to the 3′ untranslated region of its own transcript. Aberrant TDP-43 expression caused by autoregulation defects are linked to TDP-43 pathology. Therefore, interactions between TDP-43 and its own transcript are crucial to prevent TDP-43 aggregation and loss of function. However, the mechanisms that mediate this interaction remain ill-defined. We find that a central RNA sequence in the 3′ UTR, which mediates TDP-43 autoregulation, increases the liquid properties of TDP-43 phase separation. Furthermore, binding to this RNA sequence induces TDP-43 condensation in human cell lysates, suggesting that this interaction promotes TDP-43 self-assembly into dynamic ribonucleoprotein granules. In agreement with these findings, our experiments show that TDP-43 oligomerization and phase separation, mediated by the amino and carboxy-terminal domains, respectively, are essential for TDP-43 autoregulation. According to our additional observations, CLIP34-associated phase separation and autoregulation may be efficiently controlled by phosphorylation of the N-terminal domain. Importantly, we find that specific ALS-associated TDP-43 mutations, mainly M337V, and a shortened TDP-43 isoform recently tied to motor neuron toxicity in ALS, disrupt the liquid properties of TDP-43-RNA condensates as well as autoregulatory function. In addition, we find that M337V decreases the cellular clearance of TDP-43 and other RNA binding proteins associated with ALS/FTD. These observations suggest that loss of liquid properties in M337V condensates strongly affects protein homeostasis. Together, this work provides evidence for the central role of TDP-43 oligomerization and liquid-liquid phase separation linked to RNA binding in autoregulation. These mechanisms may be impaired by TDP-43 disease variants and controlled by specific cellular signaling.
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27
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Krumm J, Sekine K, Samaras P, Brazovskaja A, Breunig M, Yasui R, Kleger A, Taniguchi H, Wilhelm M, Treutlein B, Camp JG, Kuster B. High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development. Cell Rep 2022; 38:110604. [PMID: 35354033 DOI: 10.1016/j.celrep.2022.110604] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/29/2021] [Accepted: 03/09/2022] [Indexed: 11/29/2022] Open
Abstract
Primary human hepatocytes are widely used to evaluate liver toxicity of drugs, but they are scarce and demanding to culture. Stem cell-derived hepatocytes are increasingly discussed as alternatives. To obtain a better appreciation of the molecular processes during the differentiation of induced pluripotent stem cells into hepatocytes, we employ a quantitative proteomic approach to follow the expression of 9,000 proteins, 12,000 phosphorylation sites, and 800 acetylation sites over time. The analysis reveals stage-specific markers, a major molecular switch between hepatic endoderm versus immature hepatocyte-like cells impacting, e.g., metabolism, the cell cycle, kinase activity, and the expression of drug transporters. Comparing the proteomes of two- (2D) and three-dimensional (3D)-derived hepatocytes with fetal and adult liver indicates a fetal-like status of the in vitro models and lower expression of important ADME/Tox proteins. The collective data enable constructing a molecular roadmap of hepatocyte development that serves as a valuable resource for future research.
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Affiliation(s)
- Johannes Krumm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Keisuke Sekine
- Laboratory of Cancer Cell Systems, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-004, Japan
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Agnieska Brazovskaja
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Markus Breunig
- Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany
| | - Ryota Yasui
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-004, Japan
| | - Alexander Kleger
- Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany
| | - Hideki Taniguchi
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-004, Japan; Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany; Computational Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, 4056 Basel, Switzerland
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany; Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, 85354 Freising, Germany.
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28
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Lacoursiere RE, Hadi D, Shaw GS. Acetylation, Phosphorylation, Ubiquitination (Oh My!): Following Post-Translational Modifications on the Ubiquitin Road. Biomolecules 2022; 12:biom12030467. [PMID: 35327659 PMCID: PMC8946176 DOI: 10.3390/biom12030467] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 02/06/2023] Open
Abstract
Ubiquitination is controlled by a series of E1, E2, and E3 enzymes that can ligate ubiquitin to cellular proteins and dictate the turnover of a substrate and the outcome of signalling events such as DNA damage repair and cell cycle. This process is complex due to the combinatorial power of ~35 E2 and ~1000 E3 enzymes involved and the multiple lysine residues on ubiquitin that can be used to assemble polyubiquitin chains. Recently, mass spectrometric methods have identified that most enzymes in the ubiquitination cascade can be further modified through acetylation or phosphorylation under particular cellular conditions and altered modifications have been noted in different cancers and neurodegenerative diseases. This review provides a cohesive summary of ubiquitination, acetylation, and phosphorylation sites in ubiquitin, the human E1 enzyme UBA1, all E2 enzymes, and some representative E3 enzymes. The potential impacts these post-translational modifications might have on each protein function are highlighted, as well as the observations from human disease.
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29
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Molinar-Inglis O, Wozniak JM, Grimsey NJ, Orduña-Castillo L, Cheng N, Lin Y, Gonzalez Ramirez ML, Birch CA, Lapek JD, Gonzalez DJ, Trejo J. Phosphoproteomic analysis of thrombin- and p38 MAPK-regulated signaling networks in endothelial cells. J Biol Chem 2022; 298:101801. [PMID: 35257745 PMCID: PMC8987612 DOI: 10.1016/j.jbc.2022.101801] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 01/11/2023] Open
Abstract
Endothelial dysfunction is a hallmark of inflammation and is mediated by inflammatory factors that signal through G protein–coupled receptors including protease-activated receptor-1 (PAR1). PAR1, a receptor for thrombin, signals via the small GTPase RhoA and myosin light chain intermediates to facilitate endothelial barrier permeability. PAR1 also induces endothelial barrier disruption through a p38 mitogen-activated protein kinase–dependent pathway, which does not integrate into the RhoA/MLC pathway; however, the PAR1-p38 signaling pathways that promote endothelial dysfunction remain poorly defined. To identify effectors of this pathway, we performed a global phosphoproteome analysis of thrombin signaling regulated by p38 in human cultured endothelial cells using multiplexed quantitative mass spectrometry. We identified 5491 unique phosphopeptides and 2317 phosphoproteins, four distinct dynamic phosphoproteome profiles of thrombin-p38 signaling, and an enrichment of biological functions associated with endothelial dysfunction, including modulators of endothelial barrier disruption and a subset of kinases predicted to regulate p38-dependent thrombin signaling. Using available antibodies to detect identified phosphosites of key p38-regulated proteins, we discovered that inhibition of p38 activity and siRNA-targeted depletion of the p38α isoform increased basal phosphorylation of extracellular signal–regulated protein kinase 1/2, resulting in amplified thrombin-stimulated extracellular signal–regulated protein kinase 1/2 phosphorylation that was dependent on PAR1. We also discovered a role for p38 in the phosphorylation of α-catenin, a component of adherens junctions, suggesting that this phosphorylation may function as an important regulatory process. Taken together, these studies define a rich array of thrombin- and p38-regulated candidate proteins that may serve important roles in endothelial dysfunction.
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30
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Yan X, Gong X, Lin T, Lin M, Qin P, Ye J, Li H, Hong Q, Li M, Liu Y, Li Y, Wang X, Zhang Y, Ling Y, Cao H, Zhang X, Fang F. Analysis of protein phosphorylation sites in the hypothalamus tissues of pubescent goats. J Proteomics 2022; 260:104574. [DOI: 10.1016/j.jprot.2022.104574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/08/2022] [Accepted: 03/17/2022] [Indexed: 10/18/2022]
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31
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Bordet G, Kotova E, Tulin AV. Poly(ADP-ribosyl)ating pathway regulates development from stem cell niche to longevity control. Life Sci Alliance 2021; 5:5/3/e202101071. [PMID: 34949666 PMCID: PMC8739260 DOI: 10.26508/lsa.202101071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023] Open
Abstract
The regulation of poly(ADP-ribose) polymerase, the enzyme responsible for the synthesis of homopolymer ADP-ribose chains on nuclear proteins, has been extensively studied over the last decades for its involvement in tumorigenesis processes. However, the regulation of poly(ADP-ribose) glycohydrolase (PARG), the enzyme responsible for removing this posttranslational modification, has attracted little attention. Here we identified that PARG activity is partly regulated by two phosphorylation sites, ph1 and ph2, in Drosophila We showed that the disruption of these sites affects the germline stem-cells maintenance/differentiation balance as well as embryonic and larval development, but also the synchronization of egg production with the availability of a calorically sufficient food source. Moreover, these PARG phosphorylation sites play an essential role in the control of fly survivability from larvae to adults. We also showed that PARG is phosphorylated by casein kinase 2 and that this phosphorylation seems to protect PARG protein against degradation in vivo. Taken together, these results suggest that the regulation of PARG protein activity plays a crucial role in the control of several developmental processes.
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The Spliced Leader RNA Silencing (SLS) Pathway in Trypanosoma brucei Is Induced by Perturbations of Endoplasmic Reticulum, Golgi Complex, or Mitochondrial Protein Factors: Functional Analysis of SLS-Inducing Kinase PK3. mBio 2021; 12:e0260221. [PMID: 34844425 PMCID: PMC8630539 DOI: 10.1128/mbio.02602-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In the parasite Trypanosoma brucei, the causative agent of human African sleeping sickness, all mRNAs are trans-spliced to generate a common 5′ exon derived from the spliced leader (SL) RNA. Perturbations of protein translocation across the endoplasmic reticulum (ER) induce the spliced leader RNA silencing (SLS) pathway. SLS activation is mediated by a serine-threonine kinase, PK3, which translocates from the cytosolic face of the ER to the nucleus, where it phosphorylates the TATA-binding protein TRF4, leading to the shutoff of SL RNA transcription, followed by induction of programmed cell death. Here, we demonstrate that SLS is also induced by depletion of the essential ER-resident chaperones BiP and calreticulin, ER oxidoreductin 1 (ERO1), and the Golgi complex-localized quiescin sulfhydryl oxidase (QSOX). Most strikingly, silencing of Rhomboid-like 1 (TIMRHOM1), involved in mitochondrial protein import, also induces SLS. The PK3 kinase, which integrates SLS signals, is modified by phosphorylation on multiple sites. To determine which of the phosphorylation events activate PK3, several individual mutations or their combination were generated. These mutations failed to completely eliminate the phosphorylation or translocation of the kinase to the nucleus. The structures of PK3 kinase and its ATP binding domain were therefore modeled. A conserved phenylalanine at position 771 was proposed to interact with ATP, and the PK3F771L mutation completely eliminated phosphorylation under SLS, suggesting that the activation involves most if not all of the phosphorylation sites. The study suggests that the SLS occurs broadly in response to failures in protein sorting, folding, or modification across multiple compartments.
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Mukherjee S, Sanchez-Bernabeu A, Demmers LC, Wu W, Heck AJR. The HLA Ligandome Comprises a Limited Repertoire of O-GlcNAcylated Antigens Preferentially Associated With HLA-B*07:02. Front Immunol 2021; 12:796584. [PMID: 34925382 PMCID: PMC8671986 DOI: 10.3389/fimmu.2021.796584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/15/2021] [Indexed: 12/30/2022] Open
Abstract
Mass-spectrometry based immunopeptidomics has provided unprecedented insights into antigen presentation, not only charting an enormous ligandome of self-antigens, but also cancer neoantigens and peptide antigens harbouring post-translational modifications. Here we concentrate on the latter, focusing on the small subset of HLA Class I peptides (less than 1%) that has been observed to be post-translationally modified (PTM) by a O-linked N-acetylglucosamine (GlcNAc). Just like neoantigens these modified antigens may have specific immunomodulatory functions. Here we compiled from literature, and a new dataset originating from the JY B cell lymphoblastoid cell line, a concise albeit comprehensive list of O-GlcNAcylated HLA class I peptides. This cumulative list of O-GlcNAcylated HLA peptides were derived from normal and cancerous origin, as well as tissue specimen. Remarkably, the overlap in detected O-GlcNAcylated HLA peptides as well as their source proteins is strikingly high. Most of the O-GlcNAcylated HLA peptides originate from nuclear proteins, notably transcription factors. From this list, we extract that O-GlcNAcylated HLA Class I peptides are preferentially presented by the HLA-B*07:02 allele. This allele loads peptides with a Proline residue anchor at position 2, and features a binding groove that can accommodate well the recently proposed consensus sequence for O-GlcNAcylation, P(V/A/T/S)g(S/T), essentially explaining why HLA-B*07:02 is a favoured binding allele. The observations drawn from the compiled list, may assist in the prediction of novel O-GlcNAcylated HLA antigens, which will be best presented by patients harbouring HLA-B*07:02 or related alleles that use Proline as anchoring residue.
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Affiliation(s)
- Soumya Mukherjee
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
| | - Alvaro Sanchez-Bernabeu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
| | - Laura C Demmers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht University, Utrecht, Netherlands
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Characterizing the Interaction between the HTLV-1 Transactivator Tax-1 with Transcription Elongation Factor ELL2 and Its Impact on Viral Transactivation. Int J Mol Sci 2021; 22:ijms222413597. [PMID: 34948391 PMCID: PMC8705299 DOI: 10.3390/ijms222413597] [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: 10/01/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
The human T-cell leukemia virus type 1 (HTLV-1)-encoded transactivator and oncoprotein Tax-1 is essential for HTLV-1 replication. We recently found that Tax-1 interacts with transcription elongation factor for RNA polymerase II 2, ELL2, which enhances Tax-1-mediated transactivation of the HTLV-1 promotor. Here, we characterize the Tax-1:ELL2 interaction and its impact on viral transactivation by confocal imaging, co-immunoprecipitation, and luciferase assays. We found that Tax-1 and ELL2 not only co-precipitate, but also co-localize in dot-like structures in the nucleus. Tax-1:ELL2 complex formation occurred independently of Tax-1 point mutations, which are crucial for post translational modifications (PTMs) of Tax-1, suggesting that these PTMs are irrelevant for Tax-1:ELL2 interaction. In contrast, Tax-1 deletion mutants lacking either N-terminal (aa 1-37) or C-terminal regions (aa 150-353) of Tax-1 were impaired in interacting with ELL2. Contrary to Tax-1, the related, non-oncogenic Tax-2B from HTLV-2B did not interact with ELL2. Finally, we found that ELL2-R1 (aa 1-353), which carries an RNA polymerase II binding domain, and ELL2-R3 (aa 515-640) are sufficient to interact with Tax-1; however, only ELL2-truncations expressing R1 could enhance Tax-1-mediated transactivation of the HTLV-1 promoter. Together, this study identifies domains in Tax-1 and ELL2 being required for Tax-1:ELL2 complex formation and for viral transactivation.
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O-GlcNAcylation of Sox2 at threonine 258 regulates the self-renewal and early cell fate of embryonic stem cells. Exp Mol Med 2021; 53:1759-1768. [PMID: 34819616 PMCID: PMC8639819 DOI: 10.1038/s12276-021-00707-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/13/2021] [Accepted: 09/26/2021] [Indexed: 12/27/2022] Open
Abstract
Sox2 is a core transcription factor in embryonic stem cells (ESCs), and O-GlcNAcylation is a type of post-translational modification of nuclear-cytoplasmic proteins. Although both factors play important roles in the maintenance and differentiation of ESCs and the serine 248 (S248) and threonine 258 (T258) residues of Sox2 are modified by O-GlcNAcylation, the function of Sox2 O-GlcNAcylation is unclear. Here, we show that O-GlcNAcylation of Sox2 at T258 regulates mouse ESC self-renewal and early cell fate. ESCs in which wild-type Sox2 was replaced with the Sox2 T258A mutant exhibited reduced self-renewal, whereas ESCs with the Sox2 S248A point mutation did not. ESCs with the Sox2 T258A mutation heterologously introduced using the CRISPR/Cas9 system, designated E14-Sox2TA/WT, also exhibited reduced self-renewal. RNA sequencing analysis under self-renewal conditions showed that upregulated expression of early differentiation genes, rather than a downregulated expression of self-renewal genes, was responsible for the reduced self-renewal of E14-Sox2TA/WT cells. There was a significant decrease in ectodermal tissue and a marked increase in cartilage tissue in E14-Sox2TA/WT-derived teratomas compared with normal E14 ESC-derived teratomas. RNA sequencing of teratomas revealed that genes related to brain development had generally downregulated expression in the E14-Sox2TA/WT-derived teratomas. Our findings using the Sox2 T258A mutant suggest that Sox2 T258 O-GlcNAc has a positive effect on ESC self-renewal and plays an important role in the proper development of ectodermal lineage cells. Overall, our study directly links O-GlcNAcylation and early cell fate decisions.
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Vergani-Junior CA, Tonon-da-Silva G, Inan MD, Mori MA. DICER: structure, function, and regulation. Biophys Rev 2021; 13:1081-1090. [DOI: 10.1007/s12551-021-00902-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/31/2021] [Indexed: 02/06/2023] Open
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Wang Z, Gao X, Li Q, Zhu H, Zhao X, Garcia-Barrio M, Zhang J, Guo Y, Chen YE, Zeng R, Wu JR, Chang L. Inhibition of a Novel CLK1-THRAP3-PPARγ Axis Improves Insulin Sensitivity. Front Physiol 2021; 12:699578. [PMID: 34526909 PMCID: PMC8435799 DOI: 10.3389/fphys.2021.699578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
Increasing energy expenditure by promoting "browning" in adipose tissues is a promising strategy to prevent obesity and associated diabetes. To uncover potential targets of cold exposure, which induces energy expenditure, we performed phosphoproteomics profiling in brown adipose tissue of mice housed in mild cold environment at 16°C. We identified CDC2-like kinase 1 (CLK1) as one of the kinases that were significantly downregulated by mild cold exposure. In addition, genetic knockout of CLK1 or chemical inhibition in mice ameliorated diet-induced obesity and insulin resistance at 22°C. Through proteomics, we uncovered thyroid hormone receptor-associated protein 3 (THRAP3) as an interacting partner of CLK1, further confirmed by co-immunoprecipitation assays. We further demonstrated that CLK1 phosphorylates THRAP3 at Ser243, which is required for its regulatory interaction with phosphorylated peroxisome proliferator-activated receptor gamma (PPARγ), resulting in impaired adipose tissue browning and insulin sensitivity. These data suggest that CLK1 plays a critical role in controlling energy expenditure through the CLK1-THRAP3-PPARγ axis.
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Affiliation(s)
- Zhenguo Wang
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
| | - Xiaojing Gao
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qingrun Li
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
| | - Hongwen Zhu
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
| | - Xiangjie Zhao
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Minerva Garcia-Barrio
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Jifeng Zhang
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Yanhong Guo
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Y. Eugene Chen
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Rong Zeng
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
- School of Life Sciences and Technology, Shanghai Tech University, Shanghai, China
| | - Jia-Rui Wu
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
- School of Life Sciences and Technology, Shanghai Tech University, Shanghai, China
| | - Lin Chang
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
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Moesslacher CS, Kohlmayr JM, Stelzl U. Exploring absent protein function in yeast: assaying post translational modification and human genetic variation. MICROBIAL CELL (GRAZ, AUSTRIA) 2021; 8:164-183. [PMID: 34395585 PMCID: PMC8329848 DOI: 10.15698/mic2021.08.756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/13/2021] [Accepted: 06/18/2021] [Indexed: 01/08/2023]
Abstract
Yeast is a valuable eukaryotic model organism that has evolved many processes conserved up to humans, yet many protein functions, including certain DNA and protein modifications, are absent. It is this absence of protein function that is fundamental to approaches using yeast as an in vivo test system to investigate human proteins. Functionality of the heterologous expressed proteins is connected to a quantitative, selectable phenotype, enabling the systematic analyses of mechanisms and specificity of DNA modification, post-translational protein modifications as well as the impact of annotated cancer mutations and coding variation on protein activity and interaction. Through continuous improvements of yeast screening systems, this is increasingly carried out on a global scale using deep mutational scanning approaches. Here we discuss the applicability of yeast systems to investigate absent human protein function with a specific focus on the impact of protein variation on protein-protein interaction modulation.
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Affiliation(s)
- Christina S Moesslacher
- Institute of Pharmaceutical Sciences and BioTechMed-Graz, University of Graz, Graz, Austria
- Contributed equally to the writing of this review
| | - Johanna M Kohlmayr
- Institute of Pharmaceutical Sciences and BioTechMed-Graz, University of Graz, Graz, Austria
- Contributed equally to the writing of this review
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences and BioTechMed-Graz, University of Graz, Graz, Austria
- Contributed equally to the writing of this review
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Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y. O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation. Biochim Biophys Acta Gen Subj 2021; 1865:129930. [PMID: 34019948 DOI: 10.1016/j.bbagen.2021.129930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/28/2022]
Abstract
BACKGROUND Chromatin modifier metastasis-associated protein 1 (MTA1), closely associated with tumor angiogenesis in breast cancer, plays an important role in gene expression and cancer cell behavior. Recently, an association between O-GlcNAc transferase (OGT) and MTA1 was identified by mass spectroscopy. However, the potential relationship between MTA1 and O-GlcNAc modification has not yet explored. METHODS In the current study, the role of MTA1 and its O-GlcNAc modification in breast cancer cell genotoxic adaptation was investigated through quantitative proteomics, chromatin immunoprecipitation followed by sequencing (ChIP-seq), transcriptome analysis, and loss- and gain-of-function experiments. RESULTS We demonstrate that the O-GlcNAc modification promotes MTA1 to interaction with chromatin and thus changes the expression of target genes, contributing to breast cancer cell genotoxic adaptation. MTA1 is modified with O-GlcNAc residues at serine (S) residues S237/S241/S246 in adriamycin-adaptive breast cancer cells, and this modification improves the genome-wide interactions of MTA1 with gene promotor regions by enhancing its association with nucleosome remodeling and histone deacetylation (NuRD) complex. Further, O-GlcNAc modification modulates MTA1 chromatin binding, influencing the specific transcriptional regulation of genes involved in the adaptation of breast cancer cells to genotoxic stress. CONCLUSIONS Our findings reveal a previously unrecognized role for O-GlcNAc-modified MTA1 in transcriptional regulation and suggest that the O-GlcNAc modification is a key to the molecular regulation of chemoresistance in breast cancers.
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Affiliation(s)
- Xueqin Xie
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Qiutong Wu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Keren Zhang
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Yimin Liu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Nana Zhang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Qiushi Chen
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Lingyan Wang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Wenli Li
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Jianing Zhang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China..
| | - Yubo Liu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China..
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FAM20C Overview: Classic and Novel Targets, Pathogenic Variants and Raine Syndrome Phenotypes. Int J Mol Sci 2021; 22:ijms22158039. [PMID: 34360805 PMCID: PMC8348777 DOI: 10.3390/ijms22158039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 12/24/2022] Open
Abstract
FAM20C is a gene coding for a protein kinase that targets S-X-E/pS motifs on different phosphoproteins belonging to diverse tissues. Pathogenic variants of FAM20C are responsible for Raine syndrome (RS), initially described as a lethal and congenital osteosclerotic dysplasia characterized by generalized atherosclerosis with periosteal bone formation, characteristic facial dysmorphisms and intracerebral calcifications. The aim of this review is to give an overview of targets and variants of FAM20C as well as RS aspects. We performed a wide phenotypic review focusing on clinical aspects and differences between all lethal (LRS) and non-lethal (NLRS) reported cases, besides the FAM20C pathogenic variant description for each. As new targets of FAM20C kinase have been identified, we reviewed FAM20C targets and their functions in bone and other tissues, with emphasis on novel targets not previously considered. We found the classic lethal and milder non-lethal phenotypes. The milder phenotype is defined by a large spectrum ranging from osteonecrosis to osteosclerosis with additional congenital defects or intellectual disability in some cases. We discuss our current understanding of FAM20C deficiency, its mechanism in RS through classic FAM20C targets in bone tissue and its potential biological relevance through novel targets in non-bone tissues.
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Farina S, Esposito F, Battistoni M, Biamonti G, Francia S. Post-Translational Modifications Modulate Proteinopathies of TDP-43, FUS and hnRNP-A/B in Amyotrophic Lateral Sclerosis. Front Mol Biosci 2021; 8:693325. [PMID: 34291086 PMCID: PMC8287968 DOI: 10.3389/fmolb.2021.693325] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
It has been shown that protein low-sequence complexity domains (LCDs) induce liquid-liquid phase separation (LLPS), which is responsible for the formation of membrane-less organelles including P-granules, stress granules and Cajal bodies. Proteins harbouring LCDs are widely represented among RNA binding proteins often mutated in ALS. Indeed, LCDs predispose proteins to a prion-like behaviour due to their tendency to form amyloid-like structures typical of proteinopathies. Protein post-translational modifications (PTMs) can influence phase transition through two main events: i) destabilizing or augmenting multivalent interactions between phase-separating macromolecules; ii) recruiting or excluding other proteins and/or nucleic acids into/from the condensate. In this manuscript we summarize the existing evidence describing how PTM can modulate LLPS thus favouring or counteracting proteinopathies at the base of neurodegeneration in ALS.
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Affiliation(s)
- Stefania Farina
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - Consiglio Nazionale delle Ricerce (CNR), Pavia, Italy.,University School for Advanced Studies IUSS, Pavia, Italy
| | - Francesca Esposito
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - Consiglio Nazionale delle Ricerce (CNR), Pavia, Italy.,Università Degli Studi di Pavia, Pavia, Italy
| | | | - Giuseppe Biamonti
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - Consiglio Nazionale delle Ricerce (CNR), Pavia, Italy
| | - Sofia Francia
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - Consiglio Nazionale delle Ricerce (CNR), Pavia, Italy
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Wu K, Zhai X, Huang S, Jiang L, Yu Z, Huang J. Protein Kinases: Potential Drug Targets Against Schistosoma japonicum. Front Cell Infect Microbiol 2021; 11:691757. [PMID: 34277472 PMCID: PMC8282181 DOI: 10.3389/fcimb.2021.691757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022] Open
Abstract
Schistosoma japonicum (S. japonicum) infection can induce serious organ damage and cause schistosomiasis japonica which is mainly prevalent in Asia and currently one of the most seriously neglected tropical diseases. Treatment of schistosomiasis largely depends on the drug praziquantel (PZQ). However, PZQ exhibits low killing efficacy on juvenile worms and the potential emergence of its drug resistance is a continual concern. Protein kinases (PKs) are enzymes that catalyze the phosphorylation of proteins and can participate in many signaling pathways in vivo. Recent studies confirmed the essential roles of PKs in the growth and development of S. japonicum, as well as in schistosome-host interactions, and researches have screened drug targets about PKs from S. japonicum (SjPKs), which provide new opportunities of developing new treatments on schistosomiasis. The aim of this review is to present the current progress on SjPKs from classification, different functions and their potential to become drug targets compared with other schistosomes. The efficiency of related protein kinase inhibitors on schistosomes is highlighted. Finally, the current challenges and problems in the study of SjPKs are proposed, which can provide future guidance for developing anti-schistosomiasis drugs and vaccines.
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Affiliation(s)
- Kaijuan Wu
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Xingyu Zhai
- China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Shuaiqin Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, China
| | - Liping Jiang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Zheng Yu
- China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
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Liu SY, Ikegami K. Nuclear lamin phosphorylation: an emerging role in gene regulation and pathogenesis of laminopathies. Nucleus 2021; 11:299-314. [PMID: 33030403 PMCID: PMC7588210 DOI: 10.1080/19491034.2020.1832734] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Decades of studies have established that nuclear lamin polymers form the nuclear lamina, a protein meshwork that supports the nuclear envelope structure and tethers heterochromatin to the nuclear periphery. Much less is known about unpolymerized nuclear lamins in the nuclear interior, some of which are now known to undergo specific phosphorylation. A recent finding that phosphorylated lamins bind gene enhancer regions offers a new hypothesis that lamin phosphorylation may influence transcriptional regulation in the nuclear interior. In this review, we discuss the regulation, localization, and functions of phosphorylated lamins. We summarize kinases that phosphorylate lamins in a variety of biological contexts. Our discussion extends to laminopathies, a spectrum of degenerative disorders caused by lamin gene mutations, such as cardiomyopathies and progeria. We compare the prevailing hypothesis for laminopathy pathogenesis based on lamins’ function at the nuclear lamina with an emerging hypothesis based on phosphorylated lamins’ function in the nuclear interior.
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Affiliation(s)
- Sunny Yang Liu
- Department of Pediatrics, The University of Chicago , Chicago, Illinois, USA
| | - Kohta Ikegami
- Department of Pediatrics, The University of Chicago , Chicago, Illinois, USA.,Division of Molecular and Cardiovascular Biology, Cincinnati Children's Hospital Medical Center , Cincinnati, Ohio, USA
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44
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Huang Z, Ba Z, Huang N, Li Y, Luo Y. Aberrant TDP-43 phosphorylation: a key wind gap from TDP-43 to TDP-43 proteinopathy. IBRAIN 2021; 7:119-131. [PMID: 37786905 PMCID: PMC10528777 DOI: 10.1002/j.2769-2795.2021.tb00074.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/14/2021] [Accepted: 03/24/2021] [Indexed: 10/04/2023]
Abstract
TDP-43 proteinopathy is a kind of neurodegenerative diseases related to the TAR DNA-binding protein of 43-kDa molecular weight (TDP-43). The typical neurodegenerative diseases include amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD), Alzheimer's disease (AD), Parkinson's disease (PD) and so on. As the disease process cannot be blocked or slowed down, these patients have poor quality of life and poor prognosis, and bring a huge burden to the family and society. So far, the specific pathogenesis of TDP-43 proteinopathy is not clear, and there is no effective preventive measure and treatment program for this kind of disease. TDP-43 plays an important role in triggering or promoting the occurrence and progression of TDP-43 proteinopathy. The hyperphosphorylation of TDP-43 is undoubtedly an important factor in triggering or promoting the process of TDP-43 proteinopathy. Hyperphosphorylation of TDP-43 can inhibit the degradation of TDP-43, aggravate the aggregation of TDP-43 protein, increase the wrong localization of TDP-43 in cells, and enhance the cytotoxicity of TDP-43. More and more evidences show that the hyperphosphorylation of TDP-43 plays an important role in the pathogenesis of TDP-43 proteinopathy. Inhibition of TDP-43 hyperphosphorylation may be one of the important strategies for the treatment of TDP-43 proteinopathy. Therefore, this article reviews the role of TDP-43 phosphorylation in TDP-43 proteinopathy and the related mechanisms.
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Affiliation(s)
- Zi‐Qi Huang
- Department of NeurologyThird Affiliated Hospital of Zunyi Medical University & First People’s Hospital of ZunyiZunyiGuizhouChina
| | - Zhi‐Sheng Ba
- Drug Clinical Trial Institution, Third Affiliated Hospital of Zunyi Medical University & First People’s Hospital of ZunyiZunyiGuizhouChina
| | - Nan‐Qu Huang
- Drug Clinical Trial Institution, Third Affiliated Hospital of Zunyi Medical University & First People’s Hospital of ZunyiZunyiGuizhouChina
| | - Yuan‐Yuan Li
- Drug Clinical Trial Institution, Third Affiliated Hospital of Zunyi Medical University & First People’s Hospital of ZunyiZunyiGuizhouChina
| | - Yong Luo
- Department of NeurologyThird Affiliated Hospital of Zunyi Medical University & First People’s Hospital of ZunyiZunyiGuizhouChina
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45
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Kitata RB, Choong WK, Tsai CF, Lin PY, Chen BS, Chang YC, Nesvizhskii AI, Sung TY, Chen YJ. A data-independent acquisition-based global phosphoproteomics system enables deep profiling. Nat Commun 2021; 12:2539. [PMID: 33953186 PMCID: PMC8099862 DOI: 10.1038/s41467-021-22759-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/29/2021] [Indexed: 01/07/2023] Open
Abstract
Phosphoproteomics can provide insights into cellular signaling dynamics. To achieve deep and robust quantitative phosphoproteomics profiling for minute amounts of sample, we here develop a global phosphoproteomics strategy based on data-independent acquisition (DIA) mass spectrometry and hybrid spectral libraries derived from data-dependent acquisition (DDA) and DIA data. Benchmarking the method using 166 synthetic phosphopeptides shows high sensitivity (<0.1 ng), accurate site localization and reproducible quantification (~5% median coefficient of variation). As a proof-of-concept, we use lung cancer cell lines and patient-derived tissue to construct a hybrid phosphoproteome spectral library covering 159,524 phosphopeptides (88,107 phosphosites). Based on this library, our single-shot streamlined DIA workflow quantifies 36,350 phosphosites (19,755 class 1) in cell line samples within two hours. Application to drug-resistant cells and patient-derived lung cancer tissues delineates site-specific phosphorylation events associated with resistance and tumor progression, showing that our workflow enables the characterization of phosphorylation signaling with deep coverage, high sensitivity and low between-run missing values.
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Affiliation(s)
| | - Wai-Kok Choong
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Pei-Yi Lin
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Bo-Shiun Chen
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Yun-Chien Chang
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, and Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
| | - Ting-Yi Sung
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan.
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46
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Cesaro T, Hayashi Y, Borghese F, Vertommen D, Wavreil F, Michiels T. PKR activity modulation by phosphomimetic mutations of serine residues located three aminoacids upstream of double-stranded RNA binding motifs. Sci Rep 2021; 11:9188. [PMID: 33911136 PMCID: PMC8080564 DOI: 10.1038/s41598-021-88610-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 04/12/2021] [Indexed: 11/28/2022] Open
Abstract
Eukaryotic translation initiation factor 2 alpha kinase 2 (EIF2AK2), better known as PKR, plays a key role in the response to viral infections and cellular homeostasis by regulating mRNA translation. Upon binding dsRNA, PKR is activated through homodimerization and subsequent autophosphorylation on residues Thr446 and Thr451. In this study, we identified a novel PKR phosphorylation site, Ser6, located 3 amino acids upstream of the first double-stranded RNA binding motif (DRBM1). Another Ser residue occurs in PKR at position 97, the very same position relative to the DRBM2. Ser or Thr residues also occur 3 amino acids upstream DRBMs of other proteins such as ADAR1 or DICER. Phosphoinhibiting mutations (Ser-to-Ala) introduced at Ser6 and Ser97 spontaneously activated PKR. In contrast, phosphomimetic mutations (Ser-to-Asp) inhibited PKR activation following either poly (I:C) transfection or virus infection. These mutations moderately affected dsRNA binding or dimerization, suggesting a model where negative charges occurring at position 6 and 97 tighten the interaction of DRBMs with the kinase domain, thus keeping PKR in an inactive closed conformation even in the presence of dsRNA. This study provides new insights on PKR regulation mechanisms and identifies Ser6 and Ser97 as potential targets to modulate PKR activity for therapeutic purposes.
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Affiliation(s)
- Teresa Cesaro
- de Duve Institute, Université Catholique de Louvain, VIRO B1.74.07, 74, Avenue Hippocrate, 1200, Brussels, Belgium
| | - Yohei Hayashi
- de Duve Institute, Université Catholique de Louvain, VIRO B1.74.07, 74, Avenue Hippocrate, 1200, Brussels, Belgium.,Frontier Sciences Unit, Department of Medical Innovations, Otsuka Pharmaceutical Co., Ltd., Tokushima, Japan
| | - Fabian Borghese
- de Duve Institute, Université Catholique de Louvain, VIRO B1.74.07, 74, Avenue Hippocrate, 1200, Brussels, Belgium
| | - Didier Vertommen
- PHOS Unit and MASSPROT Platform, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Fanny Wavreil
- de Duve Institute, Université Catholique de Louvain, VIRO B1.74.07, 74, Avenue Hippocrate, 1200, Brussels, Belgium
| | - Thomas Michiels
- de Duve Institute, Université Catholique de Louvain, VIRO B1.74.07, 74, Avenue Hippocrate, 1200, Brussels, Belgium.
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47
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Song B, Liu D, Greco TM, Cristea IM. Post-translational modification control of viral DNA sensors and innate immune signaling. Adv Virus Res 2021; 109:163-199. [PMID: 33934827 PMCID: PMC8489191 DOI: 10.1016/bs.aivir.2021.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The vertebrate innate immune system confers host cells with mechanisms to protect against both evolutionarily ancient pathogens and newly emerging pathogenic strains. Innate immunity relies on the host cell's ability to distinguish between self and pathogen-derived molecules. To achieve this, the innate immune system uses germline encoded receptors called pattern recognition receptors (PRRs), which recognize various molecular signatures, including nucleic acids, proteins, lipids, glycans and glycolipids. Among these molecules, the recognition of pathogenic, mislocalized, or damaged DNA by cellular protein receptors, commonly called DNA sensors, represents a major surveillance pathway for initiating immune signaling. The ability of cells to temporally regulate DNA sensor activation and subsequent signal termination is critical for effective immune signaling. These same mechanisms are also co-opted by pathogens to promote their replication. Therefore, there is significant interest in understanding DNA sensor regulatory networks during microbial infections and autoimmune disease. One emerging aspect of DNA sensor regulation is through post-translational modifications (PTMs), including phosphorylation, acetylation, ubiquitination, ADP-ribosylation, SUMOylation, methylation, deamidation, glutamylation. In this chapter, we discuss how PTMs have been shown to positively or negatively impact DNA sensor functions via diverse mechanisms, including direct regulation of enzymatic activity, protein-protein and protein-DNA interactions, protein translocations and protein turnover. In addition, we highlight the ability of virus-induced PTMs to promote immune evasion. We also discuss the recent evidence linking PTMs on DNA sensors with human diseases and more broadly, highlight promising directions for future research on PTM-mediated regulation of DNA sensor-dependent immune signaling.
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Affiliation(s)
- Bokai Song
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Dawei Liu
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States.
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48
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Frankenreiter L, Gahr BM, Schmid H, Zimmermann M, Deichsel S, Hoffmeister P, Turkiewicz A, Borggrefe T, Oswald F, Nagel AC. Phospho-Site Mutations in Transcription Factor Suppressor of Hairless Impact Notch Signaling Activity During Hematopoiesis in Drosophila. Front Cell Dev Biol 2021; 9:658820. [PMID: 33937259 PMCID: PMC8079769 DOI: 10.3389/fcell.2021.658820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/25/2021] [Indexed: 11/13/2022] Open
Abstract
The highly conserved Notch signaling pathway controls a multitude of developmental processes including hematopoiesis. Here, we provide evidence for a novel mechanism of tissue-specific Notch regulation involving phosphorylation of CSL transcription factors within the DNA-binding domain. Earlier we found that a phospho-mimetic mutation of the Drosophila CSL ortholog Suppressor of Hairless [Su(H)] at Ser269 impedes DNA-binding. By genome-engineering, we now introduced phospho-specific Su(H) mutants at the endogenous Su(H) locus, encoding either a phospho-deficient [Su(H) S269A ] or a phospho-mimetic [Su(H) S269D ] isoform. Su(H) S269D mutants were defective of Notch activity in all analyzed tissues, consistent with impaired DNA-binding. In contrast, the phospho-deficient Su(H) S269A mutant did not generally augment Notch activity, but rather specifically in several aspects of blood cell development. Unexpectedly, this process was independent of the corepressor Hairless acting otherwise as a general Notch antagonist in Drosophila. This finding is in agreement with a novel mode of Notch regulation by posttranslational modification of Su(H) in the context of hematopoiesis. Importantly, our studies of the mammalian CSL ortholog (RBPJ/CBF1) emphasize a potential conservation of this regulatory mechanism: phospho-mimetic RBPJ S221D was dysfunctional in both the fly as well as two human cell culture models, whereas phospho-deficient RBPJ S221A rather gained activity during fly hematopoiesis. Thus, dynamic phosphorylation of CSL-proteins within the DNA-binding domain provides a novel means to fine-tune Notch signal transduction in a context-dependent manner.
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Affiliation(s)
- Lisa Frankenreiter
- Department of General Genetics (190g), Institute of Biology (190), University of Hohenheim, Stuttgart, Germany
| | - Bernd M Gahr
- Department of General Genetics (190g), Institute of Biology (190), University of Hohenheim, Stuttgart, Germany
| | - Hannes Schmid
- Department of General Genetics (190g), Institute of Biology (190), University of Hohenheim, Stuttgart, Germany
| | - Mirjam Zimmermann
- Department of General Genetics (190g), Institute of Biology (190), University of Hohenheim, Stuttgart, Germany
| | - Sebastian Deichsel
- Department of General Genetics (190g), Institute of Biology (190), University of Hohenheim, Stuttgart, Germany
| | - Philipp Hoffmeister
- Department of Internal Medicine 1, Center for Internal Medicine, University Medical Center Ulm, Ulm, Germany
| | | | - Tilman Borggrefe
- Institute of Biochemistry, Justus-Liebig University of Giessen, Giessen, Germany
| | - Franz Oswald
- Department of Internal Medicine 1, Center for Internal Medicine, University Medical Center Ulm, Ulm, Germany
| | - Anja C Nagel
- Department of General Genetics (190g), Institute of Biology (190), University of Hohenheim, Stuttgart, Germany
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Protein N-myristoylation: functions and mechanisms in control of innate immunity. Cell Mol Immunol 2021; 18:878-888. [PMID: 33731917 PMCID: PMC7966921 DOI: 10.1038/s41423-021-00663-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/18/2021] [Indexed: 02/08/2023] Open
Abstract
Protein N-myristoylation is an important fatty acylation catalyzed by N-myristoyltransferases (NMTs), which are ubiquitous enzymes in eukaryotes. Specifically, attachment of a myristoyl group is vital for proteins participating in various biological functions, including signal transduction, cellular localization, and oncogenesis. Recent studies have revealed unexpected mechanisms indicating that protein N-myristoylation is involved in host defense against microbial and viral infections. In this review, we describe the current understanding of protein N-myristoylation (mainly focusing on myristoyl switches) and summarize its crucial roles in regulating innate immune responses, including TLR4-dependent inflammatory responses and demyristoylation-induced innate immunosuppression during Shigella flexneri infection. Furthermore, we examine the role of myristoylation in viral assembly, intracellular host interactions, and viral spread during human immunodeficiency virus-1 (HIV-1) infection. Deeper insight into the relationship between protein N-myristoylation and innate immunity might enable us to clarify the pathogenesis of certain infectious diseases and better harness protein N-myristoylation for new therapeutics.
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50
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Reichlmeir M, Elias L, Schulte D. Posttranslational Modifications in Conserved Transcription Factors: A Survey of the TALE-Homeodomain Superclass in Human and Mouse. Front Cell Dev Biol 2021; 9:648765. [PMID: 33768097 PMCID: PMC7985065 DOI: 10.3389/fcell.2021.648765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/09/2021] [Indexed: 11/30/2022] Open
Abstract
Transcription factors (TFs) guide effector proteins like chromatin-modifying or -remodeling enzymes to distinct sites in the genome and thereby fulfill important early steps in translating the genome’s sequence information into the production of proteins or functional RNAs. TFs of the same family are often highly conserved in evolution, raising the question of how proteins with seemingly similar structure and DNA-binding properties can exert physiologically distinct functions or respond to context-specific extracellular cues. A good example is the TALE superclass of homeodomain-containing proteins. All TALE-homeodomain proteins share a characteristic, 63-amino acid long homeodomain and bind to similar sequence motifs. Yet, they frequently fulfill non-redundant functions even in domains of co-expression and are subject to regulation by different signaling pathways. Here we provide an overview of posttranslational modifications that are associated with murine and human TALE-homeodomain proteins and discuss their possible importance for the biology of these TFs.
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Affiliation(s)
- Marina Reichlmeir
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Lena Elias
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Dorothea Schulte
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
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