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Schulte S, Shin B, Rothenberg EV, Pierce NA. Multiplex, Quantitative, High-Resolution Imaging of Protein:Protein Complexes via Hybridization Chain Reaction. ACS Chem Biol 2024; 19:280-288. [PMID: 38232374 PMCID: PMC10877569 DOI: 10.1021/acschembio.3c00431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/18/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Signal amplification based on the mechanism of hybridization chain reaction (HCR) facilitates spatial exploration of gene regulatory networks by enabling multiplex, quantitative, high-resolution imaging of RNA and protein targets. Here, we extend these capabilities to the imaging of protein:protein complexes, using proximity-dependent cooperative probes to conditionally generate a single amplified signal if and only if two target proteins are colocalized within the sample. HCR probes and amplifiers combine to provide automatic background suppression throughout the protocol, ensuring that even if reagents bind nonspecifically in the sample, they will not generate amplified background. We demonstrate protein:protein imaging with a high signal-to-background ratio in human cells, mouse proT cells, and highly autofluorescent formalin-fixed paraffin-embedded (FFPE) human breast tissue sections. Further, we demonstrate multiplex imaging of three different protein:protein complexes simultaneously and validate that HCR enables accurate and precise relative quantitation of protein:protein complexes with subcellular resolution in an anatomical context. Moreover, we establish a unified framework for simultaneous multiplex, quantitative, high-resolution imaging of RNA, protein, and protein:protein targets, with one-step, isothermal, enzyme-free HCR signal amplification performed for all target classes simultaneously.
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Affiliation(s)
- Samuel
J. Schulte
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Boyoung Shin
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Ellen V. Rothenberg
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Niles A. Pierce
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
- Division
of Engineering and Applied Science, California
Institute of Technology, Pasadena, California 91125, United States
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2
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Portela M, Mukherjee S, Paul S, La Marca JE, Parsons LM, Veraksa A, Richardson HE. The Drosophila tumour suppressor Lgl and Vap33 activate the Hippo pathway through a dual mechanism. J Cell Sci 2024; 137:jcs261917. [PMID: 38240353 PMCID: PMC10911279 DOI: 10.1242/jcs.261917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/10/2024] [Indexed: 02/12/2024] Open
Abstract
The tumour suppressor, Lethal (2) giant larvae [Lgl; also known as L(2)gl], is an evolutionarily conserved protein that was discovered in the vinegar fly Drosophila, where its depletion results in tissue overgrowth and loss of cell polarity. Lgl links cell polarity and tissue growth through regulation of the Notch and the Hippo signalling pathways. Lgl regulates the Notch pathway by inhibiting V-ATPase activity via Vap33. How Lgl regulates the Hippo pathway was unclear. In this current study, we show that V-ATPase activity inhibits the Hippo pathway, whereas Vap33 acts to activate Hippo signalling. Vap33 physically and genetically interacts with the actin cytoskeletal regulators RtGEF (Pix) and Git, which also bind to the Hippo protein (Hpo) and are involved in the activation of the Hippo pathway. Additionally, we show that the ADP ribosylation factor Arf79F (Arf1), which is a Hpo interactor, is involved in the inhibition of the Hippo pathway. Altogether, our data suggest that Lgl acts via Vap33 to activate the Hippo pathway by a dual mechanism: (1) through interaction with RtGEF, Git and Arf79F, and (2) through interaction and inhibition of the V-ATPase, thereby controlling epithelial tissue growth.
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Affiliation(s)
- Marta Portela
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, 3002, Australia
| | - Swastik Mukherjee
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Sayantanee Paul
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - John E. La Marca
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
- Blood Cells and Blood Cancer Division, Water and Eliza Hall Institute, Melbourne, Victoria, 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, 3084, Australia
| | - Linda M. Parsons
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, 3002, Australia
| | - Alexey Veraksa
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Helena E. Richardson
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, 3002, Australia
- Sir Peter MacCallum Department of Oncology, Department of Anatomy and Neuroscience, Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
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Pierzynska-Mach A, Czada C, Vogel C, Gwosch E, Osswald X, Bartoschek D, Diaspro A, Kappes F, Ferrando-May E. DEK oncoprotein participates in heterochromatin replication via SUMO-dependent nuclear bodies. J Cell Sci 2023; 136:jcs261329. [PMID: 37997922 PMCID: PMC10753498 DOI: 10.1242/jcs.261329] [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: 05/12/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
The correct inheritance of chromatin structure is key for maintaining genome function and cell identity and preventing cellular transformation. DEK, a conserved non-histone chromatin protein, has recognized tumor-promoting properties, its overexpression being associated with poor prognosis in various cancer types. At the cellular level, DEK displays pleiotropic functions, influencing differentiation, apoptosis and stemness, but a characteristic oncogenic mechanism has remained elusive. Here, we report the identification of DEK bodies, focal assemblies of DEK that regularly occur at specific, yet unidentified, sites of heterochromatin replication exclusively in late S-phase. In these bodies, DEK localizes in direct proximity to active replisomes in agreement with a function in the early maturation of heterochromatin. A high-throughput siRNA screen, supported by mutational and biochemical analyses, identifies SUMO as one regulator of DEK body formation, linking DEK to the complex SUMO protein network that controls chromatin states and cell fate. This work combines and refines our previous data on DEK as a factor essential for heterochromatin integrity and facilitating replication under stress, and delineates an avenue of further study for unraveling the contribution of DEK to cancer development.
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Affiliation(s)
| | - Christina Czada
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Christopher Vogel
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Eva Gwosch
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Xenia Osswald
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Denis Bartoschek
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Alberto Diaspro
- Nanoscopy & NIC@IIT, Istituto Italiano di Tecnologia, Genoa 16152, Italy
- DIFILAB, Department of Physics, University of Genoa, Genoa 16146, Italy
| | - Ferdinand Kappes
- Duke Kunshan University, Division of Natural and Applied Sciences, Kunshan 215316, People's Republic of China
| | - Elisa Ferrando-May
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
- German Cancer Research Center, Heidelberg 69120, Germany
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4
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BHMPS Inhibits Breast Cancer Migration and Invasion by Disrupting Rab27a-Mediated EGFR and Fibronectin Secretion. Cancers (Basel) 2022; 14:cancers14020373. [PMID: 35053535 PMCID: PMC8773646 DOI: 10.3390/cancers14020373] [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: 11/08/2021] [Revised: 12/17/2021] [Accepted: 01/10/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary Numerous studies targeting Rab GTPases and its multiple effectors have been attempted since exocytosis has been shown to alter tumor malignancy by modulating cancer cell behavior and tumor microenvironment. Here, we demonstrated that BHMPS inhibits migration and invasion of breast cancer cells by blocking the interaction between Rab27a and Slp4. BHMPS interfered with vesicle trafficking and secretion by decreasing FAK and JNK activation. In addition, BHMPS suppressed tumor growth in Rab27a-overexpressing MDA-MB-231 xenograft mice. This study highlighted the importance of understanding the mechanisms of Rab27a-mediated metastasis in improving the therapeutic options for metastatic cancers. Abstract Our previous work demonstrated that (E)-N-benzyl-6-(2-(3, 4-dihydroxybenzylidene) hydrazinyl)-N-methylpyridine-3-sulfonamide (BHMPS), a novel synthetic inhibitor of Rab27aSlp(s) interaction, suppresses tumor cell invasion and metastasis. Here, we aimed to further investigate the mechanisms of action and biological significance of BHMPS. BHMPS decreased the expression of epithelial-mesenchymal transition transcription factors through inhibition of focal adhesion kinase and c-Jun N-terminal kinase activation, thereby reducing the migration and invasion of breast cancer. Additionally, knockdown of Rab27a inhibited tumor migration, with changes in related signaling molecules, whereas overexpression of Rab27a reversed this phenomenon. BHMPS effectively prevented the interaction of Rab27a and its effector Slp4, which was verified by co-localization, immunoprecipitation, and in situ proximity ligation assays. BHMPS decreased the secretion of epidermal growth factor receptor and fibronectin by interfering with vesicle trafficking, as indicated by increased perinuclear accumulation of CD63-positive vesicles. Moreover, administration of BHMPS suppressed tumor growth in Rab27a-overexpressing MDA-MB-231 xenograft mice. These findings suggest that BHMPS may be a promising candidate for attenuating tumor migration and invasion by blocking Rab27a-mediated exocytosis.
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Gao YP, Huang KJ, Wang FT, Hou YY, Xu J, Li G. Recent advances in biological detection with rolling circle amplification: design strategy, biosensing mechanism, and practical applications. Analyst 2022; 147:3396-3414. [DOI: 10.1039/d2an00556e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rolling circle amplification (RCA) is a simple and isothermal DNA amplification technique that is used to generate thousands of repeating DNA sequences using circular templates under the catalysis of DNA polymerase.
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Affiliation(s)
- Yong-ping Gao
- International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, School of Physics and Electronics, Henan University, Kaifeng, 475004, PR China
- Analysis and Testing Center, Xinyang College, Xinyang 464000, PR China
| | - Ke-Jing Huang
- Key Laboratory of Guangxi Colleges and Universities for Food Safety and Pharmaceutical Analytical Chemistry, School of Chemistry and Chemical and Engineering, Guangxi Minzu University, Nanning 530008, PR China
| | - Fu-Ting Wang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Yang-Yang Hou
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Jing Xu
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Guoqiang Li
- International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, School of Physics and Electronics, Henan University, Kaifeng, 475004, PR China
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6
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CXCR4-CCR7 Heterodimerization Is a Driver of Breast Cancer Progression. Life (Basel) 2021; 11:life11101049. [PMID: 34685420 PMCID: PMC8538406 DOI: 10.3390/life11101049] [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: 08/24/2021] [Revised: 10/01/2021] [Accepted: 10/02/2021] [Indexed: 01/11/2023] Open
Abstract
Metastatic breast cancer has one of the highest mortality rates among women in western society. Chemokine receptors CXCR4 and CCR7 have been shown to be linked to the metastatic spread of breast cancer, however, their precise function and underlying molecular pathways leading to the acquisition of the pro-metastatic properties remain poorly understood. We demonstrate here that the CXCR4 and CCR7 receptor ligands, CXCL12 and CCL19, cooperatively bind and selectively elicit synergistic signalling responses in invasive breast cancer cell lines as well as primary mammary human tumour cells. Furthermore, for the first time, we have documented the presence of CXCR4-CCR7 heterodimers in advanced primary mammary mouse and human tumours where number of CXCR4-CCR7 complexes directly correlate with the severity of the disease. The functional significance of the CXCR4-CCR7 association was also demonstrated when their forced heterodimerization led to the acquisition of invasive phenotype in non-metastatic breast cancer cells. Taken together, our data establish the CXCR4-CCR7 receptor complex as a new functional unit, which is responsible for the acquisition of breast cancer cell metastatic phenotype and which may serve as a novel biomarker for invasive mammary tumours.
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7
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Miller MR, Koch SR, Choi H, Lamb FS, Stark RJ. Apoptosis signal-regulating kinase 1 (ASK1) inhibition reduces endothelial cytokine production without improving permeability after toll-like receptor 4 (TLR4) challenge. Transl Res 2021; 235:115-128. [PMID: 33857660 PMCID: PMC8328918 DOI: 10.1016/j.trsl.2021.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022]
Abstract
Sepsis represents a life-threatening event often mediated by the host's response to pathogens such as gram-negative organisms, which release the proinflammatory lipopolysaccharide (LPS). Within the endothelium, the mitogen-activated protein kinase (MAPK) pathway is an important driver of endothelial injury during sepsis, of which oxidant-sensitive apoptosis signal-regulating kinase 1 (ASK1) is postulated to be a critical upstream regulator. We hypothesized that ASK1 would play a key role in endothelial inflammation during bacterial challenge. Utilizing RNA sequencing data from patients and cultured human microvascular endothelial cells (HMVECs), ASK1 expression was increased in sepsis and after LPS challenge. Two ASK1 inhibitors, GS444217 and MSC2023964A, reduced cytokine production in HMVECs following LPS stimulation, but had no effect on permeability as measured by transendothelial electrical resistance and intercellular space. MAPKs are known to interact with endothelial nitric oxide synthase (eNOS) and ASK1 expression levels correlated with eNOS expression in patients with septic shock. In addition, eNOS physically interacted with ASK1, though this interaction was not altered by ASK1 inhibition, nor did inhibition alter MAPK p38 activity. Instead, among MAPKs, ASK1 inhibition only impaired LPS-induced JNK phosphorylation. The reduction in JNK activation caused by ASK1 inhibition impaired JNK-mediated cytokine production without affecting permeability. Thus, LPS triggers JNK-dependent cytokine production that requires ASK1 activation, but both its effects on permeability and activation of p38 are ASK1-independent. These data demonstrate how distinct MAPK signaling pathways regulate endothelial inflammatory outputs during acute infectious challenge.
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Affiliation(s)
- Michael R Miller
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Stephen R Koch
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hyehun Choi
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Fred S Lamb
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ryan J Stark
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee.
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8
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Zhang J, Bellani MA, Huang J, James RC, Pokharel D, Gichimu J, Gali H, Stewart G, Seidman MM. Replication of the Mammalian Genome by Replisomes Specific for Euchromatin and Heterochromatin. Front Cell Dev Biol 2021; 9:729265. [PMID: 34532320 PMCID: PMC8438199 DOI: 10.3389/fcell.2021.729265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/10/2021] [Indexed: 11/26/2022] Open
Abstract
Replisomes follow a schedule in which replication of DNA in euchromatin is early in S phase while sequences in heterochromatin replicate late. Impediments to DNA replication, referred to as replication stress, can stall replication forks triggering activation of the ATR kinase and downstream pathways. While there is substantial literature on the local consequences of replisome stalling-double strand breaks, reversed forks, or genomic rearrangements-there is limited understanding of the determinants of replisome stalling vs. continued progression. Although many proteins are recruited to stalled replisomes, current models assume a single species of "stressed" replisome, independent of genomic location. Here we describe our approach to visualizing replication fork encounters with the potent block imposed by a DNA interstrand crosslink (ICL) and our discovery of an unexpected pathway of replication restart (traverse) past an intact ICL. Additionally, we found two biochemically distinct replisomes distinguished by activity in different stages of S phase and chromatin environment. Each contains different proteins that contribute to ICL traverse.
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Affiliation(s)
- Jing Zhang
- Department of Neurosurgery, Institute for Advanced Study, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Marina A. Bellani
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Jing Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, China
| | - Ryan C. James
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Durga Pokharel
- Horizon Discovery Group plc, Lafayette, CO, United States
| | - Julia Gichimu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Himabindu Gali
- Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Grant Stewart
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, United Kingdom
| | - Michael M. Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
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Proximity ligation assay: an ultrasensitive method for protein quantification and its applications in pathogen detection. Appl Microbiol Biotechnol 2021; 105:923-935. [PMID: 33427935 DOI: 10.1007/s00253-020-11049-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/27/2020] [Accepted: 12/09/2020] [Indexed: 01/08/2023]
Abstract
It is of great significance to establish sensitive and accurate pathogen detection methods, considering the continuous emergence or re-emergence of infectious diseases seriously influences the safety of human and animals. Proximity ligation assay (PLA) is developed for the sensitive protein detection and also can be used for the detection of pathogens. PLA employs aptamer or monoclonal/polyclonal antibody-nucleic acid complexes as proximity probes. When the paired proximity probes bind to the same target protein or protein complex, they will be adjacent to each other and form an amplifiable DNA sequence through ligation. Combining the specificity of enzyme-linked immunosorbent assay (ELISA) and sensitivity of polymerase chain reaction (PCR), PLA transforms the detection of protein into the detection of DNA nucleic acid sequence. Therefore, as an ultrasensitive protein assay, PLA has great potential for quantification, localization of protein, and clinical diagnostics. In this review, we summarize the basic principles of PLA and its applications in pathogen detection. KEY POINTS: • Different forms of proximity ligation assay are introduced. • Applications of proximity ligation assay in pathogen detection are summarized. • Proximity ligation assay is an ultrasensitive method to quantify protein and pathogen.
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10
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Karakostis K, Vadivel Gnanasundram S, López I, Thermou A, Wang L, Nylander K, Olivares-Illana V, Fåhraeus R. A single synonymous mutation determines the phosphorylation and stability of the nascent protein. J Mol Cell Biol 2020; 11:187-199. [PMID: 30252118 DOI: 10.1093/jmcb/mjy049] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/29/2018] [Accepted: 06/19/2018] [Indexed: 01/06/2023] Open
Abstract
p53 is an intrinsically disordered protein with a large number of post-translational modifications and interacting partners. The hierarchical order and subcellular location of these events are still poorly understood. The activation of p53 during the DNA damage response (DDR) requires a switch in the activity of the E3 ubiquitin ligase MDM2 from a negative to a positive regulator of p53. This is mediated by the ATM kinase that regulates the binding of MDM2 to the p53 mRNA facilitating an increase in p53 synthesis. Here we show that the binding of MDM2 to the p53 mRNA brings ATM to the p53 polysome where it phosphorylates the nascent p53 at serine 15 and prevents MDM2-mediated degradation of p53. A single synonymous mutation in p53 codon 22 (L22L) prevents the phosphorylation of the nascent p53 protein and the stabilization of p53 following genotoxic stress. The ATM trafficking from the nucleus to the p53 polysome is mediated by MDM2, which requires its interaction with the ribosomal proteins RPL5 and RPL11. These results show how the ATM kinase phosphorylates the p53 protein while it is being synthesized and offer a novel mechanism whereby a single synonymous mutation controls the stability and activity of the encoded protein.
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Affiliation(s)
- Konstantinos Karakostis
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, 27 Rue Juliette Dodu, Paris, France
| | | | - Ignacio López
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, 27 Rue Juliette Dodu, Paris, France
| | - Aikaterini Thermou
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, 27 Rue Juliette Dodu, Paris, France
| | - Lixiao Wang
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Karin Nylander
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | | | - Robin Fåhraeus
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, 27 Rue Juliette Dodu, Paris, France.,Department of Medical Biosciences, Umeå University, Umeå, Sweden.,RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, Brno, Czech Republic
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11
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Direct Interaction of PP2A Phosphatase with GABA B Receptors Alters Functional Signaling. J Neurosci 2020; 40:2808-2816. [PMID: 32111696 PMCID: PMC7117905 DOI: 10.1523/jneurosci.2654-19.2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/02/2020] [Accepted: 02/18/2020] [Indexed: 01/16/2023] Open
Abstract
Addictive drugs usurp the brain's intrinsic mechanism for reward, leading to compulsive and destructive behaviors. In the ventral tegmental area (VTA), the center of the brain's reward circuit, GABAergic neurons control the excitability of dopamine (DA) projection neurons and are the site of initial psychostimulant-dependent changes in signaling. Previous work established that cocaine/methamphetamine exposure increases protein phosphatase 2A (PP2A) activity, which dephosphorylates the GABABR2 subunit, promotes internalization of the GABAB receptor (GABABR) and leads to smaller GABABR-activated G-protein-gated inwardly rectifying potassium (GIRK) currents in VTA GABA neurons. How the actions of PP2A become selective for a particular signaling pathway is poorly understood. Here, we demonstrate that PP2A can associate directly with a short peptide sequence in the C terminal domain of the GABABR1 subunit, and that GABABRs and PP2A are in close proximity in rodent neurons (mouse/rat; mixed sexes). We show that this PP2A-GABABR interaction can be regulated by intracellular Ca2+ Finally, a peptide that potentially reduces recruitment of PP2A to GABABRs and thereby limits receptor dephosphorylation increases the magnitude of baclofen-induced GIRK currents. Thus, limiting PP2A-dependent dephosphorylation of GABABRs may be a useful strategy to increase receptor signaling for treating diseases.SIGNIFICANCE STATEMENT Dysregulation of GABAB receptors (GABABRs) underlies altered neurotransmission in many neurological disorders. Protein phosphatase 2A (PP2A) is involved in dephosphorylating and subsequent internalization of GABABRs in models of addiction and depression. Here, we provide new evidence that PP2A B55 regulatory subunit interacts directly with a small region of the C-terminal domain of the GABABR1 subunit, and that this interaction is sensitive to intracellular Ca2+ We demonstrate that a short peptide corresponding to the PP2A interaction site on GABABR1 competes for PP2A binding, enhances phosphorylation GABABR2 S783, and affects functional signaling through GIRK channels. Our study highlights how targeting PP2A dependent dephosphorylation of GABABRs may provide a specific strategy to modulate GABABR signaling in disease conditions.
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12
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Portela M, Venkataramani V, Fahey-Lozano N, Seco E, Losada-Perez M, Winkler F, Casas-Tintó S. Glioblastoma cells vampirize WNT from neurons and trigger a JNK/MMP signaling loop that enhances glioblastoma progression and neurodegeneration. PLoS Biol 2019; 17:e3000545. [PMID: 31846454 PMCID: PMC6917273 DOI: 10.1371/journal.pbio.3000545] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022] Open
Abstract
Glioblastoma (GB) is the most lethal brain tumor, and Wingless (Wg)-related integration site (WNT) pathway activation in these tumors is associated with a poor prognosis. Clinically, the disease is characterized by progressive neurological deficits. However, whether these symptoms result from direct or indirect damage to neurons is still unresolved. Using Drosophila and primary xenografts as models of human GB, we describe, here, a mechanism that leads to activation of WNT signaling (Wg in Drosophila) in tumor cells. GB cells display a network of tumor microtubes (TMs) that enwrap neurons, accumulate Wg receptor Frizzled1 (Fz1), and, thereby, deplete Wg from neurons, causing neurodegeneration. We have defined this process as “vampirization.” Furthermore, GB cells establish a positive feedback loop to promote their expansion, in which the Wg pathway activates cJun N-terminal kinase (JNK) in GB cells, and, in turn, JNK signaling leads to the post-transcriptional up-regulation and accumulation of matrix metalloproteinases (MMPs), which facilitate TMs’ infiltration throughout the brain, TMs’ network expansion, and further Wg depletion from neurons. Consequently, GB cells proliferate because of the activation of the Wg signaling target, β-catenin, and neurons degenerate because of Wg signaling extinction. Our findings reveal a molecular mechanism for TM production, infiltration, and maintenance that can explain both neuron-dependent tumor progression and also the neural decay associated with GB. Glioblastoma is the most lethal brain tumor and is characterized by progressive neurological deficits. However, whether these symptoms result from direct or indirect damage to neurons is still unresolved. This study shows that glioblastoma cells compete with healthy neurons for survival, depleting the signaling molecule Wg and causing neurodegeneration.
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Affiliation(s)
- Marta Portela
- Instituto Cajal-CSIC, Madrid, Spain
- * E-mail: (SCT); (MP)
| | - Varun Venkataramani
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | | | | | | | - Frank Winkler
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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13
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Atakpa P, Thillaiappan NB, Mataragka S, Prole DL, Taylor CW. IP 3 Receptors Preferentially Associate with ER-Lysosome Contact Sites and Selectively Deliver Ca 2+ to Lysosomes. Cell Rep 2019; 25:3180-3193.e7. [PMID: 30540949 PMCID: PMC6302550 DOI: 10.1016/j.celrep.2018.11.064] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/30/2018] [Accepted: 11/15/2018] [Indexed: 12/22/2022] Open
Abstract
Inositol 1,4,5-trisphosphate (IP3) receptors (IP3Rs) allow extracellular stimuli to redistribute Ca2+ from the ER to cytosol or other organelles. We show, using small interfering RNA (siRNA) and vacuolar H+-ATPase (V-ATPase) inhibitors, that lysosomes sequester Ca2+ released by all IP3R subtypes, but not Ca2+ entering cells through store-operated Ca2+ entry (SOCE). A low-affinity Ca2+ sensor targeted to lysosomal membranes reports large, local increases in cytosolic [Ca2+] during IP3-evoked Ca2+ release, but not during SOCE. Most lysosomes associate with endoplasmic reticulum (ER) and dwell at regions populated by IP3R clusters, but IP3Rs do not assemble ER-lysosome contacts. Increasing lysosomal pH does not immediately prevent Ca2+ uptake, but it causes lysosomes to slowly redistribute and enlarge, reduces their association with IP3Rs, and disrupts Ca2+ exchange with ER. In a "piston-like" fashion, ER concentrates cytosolic Ca2+ and delivers it, through large-conductance IP3Rs, to a low-affinity lysosomal uptake system. The involvement of IP3Rs allows extracellular stimuli to regulate Ca2+ exchange between the ER and lysosomes.
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Affiliation(s)
- Peace Atakpa
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | | | - Stefania Mataragka
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - David L Prole
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Colin W Taylor
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK.
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14
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Karakostis K, Fåhraeus R. Shaping the regulation of the p53 mRNA tumour suppressor: the co-evolution of genetic signatures. BMC Cancer 2019; 19:915. [PMID: 31519161 PMCID: PMC6743176 DOI: 10.1186/s12885-019-6118-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Structured RNA regulatory motifs exist from the prebiotic stages of the RNA world to the more complex eukaryotic systems. In cases where a functional RNA structure is within the coding sequence a selective pressure drives a parallel co-evolution of the RNA structure and the encoded peptide domain. The p53-MDM2 axis, describing the interactions between the p53 tumor suppressor and the MDM2 E3 ubiquitin ligase, serves as particularly useful model revealing how secondary RNA structures have co-evolved along with corresponding interacting protein motifs, thus having an impact on protein - RNA and protein - protein interactions; and how such structures developed signal-dependent regulation in mammalian systems. The p53(BOX-I) RNA sequence binds the C-terminus of MDM2 and controls p53 synthesis while the encoded peptide domain binds MDM2 and controls p53 degradation. The BOX-I peptide domain is also located within p53 transcription activation domain. The folding of the p53 mRNA structure has evolved from temperature-regulated in pre-vertebrates to an ATM kinase signal-dependent pathway in mammalian cells. The protein - protein interaction evolved in vertebrates and became regulated by the same signaling pathway. At the same time the protein - RNA and protein - protein interactions evolved, the p53 trans-activation domain progressed to become integrated into a range of cellular pathways. We discuss how a single synonymous mutation in the BOX-1, the p53(L22 L), observed in a chronic lymphocyte leukaemia patient, prevents the activation of p53 following DNA damage. The concepts analysed and discussed in this review may serve as a conceptual mechanistic paradigm of the co-evolution and function of molecules having roles in cellular regulation, or the aetiology of genetic diseases and how synonymous mutations can affect the encoded protein.
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Affiliation(s)
| | - Robin Fåhraeus
- Université Paris 7, INSERM UMR 1131, 27 Rue Juliette Dodu, 75010 Paris, France
- Department of Medical Biosciences, Umea University, SE-90185 Umea, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
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15
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Chakraborty I, Rahamim G, Avinery R, Roichman Y, Beck R. Nanoparticle Mobility over a Surface as a Probe for Weak Transient Disordered Peptide-Peptide Interactions. NANO LETTERS 2019; 19:6524-6534. [PMID: 31456409 DOI: 10.1021/acs.nanolett.9b02764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Weak interactions form the core basis of a vast number of biological processes, in particular, those involving intrinsically disordered proteins. Here, we establish a new technique capable of probing these weak interactions between synthetic unfolded polypeptides using a convenient yet efficient, quantitative method based on single particle tracking of peptide-coated gold nanoparticles over peptide-coated surfaces. We demonstrate that our technique is sensitive enough to observe the influence of a single amino acid mutation on the transient peptide-peptide interactions. Furthermore, the effects of buffer salinity, which are expected to alter weak electrostatic interactions, are also readily detected and examined in detail. The method presented here has the potential to evaluate, in a high-throughput manner, weak interactions for a wide range of disordered proteins, polypeptides, and other biomolecules.
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Affiliation(s)
| | - Gil Rahamim
- School of Physics and Astronomy , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Ram Avinery
- School of Physics and Astronomy , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Yael Roichman
- School of Chemistry , Tel Aviv University , Tel Aviv 6997801 , Israel
- School of Physics and Astronomy , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Roy Beck
- School of Physics and Astronomy , Tel Aviv University , Tel Aviv 6997801 , Israel
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16
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Amplified fluorescence imaging of HER2 dimerization on cancer cells by using a co-localization triggered DNA nanoassembly. Mikrochim Acta 2019; 186:439. [PMID: 31197538 DOI: 10.1007/s00604-019-3549-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 05/24/2019] [Indexed: 12/18/2022]
Abstract
Convenient and sensitive detection of human epidermal growth factor receptor 2 (HER2) dimerization is highly desirable for molecule subtyping and guiding personalized HER2 targeted therapy of breast cancer. A colocalization-triggered DNA nanoassembly (CtDNA) strategy was developed for amplified imaging of HER2 dimerization. It exploits (a) the advantage of the specificity of aptamer proximity hybridization, and (b) the high sensitivity of hairpin-free nonlinear HCR. The mechanism of step-by-step hairpin-free nonlinear HCR for DNA dendritic nanoassembly was studied by native polyacrylamide gel electrophoresis, atomic force microscopy and fluorometry. The results revealed a high specificity, sensitivity, and excellent controllability of the DNA dendritic nanoassembly. The method was used to identify HER2 homodimers and HER2/HER3 heterodimers in various breast cancer cell lines using fluorescence microscopy. It was then extended to image and quantitatively evaluate HER2 homodimers in clinical formalin-fixed paraffin-embedded breast cancer tissue specimens. This revealed its remarkable accuracy and practicality for clinical diagnostics. Graphical abstract Schematic presentation of amplified imaging of human epidermal growth factor receptor 2 (HER2) dimerization on cancer cell surfaces by using a co-localization triggered DNA nanoassembly (CtDNA).
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17
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Song KH, Jung SY, Park JI, Ahn J, Park JK, Um HD, Park IC, Hwang SG, Ha H, Song JY. Inhibition of Karyopherin-α2 Augments Radiation-Induced Cell Death by Perturbing BRCA1-Mediated DNA Repair. Int J Mol Sci 2019; 20:ijms20112843. [PMID: 31212646 PMCID: PMC6600173 DOI: 10.3390/ijms20112843] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 12/18/2022] Open
Abstract
Ionizing radiation (IR) has been widely used in the treatment of cancer. Radiation-induced DNA damage triggers the DNA damage response (DDR), which can confer radioresistance and early local recurrence by activating DNA repair pathways. Since karyopherin-α2 (KPNA2), playing an important role in nucleocytoplasmic transport, was significantly increased by IR in our previous study, we aimed to determine the function of KPNA2 with regard to DDR. Exposure to radiation upregulated KPNA2 expression in human colorectal cancer HT29 and HCT116 cells and breast carcinoma MDA-MB-231 cells together with the increased expression of DNA repair protein BRCA1. The knockdown of KPNA2 effectively increased apoptotic cell death via inhibition of BRCA1 nuclear import following IR. Therefore, we propose that KPNA2 is a potential target for overcoming radioresistance via interruption to DDR.
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Affiliation(s)
- Kyung-Hee Song
- Division of Radiation Biomedical Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Korea.
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 03760, Korea.
| | - Seung-Youn Jung
- Division of Radiation Biomedical Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Korea.
| | - Jeong-In Park
- Division of Radiation Biomedical Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Korea.
| | - Jiyeon Ahn
- Division of Radiation Biomedical Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Korea.
| | - Jong Kuk Park
- Division of Radiation Biomedical Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Korea.
| | - Hong-Duck Um
- Division of Radiation Biomedical Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Korea.
| | - In-Chul Park
- Division of Radiation Biomedical Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Korea.
| | - Sang-Gu Hwang
- Division of Radiation Biomedical Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Korea.
| | - Hunjoo Ha
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 03760, Korea.
| | - Jie-Young Song
- Division of Radiation Biomedical Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Korea.
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18
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Gauba E, Chen H, Guo L, Du H. Cyclophilin D deficiency attenuates mitochondrial F1Fo ATP synthase dysfunction via OSCP in Alzheimer's disease. Neurobiol Dis 2019; 121:138-147. [PMID: 30266287 PMCID: PMC6250052 DOI: 10.1016/j.nbd.2018.09.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/23/2018] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial dysfunction is pivotal in inducing synaptic injury and neuronal stress in Alzheimer's disease (AD). Mitochondrial F1Fo ATP synthase deregulation is a hallmark mitochondrial defect leading to oxidative phosphorylation (OXPHOS) failure in this neurological disorder. Oligomycin sensitivity conferring protein (OSCP) is a crucial F1Fo ATP synthase subunit. Decreased OSCP levels and OSCP interaction with amyloid β (Aβ) constitute key aspects of F1Fo ATP synthase pathology in AD-related conditions. However, the detailed mechanisms promoting such AD-related OSCP changes have not been fully resolved. Here, we have found increased physical interaction of OSCP with Cyclophilin D (CypD) in AD cases as well as in an AD animal model (5xFAD mice). Genetic depletion of CypD mitigates OSCP loss via ubiquitin-dependent OSCP degradation in 5xFAD mice. Moreover, the ablation of CypD also attenuates OSCP/Aβ interaction in AD mice. The relieved OSCP changes by CypD depletion in 5xFAD mice are along with preserved F1Fo ATP synthase function, restored mitochondrial bioenergetics as well as improved mouse cognition. The simplest interpretation of our results is that CypD is a critical mediator that promotes OSCP deficits in AD-related conditions. Therefore, to block the deleterious impact of CypD on OSCP has the potential to be a promising therapeutic strategy to correct mitochondrial dysfunction for AD therapy.
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Affiliation(s)
- Esha Gauba
- Department of Biological Sciences, The University of Texas at Dallas, United States
| | - Hao Chen
- Department of Biological Sciences, The University of Texas at Dallas, United States
| | - Lan Guo
- Department of Biological Sciences, The University of Texas at Dallas, United States
| | - Heng Du
- Department of Biological Sciences, The University of Texas at Dallas, United States.
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19
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Huebinger J, Spindler J, Holl KJ, Koos B. Quantification of protein mobility and associated reshuffling of cytoplasm during chemical fixation. Sci Rep 2018; 8:17756. [PMID: 30532039 PMCID: PMC6288139 DOI: 10.1038/s41598-018-36112-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/14/2018] [Indexed: 01/21/2023] Open
Abstract
To understand cellular functionalities, it is essential to unravel spatio-temporal patterns of molecular distributions and interactions within living cells. The technological progress in fluorescence microscopy now allows in principle to measure these patterns with sufficient spatial resolution. However, high resolution imaging comes with long acquisition times and high phototoxicity. Therefore, physiological live cell imaging is often unfeasible and chemical fixation is employed. Yet, fixation methods have not been rigorously investigated, in terms of pattern preservation, at the resolution at which cells can now be imaged. A key parameter for this is the time required until fixation is complete. During this time, cells are under unphysiological conditions and patterns decay. We demonstrate here that formaldehyde fixation takes more than one hour for cytosolic proteins in cultured cells. Other small aldehydes, glyoxal and acrolein, did not perform better. Associated with this, we found a distinct displacement of proteins and lipids, including their loss from cells. Fixations using glutaraldehyde were faster than four minutes and retained most cytoplasmic proteins. Surprisingly, autofluorescence produced by glutaraldehyde was almost completely absent with supplementary addition of formaldehyde without compromising fixation speed. These findings indicate, which cellular processes can actually be reliably imaged after a certain chemical fixation.
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Affiliation(s)
- Jan Huebinger
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227, Dortmund, Germany.
| | - Jessica Spindler
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227, Dortmund, Germany
| | - Kristin J Holl
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227, Dortmund, Germany
| | - Björn Koos
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227, Dortmund, Germany
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20
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Schaal CM, Bora-Singhal N, Kumar DM, Chellappan SP. Regulation of Sox2 and stemness by nicotine and electronic-cigarettes in non-small cell lung cancer. Mol Cancer 2018; 17:149. [PMID: 30322398 PMCID: PMC6190543 DOI: 10.1186/s12943-018-0901-2] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/28/2018] [Indexed: 01/03/2023] Open
Abstract
Background Lung cancer is the leading cause of cancer related deaths and its incidence is highly correlated with cigarette smoking. Nicotine, the addictive component of tobacco smoke, cannot initiate tumors, but can promote proliferation, migration, and invasion of cells in vitro and promote tumor growth and metastasis in vivo. This nicotine-mediated tumor promotion is facilitated through the activation of nicotinic acetylcholine receptors (nAChRs), specifically the α7 subunit. More recently, nicotine has been implicated in promoting self-renewal of stem-like side-population cells from lung cancers. This subpopulation of cancer stem-like cells has been implicated in tumor initiation, generation of the heterogeneous tumor population, metastasis, dormancy, and drug resistance. Here we describe the molecular events driving nicotine and e-cigarette extract mediated stimulation of self-renewal of stem-like cells from non-small cell lung cancer. Methods Experiments were conducted using A549 and H1650 non-small cell lung cancer cell lines and human mesenchymal stem cells according to protocols described in this paper. 2 μM nicotine or e-cigarette extracts was used in all relevant experiments. Biochemical analysis using western blotting, transient transfections, RT-PCR and cell biological analysis using double immunofluorescence and confocal microscopy, as well as proximity ligation assays were conducted. Results Here we demonstrate that nicotine can induce the expression of embryonic stem cell factor Sox2, which is indispensable for self-renewal and maintenance of stem cell properties in non-small cell lung adenocarcinoma (NSCLC) cells. We further demonstrate that this occurs through a nAChR-Yap1-E2F1 signaling axis downstream of Src and Yes kinases. Our data suggests Oct4 may also play a role in this process. Over the past few years, electronic cigarettes (e-cigarettes) have been promoted as healthier alternatives to traditional cigarette smoking as they do not contain tobacco; however, they do still contain nicotine. Hence we have investigated whether e-cigarette extracts can enhance tumor promoting properties similar to nicotine; we find that they can induce expression of Sox2 as well as mesenchymal markers and enhance migration and stemness of NSCLC cells. Conclusions Our findings shed light on novel molecular mechanisms underlying the pathophysiology of smoking-related lung cancer in the context of cancer stem cell populations, and reveal new pathways involved that could potentially be exploited therapeutically. Electronic supplementary material The online version of this article (10.1186/s12943-018-0901-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Courtney M Schaal
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA.,The Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
| | - Namrata Bora-Singhal
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA
| | - Durairaj Mohan Kumar
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA
| | - Srikumar P Chellappan
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA.
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21
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TSPYL2 is a novel regulator of SIRT1 and p300 activity in response to DNA damage. Cell Death Differ 2018; 26:918-931. [PMID: 30050056 DOI: 10.1038/s41418-018-0168-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 06/13/2018] [Accepted: 07/04/2018] [Indexed: 02/05/2023] Open
Abstract
Protein acetylation and deacetylation events are finely regulated by lysine-acetyl-transferases and lysine-deacetylases and constitute an important tool for the activation or inhibition of specific cellular pathways. One of the most important lysine-acetyl-transferases is p300, which is involved in the regulation of gene expression, cell growth, DNA repair, differentiation, apoptosis, and tumorigenesis. A well-known target of p300 is constituted by the tumor suppressor protein p53, which plays a critical role in the maintenance of genomic stability and whose activity is known to be controlled by post-translational modifications, among which acetylation. p300 activity toward p53 is negatively regulated by the NAD-dependent deacetylase SIRT1, which deacetylates p53 preventing its transcriptional activation and the induction of p53-dependent apoptosis. However, the mechanisms responsible for p53 regulation by p300 and SIRT1 are still poorly understood. Here we identify the nucleosome assembly protein TSPY-Like 2 (TSPYL2, also known as TSPX, DENTT, and CDA1) as a novel regulator of SIRT1 and p300 function. We demonstrate that, upon DNA damage, TSPYL2 inhibits SIRT1, disrupting its association with target proteins, and promotes p300 acetylation and activation, finally stimulating p53 acetylation and p53-dependent cell death. Indeed, in response to DNA damage, cells silenced for TSPYL2 were found to be defective in p53 activation and apoptosis induction and these events were shown to be dependent on SIRT1 and p300 function. Collectively, our results shed new light on the regulation of p53 acetylation and activation and reveal a novel TSPYL2 function with important implications in cancerogenesis.
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22
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Portela M, Yang L, Paul S, Li X, Veraksa A, Parsons LM, Richardson HE. Lgl reduces endosomal vesicle acidification and Notch signaling by promoting the interaction between Vap33 and the V-ATPase complex. Sci Signal 2018; 11:11/533/eaar1976. [PMID: 29871910 DOI: 10.1126/scisignal.aar1976] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Epithelial cell polarity is linked to the control of tissue growth and tumorigenesis. The tumor suppressor and cell polarity protein lethal-2-giant larvae (Lgl) promotes Hippo signaling and inhibits Notch signaling to restrict tissue growth in Drosophila melanogaster Notch signaling is greater in lgl mutant tissue than in wild-type tissue because of increased acidification of endosomal vesicles, which promotes the proteolytic processing and activation of Notch by γ-secretase. We showed that the increased Notch signaling and tissue growth defects of lgl mutant tissue depended on endosomal vesicle acidification mediated by the vacuolar adenosine triphosphatase (V-ATPase). Lgl promoted the activity of the V-ATPase by interacting with Vap33 (VAMP-associated protein of 33 kDa). Vap33 physically and genetically interacted with Lgl and V-ATPase subunits and repressed V-ATPase-mediated endosomal vesicle acidification and Notch signaling. Vap33 overexpression reduced the abundance of the V-ATPase component Vha44, whereas Lgl knockdown reduced the binding of Vap33 to the V-ATPase component Vha68-3. Our data indicate that Lgl promotes the binding of Vap33 to the V-ATPase, thus inhibiting V-ATPase-mediated endosomal vesicle acidification and thereby reducing γ-secretase activity, Notch signaling, and tissue growth. Our findings implicate the deregulation of Vap33 and V-ATPase activity in polarity-impaired epithelial cancers.
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Affiliation(s)
- Marta Portela
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.,Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3002, Australia.,Department of Molecular, Cellular and Developmental Neurobiology, Cajal Institute, Avenida Doctor Arce, 37, Madrid 28002, Spain
| | - Liu Yang
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA
| | - Sayantanee Paul
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA
| | - Xia Li
- Department of Mathematics and Statistics, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Alexey Veraksa
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA
| | - Linda M Parsons
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3002, Australia.,Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Helena E Richardson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia. .,Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3002, Australia.,Sir Peter MacCallum Department of Oncology, Department of Anatomy and Neuroscience, Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
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23
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Interaction of the Mouse Polyomavirus Capsid Proteins with Importins Is Required for Efficient Import of Viral DNA into the Cell Nucleus. Viruses 2018; 10:v10040165. [PMID: 29614718 PMCID: PMC5923459 DOI: 10.3390/v10040165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/22/2018] [Accepted: 03/30/2018] [Indexed: 12/26/2022] Open
Abstract
The mechanism used by mouse polyomavirus (MPyV) to overcome the crowded cytosol to reach the nucleus has not been fully elucidated. Here, we investigated the involvement of importin α/β1 mediated transport in the delivery of MPyV genomes into the nucleus. Interactions of the virus with importin β1 were studied by co-immunoprecipitation and proximity ligation assay. For infectivity and nucleus delivery assays, the virus and its capsid proteins mutated in the nuclear localization signals (NLSs) were prepared and produced. We found that at early times post infection, virions bound importin β1 in a time dependent manner with a peak of interactions at 6 h post infection. Mutation analysis revealed that only when the NLSs of both VP1 and VP2/3 were disrupted, virus did not bind efficiently to importin β1 and its infectivity remarkably decreased (by 80%). Nuclear targeting of capsid proteins was improved when VP1 and VP2 were co-expressed. VP1 and VP2 were effectively delivered into the nucleus, even when one of the NLS, either VP1 or VP2, was disrupted. Altogether, our results showed that MPyV virions can use VP1 and/or VP2/VP3 NLSs in concert or individually to bind importins to deliver their genomes into the cell nucleus.
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24
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Klaesson A, Grannas K, Ebai T, Heldin J, Koos B, Leino M, Raykova D, Oelrich J, Arngården L, Söderberg O, Landegren U. Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes. Sci Rep 2018; 8:5400. [PMID: 29599435 PMCID: PMC5876389 DOI: 10.1038/s41598-018-23582-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 03/14/2018] [Indexed: 12/26/2022] Open
Abstract
We have redesigned probes for in situ proximity ligation assay (PLA), resulting in more efficient localized detection of target proteins. In situ PLA depends on recognition of target proteins by pairs of antibody-oligonucleotide conjugates (PLA probes), which jointly give rise to DNA circles that template localized rolling circle amplification reactions. The requirement for dual recognition of the target proteins improves selectivity by ignoring any cross-reactivity not shared by the antibodies, and it allows detection of protein-protein interactions and post-translational modifications. We herein describe an improved design of the PLA probes –UnFold probes – where all elements required for formation of circular DNA strands are incorporated in the probes. Premature interactions between the UnFold probes are prevented by including an enzymatic “unfolding” step in the detection reactions. This allows DNA circles to form by pairs of reagents only after excess reagents have been removed. We demonstrate the performance of UnFold probes for detection of protein-protein interactions and post-translational modifications in fixed cells and tissues, revealing considerably more efficient signal generation. We also apply the UnFold probes to detect IL-6 in solution phase after capture on solid supports, demonstrating increased sensitivity over both normal sandwich enzyme-linked immunosorbent assays and conventional PLA assays.
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Affiliation(s)
- Axel Klaesson
- Department of Pharmaceutical Biosciences, Pharmaceutical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Karin Grannas
- Department of Pharmaceutical Biosciences, Pharmaceutical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Tonge Ebai
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Heldin
- Department of Pharmaceutical Biosciences, Pharmaceutical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Björn Koos
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Mattias Leino
- Department of Pharmaceutical Biosciences, Pharmaceutical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Doroteya Raykova
- Department of Pharmaceutical Biosciences, Pharmaceutical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Johan Oelrich
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Linda Arngården
- Department of Pharmaceutical Biosciences, Pharmaceutical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Pharmaceutical Cell Biology, Uppsala University, Uppsala, Sweden.
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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25
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Koos B, Christmann J, Plettenberg S, Käding D, Becker J, Keteku M, Klein C, Imtiaz S, Janning P, Bastiaens PIH, Wehner F. Hypertonicity-induced cation channels in HepG2 cells: architecture and role in proliferation vs. apoptosis. J Physiol 2018; 596:1227-1241. [PMID: 29369356 DOI: 10.1113/jp275827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 01/18/2018] [Indexed: 12/25/2022] Open
Abstract
KEY POINTS Na+ conducting hypertonicity-induced cation channels (HICCs) are key players in the volume restoration of osmotically shrunken cells and, under isotonic conditions, considered as mediators of proliferation - thereby opposing apoptosis. In an siRNA screen of ion channels and transporters in HepG2 cells, with the regulatory volume increase (RVI) as read-out, δENaC, TRPM2 and TRPM5 were identified as HICCs. Subsequently, all permutations of these channels were tested in RVI and patch-clamp recordings and, at first sight, HICCs were found to operate in an independent mode. However, there was synergy in the siRNA perturbations of HICC currents. Accordingly, proximity ligation assays showed that δENaC was located in proximity to TRPM2 and TRPM5 suggesting a physical interaction. Furthermore, δENaC, TRPM2 and TRPM5 were identified as mediators of HepG2 proliferation - their silencing enhanced apoptosis. Our study defines the architecture of HICCs in human hepatocytes as well as their molecular functions. ABSTRACT Hypertonicity-induced cation channels (HICCs) are a substantial element in the regulatory volume increase (RVI) of osmotically shrunken cells. Under isotonic conditions, they are key effectors in the volume gain preceding proliferation; HICC repression, in turn, significantly increases apoptosis rates. Despite these fundamental roles of HICCs in cell physiology, very little is known concerning the actual molecular architecture of these channels. Here, an siRNA screening of putative ion channels and transporters was performed, in HepG2 cells, with the velocity of RVI as the read-out; in this first run, δENaC, TRPM2 and TRPM5 could be identified as HICCs. In the second run, all permutations of these channels were tested in RVI and patch-clamp recordings, with special emphasis on the non-additivity and additivity of siRNAs - which would indicate molecular interactions or independent ways of channel functioning. At first sight, the HICCs in HepG2 cells appeared to operate rather independently. However, a proximity ligation assay revealed that δENaC was located in proximity to both TRPM2 and TRPM5. Furthermore, a clear synergy of HICC current knock-downs (KDs) was observed. δENaC, TRPM2 and TRPM5 were defined as mediators of HepG2 cell proliferation and their silencing increased the rates of apoptosis. This study provides a molecular characterization of the HICCs in human hepatocytes and of their role in RVI, cell proliferation and apoptosis.
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Affiliation(s)
- Björn Koos
- Max Planck Institute of Molecular Physiology, Department of Systemic Cell Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Jens Christmann
- Max Planck Institute of Molecular Physiology, Department of Systemic Cell Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Sandra Plettenberg
- Max Planck Institute of Molecular Physiology, Department of Systemic Cell Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Domenic Käding
- Max Planck Institute of Molecular Physiology, Department of Systemic Cell Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Julia Becker
- Max Planck Institute of Molecular Physiology, Department of Systemic Cell Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Melody Keteku
- Max Planck Institute of Molecular Physiology, Department of Systemic Cell Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Christian Klein
- Max Planck Institute of Molecular Physiology, Department of Systemic Cell Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Sarah Imtiaz
- Max Planck Institute of Molecular Physiology, Department of Systemic Cell Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Petra Janning
- Max Planck Institute of Molecular Physiology, Department of Systemic Cell Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Philippe I H Bastiaens
- Max Planck Institute of Molecular Physiology, Department of Systemic Cell Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Frank Wehner
- Max Planck Institute of Molecular Physiology, Department of Systemic Cell Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
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Mohtar MA, Hernychova L, O'Neill JR, Lawrence ML, Murray E, Vojtesek B, Hupp TR. The Sequence-specific Peptide-binding Activity of the Protein Sulfide Isomerase AGR2 Directs Its Stable Binding to the Oncogenic Receptor EpCAM. Mol Cell Proteomics 2018; 17:737-763. [PMID: 29339412 PMCID: PMC5880107 DOI: 10.1074/mcp.ra118.000573] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 12/30/2022] Open
Abstract
AGR2 is an oncogenic endoplasmic reticulum (ER)-resident protein disulfide isomerase. AGR2 protein has a relatively unique property for a chaperone in that it can bind sequence-specifically to a specific peptide motif (TTIYY). A synthetic TTIYY-containing peptide column was used to affinity-purify AGR2 from crude lysates highlighting peptide selectivity in complex mixtures. Hydrogen-deuterium exchange mass spectrometry localized the dominant region in AGR2 that interacts with the TTIYY peptide to within a structural loop from amino acids 131–135 (VDPSL). A peptide binding site consensus of Tx[IL][YF][YF] was developed for AGR2 by measuring its activity against a mutant peptide library. Screening the human proteome for proteins harboring this motif revealed an enrichment in transmembrane proteins and we focused on validating EpCAM as a potential AGR2-interacting protein. AGR2 and EpCAM proteins formed a dose-dependent protein-protein interaction in vitro. Proximity ligation assays demonstrated that endogenous AGR2 and EpCAM protein associate in cells. Introducing a single alanine mutation in EpCAM at Tyr251 attenuated its binding to AGR2 in vitro and in cells. Hydrogen-deuterium exchange mass spectrometry was used to identify a stable binding site for AGR2 on EpCAM, adjacent to the TLIYY motif and surrounding EpCAM's detergent binding site. These data define a dominant site on AGR2 that mediates its specific peptide-binding function. EpCAM forms a model client protein for AGR2 to study how an ER-resident chaperone can dock specifically to a peptide motif and regulate the trafficking a protein destined for the secretory pathway.
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Affiliation(s)
- M Aiman Mohtar
- From the ‡University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland, United Kingdom, EH4 2XR.,§National University of Malaysia, UKM Medical Molecular Biology Institute (UMBI), 56000 Kuala Lumpur, Malaysia
| | - Lenka Hernychova
- ¶Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - J Robert O'Neill
- From the ‡University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland, United Kingdom, EH4 2XR
| | - Melanie L Lawrence
- From the ‡University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland, United Kingdom, EH4 2XR
| | - Euan Murray
- From the ‡University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland, United Kingdom, EH4 2XR.,¶Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Borek Vojtesek
- ¶Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Ted R Hupp
- From the ‡University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland, United Kingdom, EH4 2XR; .,¶Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic.,‖University of Gdansk, International Centre for Cancer Vaccine Science, ul. Wita Stwosza 63, 80-308 Gdansk, Poland
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27
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Chien T, Weng YT, Chang SY, Lai HL, Chiu FL, Kuo HC, Chuang DM, Chern Y. GSK3β negatively regulates TRAX, a scaffold protein implicated in mental disorders, for NHEJ-mediated DNA repair in neurons. Mol Psychiatry 2018; 23:2375-2390. [PMID: 29298990 PMCID: PMC6294740 DOI: 10.1038/s41380-017-0007-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/28/2017] [Accepted: 10/30/2017] [Indexed: 12/27/2022]
Abstract
Translin-associated protein X (TRAX) is a scaffold protein with various functions and has been associated with mental illnesses, including schizophrenia. We have previously demonstrated that TRAX interacts with a Gsα protein-coupled receptor, the A2A adenosine receptor (A2AR), and mediates the function of this receptor in neuritogenesis. In addition, stimulation of the A2AR markedly ameliorates DNA damage evoked by elevated oxidative stress in neurons derived from induced pluripotent stem cells (iPSCs). Here, we report that glycogen synthase kinase 3 beta (GSK3β) and disrupted-in-schizophrenia 1 (DISC1) are two novel interacting proteins of TRAX. We present evidence to suggest that the stimulation of A2AR markedly facilitated DNA repair through the TRAX/DISC1/GSK3β complex in a rat neuronal cell line (PC12), primary mouse neurons, and human medium spiny neurons derived from iPSCs. A2AR stimulation led to the inhibition of GSK3β, thus dissociating the TRAX/DISC1/GSK3β complex and facilitating the non-homologous end-joining pathway (NHEJ) by enhancing the activation of a DNA-dependent protein kinase via phosphorylation at Thr2609. Similarly, pharmacological inhibition of GSK3β by SB216763 also facilitated the TRAX-mediated repair of oxidative DNA damage. Collectively, GSK3β binds with TRAX and negatively affects its ability to facilitate NHEJ repair. The suppression of GSK3β by A2AR activation or a GSK3β inhibitor releases TRAX for the repair of oxidative DNA damage. Our findings shed new light on the molecular mechanisms underlying diseases associated with DNA damage and provides a novel target (i.e., the TRAX/DISC1/GSK3β complex) for future therapeutic development for mental disorders.
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Affiliation(s)
- Ting Chien
- 0000 0004 0634 0356grid.260565.2Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan ,0000 0004 0633 7958grid.482251.8Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yu-Ting Weng
- 0000 0004 0633 7958grid.482251.8Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan ,0000 0001 2287 1366grid.28665.3fProgram in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan
| | - Shu-Yung Chang
- 0000 0004 0633 7958grid.482251.8Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan ,0000 0001 0425 5914grid.260770.4Institute of Neuroscience, National Yang-Ming University, Taipei, Taiwan
| | - Hsing-Lin Lai
- 0000 0004 0633 7958grid.482251.8Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Feng-Lan Chiu
- 0000 0001 2287 1366grid.28665.3fInstitute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Hung-Chih Kuo
- 0000 0001 2287 1366grid.28665.3fInstitute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - De-Maw Chuang
- 0000 0004 0464 0574grid.416868.5Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD USA
| | - Yijuang Chern
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan. .,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan. .,Institute of Neuroscience, National Yang-Ming University, Taipei, Taiwan. .,Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan.
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28
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Meese S, Cepeda AP, Gahlen F, Adams CM, Ficner R, Ricci AJ, Heller S, Reisinger E, Herget M. Activity-Dependent Phosphorylation by CaMKIIδ Alters the Ca 2+ Affinity of the Multi-C 2-Domain Protein Otoferlin. Front Synaptic Neurosci 2017; 9:13. [PMID: 29046633 PMCID: PMC5632675 DOI: 10.3389/fnsyn.2017.00013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/11/2017] [Indexed: 01/20/2023] Open
Abstract
Otoferlin is essential for fast Ca2+-triggered transmitter release from auditory inner hair cells (IHCs), playing key roles in synaptic vesicle release, replenishment and retrieval. Dysfunction of otoferlin results in profound prelingual deafness. Despite its crucial role in cochlear synaptic processes, mechanisms regulating otoferlin activity have not been studied to date. Here, we identified Ca2+/calmodulin-dependent serine/threonine kinase II delta (CaMKIIδ) as an otoferlin binding partner by pull-downs from chicken utricles and reassured interaction by a co-immunoprecipitation with heterologously expressed proteins in HEK cells. We confirmed the expression of CaMKIIδ in rodent IHCs by immunohistochemistry and real-time PCR. A proximity ligation assay indicates close proximity of the two proteins in rat IHCs, suggesting that otoferlin and CaMKIIδ also interact in mammalian IHCs. In vitro phosphorylation of otoferlin by CaMKIIδ revealed ten phosphorylation sites, five of which are located within C2-domains. Exchange of serines/threonines at phosphorylated sites into phosphomimetic aspartates reduces the Ca2+ affinity of the recombinant C2F domain 10-fold, and increases the Ca2+ affinity of the C2C domain. Concordantly, we show that phosphorylation of otoferlin and/or its interaction partners are enhanced upon hair cell depolarization and blocked by pharmacological CaMKII inhibition. We therefore propose that otoferlin activity is regulated by CaMKIIδ in IHCs.
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Affiliation(s)
- Sandra Meese
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, and Collaborative Research Center 889, University of Göttingen, Göttingen, Germany.,Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, Göttingen, Germany
| | - Andreia P Cepeda
- Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, Göttingen, Germany.,Molecular Biology of Cochlear Neurotransmission Group, Department of Otorhinolaryngology, University Medical Center Göttingen, and Collaborative Research Center 889, University of Göttingen, Göttingen, Germany
| | - Felix Gahlen
- Department of Otorhinolaryngology, Head and Neck Surgery, Ruhr-University Bochum, Bochum, Germany
| | - Christopher M Adams
- Stanford University Mass Spectrometry, Stanford University, Stanford, CA, United States
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, and Collaborative Research Center 889, University of Göttingen, Göttingen, Germany
| | - Anthony J Ricci
- Department of Otolaryngology, Head and Neck Surgery, Stanford School of Medicine, Stanford, CA, United States
| | - Stefan Heller
- Department of Otolaryngology, Head and Neck Surgery, Stanford School of Medicine, Stanford, CA, United States
| | - Ellen Reisinger
- Molecular Biology of Cochlear Neurotransmission Group, Department of Otorhinolaryngology, University Medical Center Göttingen, and Collaborative Research Center 889, University of Göttingen, Göttingen, Germany
| | - Meike Herget
- Department of Otolaryngology, Head and Neck Surgery, Stanford School of Medicine, Stanford, CA, United States
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29
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Way L, Faktor J, Dvorakova P, Nicholson J, Vojtesek B, Graham D, Ball KL, Hupp T. Rearrangement of mitochondrial pyruvate dehydrogenase subunit dihydrolipoamide dehydrogenase protein-protein interactions by the MDM2 ligand nutlin-3. Proteomics 2017; 16:2327-44. [PMID: 27273042 PMCID: PMC5026170 DOI: 10.1002/pmic.201500501] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 04/27/2016] [Accepted: 06/03/2016] [Indexed: 12/22/2022]
Abstract
Drugs targeting MDM2's hydrophobic pocket activate p53. However, these agents act allosterically and have agonist effects on MDM2's protein interaction landscape. Dominant p53‐independent MDM2‐drug responsive‐binding proteins have not been stratified. We used as a variable the differential expression of MDM2 protein as a function of cell density to identify Nutlin‐3 responsive MDM2‐binding proteins that are perturbed independent of cell density using SWATH‐MS. Dihydrolipoamide dehydrogenase, the E3 subunit of the mitochondrial pyruvate dehydrogenase complex, was one of two Nutlin‐3 perturbed proteins identified fours hour posttreatment at two cell densities. Immunoblotting confirmed that dihydrolipoamide dehydrogenase was induced by Nutlin‐3. Depletion of MDM2 using siRNA also elevated dihydrolipoamide dehydrogenase in Nutlin‐3 treated cells. Mitotracker confirmed that Nutlin‐3 inhibits mitochondrial activity. Enrichment of mitochondria using TOM22+ immunobeads and TMT labeling defined key changes in the mitochondrial proteome after Nutlin‐3 treatment. Proximity ligation identified rearrangements of cellular protein–protein complexes in situ. In response to Nutlin‐3, a reduction of dihydrolipoamide dehydrogenase/dihydrolipoamide acetyltransferase protein complexes highlighted a disruption of the pyruvate dehydrogenase complex. This coincides with an increase in MDM2/dihydrolipoamide dehydrogenase complexes in the nucleus that was further enhanced by the nuclear export inhibitor Leptomycin B. The data suggest one therapeutic impact of MDM2 drugs might be on the early perturbation of specific protein–protein interactions within the mitochondria. This methodology forms a blueprint for biomarker discovery that can identify rearrangements of MDM2 protein–protein complexes in drug‐treated cells.
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Affiliation(s)
- Luke Way
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Jakub Faktor
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Petra Dvorakova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Judith Nicholson
- CRUK & MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Borek Vojtesek
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Duncan Graham
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Kathryn L Ball
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK.,Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ted Hupp
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK. .,Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic.
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30
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Spatial cycles mediated by UNC119 solubilisation maintain Src family kinases plasma membrane localisation. Nat Commun 2017; 8:114. [PMID: 28740133 PMCID: PMC5524651 DOI: 10.1038/s41467-017-00116-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 06/02/2017] [Indexed: 12/12/2022] Open
Abstract
The peripheral membrane proto-oncogene Src family protein tyrosine kinases relay growth factor signals to the cytoplasm of mammalian cells. We unravel the spatial cycles of solubilisation, trapping on perinuclear membrane compartments and vesicular transport that counter entropic equilibration to endomembranes for maintaining the enrichment and activity of Src family protein tyrosine kinases at the plasma membrane. The solubilising factor UNC119 sequesters myristoylated Src family protein tyrosine kinases from the cytoplasm, enhancing their diffusion to effectively release Src family protein tyrosine kinases on the recycling endosome by localised Arl2/3 activity. Src is then trapped on the recycling endosome via electrostatic interactions, whereas Fyn is quickly released to be kinetically trapped on the Golgi by palmitoyl acyl-transferase activity. Vesicular trafficking from these compartments restores enrichment of the Src family protein tyrosine kinases to the plasma membrane. Interference with these spatial cycles by UNC119 knockdown disrupts Src family protein tyrosine kinase localisation and signalling activity, indicating that UNC119 could be a drug target to affect oncogenic Src family protein tyrosine kinase signalling. The peripheral membrane proto-oncogene Src family protein tyrosine kinases (SFKs) transmit growth factor signals to the cytoplasm. Here the authors show that the solubilising factor UNC119 sequesters myristoylated SFKs to maintain its enrichment at the plasma membrane to enable signal transduction.
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31
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Kirschman JL, Bhosle S, Vanover D, Blanchard EL, Loomis KH, Zurla C, Murray K, Lam BC, Santangelo PJ. Characterizing exogenous mRNA delivery, trafficking, cytoplasmic release and RNA-protein correlations at the level of single cells. Nucleic Acids Res 2017; 45:e113. [PMID: 28449134 PMCID: PMC5499550 DOI: 10.1093/nar/gkx290] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/06/2017] [Accepted: 04/11/2017] [Indexed: 12/25/2022] Open
Abstract
The use of synthetic messenger ribonucleic acid (mRNA) to express specific proteins is a highly promising therapeutic and vaccine approach that avoids many safety issues associated with viral or DNA-based systems. However, in order to optimize mRNA designs and delivery, technology advancements are required to study fundamental mechanisms of mRNA uptake and localization at the single-cell and tissue level. Here, we present a single RNA sensitive fluorescent labeling method which allows us to label and visualize synthetic mRNA without significantly affecting function. This approach enabled single cell characterization of mRNA uptake and release kinetics from endocytic compartments, the measurement of mRNA/protein correlations, and motivated the investigation of mRNA induced cellular stress, all important mechanisms influencing protein production. In addition, we demonstrated this approach can facilitate near-infrared imaging of mRNA localization in vivo and in ex-vivo tissue sections, which will facilitate mRNA trafficking studies in pre-clinical models. Overall, we demonstrate the ability to study fundamental mechanisms necessary to optimize delivery and therapeutic strategies, in order to design the next generation of novel mRNA therapeutics and vaccines.
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Affiliation(s)
- Jonathan L. Kirschman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Sushma Bhosle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Daryll Vanover
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Emmeline L. Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Kristin H. Loomis
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Chiara Zurla
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Kathryn Murray
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Blaine C. Lam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Philip J. Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, UA Whitaker Building, 313 Ferst Drive, Atlanta, GA 30332, USA
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32
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Finn CE, Chong A, Cooper KG, Starr T, Steele-Mortimer O. A second wave of Salmonella T3SS1 activity prolongs the lifespan of infected epithelial cells. PLoS Pathog 2017; 13:e1006354. [PMID: 28426838 PMCID: PMC5413073 DOI: 10.1371/journal.ppat.1006354] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 05/02/2017] [Accepted: 04/14/2017] [Indexed: 11/19/2022] Open
Abstract
Type III secretion system 1 (T3SS1) is used by the enteropathogen Salmonella enterica serovar Typhimurium to establish infection in the gut. Effector proteins translocated by this system across the plasma membrane facilitate invasion of intestinal epithelial cells. One such effector, the inositol phosphatase SopB, contributes to invasion and mediates activation of the pro-survival kinase Akt. Following internalization, some bacteria escape from the Salmonella-containing vacuole into the cytosol and there is evidence suggesting that T3SS1 is expressed in this subpopulation. Here, we investigated the post-invasion role of T3SS1, using SopB as a model effector. In cultured epithelial cells, SopB-dependent Akt phosphorylation was observed at two distinct stages of infection: during and immediately after invasion, and later during peak cytosolic replication. Single cell analysis revealed that cytosolic Salmonella deliver SopB via T3SS1. Although intracellular replication was unaffected in a SopB deletion mutant, cells infected with ΔsopB demonstrated a lack of Akt phosphorylation, earlier time to death, and increased lysis. When SopB expression was induced specifically in cytosolic Salmonella, these effects were restored to levels observed in WT infected cells, indicating that the second wave of SopB protects this infected population against cell death via Akt activation. Thus, T3SS1 has two, temporally distinct roles during epithelial cell colonization. Additionally, we found that delivery of SopB by cytosolic bacteria was translocon-independent, in contrast to canonical effector translocation across eukaryotic membranes, which requires formation of a translocon pore. This mechanism was also observed for another T3SS1 effector, SipA. These findings reveal the functional and mechanistic adaptability of a T3SS that can be harnessed in different microenvironments.
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Affiliation(s)
- Ciaran E. Finn
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Audrey Chong
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Kendal G. Cooper
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Tregei Starr
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Olivia Steele-Mortimer
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail:
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A Cytoplasmic RNA Virus Alters the Function of the Cell Splicing Protein SRSF2. J Virol 2017; 91:JVI.02488-16. [PMID: 28077658 DOI: 10.1128/jvi.02488-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 01/05/2017] [Indexed: 11/20/2022] Open
Abstract
To replicate efficiently, viruses must create favorable cell conditions and overcome cell antiviral responses. We previously reported that the reovirus protein μ2 from strain T1L, but not strain T3D, represses one antiviral response: alpha/beta interferon signaling. We report here that T1L, but not T3D, μ2 localizes to nuclear speckles, where it forms a complex with the mRNA splicing factor SRSF2 and alters its subnuclear localization. Reovirus replicates in cytoplasmic viral factories, and there is no evidence that reovirus genomic or messenger RNAs are spliced, suggesting that T1L μ2 might target splicing of cell RNAs. Indeed, RNA sequencing revealed that reovirus T1L, but not T3D, infection alters the splicing of transcripts for host genes involved in mRNA posttranscriptional modifications. Moreover, depletion of SRSF2 enhanced reovirus replication and cytopathic effect, suggesting that T1L μ2 modulation of splicing benefits the virus. This provides the first report of viral antagonism of the splicing factor SRSF2 and identifies the viral protein that determines strain-specific differences in cell RNA splicing.IMPORTANCE Efficient viral replication requires that the virus create favorable cell conditions. Many viruses accomplish this by repressing specific antiviral responses. We demonstrate here that some mammalian reoviruses, RNA viruses that replicate strictly in the cytoplasm, express a protein variant that localizes to nuclear speckles, where it targets a cell mRNA splicing factor. Infection with a reovirus strain that targets this splicing factor alters splicing of cell mRNAs involved in the maturation of many other cell mRNAs. Depletion of this cell splicing factor enhances reovirus replication and cytopathic effect. Our results provide the first evidence of viral antagonism of this splicing factor and suggest that downstream consequences to the cell are global and benefit the virus.
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Abstract
The invention of the microscope has been fundamental for the understanding of tissue architecture and subcellular structures. With the advancement of higher magnification microscopes came the development of various molecular biology tools such as Förster resonance energy transfer (FRET) and in situ proximity ligation assay (in situ PLA) to monitor protein interactions. Microscopy has become a commonly used method for the investigation of molecular events within the cell, for the identification of key players in signaling networks, and the activation of these pathways. Multiple approaches are available for functional analyses in single cells. They provide information not only on the localization of proteins at a given time point, but also on their expression levels and activity states, allowing us to pinpoint hallmarks of different cellular identities within tissues in health and disease. Clever solutions to increase the sensitivity of molecular tools, the possibilities for multiplexing, as well as image resolution have recently been introduced; however, these methods have their pros and cons. Therefore, one needs to carefully consider the biological question of interest along with the nature of the sample before choosing the most suitable method or combination of methods. Herein, we review a few of the most exciting microscopy-based molecular techniques for proteomic analysis and cover the benefits as well as the disadvantages of their use.
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Gabriel CH, Gross F, Karl M, Stephanowitz H, Hennig AF, Weber M, Gryzik S, Bachmann I, Hecklau K, Wienands J, Schuchhardt J, Herzel H, Radbruch A, Krause E, Baumgrass R. Identification of Novel Nuclear Factor of Activated T Cell (NFAT)-associated Proteins in T Cells. J Biol Chem 2016; 291:24172-24187. [PMID: 27637333 DOI: 10.1074/jbc.m116.739326] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 09/13/2016] [Indexed: 12/12/2022] Open
Abstract
Transcription factors of the nuclear factor of activated T cell (NFAT) family are essential for antigen-specific T cell activation and differentiation. Their cooperative DNA binding with other transcription factors, such as AP1 proteins (FOS, JUN, and JUNB), FOXP3, IRFs, and EGR1, dictates the gene regulatory action of NFATs. To identify as yet unknown interaction partners of NFAT, we purified biotin-tagged NFATc1/αA, NFATc1/βC, and NFATc2/C protein complexes and analyzed their components by stable isotope labeling by amino acids in cell culture-based mass spectrometry. We revealed more than 170 NFAT-associated proteins, half of which are involved in transcriptional regulation. Among them are many hitherto unknown interaction partners of NFATc1 and NFATc2 in T cells, such as Raptor, CHEK1, CREB1, RUNX1, SATB1, Ikaros, and Helios. The association of NFATc2 with several other transcription factors is DNA-dependent, indicating cooperative DNA binding. Moreover, our computational analysis discovered that binding motifs for RUNX and CREB1 are found preferentially in the direct vicinity of NFAT-binding motifs and in a distinct orientation to them. Furthermore, we provide evidence that mTOR and CHEK1 kinase activity influence NFAT's transcriptional potency. Finally, our dataset of NFAT-associated proteins provides a good basis to further study NFAT's diverse functions and how these are modulated due to the interplay of multiple interaction partners.
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Affiliation(s)
- Christian H Gabriel
- From the German Rheumatism Research Center (DRFZ), Leibniz Institute, 10117 Berlin
| | - Fridolin Gross
- the Institute for Theoretical Biology, Charité and Humboldt University Berlin, 10015 Berlin
| | - Martin Karl
- From the German Rheumatism Research Center (DRFZ), Leibniz Institute, 10117 Berlin
| | | | - Anna Floriane Hennig
- From the German Rheumatism Research Center (DRFZ), Leibniz Institute, 10117 Berlin
| | - Melanie Weber
- From the German Rheumatism Research Center (DRFZ), Leibniz Institute, 10117 Berlin
| | - Stefanie Gryzik
- From the German Rheumatism Research Center (DRFZ), Leibniz Institute, 10117 Berlin
| | | | - Katharina Hecklau
- From the German Rheumatism Research Center (DRFZ), Leibniz Institute, 10117 Berlin
| | - Jürgen Wienands
- the Institute of Cellular and Molecular Immunology, Georg-August-University of Göttingen, 37073 Göttingen, Germany
| | | | - Hanspeter Herzel
- the Institute for Theoretical Biology, Charité and Humboldt University Berlin, 10015 Berlin
| | - Andreas Radbruch
- From the German Rheumatism Research Center (DRFZ), Leibniz Institute, 10117 Berlin
| | - Eberhard Krause
- the Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin
| | - Ria Baumgrass
- From the German Rheumatism Research Center (DRFZ), Leibniz Institute, 10117 Berlin,
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36
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Di Maio R, Barrett PJ, Hoffman EK, Barrett CW, Zharikov A, Borah A, Hu X, McCoy J, Chu CT, Burton EA, Hastings TG, Greenamyre JT. α-Synuclein binds to TOM20 and inhibits mitochondrial protein import in Parkinson's disease. Sci Transl Med 2016; 8:342ra78. [PMID: 27280685 PMCID: PMC5016095 DOI: 10.1126/scitranslmed.aaf3634] [Citation(s) in RCA: 377] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/17/2016] [Indexed: 12/16/2022]
Abstract
α-Synuclein accumulation and mitochondrial dysfunction have both been strongly implicated in the pathogenesis of Parkinson's disease (PD), and the two appear to be related. Mitochondrial dysfunction leads to accumulation and oligomerization of α-synuclein, and increased levels of α-synuclein cause mitochondrial impairment, but the basis for this bidirectional interaction remains obscure. We now report that certain posttranslationally modified species of α-synuclein bind with high affinity to the TOM20 (translocase of the outer membrane 20) presequence receptor of the mitochondrial protein import machinery. This binding prevented the interaction of TOM20 with its co-receptor, TOM22, and impaired mitochondrial protein import. Consequently, there were deficient mitochondrial respiration, enhanced production of reactive oxygen species, and loss of mitochondrial membrane potential. Examination of postmortem brain tissue from PD patients revealed an aberrant α-synuclein-TOM20 interaction in nigrostriatal dopaminergic neurons that was associated with loss of imported mitochondrial proteins, thereby confirming this pathogenic process in the human disease. Modest knockdown of endogenous α-synuclein was sufficient to maintain mitochondrial protein import in an in vivo model of PD. Furthermore, in in vitro systems, overexpression of TOM20 or a mitochondrial targeting signal peptide had beneficial effects and preserved mitochondrial protein import. This study characterizes a pathogenic mechanism in PD, identifies toxic species of wild-type α-synuclein, and reveals potential new therapeutic strategies for neuroprotection.
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Affiliation(s)
- Roberto Di Maio
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA. Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA. Ri.MED Foundation, Palermo, Italy
| | - Paul J Barrett
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA. Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Eric K Hoffman
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA. Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Caitlyn W Barrett
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA. Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Alevtina Zharikov
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA. Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA. Geriatric Research Education and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA 15240, USA
| | - Anupom Borah
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA. Department of Life Science and Bioinformatics, Assam University, Silchar 788011, India
| | - Xiaoping Hu
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA. Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jennifer McCoy
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA. Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Charleen T Chu
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA. Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Edward A Burton
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA. Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA. Geriatric Research Education and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA 15240, USA
| | - Teresa G Hastings
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA. Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - J Timothy Greenamyre
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA 15213, USA. Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA. Geriatric Research Education and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA 15240, USA.
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37
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Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016; 11:738-56. [PMID: 26864455 PMCID: PMC7162211 DOI: 10.1002/cmdc.201500495] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/08/2016] [Indexed: 12/14/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
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Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
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38
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Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016. [PMID: 26864455 DOI: 10.1002/cmdc.201500495.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
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Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China. .,State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
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39
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Howe MK, Speer BL, Hughes PF, Loiselle DR, Vasudevan S, Haystead TAJ. An inducible heat shock protein 70 small molecule inhibitor demonstrates anti-dengue virus activity, validating Hsp70 as a host antiviral target. Antiviral Res 2016; 130:81-92. [PMID: 27058774 DOI: 10.1016/j.antiviral.2016.03.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/31/2016] [Accepted: 03/31/2016] [Indexed: 12/27/2022]
Abstract
An estimated three billion people are at risk of Dengue virus (DENV) infection worldwide and there are currently no approved therapeutic interventions for DENV infection. Due to the relatively small size of the DENV genome, DENV is reliant on host factors throughout the viral life cycle. The inducible form of Heat Shock Protein 70 (Hsp70i) has been implicated as a host factor in DENV pathogenesis, however the complete role remains to be elucidated. Here we further illustrate the importance of Hsp70i in dengue virus pathogenesis and describe the antiviral activity of the allosteric small molecule inhibitor that is selective for Hsp70i, called HS-72. In monocytes, Hsp70i is expressed at low levels preceding DENV infection, but Hsp70i expression is induced upon DENV infection. Targeting Hsp70i with HS-72, results in a dose dependent reduction in DENV infected monocytes, while cell viability was maintained. HS-72 works to reduce DENV infection by inhibiting the entry stage of the viral life cycle, through disrupting the association of Hsp70i with the DENV receptor complex. This work highlights Hsp70i as an antiviral target and HS-72 as a potential anti-DENV therapeutic agent.
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Affiliation(s)
- Matthew K Howe
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Brittany L Speer
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Philip F Hughes
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - David R Loiselle
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Subhash Vasudevan
- Emerging Infectious Diseases Program, Duke-NUS Graduate and Medical School, Singapore
| | - Timothy A J Haystead
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
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40
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Roussis IM, Guille M, Myers FA, Scarlett GP. RNA Whole-Mount In situ Hybridisation Proximity Ligation Assay (rISH-PLA), an Assay for Detecting RNA-Protein Complexes in Intact Cells. PLoS One 2016; 11:e0147967. [PMID: 26824753 PMCID: PMC4732756 DOI: 10.1371/journal.pone.0147967] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/11/2016] [Indexed: 11/19/2022] Open
Abstract
Techniques for studying RNA-protein interactions have lagged behind those for DNA-protein complexes as a consequence of the complexities associated with working with RNA. Here we present a method for the modification of the existing In Situ Hybridisation-Proximity Ligation Assay (ISH-PLA) protocol to adapt it to the study of RNA regulation (rISH-PLA). As proof of principle we used the well-characterised interaction of the Xenopus laevis Staufen RNA binding protein with Vg1 mRNA, the complex of which co-localises to the vegetal pole of Xenopus oocytes. The applicability of both the Stau1 antibody and the Locked Nucleic Acid probe (LNA) recognising Vg1 mRNA were independently validated by whole-mount Immunohistochemistry and whole-mount in situ hybridisation assays respectively prior to combining them in the rISH-PLA assay. The rISH-PLA assay allows the identification of a given RNA-protein complex at subcellular and single cell resolution, thus avoiding the lack of spatial resolution and sensitivity associated with assaying heterogenous cell populations from which conventional RNA-protein interaction detection techniques suffer. This technique will be particularly usefully for studying the activity of RNA binding proteins (RBPs) in complex mixtures of cells, for example tissue sections or whole embryos.
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Affiliation(s)
- Ioannis M. Roussis
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, United Kingdom
| | - Matthew Guille
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, United Kingdom
| | - Fiona A. Myers
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, United Kingdom
| | - Garry P. Scarlett
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, United Kingdom
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41
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Snider J, Kotlyar M, Saraon P, Yao Z, Jurisica I, Stagljar I. Fundamentals of protein interaction network mapping. Mol Syst Biol 2015; 11:848. [PMID: 26681426 PMCID: PMC4704491 DOI: 10.15252/msb.20156351] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Studying protein interaction networks of all proteins in an organism (“interactomes”) remains one of the major challenges in modern biomedicine. Such information is crucial to understanding cellular pathways and developing effective therapies for the treatment of human diseases. Over the past two decades, diverse biochemical, genetic, and cell biological methods have been developed to map interactomes. In this review, we highlight basic principles of interactome mapping. Specifically, we discuss the strengths and weaknesses of individual assays, how to select a method appropriate for the problem being studied, and provide general guidelines for carrying out the necessary follow‐up analyses. In addition, we discuss computational methods to predict, map, and visualize interactomes, and provide a summary of some of the most important interactome resources. We hope that this review serves as both a useful overview of the field and a guide to help more scientists actively employ these powerful approaches in their research.
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Affiliation(s)
- Jamie Snider
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Max Kotlyar
- Princess Margaret Cancer Center, IBM Life Sciences Discovery Centre, University Health Network, Ontario, Canada
| | - Punit Saraon
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Zhong Yao
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Igor Jurisica
- Princess Margaret Cancer Center, IBM Life Sciences Discovery Centre, University Health Network, Ontario, Canada
| | - Igor Stagljar
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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42
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Abstract
G protein-coupled receptors (GPCRs) compose one of the largest families of membrane proteins involved in intracellular signaling. They are involved in numerous physiological and pathological processes and are prime candidates for drug development. Over the past decade, an increasing number of studies have reported heteromerization between GPCRs. Many investigations in heterologous systems have provided important indications of potential novel pharmacology; however, the physiological relevance of these findings has yet to be established with endogenous receptors in native tissues. In this review, we focus on family A GPCRs and describe the techniques and criteria to assess their heteromerization. We conclude that advances in approaches to study receptor complex functionality in heterologous systems, coupled with techniques that enable specific examination of native receptor heteromers in vivo, are likely to establish GPCR heteromers as novel therapeutic targets.
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Affiliation(s)
- Ivone Gomes
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029;
| | - Mohammed Akli Ayoub
- Biologie et Bioinformatique des Systèmes de Signalisation (BIOS) Group, INRA, UMR85, Unité Physiologie de la Reproduction et des Comportements; CNRS, UMR7247, F-37380 Nouzilly, France
- LE STUDIUM Loire Valley Institute for Advanced Studies, F-45000 Orleans, France
| | - Wakako Fujita
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029;
- Current address: Department of Frontier Life Sciences, Nagasaki University, Nagasaki City, Nagasaki Prefecture 852-8588, Japan
| | - Werner C Jaeger
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Kevin D G Pfleger
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Dimerix Bioscience Limited, Nedlands, Western Australia 6009, Australia
| | - Lakshmi A Devi
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029;
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Zanconato F, Forcato M, Battilana G, Azzolin L, Quaranta E, Bodega B, Rosato A, Bicciato S, Cordenonsi M, Piccolo S. Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth. Nat Cell Biol 2015; 17:1218-27. [PMID: 26258633 PMCID: PMC6186417 DOI: 10.1038/ncb3216] [Citation(s) in RCA: 756] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 07/02/2015] [Indexed: 12/14/2022]
Abstract
YAP/TAZ are nuclear effectors of the Hippo pathway regulating organ growth and tumorigenesis. Yet, their function as transcriptional regulators remains underinvestigated. By ChIP-seq analyses in breast cancer cells, we discovered that the YAP/TAZ transcriptional response is pervasively mediated by a dual element: TEAD factors, through which YAP/TAZ bind to DNA, co-occupying chromatin with activator protein-1 (AP-1, dimer of JUN and FOS proteins) at composite cis-regulatory elements harbouring both TEAD and AP-1 motifs. YAP/TAZ/TEAD and AP-1 form a complex that synergistically activates target genes directly involved in the control of S-phase entry and mitosis. This control occurs almost exclusively from distal enhancers that contact target promoters through chromatin looping. YAP/TAZ-induced oncogenic growth is strongly enhanced by gain of AP-1 and severely blunted by its loss. Conversely, AP-1-promoted skin tumorigenesis is prevented in YAP/TAZ conditional knockout mice. This work highlights a new layer of signalling integration, feeding on YAP/TAZ function at the chromatin level.
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Affiliation(s)
- Francesca Zanconato
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy
| | - Mattia Forcato
- Center for Genome Research, Department of Biomedical Sciences, University of Modena and Reggio Emilia, via G. Campi 287, 41100 Modena, Italy
| | - Giusy Battilana
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy
| | - Luca Azzolin
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy
| | - Erika Quaranta
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy
| | - Beatrice Bodega
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare (INGM) 'Romeo and Enrica Invernizzi', via Francesco Sforza 35, Milan 20126, Italy
| | - Antonio Rosato
- Department of Surgery, Oncology and Gastroenterology, University of Padua School of Medicine, Via Gattamelata 64, 35126 Padua, Italy
- Istituto Oncologico Veneto IRCCS, Via Gattamelata 64, 35126 Padua, Italy
| | - Silvio Bicciato
- Center for Genome Research, Department of Biomedical Sciences, University of Modena and Reggio Emilia, via G. Campi 287, 41100 Modena, Italy
| | - Michelangelo Cordenonsi
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy
| | - Stefano Piccolo
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy
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44
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Szymaniak AD, Mahoney JE, Cardoso WV, Varelas X. Crumbs3-Mediated Polarity Directs Airway Epithelial Cell Fate through the Hippo Pathway Effector Yap. Dev Cell 2015; 34:283-96. [PMID: 26235047 DOI: 10.1016/j.devcel.2015.06.020] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 05/02/2015] [Accepted: 06/19/2015] [Indexed: 12/31/2022]
Abstract
Epithelial cells undergo dynamic polarity changes as organs pattern, but the relationship between epithelial polarity and cell fate is poorly understood. Using the developing lung as a model, we found that distinct alterations in apical-basal polarity dictate airway epithelial differentiation. We demonstrate that Crb3, a Crumbs isoform that determines epithelial apical domain identity, is required for airway differentiation by controlling the localization of the transcriptional regulator Yap. We show that Crb3 promotes the interaction between Yap and the Hippo pathway kinases Lats1/2 at apical cell junctions to induce Yap phosphorylation and cytoplasmic retention, which drive cell differentiation. Loss of Crb3 in developing mouse airways or isolated adult airway progenitors results in unrestricted nuclear Yap activity and consequent cell differentiation defects. Our findings demonstrate that polarity-dependent cues control airway cell differentiation, offering important molecular insights into organ patterning.
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Affiliation(s)
| | - John E Mahoney
- Department of Pathology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Wellington V Cardoso
- Department of Pathology, Boston University School of Medicine, Boston, MA 02118, USA; Columbia Center for Human Development, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA.
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45
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Koos B, Cane G, Grannas K, Löf L, Arngården L, Heldin J, Clausson CM, Klaesson A, Hirvonen MK, de Oliveira FMS, Talibov VO, Pham NT, Auer M, Danielson UH, Haybaeck J, Kamali-Moghaddam M, Söderberg O. Proximity-dependent initiation of hybridization chain reaction. Nat Commun 2015; 6:7294. [PMID: 26065580 PMCID: PMC4490387 DOI: 10.1038/ncomms8294] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/24/2015] [Indexed: 11/09/2022] Open
Abstract
Sensitive detection of protein interactions and post-translational modifications of native proteins is a challenge for research and diagnostic purposes. A method for this, which could be used in point-of-care devices and high-throughput screening, should be reliable, cost effective and robust. To achieve this, here we design a method (proxHCR) that combines the need for proximal binding with hybridization chain reaction (HCR) for signal amplification. When two oligonucleotide hairpins conjugated to antibodies bind in close proximity, they can be activated to reveal an initiator sequence. This starts a chain reaction of hybridization events between a pair of fluorophore-labelled oligonucleotide hairpins, generating a fluorescent product. In conclusion, we show the applicability of the proxHCR method for the detection of protein interactions and posttranslational modifications in microscopy and flow cytometry. As no enzymes are needed, proxHCR may be an inexpensive and robust alternative to proximity ligation assays. Proximity ligation assays are a sensitive method for detecting protein interactions, but require the addition of enzymes. Here the authors introduce proxHCR, an enzyme-free method of detecting interactions in close proximity by inducing a hybribization chain reaction (HCR) of fluorescently labelled oligonucleotides.
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Affiliation(s)
- Björn Koos
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Gaëlle Cane
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Karin Grannas
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Liza Löf
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Linda Arngården
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Johan Heldin
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Carl-Magnus Clausson
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Axel Klaesson
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - M Karoliina Hirvonen
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Felipe M S de Oliveira
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Vladimir O Talibov
- Department of Chemistry-BMC, Box 256, Uppsala University, SE-75123 Uppsala, Sweden
| | - Nhan T Pham
- School of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, C H Waddington Building, Max Born Cresent, Kings Buildings, Edinburgh EH9 3BF, UK
| | - Manfred Auer
- School of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, C H Waddington Building, Max Born Cresent, Kings Buildings, Edinburgh EH9 3BF, UK
| | - U Helena Danielson
- Department of Chemistry-BMC, Box 256, Uppsala University, SE-75123 Uppsala, Sweden
| | - Johannes Haybaeck
- Institute of Pathology, Medical University of Graz, A-8036 Graz, Austria
| | - Masood Kamali-Moghaddam
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Ola Söderberg
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
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Greenwood C, Ruff D, Kirvell S, Johnson G, Dhillon HS, Bustin SA. Proximity assays for sensitive quantification of proteins. BIOMOLECULAR DETECTION AND QUANTIFICATION 2015; 4:10-6. [PMID: 27077033 PMCID: PMC4822221 DOI: 10.1016/j.bdq.2015.04.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 04/23/2015] [Indexed: 12/22/2022]
Abstract
Proximity assays are immunohistochemical tools that utilise two or more DNA-tagged aptamers or antibodies binding in close proximity to the same protein or protein complex. Amplification by PCR or isothermal methods and hybridisation of a labelled probe to its DNA target generates a signal that enables sensitive and robust detection of proteins, protein modifications or protein-protein interactions. Assays can be carried out in homogeneous or solid phase formats and in situ assays can visualise single protein molecules or complexes with high spatial accuracy. These properties highlight the potential of proximity assays in research, diagnostic, pharmacological and many other applications that require sensitive, specific and accurate assessments of protein expression.
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Affiliation(s)
- Christina Greenwood
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
| | - David Ruff
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Sara Kirvell
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
| | - Gemma Johnson
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
| | - Harvinder S Dhillon
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
| | - Stephen A Bustin
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex CM1 1SQ, UK
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Galler K, Bräutigam K, Große C, Popp J, Neugebauer U. Making a big thing of a small cell--recent advances in single cell analysis. Analyst 2015; 139:1237-73. [PMID: 24495980 DOI: 10.1039/c3an01939j] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single cell analysis is an emerging field requiring a high level interdisciplinary collaboration to provide detailed insights into the complex organisation, function and heterogeneity of life. This review is addressed to life science researchers as well as researchers developing novel technologies. It covers all aspects of the characterisation of single cells (with a special focus on mammalian cells) from morphology to genetics and different omics-techniques to physiological, mechanical and electrical methods. In recent years, tremendous advances have been achieved in all fields of single cell analysis: (1) improved spatial and temporal resolution of imaging techniques to enable the tracking of single molecule dynamics within single cells; (2) increased throughput to reveal unexpected heterogeneity between different individual cells raising the question what characterizes a cell type and what is just natural biological variation; and (3) emerging multimodal approaches trying to bring together information from complementary techniques paving the way for a deeper understanding of the complexity of biological processes. This review also covers the first successful translations of single cell analysis methods to diagnostic applications in the field of tumour research (especially circulating tumour cells), regenerative medicine, drug discovery and immunology.
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Affiliation(s)
- Kerstin Galler
- Integrated Research and Treatment Center "Center for Sepsis Control and Care", Jena University Hospital, Erlanger Allee 101, 07747 Jena, Germany
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Genetet S, Ripoche P, Le Van Kim C, Colin Y, Lopez C. Evidence of a structural and functional ammonium transporter RhBG·anion exchanger 1·ankyrin-G complex in kidney epithelial cells. J Biol Chem 2015; 290:6925-36. [PMID: 25616663 DOI: 10.1074/jbc.m114.610048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The renal ammonium transporter RhBG and anion exchanger 1 kAE1 colocalize in the basolateral domain of α-intercalated cells in the distal nephron. Although we have previously shown that RhBG is linked to the spectrin-based skeleton through ankyrin-G and that its NH3 transport activity is dependent on this association, there is no evidence for an interaction of kAE1 with this adaptor protein. We report here that the kAE1 cytoplasmic N terminus actually binds to ankyrin-G, both in yeast two-hybrid analysis and by coimmunoprecipitation in situ in HEK293 cells expressing recombinant kAE1. A site-directed mutagenesis study allowed the identification of three dispersed regions on kAE1 molecule linking the third and fourth repeat domains of ankyrin-G. One secondary docking site corresponds to a major interacting loop of the erythroid anion exchanger 1 (eAE1) with ankyrin-R, whereas the main binding region of kAE1 does not encompass any eAE1 determinant. Stopped flow spectrofluorometry analysis of recombinant HEK293 cells revealed that the Cl(-)/HCO3 (-) exchange activity of a kAE1 protein mutated on the ankyrin-G binding site was abolished. This disruption impaired plasma membrane expression of kAE1 leading to total retention on cytoplasmic structures in polarized epithelial Madin-Darby canine kidney cell transfectants. kAE1 also directly interacts with RhBG without affecting its surface expression and NH3 transport function. This is the first description of a structural and functional RhBG·kAE1·ankyrin-G complex at the plasma membrane of kidney epithelial cells, comparable with the well known Rh·eAE1·ankyrin-R complex in the red blood cell membrane. This renal complex could participate in the regulation of acid-base homeostasis.
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Affiliation(s)
- Sandrine Genetet
- From INSERM U1134, 75739 Paris, France, the Université Paris Diderot, Sorbonne Paris Cité, UMR_S1134, 75739 Paris, France, the Institut National de la Transfusion Sanguine, 75739 Paris, France, and the Laboratoire d'Excellence GR-Ex, 75238 Paris, France
| | - Pierre Ripoche
- From INSERM U1134, 75739 Paris, France, the Université Paris Diderot, Sorbonne Paris Cité, UMR_S1134, 75739 Paris, France, the Institut National de la Transfusion Sanguine, 75739 Paris, France, and the Laboratoire d'Excellence GR-Ex, 75238 Paris, France
| | - Caroline Le Van Kim
- From INSERM U1134, 75739 Paris, France, the Université Paris Diderot, Sorbonne Paris Cité, UMR_S1134, 75739 Paris, France, the Institut National de la Transfusion Sanguine, 75739 Paris, France, and the Laboratoire d'Excellence GR-Ex, 75238 Paris, France
| | - Yves Colin
- From INSERM U1134, 75739 Paris, France, the Université Paris Diderot, Sorbonne Paris Cité, UMR_S1134, 75739 Paris, France, the Institut National de la Transfusion Sanguine, 75739 Paris, France, and the Laboratoire d'Excellence GR-Ex, 75238 Paris, France
| | - Claude Lopez
- From INSERM U1134, 75739 Paris, France, the Université Paris Diderot, Sorbonne Paris Cité, UMR_S1134, 75739 Paris, France, the Institut National de la Transfusion Sanguine, 75739 Paris, France, and the Laboratoire d'Excellence GR-Ex, 75238 Paris, France
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Kim TH, Yoo JY, Kim HI, Gilbert J, Ku BJ, Li J, Mills GB, Broaddus RR, Lydon JP, Lim JM, Yoon HG, Jeong JW. Mig-6 suppresses endometrial cancer associated with Pten deficiency and ERK activation. Cancer Res 2014; 74:7371-82. [PMID: 25377472 PMCID: PMC4268053 DOI: 10.1158/0008-5472.can-14-0794] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PTEN mutations are the most common genetic alterations in endometrial cancer. Loss of PTEN and subsequent AKT activation stimulate estrogen receptor α-dependent pathways that play an important role in endometrial tumorigenesis. The major pathologic phenomenon of endometrial cancer is the loss of ovarian steroid hormone control over uterine epithelial cell proliferation and apoptosis. However, the precise mechanism of PTEN/AKT signaling in endometrial cancer remains poorly understood. The progesterone signaling mediator MIG-6 suppresses estrogen signaling and it has been implicated previously as a tumor suppressor in endometrial cancer. In this study, we show that MIG-6 also acts as a tumor suppressor in endometrial cancers associated with PTEN deficiency. Transgenic mice, where Mig-6 was overexpressed in progesterone receptor-expressing cells, exhibited a relative reduction in uterine tumorigenesis caused by Pten deficiency. ERK1/2 was phosphorylated in uterine tumors and administration of an ERK1/2 inhibitor suppressed cancer progression in PR(cre/+)Pten(f/f) mice. In clinical specimens of endometrial cancer, MIG-6 expression correlated inversely with ERK1/2 phosphorylation during progression. Taken together, our findings suggest that Mig-6 regulates ERK1/2 phosphorylation and that it is crucial for progression of PTEN-mutant endometrial cancers, providing a mechanistic rationale for the evaluation of ERK1/2 inhibitors as a therapeutic treatment in human endometrial cancer.
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Affiliation(s)
- Tae Hoon Kim
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University College of Human Medicine, Grand Rapids, MI 49503, USA
| | - Jung-Yoon Yoo
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University College of Human Medicine, Grand Rapids, MI 49503, USA,Department of Biochemistry and Molecular Biology, Brain Korea 21 PLUS Project for Medicine Science, Yonsei University College of Medicine, Seoul 120-752, South Korea
| | - Hong Im Kim
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University College of Human Medicine, Grand Rapids, MI 49503, USA
| | - Jenifer Gilbert
- Institute of Immunology, National University of Ireland, Maynooth, Ireland
| | - Bon Jeong Ku
- Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, 301-721, South Korea
| | - Jane Li
- Department of Systems Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B. Mills
- Department of Systems Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Russell R. Broaddus
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - John P. Lydon
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeong Mook Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, South Korea
| | - Ho-Geun Yoon
- Department of Biochemistry and Molecular Biology, Brain Korea 21 PLUS Project for Medicine Science, Yonsei University College of Medicine, Seoul 120-752, South Korea,Correspondence to: Jae-Wook Jeong, Ph.D., Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University College of Human Medicine, 333 Bostwick Avenue NE, Suite 4024, Grand Rapids, MI 49503, Phone: 616-234-0987, Fax: 616-234-0990, . Ho-Geun Yoon, Ph.D., Department of Biochemistry and Molecular Biology, Severance Medical Research Institute, Yonsei University College of Medicine,134 Shinchon-dong, Seodaemoon-gu, 120-752, Seoul, South Korea, Tel: +82-2-2228-1683, Fax: +82-2-312-5041,
| | - Jae-Wook Jeong
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University College of Human Medicine, Grand Rapids, MI 49503, USA,Correspondence to: Jae-Wook Jeong, Ph.D., Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University College of Human Medicine, 333 Bostwick Avenue NE, Suite 4024, Grand Rapids, MI 49503, Phone: 616-234-0987, Fax: 616-234-0990, . Ho-Geun Yoon, Ph.D., Department of Biochemistry and Molecular Biology, Severance Medical Research Institute, Yonsei University College of Medicine,134 Shinchon-dong, Seodaemoon-gu, 120-752, Seoul, South Korea, Tel: +82-2-2228-1683, Fax: +82-2-312-5041,
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Abstract
Dissecting the subcellular distribution of a fatty-acylated protein is key to the understanding of the molecular mechanisms regulating protein movement and function in a cell. This protocol describes how to perform single-cell imaging of palmitoylation in a fatty-acylated protein of interest with high sensitivity using click chemistry, proximity ligation and fluorescence microscopy. The initial steps in this protocol involve optimization of conditions for (i) metabolic incorporation of an alkynyl analog of palmitic acid into cellular proteins coupled with click chemistry and (ii) detecting a specific protein of interest with primary antibodies using automated fluorescence microscopy, followed by (iii) imaging palmitoylation of the target fatty-acylated protein of interest, such as Wnt, Sonic Hedgehog or H-Ras. Furthermore, we outline strategies for imaging specific fatty-acylated proteins with subcellular organelles and/or total proteome palmitoylation, and we discuss special considerations that need to be given depending on the experimental design. The use of clickable fatty acids with proximity ligation may have promising applications to the investigation of fatty acylation cell biology. The entire protocol takes ∼3 weeks to complete.
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