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Frolikova M, Sur VP, Novotny I, Blazikova M, Vondrakova J, Simonik O, Ded L, Valaskova E, Koptasikova L, Benda A, Postlerova P, Horvath O, Komrskova K. Juno and CD9 protein network organization in oolemma of mouse oocyte. Front Cell Dev Biol 2023; 11:1110681. [PMID: 37635875 PMCID: PMC10450504 DOI: 10.3389/fcell.2023.1110681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
Juno and CD9 protein, expressed in oolemma, are known to be essential for sperm-oocyte binding and fusion. Although evidence exists that these two proteins cooperate, their interaction has not yet been demonstrated. Here in, we present Juno and CD9 mutual localization over the surface of mouse metaphase II oocytes captured using the 3D STED super-resolution technique. The precise localization of examined proteins was identified in different compartments of oolemma such as the microvillar membrane, planar membrane between individual microvilli, and the membrane of microvilli-free region. Observed variance in localization of Juno and CD9 was confirmed by analysis of transmission and scanning electron microscopy images, which showed a significant difference in the presence of proteins between selected membrane compartments. Colocalization analysis of super-resolution images based on Pearson's correlation coefficient supported evidence of Juno and CD9 mutual position in the oolemma, which was identified by proximity ligation assay. Importantly, the interaction between Juno and CD9 was detected by co-immunoprecipitation and mass spectrometry in HEK293T/17 transfected cell line. For better understanding of experimental data, mouse Juno and CD9 3D structure were prepared by comparative homology modelling and several protein-protein flexible sidechain dockings were performed using the ClusPro server. The dynamic state of the proteins was studied in real-time at atomic level by molecular dynamics (MD) simulation. Docking and MD simulation predicted Juno-CD9 interactions and stability also suggesting an interactive mechanism. Using the multiscale approach, we detected close proximity of Juno and CD9 within microvillar oolemma however, not in the planar membrane or microvilli-free region. Our findings show yet unidentified Juno and CD9 interaction within the mouse oolemma protein network prior to sperm attachment. These results suggest that a Juno and CD9 interactive network could assist in primary Juno binding to sperm Izumo1 as a prerequisite to subsequent gamete membrane fusion.
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Affiliation(s)
- Michaela Frolikova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Vishma Pratap Sur
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Ivan Novotny
- Light Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Michaela Blazikova
- Light Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Jana Vondrakova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Ondrej Simonik
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Lukas Ded
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Eliska Valaskova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
| | - Lenka Koptasikova
- Imaging Methods Core Facility at BIOCEV, Faculty of Science, Charles University, Vestec, Czechia
| | - Ales Benda
- Imaging Methods Core Facility at BIOCEV, Faculty of Science, Charles University, Vestec, Czechia
| | - Pavla Postlerova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, University of Life Sciences Prague, Prague, Czechia
| | - Ondrej Horvath
- Light Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Katerina Komrskova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czechia
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
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2
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Magalhaes-Novais S, Blecha J, Naraine R, Mikesova J, Abaffy P, Pecinova A, Milosevic M, Bohuslavova R, Prochazka J, Khan S, Novotna E, Sindelka R, Machan R, Dewerchin M, Vlcak E, Kalucka J, Stemberkova Hubackova S, Benda A, Goveia J, Mracek T, Barinka C, Carmeliet P, Neuzil J, Rohlenova K, Rohlena J. Mitochondrial respiration supports autophagy to provide stress resistance during quiescence. Autophagy 2022; 18:2409-2426. [PMID: 35258392 PMCID: PMC9542673 DOI: 10.1080/15548627.2022.2038898] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Mitochondrial oxidative phosphorylation (OXPHOS) generates ATP, but OXPHOS also supports biosynthesis during proliferation. In contrast, the role of OXPHOS during quiescence, beyond ATP production, is not well understood. Using mouse models of inducible OXPHOS deficiency in all cell types or specifically in the vascular endothelium that negligibly relies on OXPHOS-derived ATP, we show that selectively during quiescence OXPHOS provides oxidative stress resistance by supporting macroautophagy/autophagy. Mechanistically, OXPHOS constitutively generates low levels of endogenous ROS that induce autophagy via attenuation of ATG4B activity, which provides protection from ROS insult. Physiologically, the OXPHOS-autophagy system (i) protects healthy tissue from toxicity of ROS-based anticancer therapy, and (ii) provides ROS resistance in the endothelium, ameliorating systemic LPS-induced inflammation as well as inflammatory bowel disease. Hence, cells acquired mitochondria during evolution to profit from oxidative metabolism, but also built in an autophagy-based ROS-induced protective mechanism to guard against oxidative stress associated with OXPHOS function during quiescence. Abbreviations: AMPK: AMP-activated protein kinase; AOX: alternative oxidase; Baf A: bafilomycin A1; CI, respiratory complexes I; DCF-DA: 2′,7′-dichlordihydrofluorescein diacetate; DHE: dihydroethidium; DSS: dextran sodium sulfate; ΔΨmi: mitochondrial inner membrane potential; EdU: 5-ethynyl-2’-deoxyuridine; ETC: electron transport chain; FA: formaldehyde; HUVEC; human umbilical cord endothelial cells; IBD: inflammatory bowel disease; LC3B: microtubule associated protein 1 light chain 3 beta; LPS: lipopolysaccharide; MEFs: mouse embryonic fibroblasts; MTORC1: mechanistic target of rapamycin kinase complex 1; mtDNA: mitochondrial DNA; NAC: N-acetyl cysteine; OXPHOS: oxidative phosphorylation; PCs: proliferating cells; PE: phosphatidylethanolamine; PEITC: phenethyl isothiocyanate; QCs: quiescent cells; ROS: reactive oxygen species; PLA2: phospholipase A2, WB: western blot.
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Affiliation(s)
- Silvia Magalhaes-Novais
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Blecha
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Ravindra Naraine
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Jana Mikesova
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Pavel Abaffy
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Alena Pecinova
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Mirko Milosevic
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Romana Bohuslavova
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Jan Prochazka
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Shawez Khan
- VIB-KU Leuven Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Eliska Novotna
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Radek Sindelka
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Radek Machan
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Mieke Dewerchin
- VIB-KU Leuven Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Erik Vlcak
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Joanna Kalucka
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus C, Denmark
| | - Sona Stemberkova Hubackova
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic.,Centre for Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Ales Benda
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Jermaine Goveia
- VIB-KU Leuven Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Tomas Mracek
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Cyril Barinka
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Peter Carmeliet
- VIB-KU Leuven Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium.,Department of Biomedicine, Aarhus University, Aarhus, Denmark.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jiri Neuzil
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic.,School of Medical Science, Griffith University, Southport, Qld, Australia
| | - Katerina Rohlenova
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic.,VIB-KU Leuven Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jakub Rohlena
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
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Aranaz-Novaliches G, Spoutil F, Bukova I, Krejzova I, Olsinova M, Dalecka M, Benda A, Rozman J, Sedlacek R, Prochazka J. Multi-Level Approach for Comprehensive Enamel Phenotyping. Curr Protoc 2022; 2:e340. [PMID: 35007410 DOI: 10.1002/cpz1.340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Enamel is the hardest tissue in mammalian organisms and is the layer covering the tooth. It consists of hydroxyapatite (HAP) crystallites, which mineralize on a protein scaffold known as the enamel matrix. Enamel matrix assembly is a very complex process mediated by enamel matrix proteins (EMPs). Altered HAP deposition or disintegration of the protein scaffold can cause enamel defects. Various methods have been established for enamel phenotyping, including MicroCT scanning with various resolutions from 9 µm for in vivo imaging to 1.5 µm for ex vivo imaging. With increasing resolution, we can see not only the enamel layer itself but also a detailed map of mineralization. To study enamel microstructure, we combine the MicroCT analysis with scanning electron microscopy (SEM), which enables us to perform element analyses such as calcium-carbon ratio. However, the methods mentioned above only show the result-already formed enamel. Stimulated emission depletion (STED) microscopy provides extra information about protein structure in the form of EMP localization and position before enamel mineralization. A combination of all these methods allows analyzing the same sample on multiple levels-starting with the live animal being scanned harmlessly and quickly, followed by sacrifice and high-resolution MicroCT scans requiring no special sample preparation. The biggest advantage is that samples remain in perfect condition for SEM or STED microscopic analysis. © 2022 Wiley Periodicals LLC. Basic Protocol 1: In vivo MicroCT scanning of mouse Basic Protocol 2: Ex vivo HR-MicroCT of the teeth Basic Protocol 3: SEM for teeth microstructure Basic Protocol 4: Stimulated emission depletion (STED) microscopy.
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Affiliation(s)
- Goretti Aranaz-Novaliches
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Frantisek Spoutil
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ivana Bukova
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Irena Krejzova
- Imaging Methods Core Facility, Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Marie Olsinova
- Imaging Methods Core Facility, Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Marketa Dalecka
- Imaging Methods Core Facility, Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Ales Benda
- Imaging Methods Core Facility, Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Jan Rozman
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Prochazka
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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Markova V, Hejnova L, Benda A, Novotny J, Melkes B. β-Arrestin 1 and 2 similarly influence μ-opioid receptor mobility and distinctly modulate adenylyl cyclase activity. Cell Signal 2021; 87:110124. [PMID: 34450275 DOI: 10.1016/j.cellsig.2021.110124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/20/2021] [Accepted: 08/22/2021] [Indexed: 01/14/2023]
Abstract
β-Arrestins are known to play a crucial role in GPCR-mediated transmembrane signaling processes. However, there are still many unanswered questions, especially those concerning the presumed similarities and differences of β-arrestin isoforms. Here, we examined the roles of β-arrestin 1 and β-arrestin 2 at different levels of μ-opioid receptor (MOR)-regulated signaling, including MOR mobility, internalization of MORs, and adenylyl cyclase (AC) activity. For this purpose, naïve HEK293 cells or HEK293 cells stably expressing YFP-tagged MOR were transfected with appropriate siRNAs to block in a specific way the expression of β-arrestin 1 or β-arrestin 2. We did not find any significant differences in the ability of β-arrestin isoforms to influence the lateral mobility of MORs in the plasma membrane. Using FRAP and line-scan FCS, we observed that knockdown of both β-arrestins similarly increased MOR lateral mobility and diminished the ability of DAMGO and endomorphin-2, respectively, to enhance and slow down receptor diffusion kinetics. However, β-arrestin 1 and β-arrestin 2 diversely affected the process of agonist-induced MOR endocytosis and exhibited distinct modulatory effects on AC function. Knockdown of β-arrestin 1, in contrast to β-arrestin 2, more effectively suppressed forskolin-stimulated AC activity and prevented the ability of activated-MORs to inhibit the enzyme activity. Moreover, we have demonstrated for the first time that β-arrestin 1, and partially β-arrestin 2, may somehow interact with AC and that this interaction is strongly supported by the enzyme activation. These data provide new insights into the functioning of β-arrestin isoforms and their distinct roles in GPCR-mediated signaling.
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Affiliation(s)
- Vendula Markova
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lucie Hejnova
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ales Benda
- IMCF at Biocev, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiri Novotny
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic.
| | - Barbora Melkes
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
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Lešták J, Fůs M, Benda A, Bartošová L, Marešová K. OCT ANGIOGRAPHY AND DOPPLER ULTRASOUND IN HYPERTENSION GLAUCOMA. Cesk Slov Oftalmol 2021; 77:130-133. [PMID: 35130704 DOI: 10.31348/2021/15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
AIMS The main aim of this work was to find out if there is a correlation between vessel density (VD) and results of measured perfusion values in ophthalmic artery and in central retinal artery of the same eye in a group with hypertension glaucoma (HTG). MATERIALS AND METHODS The file included 20 patients with HTG, thereof 13 women of average age 68.7 years (49-80 years) and 7 men of average age 58.4 years (27-81 years). Criteria for inclusion in the study: visual acuity 1,0 with possible correction less than ±3 diopters, approximately the same changes in visual fields in every patient, intraocular pressure (IOP) less than 18 mmHg, no other ocular or neurological diseases. VD was measured by Avanti RTVue XR by Optovue firm, perfusion parameters were measured using Doppler ultrasound with Affinity 70G machine by Philips firm. The peak systolic velocity (PSV) and end diastolic velocity (EDV) and resistance index (RI) were measured both in ophthalmic artery (AO) and in central retinal artery (CRA). Visual field (VF) was examined by quick threshold glaucoma program by Medmont M 700 machine. The sum of sensitivities in apostilbs (abs) was evaluated in the range 0-22 degrees of visual field. The results of sensitivities in visual field were compared to VD and perfusion parameters in CRA and AO of the same eye. RESULTS Pearsons correlation coefficient (p = 0,05) was used to assess the dependency between chosen parameters. By comparing VF and VD from measured areas, strong correlation (r = 0.64, resp. 0.65) was revealed. It was then proved that VD (WI-VDs) correlates with RICRA weakly (r = -0.35) and moderately strongly (WI-VDa r = -0.4, PP-VDs r = -0.43 and PP-VDa r = -0.45). This means that with increasing resistance index in CRA the density in VD decreases. The other correlations between VD and perfusion parameters (PSV and EDV) in CRA and AO were not significant. CONCLUSION Measured values showed that the vascular component of VD has a huge impact on the changes in visual fields in HTG. Weak to moderate influence exists between VD and RI in CRA. OCTA has proven to be more suitable than Doppler ultrasound for determining the condition of blood circulation in the eye.
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6
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Abstract
AIMS To investigate the dependence of blood vessel density and velocity in ophthalmic artery and arteria centralis retinae of the same eye in patients with normotensive glaucoma. METHODS The sample consisted of 20 patients with normotensive glaucoma (NTG). There were 17 women (mean age 56.1) and 3 men (mean age 60 years). Inclusion criteria for study: visual acuity 1.0 with correction up to ±3 dioptres, approximately equal changes in the visual field, whereby it was incipient NTG and diagnosis was confirmed by electrophysiological examination, without further ocular or neurological disease. Parameters of vessel density (VD) were evaluated by Avanti RTVue XR (Optovue). Perfusion parameters such as peak systolic velocity (PSV), end diastolic velocity (EDV) and resistive index (RI) were evaluated for ophthalmic artery (AO) and arteria centralis retinae (ACR) using Doppler sonography (Affinity 70G Philips, probe 5-12 MHz). Visual field (VF) was evaluated by automated perimeter (Medmont M700) using fast threshold glaucoma strategy test. The sum of sensitivity levels in apostilb (asb) were evaluated in range 0-22 degrees of visual field. Resulting values of VF were compared with VD and perfusion parameters in AO and ACR at the same eye. RESULTS Pearsons correlation coefficient was used to evaluate the dependence. Data shows, that changes in visual fields are mainly caused by peripapillary VD of small and all vessels, and vessels throughout measured image area also. Correlation of small vessels throughout measured image area was weak (r = 0.23). Moderate negative correlation was found for PSV in AO and peripapillary small VD (r = -0.46), all peripapillary VD (r = -0.49), VD in whole area (r = -0.45), then between EDV in AO and VD in whole area (r = -0.42). Other correlations between VD and perfusion parameter were insignificant. CONCLUSIONS Study confirms, that changes of visual field in NTG patients are mainly caused by VD rather than perfusion parameters, especially in AO. Perfusion parameters in ACR are not significantly correlated with changes of VF in NTG patients.
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Vennin C, Mélénec P, Rouet R, Nobis M, Cazet AS, Murphy KJ, Herrmann D, Reed DA, Lucas MC, Warren SC, Elgundi Z, Pinese M, Kalna G, Roden D, Samuel M, Zaratzian A, Grey ST, Da Silva A, Leung W, Mathivanan S, Wang Y, Braithwaite AW, Christ D, Benda A, Parkin A, Phillips PA, Whitelock JM, Gill AJ, Sansom OJ, Croucher DR, Parker BL, Pajic M, Morton JP, Cox TR, Timpson P. CAF hierarchy driven by pancreatic cancer cell p53-status creates a pro-metastatic and chemoresistant environment via perlecan. Nat Commun 2019; 10:3637. [PMID: 31406163 PMCID: PMC6691013 DOI: 10.1038/s41467-019-10968-6] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 06/11/2019] [Indexed: 12/15/2022] Open
Abstract
Heterogeneous subtypes of cancer-associated fibroblasts (CAFs) coexist within pancreatic cancer tissues and can both promote and restrain disease progression. Here, we interrogate how cancer cells harboring distinct alterations in p53 manipulate CAFs. We reveal the existence of a p53-driven hierarchy, where cancer cells with a gain-of-function (GOF) mutant p53 educate a dominant population of CAFs that establish a pro-metastatic environment for GOF and null p53 cancer cells alike. We also demonstrate that CAFs educated by null p53 cancer cells may be reprogrammed by either GOF mutant p53 cells or their CAFs. We identify perlecan as a key component of this pro-metastatic environment. Using intravital imaging, we observe that these dominant CAFs delay cancer cell response to chemotherapy. Lastly, we reveal that depleting perlecan in the stroma combined with chemotherapy prolongs mouse survival, supporting it as a potential target for anti-stromal therapies in pancreatic cancer.
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Affiliation(s)
- Claire Vennin
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
- Molecular Pathology department, the Netherlands Cancer Institute, Amsterdam, 1066CX, the Netherlands
| | - Pauline Mélénec
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Romain Rouet
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Max Nobis
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Aurélie S Cazet
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Kendelle J Murphy
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - David Herrmann
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Daniel A Reed
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Morghan C Lucas
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Sean C Warren
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Zehra Elgundi
- Graduate school of Biomedical Engineering, University of New South Wales Sydney, Sydney, NSW, 2052, Australia
| | - Mark Pinese
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Gabriella Kalna
- Cancer Research UK Beatson Institute, Glasgow Scotland, G61 BD, UK
| | - Daniel Roden
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Monisha Samuel
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Anaiis Zaratzian
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
| | - Shane T Grey
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Andrew Da Silva
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
| | - Wilfred Leung
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Suresh Mathivanan
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, 92121, USA
| | - Anthony W Braithwaite
- Children's Medical Research Institute, University of Sydney, Sydney, NSW, 2006, Australia
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
- Maurice Wilkins Centre, University of Otago, Dunedin, 9054, New Zealand
| | - Daniel Christ
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Ales Benda
- Biomedical imaging facility, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Ashleigh Parkin
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Phoebe A Phillips
- Pancreatic Cancer Translational Research Group, Lowy Cancer Research Centre, School of Medical Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Australian Centre for Nanomedicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - John M Whitelock
- Graduate school of Biomedical Engineering, University of New South Wales Sydney, Sydney, NSW, 2052, Australia
| | - Anthony J Gill
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, Sydney, NSW, 2065, Australia
- Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, St Leonards, NSW, 2065, Australia
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow Scotland, G61 BD, UK
| | - David R Croucher
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Benjamin L Parker
- Schools of Life and Environmental Sciences, the Charles Perkin Centre, the University of Sydney, Sydney, NSW, 2006, Australia
| | - Marina Pajic
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | | | - Thomas R Cox
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia.
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia.
| | - Paul Timpson
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia.
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia.
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8
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Kostrouchová M, Kostrouchová V, Yilma P, Benda A, Mandys V, Kostrouchová M. Valproic Acid Decreases the Nuclear Localization of MDT-28, the Nematode Orthologue of MED28. Folia Biol (Praha) 2018; 64:1-9. [PMID: 29871732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mediator is a multiprotein complex that connects regulation mediated by transcription factors with RNA polymerase II transcriptional machinery and integrates signals from the cell regulatory cascades with gene expression. One of the Mediator subunits, Mediator complex subunit 28 (MED28), has a dual nuclear and cytoplasmic localization and function. In the nucleus, MED28 functions as part of Mediator and in the cytoplasm, it interacts with cytoskeletal proteins and is part of the regulatory cascades including that of Grb2. MED28 thus has the potential to bring cytoplasmic regulatory interactions towards the centre of gene expression regulation. In this study, we identified MDT-28, the nematode orthologue of MED28, as a likely target of lysine acetylation using bioinformatic prediction of posttranslational modifications. Lysine acetylation was experimentally confirmed using anti-acetyl lysine antibody on immunoprecipitated GFP::MDT-28 expressed in synchronized C. elegans. Valproic acid (VPA), a known inhibitor of lysine deacetylases, enhanced the lysine acetylation of GFP::MDT-28. At the subcellular level, VPA decreased the nuclear localization of GFP::MDT-28 detected by fluorescencelifetime imaging microscopy (FLIM). This indicates that the nuclear pool of MDT-28 is regulated by a mechanism sensitive to VPA and provides an indirect support for a variable relative proportion of MED28 orthologues with other Mediator subunits.
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Affiliation(s)
- M Kostrouchová
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Department of Pathology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - V Kostrouchová
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - P Yilma
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - A Benda
- Imaging Methods Core Facility, Biocev, Faculty of Science, Charles University, Prague, Czech Republic
| | - V Mandys
- Department of Pathology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - M Kostrouchová
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
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9
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Kollárová J, Kostrouchová M, Benda A, Kostrouchová M. ALKB-8, a 2-Oxoglutarate-Dependent Dioxygenase and S-Adenosine Methionine-Dependent Methyltransferase Modulates Metabolic Events Linked to Lysosome-Related Organelles and Aging in C. elegans. Folia Biol (Praha) 2018; 64:46-58. [PMID: 30338756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
ALKB-8 is a 2-oxoglutarate-dependent dioxygenase homologous to bacterial AlkB, which oxidatively demethylates DNA substrates. The mammalian AlkB family contains AlkB homologues denominated ALKBH1 to 8 and FTO. The C. elegans genome includes five AlkB-related genes, homologues of ALKBH1, 4, 6, 7, and 8, but lacks homologues of ALKBH2, 3, and 5 and FTO. ALKBH8 orthologues differ from other AlkB family members by possessing an additional methyltransferase module and an RNA binding N-terminal module. The ALKBH8 methyltransferase domain generates the wobble nucleoside 5-methoxycarbonylmethyluridine from its precursor 5-carboxymethyluridine and its (R)- and (S)-5-methoxycarbonylhydroxymethyluridine hydroxylated forms in tRNA Arg/UCG and tRNA Gly/UCC. The ALKBH8/ALKB-8 methyltransferase domain is highly similar to yeast TRM9, which selectively modulates translation of mRNAs enriched with AGA and GAA codons under both normal and stress conditions. In this report, we studied the role of alkb-8 in C. elegans. We show that downregulation of alkb-8 increases detection of lysosome-related organelles visualized by Nile red in vivo. Reversely, forced expression of alkb-8 strongly decreases the detection of this compartment. In addition, overexpression of alkb-8 applied in a pulse during the L1 larval stage increases the C. elegans lifespan.
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Affiliation(s)
- J Kollárová
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - M Kostrouchová
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
- Department of Pathology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - A Benda
- Imaging Methods Core Facility, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - M Kostrouchová
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
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10
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Danko M, Hrdlovič P, Martinická A, Benda A, Cigáň M. Spectral properties of ionic benzotristhiazole based donor-acceptor NLO-phores in polymer matrices and their one- and two-photon cellular imaging ability. Photochem Photobiol Sci 2017; 16:1832-1844. [PMID: 29143829 DOI: 10.1039/c7pp00239d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A series of ionic benzotristhiazolium (BTT) push-pull chromophores, with different nitrogen donor groups and different lengths of conjugated bridges, was successfully doped in polar polymer matrices (PVC and PSS). The spectral (photophysical) properties of their low concentration thin polymeric films are compared with those in solution and are discussed in terms of matrix polarity/viscosity influence, specific polymer-chromophore interaction, structure-spectral property relationship and Twisted Intramolecular Charge-Transfer (TICT) state formation. The elimination of a non-emissive phantom and TICT state formation by restricted intramolecular rotations in the polymer matrix or viscous solvent results in a relatively high ΦF of all the investigated NLO-phores; particularly for near-infrared NIR molecular rotors bearing diphenylamino and julolidine donor groups. Because of cationic characteristics, small molecular weight, calculated high second hyperpolarizability and significant emission efficiency dependence on surroundings' viscosity (rigidochromic effect), two dyes were chosen as candidates for potential fluorescent probes for one-photon (1P) and two photon (2P) cellular imaging. The selected BTT NLO-phore with a julolidine donor is promising as a mitochondria-specific fluorescent small molecular probe for live cell super-resolution imaging with low cytotoxicity and good photostability, and is also potentially suitable for super-resolution STED imaging.
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Affiliation(s)
- M Danko
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovak Republic.
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11
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Huranová M, Ivani I, Benda A, Poser I, Brody Y, Hof M, Shav-Tal Y, Neugebauer KM, Stanek D. The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells. ACTA ACUST UNITED AC 2010; 191:75-86. [PMID: 20921136 PMCID: PMC2953428 DOI: 10.1083/jcb.201004030] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
GFP-tagged snRNP components reveal the dynamics and rate for spliceosome assembly in vivo. Precursor messenger RNA (pre-mRNA) splicing is catalyzed by the spliceosome, a large ribonucleoprotein (RNP) complex composed of five small nuclear RNP particles (snRNPs) and additional proteins. Using live cell imaging of GFP-tagged snRNP components expressed at endogenous levels, we examined how the spliceosome assembles in vivo. A comprehensive analysis of snRNP dynamics in the cell nucleus enabled us to determine snRNP diffusion throughout the nucleoplasm as well as the interaction rates of individual snRNPs with pre-mRNA. Core components of the spliceosome, U2 and U5 snRNPs, associated with pre-mRNA for 15–30 s, indicating that splicing is accomplished within this time period. Additionally, binding of U1 and U4/U6 snRNPs with pre-mRNA occurred within seconds, indicating that the interaction of individual snRNPs with pre-mRNA is distinct. These results are consistent with the predictions of the step-wise model of spliceosome assembly and provide an estimate on the rate of splicing in human cells.
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Affiliation(s)
- Martina Huranová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic
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12
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Říhová B, Etrych T, Šírová M, Kovář L, Hovorka O, Kovář M, Benda A, Ulbrich K. Synergistic Action of Doxorubicin Bound to the Polymeric Carrier Based on N-(2-Hydroxypropyl)methacrylamide Copolymers through an Amide or Hydrazone Bond. Mol Pharm 2010; 7:1027-40. [DOI: 10.1021/mp100121g] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- B. Říhová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic, Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovsky Sq. 2, 162 06 Prague 6, Czech Republic, and J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejskova 2155/3, 182 23 Prague 8, Czech Republic
| | - T. Etrych
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic, Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovsky Sq. 2, 162 06 Prague 6, Czech Republic, and J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejskova 2155/3, 182 23 Prague 8, Czech Republic
| | - M. Šírová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic, Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovsky Sq. 2, 162 06 Prague 6, Czech Republic, and J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejskova 2155/3, 182 23 Prague 8, Czech Republic
| | - L. Kovář
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic, Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovsky Sq. 2, 162 06 Prague 6, Czech Republic, and J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejskova 2155/3, 182 23 Prague 8, Czech Republic
| | - O. Hovorka
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic, Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovsky Sq. 2, 162 06 Prague 6, Czech Republic, and J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejskova 2155/3, 182 23 Prague 8, Czech Republic
| | - M. Kovář
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic, Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovsky Sq. 2, 162 06 Prague 6, Czech Republic, and J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejskova 2155/3, 182 23 Prague 8, Czech Republic
| | - A. Benda
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic, Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovsky Sq. 2, 162 06 Prague 6, Czech Republic, and J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejskova 2155/3, 182 23 Prague 8, Czech Republic
| | - K. Ulbrich
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic, Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovsky Sq. 2, 162 06 Prague 6, Czech Republic, and J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejskova 2155/3, 182 23 Prague 8, Czech Republic
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13
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Humpolícková J, Benda A, Enderlein J. Optical saturation as a versatile tool to enhance resolution in confocal microscopy. Biophys J 2010; 97:2623-9. [PMID: 19883606 DOI: 10.1016/j.bpj.2009.08.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/16/2009] [Accepted: 08/03/2009] [Indexed: 11/15/2022] Open
Abstract
One of the most actively developing areas in fluorescence microscopy is the achievement of spatial resolution below Abbe's diffraction limit, which restricts the resolution to several hundreds of nanometers. Most of the approaches in use at this time require a complex optical setup, a difficult mathematical treatment, or usage of dyes with special photophysical properties. In this work, we present a new, to our knowledge, approach in confocal microscopy that enhances the resolution moderately but is both technically and computationally simple. As it is based on the saturation of the transition from the ground state to the first excited state, it is universally applicable with respect to the dye used. The idea of the method presented is based on a principle similar to that underlying saturation excitation microscopy, but instead of applying harmonically modulated excitation light, the fluorophores are excited by picosecond laser pulses at different intensities, resulting in different levels of saturation. We show that the method can be easily combined with the concept of triplet relaxation, which by tuning the dark periods between pulses helps to suppress the formation of a photolabile triplet state and effectively reduces photobleaching. We demonstrate our approach imaging GFP-labeled protein patches within the plasma membrane of yeast cells.
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Affiliation(s)
- Jana Humpolícková
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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14
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Huranová M, Jablonski JA, Benda A, Hof M, Stanek D, Caputi M. In vivo detection of RNA-binding protein interactions with cognate RNA sequences by fluorescence resonance energy transfer. RNA 2009; 15:2063-2071. [PMID: 19767419 PMCID: PMC2764471 DOI: 10.1261/rna.1678209] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 08/12/2009] [Indexed: 05/28/2023]
Abstract
Expression of the nascent RNA transcript is regulated by its interaction with a number of proteins. The misregulation of such interactions can often result in impaired cellular functions that can lead to cancer and a number of diseases. Thus, our understanding of RNA-protein interactions within the cellular context is essential for the development of novel diagnostic and therapeutic tools. While there are many in vitro methods that analyze RNA-protein interactions in vivo approaches are scarce. Here we established a method based on fluorescence resonance energy transfer (FRET), which we term RNA-binding mediated FRET (RB-FRET), which determines RNA-protein interaction inside cells and tested it on hnRNP H protein binding to its cognate RNA. Using two different approaches, we provide evidence that RB-FRET is sensitive enough to detect specific RNA-protein interactions in the cell, providing a powerful tool to study spatial and temporal localization of specific RNA-protein complexes.
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Affiliation(s)
- Martina Huranová
- Department of RNA Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, CZ-14220 Prague 4, Czech Republic
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15
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Miszta A, Machán R, Benda A, Ouellette AJ, Hermens WT, Hof M. Combination of ellipsometry, laser scanning microscopy and Z-scan fluorescence correlation spectroscopy elucidating interaction of cryptdin-4 with supported phospholipid bilayers. J Pept Sci 2008; 14:503-9. [PMID: 17994618 DOI: 10.1002/psc.938] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The present study has two main objectives. The first is to characterize antimicrobial peptide (AMP) cryptdin-4 (Crp-4) interactions with biological membranes and to compare those interactions with those of magainin 2. The second is to combine the complementary experimental approaches of laser scanning microscopy (LSM), ellipsometry, and Z-scan fluorescence correlation spectroscopy (FCS) to acquire comprehensive information on mechanisms of AMP interactions with supported phospholipid bilayers (SPBs)-a popular model of biological membranes. LSM shows appearance of inhomogeneities in spatial distribution of lipids in the bilayer after treatment with Crp-4. Ellipsometric measurements show that binding of Crp-4 does not significantly change the lipid structure of the bilayer (increase in adsorbed mass without a change in thickness of adsorbed layer). Furthermore, Crp-4 slows the lateral diffusion of lipids within the membrane as shown by Z-scan FCS. All changes of the bilayer induced by Crp-4 can be partially reversed by flushing the sample with excess of buffer. Bilayer interactions of magainin 2 are significantly different, causing large loss of lipids and extensive damage to the bilayer. It seems likely that differences in peptide mode of action, readily distinguished using these combined experimental methods, are related to the distinctive beta-sheet and alpha-helical structures of the respective peptides.
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Affiliation(s)
- Adam Miszta
- J. Heyrovský Institute of Physical Chemistry v.v.i., Academy of Sciences of the Czech Republic, Czech Republic
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16
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Affiliation(s)
- J Hohlbein
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany
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17
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Abstract
This article explains the basic principles of FLCS, a genuine fusion of Time-Correlated Single Photon Counting (TCSPC) and Fluorescence Correlation Spectroscopy (FCS), using common terms and minimum mathematics. The usefulness of the method is demonstrated on simple FCS experiments. The method makes possible to separate the autocorrelation function of individual components of a mixture of fluorophores, as well as purging the result from parasitic contributions like scattered light or detector afterpulsing.
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Affiliation(s)
- Peter Kapusta
- PicoQuant GmbH, Rudower Chaussee 29, 12489 Berlin, Germany.
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18
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Benda A, Fagul'ová V, Deyneka A, Enderlein J, Hof M. Fluorescence lifetime correlation spectroscopy combined with lifetime tuning: new perspectives in supported phospholipid bilayer research. Langmuir 2006; 22:9580-5. [PMID: 17073482 DOI: 10.1021/la061573d] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A new concept based on fluorescence lifetime correlation spectroscopy (FLCS) is presented allowing the simultaneous determination of diffusion coefficients of identical molecules located in different environments. The difference in fluorescence lifetimes, which is the main prerequisite for FLCS, is reached by locating one population of the dye close to a light-absorbing surface. Since such surfaces quench fluorescence, the fluorescence lifetime of chromophores located close to these surfaces can be tuned in a specific manner. This approach has been demonstrated for a BODIPY-tail-labeled lipid in supported phospholipid bilayers (SPBs) as well as in phospholipid multilayers adsorbed onto solid supports. In particular, the effect of the solid support type on the fluorescence lifetime as well as its dependence on the BODIPY-support distance has been characterized and verified by theoretical considerations based on precise determination of refractive indices of the used supports. While the fluorescence lifetime of BODIPY dye is 5.6 ns in small unilamellar vesicles (SUVs) composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dioleoyl-sn-glycero-3-[phospho-L-serine] (DOPS), the lifetime is 1.8 ns in DOPC/DOPS SPBs adsorbed onto ITO-covered glass or 3.0 ns in a DOPC/DOPS monolayer adsorbed onto seven 1,2-dipalmitoyl-sn-glycero-3-phosphate (DPPA) layers on oxidized silicon. Using these particular systems, we demonstrated that FLCS enables one to characterize simultaneously two-dimensional lipid diffusion in the planar lipid layers and three-dimensional vesicle diffusion in bulk above the lipid layers using single dye labeling. The autocorrelation functions obtained by this new approach do agree with those obtained by standard FCS on isolated SPBs or vesicles. Possible applications of this virtual two-channel measurement using single dye labeling as well as one detection channel are discussed.
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Affiliation(s)
- Ales Benda
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejskova 3, 18223 Praha 8, Czech Republic
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19
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Dertinger T, von der Hocht I, Benda A, Hof M, Enderlein J. Surface sticking and lateral diffusion of lipids in supported bilayers. Langmuir 2006; 22:9339-44. [PMID: 17042551 DOI: 10.1021/la061389s] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The diffusion of fluorescently labeled lipids in supported bilayers is studied using two different methods: Z-scan fluorescence correlation spectroscopy (z-scan FCS) and two-focus fluorescence correlation spectroscopy (2f-FCS). It is found that the data can be fitted consistently only when taking into account partial sticking of the labeled lipids to the supporting glass surface. A kinetic reaction-diffusion model is developed and applied to the data. We find a very slow sticking rate which, however, when neglected, leads to strongly varying estimates of the free diffusion coefficient. The study reveals a strong sensitivity of FCS on even slight binding/unbinding kinetics of the labeled molecules, which has significance for related diffusion measurements in cellular lipid membranes.
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Affiliation(s)
- Thomas Dertinger
- Institute for Biological Information Processing I, Forschungszentrum Jülich, D-52425 Jülich, Germany
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20
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Przybylo M, Sýkora J, Humpolíckova J, Benda A, Zan A, Hof M. Lipid diffusion in giant unilamellar vesicles is more than 2 times faster than in supported phospholipid bilayers under identical conditions. Langmuir 2006; 22:9096-9. [PMID: 17042516 DOI: 10.1021/la061934p] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The lateral diffusion coefficients of a BODIPY tail-labeled lipid in two model systems, namely, free-standing giant unilamellar vesicles (GUVs) and supported phospholipid bilayers (SPBs), were determined by fluorescence correlation spectroscopy (FCS) using the Z-scan approach. For the first time, the performed measurements on 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers maintain exactly the same experimental conditions for both systems, which allows for a quantitative comparison of lipid diffusion in these two commonly used model membranes. The results obtained revealed that the lipid mobility in free-standing bilayers (D=7.8+/-0.8 microm2 s-1) is significantly higher than in the bilayer created on the solid support (mica) (D=3.1+/-0.3 microm2 s-1).
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Affiliation(s)
- Magdalena Przybylo
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejskova 3, 18223 Prague 8, Czech Republic
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21
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Humpolícková J, Gielen E, Benda A, Fagulova V, Vercammen J, Vandeven M, Hof M, Ameloot M, Engelborghs Y. Probing diffusion laws within cellular membranes by Z-scan fluorescence correlation spectroscopy. Biophys J 2006; 91:L23-5. [PMID: 16751239 PMCID: PMC1563743 DOI: 10.1529/biophysj.106.089474] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The plasma membrane of various mammalian cell types is heterogeneous in structure and may contain microdomains, which can impose constraints on the lateral diffusion of its constituents. Fluorescence correlation spectroscopy (FCS) can be used to investigate the dynamic properties of the plasma membrane of living cells. Very recently, Wawrezinieck et al. (Wawrezinieck, L., H. Rigneault, D. Marguet, and P. F. Lenne. 2005. Biophys. J. 89:4029-4042) described a method to probe the nature of the lateral microheterogeneities of the membrane by varying the beam size in the FCS instrument. The dependence of the width of the autocorrelation function at half-maximum, i.e., the diffusion time, on the transverse area of the confocal volume gives information on the nature of the imposed confinement. We describe an alternative approach that yields essentially the same information, and can readily be applied on commercial FCS instruments by measuring the diffusion time and the particle number at various relative positions of the cell membrane with respect to the waist of the laser beam, i.e., by performing a Z-scan.
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Affiliation(s)
- Jana Humpolícková
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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22
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Benes M, Billy D, Benda A, Speijer H, Hof M, Hermens WT. Surface-dependent transitions during self-assembly of phospholipid membranes on mica, silica, and glass. Langmuir 2004; 20:10129-10137. [PMID: 15518504 DOI: 10.1021/la048811u] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Formation of supported membranes by exposure of solid surfaces to phospholipid vesicles is a much-used technique in membrane research. Freshly cleaved mica, because of its superior flatness, is a preferred support, and we used ellipsometry to study membrane formation kinetics on mica. Neutral dioleoyl-phosphatidylcholine (DOPC) and negatively charged dioleoyl-phosphatidylserine/dioleoyl-phosphatidylcholine (20% DOPS/80% DOPC) vesicles were prepared by sonication. Results were compared with membrane formation on silica and glass, and the influence of stirring, buffer, and calcium was assessed. Without calcium, DOPC vesicles had a low affinity (Kd approximately 30 microM) for mica, and DOPS/DOPC vesicles hardly adsorbed. Addition of calcium promptly caused condensation of the adhering vesicles, with either loss of excess lipid or rapid additional lipid adsorption up to full surface coverage. Vesicle-mica interactions dominate the adsorption process, but vesicle-vesicle interactions also seem to be required for the condensation process. Membranes on mica proved unstable in Tris-HCl buffer. For glass, transport-limited adsorption of DOPC and DOPS/DOPC vesicles with immediate condensation into bilayers was observed, with and without calcium. For silica, vesicle adsorption was also rapid, even in the absence of calcium, but the transition to condensed layers required a critical surface coverage of about 50% of bilayer mass, indicating vesicle-vesicle interaction. For all three surfaces, additional adsorption of DOPC (but not DOPS/DOPC) vesicles to condensed membranes was observed. DOPC membranes on mica were rapidly degraded by phospholipase A2 (PLA2), which pleads against the role of membrane defects as initial PLA2 targets. During degradation, layer thickness remained unchanged while layer density decreased, in accordance with recent atomic force microscopy measurements of gel-phase phospholipid degradation by PLA2.
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Affiliation(s)
- Martin Benes
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Centre for Complex Molecular Systems and Biomolecules, Dolejskova 3, 18223 Prague, Czech Republic
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Sheynis T, Sykora J, Benda A, Kolusheva S, Hof M, Jelinek R. Bilayer localization of membrane-active peptides studied in biomimetic vesicles by visible and fluorescence spectroscopies. ACTA ACUST UNITED AC 2003; 270:4478-87. [PMID: 14622276 DOI: 10.1046/j.1432-1033.2003.03840.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Depth of bilayer penetration and effects on lipid mobility conferred by the membrane-active peptides magainin, melittin, and a hydrophobic helical sequence KKA(LA)7KK (denoted KAL), were investigated by colorimetric and time-resolved fluorescence techniques in biomimetic phospholipid/poly(diacetylene) vesicles. The experiments demonstrated that the extent of bilayer permeation and peptide localization within the membrane was dependent upon the bilayer composition, and that distinct dynamic modifications were induced by each peptide within the head-group environment of the phospholipids. Solvent relaxation, fluorescence correlation spectroscopy and fluorescence quenching analyses, employing probes at different locations within the bilayer, showed that magainin and melittin inserted close to the glycerol residues in bilayers incorporating negatively charged phospholipids, but predominant association at the lipid-water interface occurred in bilayers containing zwitterionic phospholipids. The fluorescence and colorimetric analyses also exposed the different permeation properties and distinct dynamic influence of the peptides: magainin exhibited the most pronounced interfacial attachment onto the vesicles, melittin penetrated more into the bilayers, while the KAL peptide inserted deepest into the hydrophobic core of the lipid assemblies. The solvent relaxation results suggest that decreasing the lipid fluidity might be an important initial factor contributing to the membrane activity of antimicrobial peptides.
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Affiliation(s)
- Tanya Sheynis
- Department of Chemistry and the Stadler Minerva Center for Mesoscopic Macromolecular Engineering, Ben Gurion University of the Negev, Beersheva, Israel
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Gräfner G, Eichhorn G, Benda A. [The role of the roe deer in the contamination of cattle pastures with lung worm larvae]. Monatsh Veterinarmed 1969; 24:412-4. [PMID: 4248377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Gräfner G, Graubmann HD, Benda A. [Propagation and impacts of hare's coccidiosis in Schwerin District]. Monatsh Veterinarmed 1967; 22:449-52. [PMID: 5627637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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