1
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Schaart JM, Kea-Te Lindert M, Roverts R, Nijhuis WH, Sommerdijk N, Akiva A. Cell-induced collagen alignment in a 3D in vitro culture during extracellular matrix production. J Struct Biol 2024; 216:108096. [PMID: 38697586 DOI: 10.1016/j.jsb.2024.108096] [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] [Received: 01/19/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/05/2024]
Abstract
The bone extracellular matrix consists of a highly organized collagen matrix that is mineralized with carbonated hydroxyapatite. Even though the structure and composition of bone have been studied extensively, the mechanisms underlying collagen matrix organization remain elusive. In this study, we used a 3D cell culture system in which osteogenic cells deposit and orient the collagen matrix that is subsequently mineralized. Using live fluorescence imaging combined with volume electron microscopy, we visualize the organization of the cells and collagen in the cell culture. We show that the osteogenically induced cells are organizing the collagen matrix during development. Based on the observation of tunnel-like structures surrounded by aligned collagen in the center of the culture, we propose that osteoblasts organize the deposited collagen during migration through the culture. Overall, we show that cell-matrix interactions are involved in collagen alignment during early-stage osteogenic differentiation and that the matrix is organized by the osteoblasts in the absence of osteoclast activity.
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Affiliation(s)
- Judith M Schaart
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525GA Nijmegen, The Netherlands
| | - Mariska Kea-Te Lindert
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525GA Nijmegen, The Netherlands; Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud University Medical Center, Geert Grooteplein Noord 29, 6525EZ Nijmegen, The Netherlands
| | - Rona Roverts
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525GA Nijmegen, The Netherlands; Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud University Medical Center, Geert Grooteplein Noord 29, 6525EZ Nijmegen, The Netherlands
| | - Wouter H Nijhuis
- Department of Orthopaedic Surgery, University Medical Centre Utrecht, Wilhelmina Children's Hospital, 3508GA Utrecht, The Netherlands
| | - Nico Sommerdijk
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525GA Nijmegen, The Netherlands; Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud University Medical Center, Geert Grooteplein Noord 29, 6525EZ Nijmegen, The Netherlands.
| | - Anat Akiva
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525GA Nijmegen, The Netherlands; Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud University Medical Center, Geert Grooteplein Noord 29, 6525EZ Nijmegen, The Netherlands.
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2
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Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, van der Net A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proc Natl Acad Sci U S A 2024; 121:e2313162121. [PMID: 38451946 PMCID: PMC10945838 DOI: 10.1073/pnas.2313162121] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/30/2023] [Indexed: 03/09/2024] Open
Abstract
Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water-collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H[Formula: see text]O/D[Formula: see text]O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H[Formula: see text]O and D[Formula: see text]O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D[Formula: see text]O than in H[Formula: see text]O, and collagen in D[Formula: see text]O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H[Formula: see text]O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D[Formula: see text]O is less hydrated than in H[Formula: see text]O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen-water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.
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Affiliation(s)
- Giulia Giubertoni
- Van ’t Hoff Institute for Molecular Sciences, Department of Molecular Photonics, University of Amsterdam, Amsterdam1090 GD, The Netherlands
| | - Liru Feng
- Van ’t Hoff Institute for Molecular Sciences, Department of Molecular Photonics, University of Amsterdam, Amsterdam1090 GD, The Netherlands
| | - Kevin Klein
- Institute of Science and Technology Austria, Division of Mathematical and Physical Sciences, Klosterneuburg3400, Austria
- University College London, Division of Physics and Astronomy, LondonWC1E 6BT, United Kingdom
| | - Guido Giannetti
- Van ’t Hoff Institute for Molecular Sciences, Department of Molecular Photonics, University of Amsterdam, Amsterdam1090 GD, The Netherlands
| | - Luco Rutten
- Electron Microscopy Center, Radboud Technology Center Microscopy, Department of Medical BioSciences, Radboud University Medical Center, Nijmegen6525 GA, The Netherlands
| | - Yeji Choi
- Max Planck Institute for Polymer Research, Molecular Spectroscopy Department, Mainz55128, Germany
| | - Anouk van der Net
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft2628 HZ, The Netherlands
| | - Gerard Castro-Linares
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft2628 HZ, The Netherlands
| | - Federico Caporaletti
- Van ’t Hoff Institute for Molecular Sciences, Department of Molecular Photonics, University of Amsterdam, Amsterdam1090 GD, The Netherlands
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, Amsterdam1090 GL, The Netherlands
| | - Dimitra Micha
- Amsterdam University Medical Centers, Human Genetics Department, Vrije Universiteit, Amsterdam1007 MB, The Netherlands
| | - Johannes Hunger
- Max Planck Institute for Polymer Research, Molecular Spectroscopy Department, Mainz55128, Germany
| | - Antoine Deblais
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, Amsterdam1090 GL, The Netherlands
| | - Daniel Bonn
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, Amsterdam1090 GL, The Netherlands
| | - Nico Sommerdijk
- Electron Microscopy Center, Radboud Technology Center Microscopy, Department of Medical BioSciences, Radboud University Medical Center, Nijmegen6525 GA, The Netherlands
| | - Andela Šarić
- Institute of Science and Technology Austria, Division of Mathematical and Physical Sciences, Klosterneuburg3400, Austria
| | - Ioana M. Ilie
- Van ’t Hoff Institute for Molecular Sciences, Department of Molecular Photonics, University of Amsterdam, Amsterdam1090 GD, The Netherlands
- Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam1090 GD, The Netherlands
| | - Gijsje H. Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft2628 HZ, The Netherlands
| | - Sander Woutersen
- Van ’t Hoff Institute for Molecular Sciences, Department of Molecular Photonics, University of Amsterdam, Amsterdam1090 GD, The Netherlands
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3
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Papadopoulou P, van der Pol R, van Hilten N, van Os WL, Pattipeiluhu R, Arias-Alpizar G, Knol RA, Noteborn W, Moradi MA, Ferraz MJ, Aerts JMFG, Sommerdijk N, Campbell F, Risselada HJ, Sevink GJA, Kros A. Phase-Separated Lipid-Based Nanoparticles: Selective Behavior at the Nano-Bio Interface. Adv Mater 2024; 36:e2310872. [PMID: 37988682 DOI: 10.1002/adma.202310872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 10/18/2023] [Indexed: 11/23/2023]
Abstract
The membrane-protein interface on lipid-based nanoparticles influences their in vivo behavior. Better understanding may evolve current drug delivery methods toward effective targeted nanomedicine. Previously, the cell-selective accumulation of a liposome formulation in vivo is demonstrated, through the recognition of lipid phase-separation by triglyceride lipases. This exemplified how liposome morphology and composition can determine nanoparticle-protein interactions. Here, the lipase-induced compositional and morphological changes of phase-separated liposomes-which bear a lipid droplet in their bilayer- are investigated, and the mechanism upon which lipases recognize and bind to the particles is unravelled. The selective lipolytic degradation of the phase-separated lipid droplet is observed, while nanoparticle integrity remains intact. Next, the Tryptophan-rich loop of the lipase is identified as the region with which the enzymes bind to the particles. This preferential binding is due to lipid packing defects induced on the liposome surface by phase separation. In parallel, the existing knowledge that phase separation leads to in vivo selectivity, is utilized to generate phase-separated mRNA-LNPs that target cell-subsets in zebrafish embryos, with subsequent mRNA delivery and protein expression. Together, these findings can expand the current knowledge on selective nanoparticle-protein communications and in vivo behavior, aspects that will assist to gain control of lipid-based nanoparticles.
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Affiliation(s)
- Panagiota Papadopoulou
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Rianne van der Pol
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Niek van Hilten
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Winant L van Os
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Roy Pattipeiluhu
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Gabriela Arias-Alpizar
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Renzo Aron Knol
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Willem Noteborn
- NeCEN, Leiden University, Einsteinweg 55, Leiden, 2333 AL, The Netherlands
| | - Mohammad-Amin Moradi
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P. O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - Maria Joao Ferraz
- Department of Medical Biochemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | | | - Nico Sommerdijk
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P. O. Box 513, Eindhoven, 5600 MB, The Netherlands
- Department of Medical BioSciences and Radboud Technology Center - Electron Microscopy, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Frederick Campbell
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Herre Jelger Risselada
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
- Department of Physics, Technical University Dortmund, 44221, Dortmund, Germany
| | - Geert Jan Agur Sevink
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Alexander Kros
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
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4
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Hassani Besheli N, Martens M, Macías-Sánchez E, Olijve J, Yang F, Sommerdijk N, Leeuwenburgh SCG. Unraveling the Formation of Gelatin Nanospheres by Means of Desolvation. Nano Lett 2023; 23:11091-11098. [PMID: 37967168 PMCID: PMC10722596 DOI: 10.1021/acs.nanolett.3c03459] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023]
Abstract
Gelatin nanoparticles (GNPs) have been widely studied for a plethora of biomedical applications, but their formation mechanism remains poorly understood, which precludes precise control over their physicochemical properties. This leads to time-consuming parameter adjustments without a fundamental grasp of the underlying mechanism. Here, we analyze and visualize in a time-resolved manner the mechanism by which GNPs are formed during desolvation of gelatin as a function of gelatin molecular weight and type of desolvating agent. Through various analytical and imaging techniques, we unveil a multistage process that is initiated by the formation of primary particles that are ∼18 nm in diameter (wet state). These primary particles subsequently assemble into colloidally stable GNPs with a raspberry-like structure and a hydrodynamic diameter of ∼300 nm. Our results create a basic understanding of the formation mechanism of gelatin nanoparticles, which opens new opportunities for precisely tuning their physicochemical and biofunctional properties.
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Affiliation(s)
- Negar Hassani Besheli
- Department
of Dentistry-Regenerative Biomaterials, Radboud University Medical Center, 6525 EX Nijmegen, The Netherlands
| | - Martijn Martens
- Department
of Medical BioSciences, Radboud University
Medical Center, Geert-Grooteplein
Zuid 28, 6525 GA Nijmegen, The Netherlands
- Electron
Microscopy Centre Radboudumc, Technology Center Microscopy, Radboud University Medical Center, Geert-Grooteplein Noord 29, 6525 GA Nijmegen, The Netherlands
| | - Elena Macías-Sánchez
- Department
of Medical BioSciences, Radboud University
Medical Center, Geert-Grooteplein
Zuid 28, 6525 GA Nijmegen, The Netherlands
- Department
of Stratigraphy and Paleontology, University
of Granada, Avenida de
la Fuente Nueva S/N, CP 18071 Granada, Spain
| | - Jos Olijve
- Rousselot
BV, Port Arthurlaan 173, 9000 Ghent, Belgium
| | - Fang Yang
- Department
of Dentistry-Regenerative Biomaterials, Radboud University Medical Center, 6525 EX Nijmegen, The Netherlands
| | - Nico Sommerdijk
- Department
of Medical BioSciences, Radboud University
Medical Center, Geert-Grooteplein
Zuid 28, 6525 GA Nijmegen, The Netherlands
- Electron
Microscopy Centre Radboudumc, Technology Center Microscopy, Radboud University Medical Center, Geert-Grooteplein Noord 29, 6525 GA Nijmegen, The Netherlands
| | - Sander C. G. Leeuwenburgh
- Department
of Dentistry-Regenerative Biomaterials, Radboud University Medical Center, 6525 EX Nijmegen, The Netherlands
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5
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Rutten L, de Beer M, Roverts R, Sánchez EM, Sommerdijk N. A Cryo-/Liquid Phase Correlative Light Electron Microscopy Workflow to Visualize Crystallization Processes in Graphene Liquid Cells. Microsc Microanal 2023; 29:1935-1936. [PMID: 37612957 DOI: 10.1093/micmic/ozad067.1002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Luco Rutten
- Department of Medical BioSciences, Research Institute for Medical Innovations, Radboud University Medical Center, Nijmegen, Netherlands
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marit de Beer
- Department of Medical BioSciences, Research Institute for Medical Innovations, Radboud University Medical Center, Nijmegen, Netherlands
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud University Medical Center, Nijmegen, Netherlands
| | - Rona Roverts
- Department of Medical BioSciences, Research Institute for Medical Innovations, Radboud University Medical Center, Nijmegen, Netherlands
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud University Medical Center, Nijmegen, Netherlands
| | - Elena Macías Sánchez
- Department of Medical BioSciences, Research Institute for Medical Innovations, Radboud University Medical Center, Nijmegen, Netherlands
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Stratigraphy and Palaeontolgy, University of Granada, Granada, Spain
| | - Nico Sommerdijk
- Department of Medical BioSciences, Research Institute for Medical Innovations, Radboud University Medical Center, Nijmegen, Netherlands
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud University Medical Center, Nijmegen, Netherlands
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6
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Carotti V, van Megen WH, Rigalli JP, Barros ER, Sommers V, Rutten L, Sommerdijk N, Peters DJM, van Asbeck-van der Wijst J, Hoenderop JGJ. Extracellular vesicles contribute to early cyst development in autosomal dominant polycystic kidney disease by cell-to-cell communication. FASEB J 2023; 37:e23006. [PMID: 37249915 DOI: 10.1096/fj.202300490r] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 05/31/2023]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is characterized by the formation of fluid-filled cysts within the kidney due to mutations in PKD1 or PKD2. Although the disease remains incompletely understood, one of the factors associated with ADPKD progression is the release of nucleotides (including ATP), which can initiate autocrine or paracrine purinergic signaling by binding to their receptors. Recently, we and others have shown that increased extracellular vesicle (EVs) release from PKD1 knockout cells can stimulate cyst growth through effects on recipient cells. Given that EVs are an important communicator between different nephron segments, we hypothesize that EVs released from PKD1 knockout distal convoluted tubule (DCT) cells can stimulate cyst growth in the downstream collecting duct (CD). Here, we show that administration of EVs derived from Pkd1-/- mouse distal convoluted tubule (mDCT15) cells result in a significant increase in extracellular ATP release from Pkd1-/- mouse inner medullary collecting duct (iMCD3) cells. In addition, exposure of Pkd1-/- iMCD3 cells to EVs derived from Pkd1-/- mDCT15 cells led to an increase in the phosphorylation of the serine/threonine-specific protein Akt, suggesting activation of proliferative pathways. Finally, the exposure of iMCD3 Pkd1-/- cells to mDCT15 Pkd1-/- EVs increased cyst size in Matrigel. These findings indicate that EVs could be involved in intersegmental communication between the distal convoluted tubule and the collecting duct and potentially stimulate cyst growth.
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Affiliation(s)
- Valentina Carotti
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wouter H van Megen
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Juan P Rigalli
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Eric R Barros
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Vera Sommers
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Luco Rutten
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nico Sommerdijk
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Joost G J Hoenderop
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
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7
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de Beer M, Daviran D, Roverts R, Rutten L, Macías-Sánchez E, Metz JR, Sommerdijk N, Akiva A. Precise targeting for 3D cryo-correlative light and electron microscopy volume imaging of tissues using a FinderTOP. Commun Biol 2023; 6:510. [PMID: 37169904 PMCID: PMC10175257 DOI: 10.1038/s42003-023-04887-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/28/2023] [Indexed: 05/13/2023] Open
Abstract
Cryo-correlative light and electron microscopy (cryoCLEM) is a powerful strategy to high resolution imaging in the unperturbed hydrated state. In this approach fluorescence microscopy aids localizing the area of interest, and cryogenic focused ion beam/scanning electron microscopy (cryoFIB/SEM) allows preparation of thin cryo-lamellae for cryoET. However, the current method cannot be accurately applied on bulky (3D) samples such as tissues and organoids. 3D cryo-correlative imaging of large volumes is needed to close the resolution gap between cryo-light microscopy and cryoET, placing sub-nanometer observations in a larger biological context. Currently technological hurdles render 3D cryoCLEM an unexplored approach. Here we demonstrate a cryoCLEM workflow for tissues, correlating cryo-Airyscan confocal microscopy with 3D cryoFIB/SEM volume imaging. Accurate correlation is achieved by imprinting a FinderTOP pattern in the sample surface during high pressure freezing, and allows precise targeting for cryoFIB/SEM volume imaging.
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Affiliation(s)
- Marit de Beer
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Deniz Daviran
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rona Roverts
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Luco Rutten
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elena Macías-Sánchez
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Stratigraphy and Paleontology, University of Granada, Granada, Spain
| | - Juriaan R Metz
- Department of Animal Ecology and Physiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Nico Sommerdijk
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands.
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Anat Akiva
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands.
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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8
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Arias-Alpizar G, Papadopoulou P, Rios X, Pulagam KR, Moradi MA, Pattipeiluhu R, Bussmann J, Sommerdijk N, Llop J, Kros A, Campbell F. Phase-Separated Liposomes Hijack Endogenous Lipoprotein Transport and Metabolism Pathways to Target Subsets of Endothelial Cells In Vivo. Adv Healthc Mater 2022; 12:e2202709. [PMID: 36565694 DOI: 10.1002/adhm.202202709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/14/2022] [Indexed: 12/25/2022]
Abstract
Plasma lipid transport and metabolism are essential to ensure correct cellular function throughout the body. Dynamically regulated in time and space, the well-characterized mechanisms underpinning plasma lipid transport and metabolism offers an enticing, but as yet underexplored, rationale to design synthetic lipid nanoparticles with inherent cell/tissue selectivity. Herein, a systemically administered liposome formulation, composed of just two lipids, that is capable of hijacking a triglyceride lipase-mediated lipid transport pathway resulting in liposome recognition and uptake within specific endothelial cell subsets is described. In the absence of targeting ligands, liposome-lipase interactions are mediated by a unique, phase-separated ("parachute") liposome morphology. Within the embryonic zebrafish, selective liposome accumulation is observed at the developing blood-brain barrier. In mice, extensive liposome accumulation within the liver and spleen - which is reduced, but not eliminated, following small molecule lipase inhibition - supports a role for endothelial lipase but highlights these liposomes are also subject to significant "off-target" by reticuloendothelial system organs. Overall, these compositionally simplistic liposomes offer new insights into the discovery and design of lipid-based nanoparticles that can exploit endogenous lipid transport and metabolism pathways to achieve cell selective targeting in vivo.
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Affiliation(s)
- Gabriela Arias-Alpizar
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, Leiden, 2300, The Netherlands.,Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, Leiden, 2300, The Netherlands
| | - Panagiota Papadopoulou
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, Leiden, 2300, The Netherlands
| | - Xabier Rios
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), San Sebastián, 20014, Spain
| | - Krishna Reddy Pulagam
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), San Sebastián, 20014, Spain
| | - Mohammad-Amin Moradi
- Materials and Interface Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600, The Netherlands
| | - Roy Pattipeiluhu
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, Leiden, 2300, The Netherlands
| | - Jeroen Bussmann
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, Leiden, 2300, The Netherlands.,Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, Leiden, 2300, The Netherlands
| | - Nico Sommerdijk
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525, The Netherlands.,Electron Microscopy Centre, Radboudumc Technology Center Microscopy, Radboud University Medical Center, Geert Grooteplein Zuid 28, Nijmegen, 6525, The Netherlands
| | - Jordi Llop
- Materials and Interface Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600, The Netherlands
| | - Alexander Kros
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, Leiden, 2300, The Netherlands
| | - Frederick Campbell
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, Leiden, 2300, The Netherlands
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9
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Kunnas P, Moradi MA, Sommerdijk N, de Jonge N. Strategy for optimizing experimental settings for studying low atomic number colloidal assemblies using liquid phase scanning transmission electron microscopy. Ultramicroscopy 2022; 240:113596. [PMID: 35908325 DOI: 10.1016/j.ultramic.2022.113596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 07/08/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022]
Abstract
Observing processes of nanoscale materials of low atomic number is possible using liquid phase electron microscopy (LP-EM). However, the achievable spatial resolution (d) is limited by radiation damage. Here, we examine a strategy for optimizing LP-EM experiments based on an analytical model and experimental measurements, and develop a method for quantifying image quality at ultra low electron dose De using scanning transmission electron microscopy (STEM). As experimental test case we study the formation of a colloidal binary system containing 30 nm diameter SiO2 nanoparticles (SiONPs), and 100 nm diameter polystyrene microspheres (PMs). We show that annular dark field (DF) STEM is preferred over bright field (BF) STEM for practical reasons. Precise knowledge of the material's density is crucial for the calculations in order to match experimental data. To calculate the detectability of nano-objects in an image, the Rose criterion for single pixels is expanded to a model of the signal to noise ratio obtained for multiple pixels spanning the image of an object. Using optimized settings, it is possible to visualize the radiation-sensitive, hierarchical low-Z binary structures, and identify both components.
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Affiliation(s)
- Peter Kunnas
- INM- Leibniz Institute for New Materials, Saarbrücken 66123, Germany; Faculty of Physics, Quantum Imaging and Biophysics, University of Vienna, Vienna 1090, Austria
| | - Mohammad-Amin Moradi
- Department of Chemical Engineering and Chemistry, Laboratory of Physical Chemistry, Eindhoven University of Technology, Eindhoven 5600 MB, the Netherlands
| | - Nico Sommerdijk
- Department of Biochemistry, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands
| | - Niels de Jonge
- INM- Leibniz Institute for New Materials, Saarbrücken 66123, Germany; Department of Physics, Saarland University, Saarbrücken 66123, Germany.
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10
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Pattipeiluhu R, Arias-Alpizar G, Basha G, Chan KYT, Bussmann J, Sharp TH, Moradi MA, Sommerdijk N, Harris EN, Cullis PR, Kros A, Witzigmann D, Campbell F. Anionic Lipid Nanoparticles Preferentially Deliver mRNA to the Hepatic Reticuloendothelial System. Adv Mater 2022; 34:e2201095. [PMID: 35218106 PMCID: PMC9461706 DOI: 10.1002/adma.202201095] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [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: 02/02/2022] [Indexed: 05/04/2023]
Abstract
Lipid nanoparticles (LNPs) are the leading nonviral technologies for the delivery of exogenous RNA to target cells in vivo. As systemic delivery platforms, these technologies are exemplified by Onpattro, an approved LNP-based RNA interference therapy, administered intravenously and targeted to parenchymal liver cells. The discovery of systemically administered LNP technologies capable of preferential RNA delivery beyond hepatocytes has, however, proven more challenging. Here, preceded by comprehensive mechanistic understanding of in vivo nanoparticle biodistribution and bodily clearance, an LNP-based messenger RNA (mRNA) delivery platform is rationally designed to preferentially target the hepatic reticuloendothelial system (RES). Evaluated in embryonic zebrafish, validated in mice, and directly compared to LNP-mRNA systems based on the lipid composition of Onpattro, RES-targeted LNPs significantly enhance mRNA expression both globally within the liver and specifically within hepatic RES cell types. Hepatic RES targeting requires just a single lipid change within the formulation of Onpattro to switch LNP surface charge from neutral to anionic. This technology not only provides new opportunities to treat liver-specific and systemic diseases in which RES cell types play a key role but, more importantly, exemplifies that rational design of advanced RNA therapies must be preceded by a robust understanding of the dominant nano-biointeractions involved.
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Affiliation(s)
- Roy Pattipeiluhu
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333 CC, The Netherlands
- BioNanoPatterning, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, 2333 RC, The Netherlands
| | - Gabriela Arias-Alpizar
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333 CC, The Netherlands
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, 2333 CC, The Netherlands
| | - Genc Basha
- NanoMedicines Research Group, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Karen Y T Chan
- NanoMedicines Research Group, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Jeroen Bussmann
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, 2333 CC, The Netherlands
| | - Thomas H Sharp
- BioNanoPatterning, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, 2333 RC, The Netherlands
| | - Mohammad-Amin Moradi
- Materials and Interface Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Nico Sommerdijk
- Department of Biochemistry, Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Edward N Harris
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA
| | - Pieter R Cullis
- NanoMedicines Research Group, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, V6T 1Z3, Canada
- NanoMedicines Innovation Network (NMIN), University of British Columbia, Vancouver, V6T 1Z3, Canada
- NanoVation Therapeutics Inc., 2405 Wesbrook Mall 4th Floor, Vancouver, V6T 1Z3, Canada
| | - Alexander Kros
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333 CC, The Netherlands
| | - Dominik Witzigmann
- NanoMedicines Research Group, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, V6T 1Z3, Canada
- NanoMedicines Innovation Network (NMIN), University of British Columbia, Vancouver, V6T 1Z3, Canada
- NanoVation Therapeutics Inc., 2405 Wesbrook Mall 4th Floor, Vancouver, V6T 1Z3, Canada
| | - Frederick Campbell
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333 CC, The Netherlands
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11
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Carotti V, van der Wijst J, Verschuren EHJ, Rutten L, Sommerdijk N, Kaffa C, Sommers V, Rigalli JP, Hoenderop JGJ. Involvement of ceramide biosynthesis in increased extracellular vesicle release in Pkd1 knock out cells. Front Endocrinol (Lausanne) 2022; 13:1005639. [PMID: 36299464 PMCID: PMC9589111 DOI: 10.3389/fendo.2022.1005639] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Autosomal Dominant Polycystic Kidney Disease (ADPKD) is an inherited disorder characterized by the development of renal cysts, which frequently leads to renal failure. Hypertension and other cardiovascular symptoms contribute to the high morbidity and mortality of the disease. ADPKD is caused by mutations in the PKD1 gene or, less frequently, in the PKD2 gene. The disease onset and progression are highly variable between patients, whereby the underlying mechanisms are not fully elucidated. Recently, a role of extracellular vesicles (EVs) in the progression of ADPKD has been postulated. However, the mechanisms stimulating EV release in ADPKD have not been addressed and the participation of the distal nephron segments is still uninvestigated. Here, we studied the effect of Pkd1 deficiency on EV release in wild type and Pkd1-/- mDCT15 and mIMCD3 cells as models of the distal convoluted tubule (DCT) and inner medullary collecting duct (IMCD), respectively. By using nanoparticle tracking analysis, we observed a significant increase in EV release in Pkd1-/- mDCT15 and mIMCD3 cells, with respect to the wild type cells. The molecular mechanisms leading to the changes in EV release were further investigated in mDCT15 cells through RNA sequencing and qPCR studies. Specifically, we assessed the relevance of purinergic signaling and ceramide biosynthesis enzymes. Pkd1-/- mDCT15 cells showed a clear upregulation of P2rx7 expression compared to wild type cells. Depletion of extracellular ATP by apyrase (ecto-nucleotidase) inhibited EV release only in wild type cells, suggesting an exacerbated signaling of the extracellular ATP/P2X7 pathway in Pkd1-/- cells. In addition, we identified a significant up-regulation of the ceramide biosynthesis enzymes CerS6 and Smpd3 in Pkd1-/- cells. Altogether, our findings suggest the involvement of the DCT in the EV-mediated ADPKD progression and points to the induction of ceramide biosynthesis as an underlying molecular mechanism. Further studies should be performed to investigate whether CerS6 and Smpd3 can be used as biomarkers of ADPKD onset, progression or severity.
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Affiliation(s)
- Valentina Carotti
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jenny van der Wijst
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Eric H. J. Verschuren
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Luco Rutten
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nico Sommerdijk
- Electron Microscopy Center, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Charlotte Kaffa
- Radboud Technology Center for Bioinformatics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Vera Sommers
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Juan P. Rigalli
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Joost G. J. Hoenderop
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
- *Correspondence: Joost G. J. Hoenderop,
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12
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Jansen J, Reimer KC, Nagai JS, Varghese FS, Overheul GJ, de Beer M, Roverts R, Daviran D, Fermin LA, Willemsen B, Beukenboom M, Djudjaj S, von Stillfried S, van Eijk LE, Mastik M, Bulthuis M, Dunnen WD, van Goor H, Hillebrands JL, Triana SH, Alexandrov T, Timm MC, van den Berge BT, van den Broek M, Nlandu Q, Heijnert J, Bindels EM, Hoogenboezem RM, Mooren F, Kuppe C, Miesen P, Grünberg K, Ijzermans T, Steenbergen EJ, Czogalla J, Schreuder MF, Sommerdijk N, Akiva A, Boor P, Puelles VG, Floege J, Huber TB, van Rij RP, Costa IG, Schneider RK, Smeets B, Kramann R, Achdout H, Aimon A, Bar-David E, Barr H, Ben-Shmuel A, Bennett J, Boby ML, Borden B, Bowman GR, Brun J, BVNBS S, Calmiano M, Carbery A, Cattermole E, Chernychenko E, Choder JD, Clyde A, Coffland JE, Cohen G, Cole J, Contini A, Cox L, Cvitkovic M, Dias A, Donckers K, Dotson DL, Douangamath A, Duberstein S, Dudgeon T, Dunnett L, Eastman PK, Erez N, Eyermann CJ, Fairhead M, Fate G, Fearon D, Federov O, Ferla M, Fernandes RS, Ferrins L, Foster R, Foster H, Gabizon R, Garcia-Sastre A, Gawriljuk VO, Gehrtz P, Gileadi C, Giroud C, Glass WG, Glen R, Itai glinert, Godoy AS, Gorichko M, Gorrie-Stone T, Griffen EJ, Hart SH, Heer J, Henry M, Hill M, Horrell S, Hurley MF, Israely T, Jajack A, Jnoff E, Jochmans D, John T, De Jonghe S, Kantsadi AL, Kenny PW, Kiappes J, Koekemoer L, Kovar B, Krojer T, Lee AA, Lefker BA, Levy H, London N, Lukacik P, Macdonald HB, Maclean B, Malla TR, Matviiuk T, McCorkindale W, McGovern BL, Melamed S, Michurin O, Mikolajek H, Milne BF, Morris A, Morris GM, Morwitzer MJ, Moustakas D, Nakamura AM, Neto JB, Neyts J, Nguyen L, Noske GD, Oleinikovas V, Oliva G, Overheul GJ, Owen D, Psenak V, Pai R, Pan J, Paran N, Perry B, Pingle M, Pinjari J, Politi B, Powell A, Puni R, Rangel VL, Reddi RN, Reid SP, Resnick E, Ripka EG, Robinson MC, Robinson RP, Rodriguez-Guerra J, Rosales R, Rufa D, Schofield C, Shafeev M, Shaikh A, Shi J, Shurrush K, Sing S, Sittner A, Skyner R, Smalley A, Smilova MD, Solmesky LJ, Spencer J, Strain-Damarell C, Swamy V, Tamir H, Tennant R, Thompson W, Thompson A, Thompson W, Tomasia S, Tumber A, Vakonakis I, van Rij RP, van Geel L, Varghese FS, Vaschetto M, Vitner EB, Voelz V, Volkamer A, von Delft F, von Delft A, Walsh M, Ward W, Weatherall C, Weiss S, White KM, Wild CF, Wittmann M, Wright N, Yahalom-Ronen Y, Zaidmann D, Zidane H, Zitzmann N. SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids. Cell Stem Cell 2021; 29:217-231.e8. [PMID: 35032430 PMCID: PMC8709832 DOI: 10.1016/j.stem.2021.12.010] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 09/03/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022]
Abstract
Kidney failure is frequently observed during and after COVID-19, but it remains elusive whether this is a direct effect of the virus. Here, we report that SARS-CoV-2 directly infects kidney cells and is associated with increased tubule-interstitial kidney fibrosis in patient autopsy samples. To study direct effects of the virus on the kidney independent of systemic effects of COVID-19, we infected human-induced pluripotent stem-cell-derived kidney organoids with SARS-CoV-2. Single-cell RNA sequencing indicated injury and dedifferentiation of infected cells with activation of profibrotic signaling pathways. Importantly, SARS-CoV-2 infection also led to increased collagen 1 protein expression in organoids. A SARS-CoV-2 protease inhibitor was able to ameliorate the infection of kidney cells by SARS-CoV-2. Our results suggest that SARS-CoV-2 can directly infect kidney cells and induce cell injury with subsequent fibrosis. These data could explain both acute kidney injury in COVID-19 patients and the development of chronic kidney disease in long COVID. COVID-19 patients present tubulo-interstitial kidney fibrosis compared with controls SARS-CoV-2 infection stimulates profibrotic signaling in human kidney organoids SARS-CoV-2 infection can be inhibited by a protease blocker in human kidney organoids
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13
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Van Driessche AES, Van Gerven N, Joosten RRM, Ling WL, Bacia M, Sommerdijk N, Sleutel M. Nucleation of protein mesocrystals via oriented attachment. Nat Commun 2021; 12:3902. [PMID: 34162863 PMCID: PMC8222410 DOI: 10.1038/s41467-021-24171-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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] [Received: 08/26/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
Self-assembly of proteins holds great promise for the bottom-up design and production of synthetic biomaterials. In conventional approaches, designer proteins are pre-programmed with specific recognition sites that drive the association process towards a desired organized state. Although proven effective, this approach poses restrictions on the complexity and material properties of the end-state. An alternative, hierarchical approach that has found wide adoption for inorganic systems, relies on the production of crystalline nanoparticles that become the building blocks of a next-level assembly process driven by oriented attachment (OA). As it stands, OA has not yet been observed for protein systems. Here we employ cryo-transmission electron microscopy (cryoEM) in the high nucleation rate limit of protein crystals and map the self-assembly route at molecular resolution. We observe the initial formation of facetted nanocrystals that merge lattices by means of OA alignment well before contact is made, satisfying non-trivial symmetry rules in the process. As these nanocrystalline assemblies grow larger we witness imperfect docking events leading to oriented aggregation into mesocrystalline assemblies. These observations highlight the underappreciated role of the interaction between crystalline nuclei, and the impact of OA on the crystallization process of proteins.
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Affiliation(s)
| | - Nani Van Gerven
- grid.8767.e0000 0001 2290 8069Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium ,grid.11486.3a0000000104788040Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Brussels, Belgium
| | - Rick R. M. Joosten
- grid.6852.90000 0004 0398 8763Department of Chemical Engineering and Chemistry, Center of Multiscale Electron Microscopy, Eindhoven University of Technology, Eindhoven, The Netherlands ,grid.6852.90000 0004 0398 8763Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Wai Li Ling
- grid.450307.5Univ. Grenoble Alpes, CEA, CNRS, IRIG, IBS, Grenoble, France
| | - Maria Bacia
- grid.450307.5Univ. Grenoble Alpes, CEA, CNRS, IRIG, IBS, Grenoble, France
| | - Nico Sommerdijk
- grid.10417.330000 0004 0444 9382Department of Biochemistry, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein, GA Nijmegen, The Netherlands
| | - Mike Sleutel
- grid.8767.e0000 0001 2290 8069Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium ,grid.11486.3a0000000104788040Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Brussels, Belgium
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14
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Moradi MA, Eren ED, Chiappini M, Rzadkiewicz S, Goudzwaard M, van Rijt MMJ, Keizer ADA, Routh AF, Dijkstra M, de With G, Sommerdijk N, Friedrich H, Patterson JP. Spontaneous organization of supracolloids into three-dimensional structured materials. Nat Mater 2021; 20:541-547. [PMID: 33510444 DOI: 10.1038/s41563-020-00900-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 12/04/2020] [Indexed: 05/16/2023]
Abstract
Periodic nano- or microscale structures are used to control light, energy and mass transportation. Colloidal organization is the most versatile method used to control nano- and microscale order, and employs either the enthalpy-driven self-assembly of particles at a low concentration or the entropy-driven packing of particles at a high concentration. Nonetheless, it cannot yet provide the spontaneous three-dimensional organization of multicomponent particles at a high concentration. Here we combined these two concepts into a single strategy to achieve hierarchical multicomponent materials. We tuned the electrostatic attraction between polymer and silica nanoparticles to create dynamic supracolloids whose components, on drying, reorganize by entropy into three-dimensional structured materials. Cryogenic electron tomography reveals the kinetic pathways, whereas Monte Carlo simulations combined with a kinetic model provide design rules to form the supracolloids and control the kinetic pathways. This approach may be useful to fabricate hierarchical hybrid materials for distinct technological applications.
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Affiliation(s)
- Mohammad-Amin Moradi
- Laboratory of Materials and Interface Chemistry and Centre for Multiscale Electron Microscopy, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - E Deniz Eren
- Laboratory of Materials and Interface Chemistry and Centre for Multiscale Electron Microscopy, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Massimiliano Chiappini
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Sebastian Rzadkiewicz
- Laboratory of Materials and Interface Chemistry and Centre for Multiscale Electron Microscopy, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Maurits Goudzwaard
- Laboratory of Materials and Interface Chemistry and Centre for Multiscale Electron Microscopy, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Mark M J van Rijt
- Laboratory of Materials and Interface Chemistry and Centre for Multiscale Electron Microscopy, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Arthur D A Keizer
- Laboratory of Materials and Interface Chemistry and Centre for Multiscale Electron Microscopy, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Alexander F Routh
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Marjolein Dijkstra
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Gijsbertus de With
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Nico Sommerdijk
- Laboratory of Materials and Interface Chemistry and Centre for Multiscale Electron Microscopy, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Heiner Friedrich
- Laboratory of Materials and Interface Chemistry and Centre for Multiscale Electron Microscopy, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Joseph P Patterson
- Laboratory of Materials and Interface Chemistry and Centre for Multiscale Electron Microscopy, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Department of Chemistry, University of California, Irvine (UCI), Irvine, CA, USA.
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15
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Heiligenstein X, de Beer M, Heiligenstein J, Eyraud F, Manet L, Schmitt F, Lamers E, Lindenau J, Kea-Te Lindert M, Salamero J, Raposo G, Sommerdijk N, Belle M, Akiva A. HPM live μ for a full CLEM workflow. Methods Cell Biol 2021; 162:115-149. [PMID: 33707009 DOI: 10.1016/bs.mcb.2020.10.022] [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] [Indexed: 02/08/2023]
Abstract
With the development of advanced imaging methods that took place in the last decade, the spatial correlation of microscopic and spectroscopic information-known as multimodal imaging or correlative microscopy (CM)-has become a broadly applied technique to explore biological and biomedical materials at different length scales. Among the many different combinations of techniques, Correlative Light and Electron Microscopy (CLEM) has become the flagship of this revolution. Where light (mainly fluorescence) microscopy can be used directly for the live imaging of cells and tissues, for almost all applications, electron microscopy (EM) requires fixation of the biological materials. Although sample preparation for EM is traditionally done by chemical fixation and embedding in a resin, rapid cryogenic fixation (vitrification) has become a popular way to avoid the formation of artifacts related to the chemical fixation/embedding procedures. During vitrification, the water in the sample transforms into an amorphous ice, keeping the ultrastructure of the biological sample as close as possible to the native state. One immediate benefit of this cryo-arrest is the preservation of protein fluorescence, allowing multi-step multi-modal imaging techniques for CLEM. To minimize the delay separating live imaging from cryo-arrest, we developed a high-pressure freezing (HPF) system directly coupled to a light microscope. We address the optimization of sample preservation and the time needed to capture a biological event, going from live imaging to cryo-arrest using HPF. To further explore the potential of cryo-fixation related to the forthcoming transition from imaging 2D (cell monolayers) to imaging 3D samples (tissue) and the associated importance of homogeneous deep vitrification, the HPF core technology has been revisited to allow easy modification of the environmental parameters during vitrification. Lastly, we will discuss the potential of our HPM within CLEM protocols especially for correlating live imaging using the Zeiss LSM900 with electron microscopy.
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Affiliation(s)
| | - Marit de Beer
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Cell Biology, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Biochemistry, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | | | | | | | | | - Mariska Kea-Te Lindert
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Cell Biology, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jean Salamero
- SERPICO Inria Team/UMR 144 CNRS & National Biology and Health Infrastructure "France Bioimaging", Institut Curie, Paris, France
| | - Graça Raposo
- Institut Curie, PSL Research University, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France; Institut Curie, PSL Research University, CNRS, UMR144, Structure and Membrane Compartments, Paris, France
| | - Nico Sommerdijk
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Biochemistry, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Anat Akiva
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Cell Biology, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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Xu Y, Nudelman F, Eren ED, Wirix MJM, Cantaert B, Nijhuis WH, Hermida-Merino D, Portale G, Bomans PHH, Ottmann C, Friedrich H, Bras W, Akiva A, Orgel JPRO, Meldrum FC, Sommerdijk N. Intermolecular channels direct crystal orientation in mineralized collagen. Nat Commun 2020; 11:5068. [PMID: 33033251 PMCID: PMC7545172 DOI: 10.1038/s41467-020-18846-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [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] [Received: 03/20/2020] [Accepted: 08/27/2020] [Indexed: 12/27/2022] Open
Abstract
The mineralized collagen fibril is the basic building block of bone, and is commonly pictured as a parallel array of ultrathin carbonated hydroxyapatite (HAp) platelets distributed throughout the collagen. This orientation is often attributed to an epitaxial relationship between the HAp and collagen molecules inside 2D voids within the fibril. Although recent studies have questioned this model, the structural relationship between the collagen matrix and HAp, and the mechanisms by which collagen directs mineralization remain unclear. Here, we use XRD to reveal that the voids in the collagen are in fact cylindrical pores with diameters of ~2 nm, while electron microscopy shows that the HAp crystals in bone are only uniaxially oriented with respect to the collagen. From in vitro mineralization studies with HAp, CaCO3 and γ-FeOOH we conclude that confinement within these pores, together with the anisotropic growth of HAp, dictates the orientation of HAp crystals within the collagen fibril.
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Affiliation(s)
- YiFei Xu
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Center for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Fabio Nudelman
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Center for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,School of Chemistry, University of Edinburgh, Joseph Black Building, The King's Buildings, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - E Deniz Eren
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Chemical Engineering and Chemistry, Laboratory of Physical Chemistry, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Maarten J M Wirix
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Center for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Bram Cantaert
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Wouter H Nijhuis
- Department of Orthopaedic Surgery, University Medical Centre Utrecht, Wilhelmina Children's Hospital, Utrecht, The Netherlands
| | - Daniel Hermida-Merino
- Netherlands Organization for Scientific Research (NWO), DUBBLE@ESRF, BP220, F38043, Grenoble, France
| | - Giuseppe Portale
- Netherlands Organization for Scientific Research (NWO), DUBBLE@ESRF, BP220, F38043, Grenoble, France.,Macromolecular Science and New Polymeric Materials, Zernike Institute for Advanced Materials, University of Groningen, Nijemborg 4, 9747, Groningen, The Netherlands
| | - Paul H H Bomans
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Center for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Christian Ottmann
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Heiner Friedrich
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Chemical Engineering and Chemistry, Laboratory of Physical Chemistry, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Wim Bras
- Netherlands Organization for Scientific Research (NWO), DUBBLE@ESRF, BP220, F38043, Grenoble, France.,Chemical Sciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Anat Akiva
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Center for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Cell Biology, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein, 6525 GA, Nijmegen, The Netherlands
| | - Joseph P R O Orgel
- Departments of Biology, Physics and Biomedical Engineering, Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA.
| | - Fiona C Meldrum
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - Nico Sommerdijk
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Center for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands. .,Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands. .,Department of Biochemistry, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein, 6525 GA, Nijmegen, The Netherlands.
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Egorova E, van Rijt MMJ, Sommerdijk N, Gooris GS, Bouwstra JA, Boyle AL, Kros A. One Peptide for Them All: Gold Nanoparticles of Different Sizes Are Stabilized by a Common Peptide Amphiphile. ACS Nano 2020; 14:5874-5886. [PMID: 32348119 PMCID: PMC7254838 DOI: 10.1021/acsnano.0c01021] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The functionalization of gold nanoparticles (GNPs) with peptidic moieties can prevent their aggregation and facilitate their use for applications both in vitro and in vivo. To date, no peptide-based coating has been shown to stabilize GNPs larger than 30 nm in diameter; such particles are of interest for applications including vaccine development, drug delivery, and sensing. Here, GNPs with diameters of 20, 40, and 100 nm are functionalized with peptide amphiphiles. Using a combination of transmission electron microscopy, UV-vis spectroscopy, and dynamic light scattering, we show that GNPs up to 100 nm in size can be stabilized by these molecules. Moreover, we demonstrate that these peptide amphiphiles form curvature-dependent, ordered structures on the surface of the GNPs and that the GNPs remain disperse at high-salt concentrations and in the presence of competing thiol-containing molecules. These results represent the development of a peptide amphiphile-based coating system for GNPs which has the potential to be beneficial for a wide range of biological applications, in addition to image enhancement and catalysis.
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Affiliation(s)
- Elena
A. Egorova
- Department
of Supramolecular and Biomaterials Chemistry, Leiden Institute of
Chemistry, Leiden University, Leiden 2333 CC, The Netherlands
| | - Mark M. J. van Rijt
- Laboratory
of Physical Chemistry and the Centre for Multiscale Electron Microscopy,
Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven 5600 MB, The
Netherlands
| | - Nico Sommerdijk
- Radboud
Institute for Molecular Life Sciences, Radboud
University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Gert S. Gooris
- Division
of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Joke A. Bouwstra
- Division
of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Aimee L. Boyle
- Department
of Supramolecular and Biomaterials Chemistry, Leiden Institute of
Chemistry, Leiden University, Leiden 2333 CC, The Netherlands
| | - Alexander Kros
- Department
of Supramolecular and Biomaterials Chemistry, Leiden Institute of
Chemistry, Leiden University, Leiden 2333 CC, The Netherlands
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Sun W, Booth S, Myerson A, Hughes C, Pan H, Coquerel G, Brandel C, Meekes H, Mazzotti M, Fabian L, Black S, Vekilov P, Back K, Toroz D, Lovelock J, Sefcik J, Rasmuson A, Breynaert E, Sear R, Hammond R, Ward M, Threlfall T, De Yoreo J, Davey R, Ristic R, Lewtas K, Roberts K, Hare A, Gich M, Cölfen H, Likhatskiy M, ter Horst J, Sommerdijk N. Time and space resolved methods: general discussion. Faraday Discuss 2015; 179:247-67. [DOI: 10.1039/c5fd90037a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Goos JACM, Vo CD, Dey A, van den Hoogen CJ, Lousberg NJHGM, Hendrix MMRM, Tirelli N, de With G, Sommerdijk N, Sommerdijk N. Biomimetic synthesis of calcium carbonate bilayers interfaced by a diblock copolymer template. Z KRIST-CRYST MATER 2012. [DOI: 10.1524/zkri.2012.1525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
The synthesis of a new class of hybrid materials with two differently oriented layers of calcite at adjacent sides of an organic template is demonstrated. A Langmuir monolayer of the amphiphilic block copolymer poly(butyl acrylate)-b-poly(hydroxypropyl acrylate) directs the formation of a first CaCO3 phase through interaction with the hydrophilic poly(hydroxypropyl acrylate) blocks. After partial hydrolysis of the hydrophobic poly(butyl acrylate) segments a second CaCO3 phase is formed on the monolayer associated to the first mineral phase. Thus, bilayered CaCO3-based hybrid materials are obtained with two differently oriented calcite phases at opposite sides of the polymer film. By using DNA as an additive the crystal orientation in the second layer can be modified.
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