1
|
van der Beek J, de Heus C, Sanza P, Liv N, Klumperman J. Loss of the HOPS complex disrupts early-to-late endosome transition, impairs endosomal recycling and induces accumulation of amphisomes. Mol Biol Cell 2024; 35:ar40. [PMID: 38198575 PMCID: PMC10916860 DOI: 10.1091/mbc.e23-08-0328] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/22/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024] Open
Abstract
The multisubunit HOPS tethering complex is a well-established regulator of lysosome fusion with late endosomes and autophagosomes. However, the role of the HOPS complex in other stages of endo-lysosomal trafficking is not well understood. To address this, we made HeLa cells knocked out for the HOPS-specific subunits Vps39 or Vps41, or the HOPS-CORVET-core subunits Vps18 or Vps11. In all four knockout cells, we found that endocytosed cargos were trapped in enlarged endosomes that clustered in the perinuclear area. By correlative light-electron microscopy, these endosomes showed a complex ultrastructure and hybrid molecular composition, displaying markers for early (Rab5, PtdIns3P, EEA1) as well as late (Rab7, CD63, LAMP1) endosomes. These "HOPS bodies" were not acidified, contained enzymatically inactive cathepsins and accumulated endocytosed cargo and cation-independent mannose-6-phosphate receptor (CI-MPR). Consequently, CI-MPR was depleted from the TGN, and secretion of lysosomal enzymes to the extracellular space was enhanced. Strikingly, HOPS bodies also contained the autophagy proteins p62 and LC3, defining them as amphisomes. Together, these findings show that depletion of the lysosomal HOPS complex has a profound impact on the functional organization of the entire endosomal system and suggest the existence of a HOPS-independent mechanism for amphisome formation.
Collapse
Affiliation(s)
- Jan van der Beek
- Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Cecilia de Heus
- Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Paolo Sanza
- Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Nalan Liv
- Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Judith Klumperman
- Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, 3584 CX Utrecht, The Netherlands
| |
Collapse
|
2
|
de Heus C, Fermie J, Loginov S, Gerritsen HC, Klumperman J, Liv N. Correlative Live-cell-volume Electron Microscopy: Bridging Cellular Dynamics to 3D-Ultrastructure. Microsc Microanal 2023; 29:1188. [PMID: 37613701 DOI: 10.1093/micmic/ozad067.612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Cecilia de Heus
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Job Fermie
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands
| | - Sergey Loginov
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands
| | - Hans C Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands
| | - Judith Klumperman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Nalan Liv
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| |
Collapse
|
3
|
Liv N, Fermie J, Ten Brink CBM, de Heus C, Klumperman J. Functional characterization of endo-lysosomal compartments by correlative live-cell and volume electron microscopy. Methods Cell Biol 2023; 177:301-326. [PMID: 37451771 DOI: 10.1016/bs.mcb.2022.12.022] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Fluorescent biosensors are valuable tools to monitor protein activities and the functional state of organelles in live cells. However, the information provided by fluorescent microscopy (FM) is mostly limited in resolution and lacks ultrastructural context information. Protein activities are confined to organelle zones with a distinct membrane morphology, which can only be seen by electron microscopy (EM). EM, however, intrinsically lacks information on protein activities. The lack of methods to integrate these two imaging modalities has hampered understanding the functional organization of cellular organelles. Here we introduce "functional correlative microscopy" (functional CLEM) to directly infer functional information from live cells to EM with nanometer resolution. We label and visualize live cells with fluorescent biosensors after which they are processed for EM and imaged using a volume electron microscopy technique. Within a single dataset we correlate hundreds of fluorescent spots enabling quantitative analysis of the functional-ultrastructural data. We employ our method to monitor essential functional parameters of late endo-lysosomal compartments, i.e., pH, calcium, enzyme activities and cholesterol content. Our data reveal a steep functional difference in enzyme activity between late endosomes and lysosomes and unexpectedly high calcium levels in late endosomes. The presented CLEM workflow is compatible with a large repertoire of probes and paves the way for large scale functional studies of all types of cellular structures.
Collapse
Affiliation(s)
- Nalan Liv
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
| | - Job Fermie
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands; Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Corlinda B M Ten Brink
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Cecilia de Heus
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Judith Klumperman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
4
|
van der Beek J, Veenendaal T, de Heus C, van Dijk S, Ten Brink C, Liv N, Klumperman J. Ultrastructural Localization of Endogenous LC3 by On-Section Correlative Light-Electron Microscopy. J Vis Exp 2023. [PMID: 37067272 DOI: 10.3791/65067] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
The visualization of autophagic organelles at the ultrastructural level by electron microscopy (EM) is essential to establish their identity and reveal details that are important for understanding the autophagic process. However, EM methods often lack molecular information, obstructing the correlation of ultrastructural information obtained by EM to fluorescence microscopy-based localization of specific autophagy proteins. Furthermore, the rarity of autophagosomes in unaltered cellular conditions hampers investigation by EM, which requires high magnification, and hence provides a limited field of view. In answer to both challenges, an on-section correlative light-electron microscopy (CLEM) method based on fluorescent labeling was applied to correlate a common autophagosomal marker, LC3, to EM ultrastructure. The method was used to rapidly screen cells in fluorescence microscopy for LC3 labeling in combination with other relevant markers. Subsequently, the underlying ultrastructural features of selected LC3-labeled spots were identified by CLEM. The method was applied to starved cells without adding inhibitors of lysosomal acidification. In these conditions, LC3 was found predominantly on autophagosomes and rarely in autolysosomes, in which LC3 is rapidly degraded. These data show both the feasibility and sensitivity of this approach, demonstrating that CLEM can be used to provide ultrastructural insights on LC3-mediated autophagy in native conditions-without drug treatments or genetic alterations. Overall, this method presents a valuable tool for ultrastructural localization studies of autophagy proteins and other scarce antigens by bridging light microscopy to EM data.
Collapse
Affiliation(s)
- Jan van der Beek
- Center for Molecular Medicine-Cell Biology, University Medical Center Utrecht, Utrecht University
| | - Tineke Veenendaal
- Center for Molecular Medicine-Cell Biology, University Medical Center Utrecht, Utrecht University
| | - Cecilia de Heus
- Center for Molecular Medicine-Cell Biology, University Medical Center Utrecht, Utrecht University
| | - Suzanne van Dijk
- Center for Molecular Medicine-Cell Biology, University Medical Center Utrecht, Utrecht University
| | - Corlinda Ten Brink
- Center for Molecular Medicine-Cell Biology, University Medical Center Utrecht, Utrecht University
| | - Nalan Liv
- Center for Molecular Medicine-Cell Biology, University Medical Center Utrecht, Utrecht University
| | - Judith Klumperman
- Center for Molecular Medicine-Cell Biology, University Medical Center Utrecht, Utrecht University;
| |
Collapse
|
5
|
Rawat S, Chatterjee D, Marwaha R, Charak G, Kumar G, Shaw S, Khatter D, Sharma S, de Heus C, Liv N, Klumperman J, Tuli A, Sharma M. RUFY1 binds Arl8b and mediates endosome-to-TGN CI-M6PR retrieval for cargo sorting to lysosomes. J Cell Biol 2023; 222:e202108001. [PMID: 36282215 PMCID: PMC9597352 DOI: 10.1083/jcb.202108001] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/26/2022] [Accepted: 09/29/2022] [Indexed: 11/22/2022] Open
Abstract
Arl8b, an Arf-like GTP-binding protein, regulates cargo trafficking and positioning of lysosomes. However, it is unknown whether Arl8b regulates lysosomal cargo sorting. Here, we report that Arl8b binds to the Rab4 and Rab14 interaction partner, RUN and FYVE domain-containing protein (RUFY) 1, a known regulator of cargo sorting from recycling endosomes. Arl8b determines RUFY1 endosomal localization through regulating its interaction with Rab14. RUFY1 depletion led to a delay in CI-M6PR retrieval from endosomes to the TGN, resulting in impaired delivery of newly synthesized hydrolases to lysosomes. We identified the dynein-dynactin complex as an RUFY1 interaction partner, and similar to a subset of activating dynein adaptors, the coiled-coil region of RUFY1 was required for interaction with dynein and the ability to mediate dynein-dependent organelle clustering. Our findings suggest that Arl8b and RUFY1 play a novel role on recycling endosomes, from where this machinery regulates endosomes to TGN retrieval of CI-M6PR and, consequently, lysosomal cargo sorting.
Collapse
Affiliation(s)
- Shalini Rawat
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali (IISERM), Punjab, India
| | - Dhruba Chatterjee
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali (IISERM), Punjab, India
| | - Rituraj Marwaha
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali (IISERM), Punjab, India
| | - Gitanjali Charak
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali (IISERM), Punjab, India
| | - Gaurav Kumar
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Shrestha Shaw
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali (IISERM), Punjab, India
| | - Divya Khatter
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali (IISERM), Punjab, India
| | - Sheetal Sharma
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Cecilia de Heus
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Amit Tuli
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Mahak Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali (IISERM), Punjab, India
| |
Collapse
|
6
|
Ferro R, Carroll A, Mendes-Pereira A, Reen V, Roxanis I, Annunziato S, Jonkers J, Liv N, Alexander J, Quist J, Pardo M, Roumeliotis T, Choudhary J, Weekes D, Marra P, Natrajan R, Grigoriadis A, Haider S, Lord C, Tutt A. The anion channel GPR89 is a novel oncogene associated with tumour specific dependency in breast cancer. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)00934-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
7
|
Fermie J, de Jager L, Foster HE, Veenendaal T, de Heus C, van Dijk S, ten Brink C, Oorschot V, Yang L, Li W, Müller WH, Howes S, Carter AP, Förster F, Posthuma G, Gerritsen HC, Klumperman J, Liv N. Bimodal endocytic probe for three-dimensional correlative light and electron microscopy. Cell Rep Methods 2022; 2:100220. [PMID: 35637912 PMCID: PMC9142762 DOI: 10.1016/j.crmeth.2022.100220] [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] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 02/04/2022] [Accepted: 04/26/2022] [Indexed: 12/03/2022]
Abstract
We present a bimodal endocytic tracer, fluorescent BSA-gold (fBSA-Au), as a fiducial marker for 2D and 3D correlative light and electron microscopy (CLEM) applications. fBSA-Au consists of colloidal gold (Au) particles stabilized with fluorescent BSA. The conjugate is efficiently endocytosed and distributed throughout the 3D endolysosomal network of cells and has an excellent visibility in both fluorescence microscopy (FM) and electron microscopy (EM). We demonstrate that fBSA-Au facilitates rapid registration in several 2D and 3D CLEM applications using Tokuyasu cryosections, resin-embedded material, and cryoelectron microscopy (cryo-EM). Endocytosed fBSA-Au benefits from a homogeneous 3D distribution throughout the endosomal system within the cell, does not obscure any cellular ultrastructure, and enables accurate (50-150 nm) correlation of fluorescence to EM data. The broad applicability and visibility in both modalities makes fBSA-Au an excellent endocytic fiducial marker for 2D and 3D (cryo)CLEM applications.
Collapse
Affiliation(s)
- Job Fermie
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands
| | - Leanne de Jager
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Helen E. Foster
- Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Cambridge, UK
| | - Tineke Veenendaal
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Cecilia de Heus
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Suzanne van Dijk
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Corlinda ten Brink
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Viola Oorschot
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Lin Yang
- Institute of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- Institute of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wally H. Müller
- Microbiology, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Stuart Howes
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Andrew P. Carter
- Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Cambridge, UK
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - George Posthuma
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Hans C. Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands
| | - Judith Klumperman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Nalan Liv
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| |
Collapse
|
8
|
Loginov SV, Fermie J, Fokkema J, Agronskaia AV, De Heus C, Blab GA, Klumperman J, Gerritsen HC, Liv N. Correlative Organelle Microscopy: Fluorescence Guided Volume Electron Microscopy of Intracellular Processes. Front Cell Dev Biol 2022; 10:829545. [PMID: 35478966 PMCID: PMC9035751 DOI: 10.3389/fcell.2022.829545] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/04/2022] [Indexed: 01/19/2023] Open
Abstract
Intracellular processes depend on a strict spatial and temporal organization of proteins and organelles. Therefore, directly linking molecular to nanoscale ultrastructural information is crucial in understanding cellular physiology. Volume or three-dimensional (3D) correlative light and electron microscopy (volume-CLEM) holds unique potential to explore cellular physiology at high-resolution ultrastructural detail across cell volumes. However, the application of volume-CLEM is hampered by limitations in throughput and 3D correlation efficiency. In order to address these limitations, we describe a novel pipeline for volume-CLEM that provides high-precision (<100 nm) registration between 3D fluorescence microscopy (FM) and 3D electron microscopy (EM) datasets with significantly increased throughput. Using multi-modal fiducial nanoparticles that remain fluorescent in epoxy resins and a 3D confocal fluorescence microscope integrated into a Focused Ion Beam Scanning Electron Microscope (FIB.SEM), our approach uses FM to target extremely small volumes of even single organelles for imaging in volume EM and obviates the need for post-correlation of big 3D datasets. We extend our targeted volume-CLEM approach to include live-cell imaging, adding information on the motility of intracellular membranes selected for volume-CLEM. We demonstrate the power of our approach by targeted imaging of rare and transient contact sites between the endoplasmic reticulum (ER) and lysosomes within hours rather than days. Our data suggest that extensive ER-lysosome and mitochondria-lysosome interactions restrict lysosome motility, highlighting the unique capabilities of our integrated CLEM pipeline for linking molecular dynamic data to high-resolution ultrastructural detail in 3D.
Collapse
Affiliation(s)
- Sergey V. Loginov
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Job Fermie
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Jantina Fokkema
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Alexandra V. Agronskaia
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Cilia De Heus
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Gerhard A. Blab
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Judith Klumperman
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Hans C. Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Nalan Liv
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- *Correspondence: Nalan Liv,
| |
Collapse
|
9
|
Tavares S, Liv N, Pasolli M, Opdam M, Rätze MAK, Saornil M, Sluimer LM, Hengeveld RCC, van Es R, van Werkhoven E, Vos H, Rehmann H, Burgering BMT, Oosterkamp HM, Lens SMA, Klumperman J, Linn SC, Derksen PWB. FER regulates endosomal recycling and is a predictor for adjuvant taxane benefit in breast cancer. Cell Rep 2022; 39:110584. [PMID: 35385742 DOI: 10.1016/j.celrep.2022.110584] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/28/2021] [Accepted: 03/07/2022] [Indexed: 11/18/2022] Open
Abstract
Elevated expression of non-receptor tyrosine kinase FER is an independent prognosticator that correlates with poor survival of high-grade and basal/triple-negative breast cancer (TNBC) patients. Here, we show that high FER levels are also associated with improved outcomes after adjuvant taxane-based combination chemotherapy in high-risk, HER2-negative patients. In TNBC cells, we observe a causal relation between high FER levels and sensitivity to taxanes. Proteomics and mechanistic studies demonstrate that FER regulates endosomal recycling, a microtubule-dependent process that underpins breast cancer cell invasion. Using chemical genetics, we identify DCTN2 as a FER substrate. Our work indicates that the DCTN2 tyrosine 6 is essential for the development of tubular recycling domains in early endosomes and subsequent propagation of TNBC cell invasion in 3D. In conclusion, we show that high FER expression promotes endosomal recycling and represents a candidate predictive marker for the benefit of adjuvant taxane-containing chemotherapy in high-risk patients, including TNBC patients.
Collapse
Affiliation(s)
- Sandra Tavares
- Department of Pathology, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Milena Pasolli
- Cell Biology, Neurobiology, and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584CH Utrecht, the Netherlands
| | - Mark Opdam
- Department of Molecular Pathology, Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Max A K Rätze
- Department of Pathology, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Manuel Saornil
- Department of Pathology, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Lilian M Sluimer
- Department of Pathology, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Rutger C C Hengeveld
- Oncode Institute, Department of Molecular Cancer Research, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Robert van Es
- Oncode Institute, Department of Molecular Cancer Research, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Erik van Werkhoven
- Department of Molecular Pathology, Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Harmjan Vos
- Oncode Institute, Department of Molecular Cancer Research, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Holger Rehmann
- Flensburg University of Applied Sciences, 24943 Flensburg, Germany
| | - Boudewijn M T Burgering
- Oncode Institute, Department of Molecular Cancer Research, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Hendrika M Oosterkamp
- Department of Medical Oncology, Haaglanden Medisch Centrum, 2501 CK The Hague, the Netherlands
| | - Susanne M A Lens
- Oncode Institute, Department of Molecular Cancer Research, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Sabine C Linn
- Department of Pathology, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands; Department of Molecular Pathology, Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Department of Medical Oncology, Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Patrick W B Derksen
- Department of Pathology, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands.
| |
Collapse
|
10
|
Lehmann V, Schene IF, Ardisasmita AI, Liv N, Veenendaal T, Klumperman J, van der Doef HPJ, Verkade HJ, Verstegen MMA, van der Laan LJW, Jans JJM, Verhoeven‐Duif NM, van Hasselt PM, Nieuwenhuis EES, Spee B, Fuchs SA. The potential and limitations of intrahepatic cholangiocyte organoids to study inborn errors of metabolism. J Inherit Metab Dis 2022; 45:353-365. [PMID: 34671987 PMCID: PMC9298016 DOI: 10.1002/jimd.12450] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 01/09/2023]
Abstract
Inborn errors of metabolism (IEMs) comprise a diverse group of individually rare monogenic disorders that affect metabolic pathways. Mutations lead to enzymatic deficiency or dysfunction, which results in intermediate metabolite accumulation or deficit leading to disease phenotypes. Currently, treatment options for many IEMs are insufficient. Rarity of individual IEMs hampers therapy development and phenotypic and genetic heterogeneity suggest beneficial effects of personalized approaches. Recently, cultures of patient-own liver-derived intrahepatic cholangiocyte organoids (ICOs) have been established. Since most metabolic genes are expressed in the liver, patient-derived ICOs represent exciting possibilities for in vitro modeling and personalized drug testing for IEMs. However, the exact application range of ICOs remains unclear. To address this, we examined which metabolic pathways can be studied with ICOs and what the potential and limitations of patient-derived ICOs are to model metabolic functions. We present functional assays in patient ICOs with defects in branched-chain amino acid metabolism (methylmalonic acidemia), copper metabolism (Wilson disease), and transporter defects (cystic fibrosis). We discuss the broad range of functional assays that can be applied to ICOs, but also address the limitations of these patient-specific cell models. In doing so, we aim to guide the selection of the appropriate cell model for studies of a specific disease or metabolic process.
Collapse
Affiliation(s)
- Vivian Lehmann
- Department of Metabolic DiseasesUniversity Medical Center UtrechtUtrechtThe Netherlands
- Department of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Imre F. Schene
- Department of Metabolic DiseasesUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Arif I. Ardisasmita
- Department of Metabolic DiseasesUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Tineke Veenendaal
- Section Cell Biology, Center for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | | | - Henkjan J. Verkade
- Department of Pediatric GastroenterologyUniversity Medical Center GroningenGroningenThe Netherlands
- Department of HepatologyUniversity Medical Center GroningenGroningenThe Netherlands
| | | | | | - Judith J. M. Jans
- Department of Metabolic DiagnosticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | | | - Peter M. van Hasselt
- Department of Metabolic DiseasesUniversity Medical Center UtrechtUtrechtThe Netherlands
| | | | - Bart Spee
- Department of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Sabine A. Fuchs
- Department of Metabolic DiseasesUniversity Medical Center UtrechtUtrechtThe Netherlands
| |
Collapse
|
11
|
Guo S, Cázarez-Márquez F, Jiao H, Foppen E, Korpel NL, Grootemaat AE, Liv N, Gao Y, van der Wel N, Zhou B, Nie G, Yi CX. Specific Silencing of Microglial Gene Expression in the Rat Brain by Nanoparticle-Based Small Interfering RNA Delivery. ACS Appl Mater Interfaces 2022; 14:5066-5079. [PMID: 35041392 PMCID: PMC8815040 DOI: 10.1021/acsami.1c22434] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/03/2022] [Indexed: 05/02/2023]
Abstract
Microglia are the major innate immune cells in the brain and are essential for maintaining homeostasis in a neuronal microenvironment. Currently, a genetic tool to modify microglial gene expression in specific brain regions is not available. In this report, we introduce a tailor-designed method that uses lipid and polymer hybridized nanoparticles (LPNPs) for the local delivery of small interfering RNAs (siRNAs), allowing the silencing of specific microglial genes in the hypothalamus. Our physical characterization proved that this LPNP-siRNA was uniform and stable. We demonstrated that, due to their natural phagocytic behavior, microglial cells are the dominant cell type taking up these LPNPs in the hypothalamus of rats. We then tested the silencing efficiency of LPNPs carrying a cluster of differentiation molecule 11b (CD11b) or Toll-like receptor 4 (TLR4) siRNA using different in vivo and in vitro approaches. In cultured microglial cells treated with LPNP-CD11b siRNA or LPNP-TLR4 siRNA, we found a silencing efficiency at protein expression levels of 65 or 77%, respectively. In line with this finding, immunohistochemistry and western blotting results from in vivo experiments showed that LPNP-CD11b siRNA significantly inhibited microglial CD11b protein expression in the hypothalamus. Furthermore, following lipopolysaccharide (LPS) stimulation of cultured microglial cells, gene expression of the TLR4 downstream signaling component myeloid differentiation factor 88 and its associated cytokines was significantly inhibited in LPNP-TLR4 siRNA-treated microglial cells compared with cells treated with LPNP-scrambled siRNA. Finally, after LPNP-TLR4 siRNA injection into the rat hypothalamus, we observed a significant reduction in microglial activation in response to LPS compared with the control rats injected with LPNP-scrambled siRNA. Our results indicate that LPNP-siRNA is a promising tool to manipulate microglial activity locally in the brain and may serve as a prophylactic approach to prevent microglial dysfunction-associated diseases.
Collapse
Affiliation(s)
- Shanshan Guo
- Department
of Endocrinology and Metabolism, Laboratory of Endocrinology, Amsterdam
Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam
University Medical Centre (UMC), location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Fernando Cázarez-Márquez
- Department
of Endocrinology and Metabolism, Laboratory of Endocrinology, Amsterdam
Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam
University Medical Centre (UMC), location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Netherlands
Institute for Neuroscience, Institute of
the Royal Netherlands Academy of Arts and Sciences, 1105 AZ Amsterdam, The Netherlands
| | - Han Jiao
- Department
of Endocrinology and Metabolism, Laboratory of Endocrinology, Amsterdam
Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam
University Medical Centre (UMC), location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Key
Laboratory of Cardiovascular and Cerebrovascular Medicine, School
of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Ewout Foppen
- Department
of Endocrinology and Metabolism, Laboratory of Endocrinology, Amsterdam
Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam
University Medical Centre (UMC), location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Netherlands
Institute for Neuroscience, Institute of
the Royal Netherlands Academy of Arts and Sciences, 1105 AZ Amsterdam, The Netherlands
| | - Nikita L. Korpel
- Department
of Endocrinology and Metabolism, Laboratory of Endocrinology, Amsterdam
Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam
University Medical Centre (UMC), location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Netherlands
Institute for Neuroscience, Institute of
the Royal Netherlands Academy of Arts and Sciences, 1105 AZ Amsterdam, The Netherlands
| | - Anita E. Grootemaat
- Cellular
Imaging Core Facility, Amsterdam University Medical Centre (UMC),
location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Nalan Liv
- Section
Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Yuanqing Gao
- Key
Laboratory of Cardiovascular and Cerebrovascular Medicine, School
of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Nicole van der Wel
- Cellular
Imaging Core Facility, Amsterdam University Medical Centre (UMC),
location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Bing Zhou
- Institute
of Synthetic Biology, Shenzhen Institutes
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guangjun Nie
- CAS
Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Chun-Xia Yi
- Department
of Endocrinology and Metabolism, Laboratory of Endocrinology, Amsterdam
Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam
University Medical Centre (UMC), location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| |
Collapse
|
12
|
van der Beek J, de Heus C, Liv N, Klumperman J. Quantitative correlative microscopy reveals the ultrastructural distribution of endogenous endosomal proteins. J Cell Biol 2022; 221:212877. [PMID: 34817533 PMCID: PMC8624803 DOI: 10.1083/jcb.202106044] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 06/08/2021] [Revised: 10/22/2021] [Accepted: 11/01/2021] [Indexed: 02/07/2023] Open
Abstract
The key endosomal regulators Rab5, EEA1, and APPL1 are frequently applied in fluorescence microscopy to mark early endosomes, whereas Rab7 is used as a marker for late endosomes and lysosomes. However, endogenous levels of these proteins localize poorly in immuno-EM, and systematic studies on their native ultrastructural distributions are lacking. To address this gap, we here present a quantitative, on-section correlative light and electron microscopy (CLEM) approach. Using the sensitivity of fluorescence microscopy, we label hundreds of organelles that are subsequently visualized by EM and classified by ultrastructure. We show that Rab5 predominantly marks small, endocytic vesicles and early endosomes. EEA1 colocalizes with Rab5 on early endosomes, but unexpectedly also labels Rab5-negative late endosomes, which are positive for PI(3)P but lack Rab7. APPL1 is restricted to small Rab5-positive, tubulo-vesicular profiles. Rab7 primarily labels late endosomes and lysosomes. These data increase our understanding of the structural-functional organization of the endosomal system and introduce quantitative CLEM as a sensitive alternative for immuno-EM.
Collapse
Affiliation(s)
- Jan van der Beek
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Cecilia de Heus
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| |
Collapse
|
13
|
Jonker CTH, Galmes R, Veenendaal T, Ten Brink C, van der Welle REN, Liv N, de Rooij J, Peden AA, van der Sluijs P, Margadant C, Klumperman J. Author Correction: Vps3 and Vps8 control integrin trafficking from early to recycling endosomes and regulate integrin-dependent functions. Nat Commun 2021; 12:5828. [PMID: 34588435 PMCID: PMC8481545 DOI: 10.1038/s41467-021-25201-6] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Caspar T H Jonker
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.,Department of Ophthalmology, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
| | - Romain Galmes
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.,UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6DD, UK
| | - Tineke Veenendaal
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Corlinda Ten Brink
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Reini E N van der Welle
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Johan de Rooij
- Section Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht Universty, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Andrew A Peden
- Department of Biomedical Science, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Peter van der Sluijs
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.,Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH Utrecht, The Netherlands
| | - Coert Margadant
- Department of Molecular Cell Biology, Sanquin Research, Plesmanlaan 125, 1066 CX, Amsterdam, The Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
| |
Collapse
|
14
|
Calandrini C, van Hooff SR, Paassen I, Ayyildiz D, Derakhshan S, Dolman MEM, Langenberg KPS, van de Ven M, de Heus C, Liv N, Kool M, de Krijger RR, Tytgat GAM, van den Heuvel-Eibrink MM, Molenaar JJ, Drost J. Organoid-based drug screening reveals neddylation as therapeutic target for malignant rhabdoid tumors. Cell Rep 2021; 36:109568. [PMID: 34433038 DOI: 10.1016/j.celrep.2021.109568] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 11/10/2020] [Revised: 05/12/2021] [Accepted: 07/28/2021] [Indexed: 11/29/2022] Open
Abstract
Malignant rhabdoid tumors (MRTs) represent one of the most aggressive childhood malignancies. No effective treatment options are available, and prognosis is, therefore, dismal. Previous studies have demonstrated that tumor organoids capture the heterogeneity of patient tumors and can be used to predict patient response to therapy. Here, we perform drug screening on patient-derived normal and tumor organoids to identify MRT-specific therapeutic vulnerabilities. We identify neddylation inhibitor MLN4924 as a potential therapeutic agent. Mechanistically, we find increased neddylation in MRT organoids and tissues and show that MLN4924 induces a cytotoxic response via upregulation of the unfolded protein response. Lastly, we demonstrate in vivo efficacy in an MRT PDX mouse model, in which single-agent MLN4924 treatment significantly extends survival. Our study demonstrates that organoids can be used to find drugs selectively targeting tumor cells while leaving healthy cells unharmed and proposes neddylation inhibition as a therapeutic strategy in MRT.
Collapse
Affiliation(s)
- Camilla Calandrini
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Sander R van Hooff
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Irene Paassen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Dilara Ayyildiz
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Sepide Derakhshan
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - M Emmy M Dolman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Karin P S Langenberg
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Marieke van de Ven
- Preclinical Intervention Unit of the Mouse Clinic for Cancer and Ageing (MCCA), NKI, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Cecilia de Heus
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Nalan Liv
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center DKFZ and German Cancer Consortium DKTK, 69120 Heidelberg, Germany
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; University Medical Center, Department of Pathology, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Godelieve A M Tytgat
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | | | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands.
| |
Collapse
|
15
|
Özkan N, Koppers M, van Soest I, van Harten A, Jurriens D, Liv N, Klumperman J, Kapitein LC, Hoogenraad CC, Farías GG. ER - lysosome contacts at a pre-axonal region regulate axonal lysosome availability. Nat Commun 2021; 12:4493. [PMID: 34301956 PMCID: PMC8302662 DOI: 10.1038/s41467-021-24713-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
Neuronal function relies on careful coordination of organelle organization and transport. Kinesin-1 mediates transport of the endoplasmic reticulum (ER) and lysosomes into the axon and it is increasingly recognized that contacts between the ER and lysosomes influence organelle organization. However, it is unclear how organelle organization, inter-organelle communication and transport are linked and how this contributes to local organelle availability in neurons. Here, we show that somatic ER tubules are required for proper lysosome transport into the axon. Somatic ER tubule disruption causes accumulation of enlarged and less motile lysosomes at the soma. ER tubules regulate lysosome size and axonal translocation by promoting lysosome homo-fission. ER tubule - lysosome contacts often occur at a somatic pre-axonal region, where the kinesin-1-binding ER-protein P180 binds microtubules to promote kinesin-1-powered lysosome fission and subsequent axonal translocation. We propose that ER tubule - lysosome contacts at a pre-axonal region finely orchestrate axonal lysosome availability for proper neuronal function.
Collapse
Affiliation(s)
- Nazmiye Özkan
- Cell Biology, Neurobiology and Biophysics. Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Max Koppers
- Cell Biology, Neurobiology and Biophysics. Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Inge van Soest
- Cell Biology, Neurobiology and Biophysics. Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Alexandra van Harten
- Cell Biology, Neurobiology and Biophysics. Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Daphne Jurriens
- Cell Biology, Neurobiology and Biophysics. Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics. Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Casper C Hoogenraad
- Cell Biology, Neurobiology and Biophysics. Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Ginny G Farías
- Cell Biology, Neurobiology and Biophysics. Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
16
|
Tavares S, Liv N, Pasolli M, Opdam M, Ratze M, Saornil M, Sluimer L, Hengeveld R, van Es R, van Werkhoven E, Vos H, Rehmann H, Burgering B, Oosterkamp H, Lens S, Klumperman J, Linn S, Derksen P. Abstract LB203: FER regulates endosomal recycling and is a candidate predictor for taxane benefit in breast cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-lb203] [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] [Indexed: 11/16/2022]
Abstract
Abstract
To this day, targeted treatment options for patients with triple negative metastatic breast cancer (TNBC) are still virtually absent. Previously, we showed that elevated expression of the tyrosine kinase FER is an independent prognosticator that correlates with poor survival of high-grade and basal/TNBC patients. Here, we show that high FER levels are also associated with improved outcome after adjuvant taxane-based combination chemotherapy, in high-risk, HER2-negative patients. In TNBC cells, we observed a causal relation between high FER levels and sensitivity to taxanes. Our proteomics and mechanistic studies demonstrated that FER regulates endosomal recycling, a microtubule-dependent process that underpins breast cancer cell invasion. Using chemical genetics, we identified DCTN2 as a novel FER substrate. Our work indicates that the DCTN2 tyrosine 6 is essential for tubular recycling domains development in early endosomes and subsequent propagation of TNBC cell invasion in 3D. In conclusion, we show that high FER expression promotes endosomal recycling and represents a candidate predictive marker for benefit of adjuvant taxane-containing chemotherapy in high-risk patients, including TNBC patients.
Citation Format: Sandra Tavares, Nalan Liv, Milena Pasolli, Mark Opdam, Max Ratze, Manuel Saornil, Lilian Sluimer, Rutger Hengeveld, Robert van Es, Erik van Werkhoven, Harmjan Vos, Holger Rehmann, Boudewijn Burgering, Hendrika Oosterkamp, Susanne Lens, Judith Klumperman, Sabine Linn, Patrick Derksen. FER regulates endosomal recycling and is a candidate predictor for taxane benefit in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB203.
Collapse
Affiliation(s)
| | | | | | - Mark Opdam
- 4Netherlands Cancer institute, Amsterdam, Netherlands
| | | | | | | | | | | | | | | | - Holger Rehmann
- 6Flensburg University of Applied Sciences, Flensburg, Germany
| | | | | | | | | | - Sabine Linn
- 4Netherlands Cancer institute, Amsterdam, Netherlands
| | | |
Collapse
|
17
|
Dilsizoglu Senol A, Samarani M, Syan S, Guardia CM, Nonaka T, Liv N, Latour-Lambert P, Hasegawa M, Klumperman J, Bonifacino JS, Zurzolo C. α-Synuclein fibrils subvert lysosome structure and function for the propagation of protein misfolding between cells through tunneling nanotubes. PLoS Biol 2021; 19:e3001287. [PMID: 34283825 PMCID: PMC8291706 DOI: 10.1371/journal.pbio.3001287] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 05/13/2021] [Indexed: 01/06/2023] Open
Abstract
The accumulation of α-synuclein (α-syn) aggregates in specific brain regions is a hallmark of synucleinopathies including Parkinson disease (PD). α-Syn aggregates propagate in a "prion-like" manner and can be transferred inside lysosomes to recipient cells through tunneling nanotubes (TNTs). However, how lysosomes participate in the spreading of α-syn aggregates is unclear. Here, by using super-resolution (SR) and electron microscopy (EM), we find that α-syn fibrils affect the morphology of lysosomes and impair their function in neuronal cells. In addition, we demonstrate that α-syn fibrils induce peripheral redistribution of lysosomes, likely mediated by transcription factor EB (TFEB), increasing the efficiency of α-syn fibrils' transfer to neighboring cells. We also show that lysosomal membrane permeabilization (LMP) allows the seeding of soluble α-syn in cells that have taken up α-syn fibrils from the culture medium, and, more importantly, in healthy cells in coculture, following lysosome-mediated transfer of the fibrils. Moreover, we demonstrate that seeding occurs mainly at lysosomes in both donor and acceptor cells, after uptake of α-syn fibrils from the medium and following their transfer, respectively. Finally, by using a heterotypic coculture system, we determine the origin and nature of the lysosomes transferred between cells, and we show that donor cells bearing α-syn fibrils transfer damaged lysosomes to acceptor cells, while also receiving healthy lysosomes from them. These findings thus contribute to the elucidation of the mechanism by which α-syn fibrils spread through TNTs, while also revealing the crucial role of lysosomes, working as a Trojan horse for both seeding and propagation of disease pathology.
Collapse
Affiliation(s)
- Aysegul Dilsizoglu Senol
- Unité de Trafic Membranaire et Pathogénèse, Département de Biologie Cellulaire et de l’Infection, Institut Pasteur, Paris, France
| | - Maura Samarani
- Unité de Trafic Membranaire et Pathogénèse, Département de Biologie Cellulaire et de l’Infection, Institut Pasteur, Paris, France
| | - Sylvie Syan
- Unité de Trafic Membranaire et Pathogénèse, Département de Biologie Cellulaire et de l’Infection, Institut Pasteur, Paris, France
| | - Carlos M. Guardia
- Neurosciences and Cellular and Structural Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Takashi Nonaka
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Patricia Latour-Lambert
- Dynamique des Interaction Hôte–Pathogène, Département de Biologie Cellulaire et de l’Infection, Institut Pasteur, Paris, France
| | - Masato Hasegawa
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Juan S. Bonifacino
- Neurosciences and Cellular and Structural Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chiara Zurzolo
- Unité de Trafic Membranaire et Pathogénèse, Département de Biologie Cellulaire et de l’Infection, Institut Pasteur, Paris, France
| |
Collapse
|
18
|
van der Welle REN, Jobling R, Burns C, Sanza P, van der Beek JA, Fasano A, Chen L, Zwartkruis FJ, Zwakenberg S, Griffin EF, ten Brink C, Veenendaal T, Liv N, van Ravenswaaij‐Arts CMA, Lemmink HH, Pfundt R, Blaser S, Sepulveda C, Lozano AM, Yoon G, Santiago‐Sim T, Asensio CS, Caldwell GA, Caldwell KA, Chitayat D, Klumperman J. Neurodegenerative VPS41 variants inhibit HOPS function and mTORC1-dependent TFEB/TFE3 regulation. EMBO Mol Med 2021; 13:e13258. [PMID: 33851776 PMCID: PMC8103106 DOI: 10.15252/emmm.202013258] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 08/07/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/09/2022] Open
Abstract
Vacuolar protein sorting 41 (VPS41) is as part of the Homotypic fusion and Protein Sorting (HOPS) complex required for lysosomal fusion events and, independent of HOPS, for regulated secretion. Here, we report three patients with compound heterozygous mutations in VPS41 (VPS41S285P and VPS41R662* ; VPS41c.1423-2A>G and VPS41R662* ) displaying neurodegeneration with ataxia and dystonia. Cellular consequences were investigated in patient fibroblasts and VPS41-depleted HeLa cells. All mutants prevented formation of a functional HOPS complex, causing delayed lysosomal delivery of endocytic and autophagic cargo. By contrast, VPS41S285P enabled regulated secretion. Strikingly, loss of VPS41 function caused a cytosolic redistribution of mTORC1, continuous nuclear localization of Transcription Factor E3 (TFE3), enhanced levels of LC3II, and a reduced autophagic response to nutrient starvation. Phosphorylation of mTORC1 substrates S6K1 and 4EBP1 was not affected. In a C. elegans model of Parkinson's disease, co-expression of VPS41S285P /VPS41R662* abolished the neuroprotective function of VPS41 against α-synuclein aggregates. We conclude that the VPS41 variants specifically abrogate HOPS function, which interferes with the TFEB/TFE3 axis of mTORC1 signaling, and cause a neurodegenerative disease.
Collapse
Affiliation(s)
- Reini E N van der Welle
- Section Cell BiologyCenter for Molecular MedicineInstitute of BiomembranesUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Rebekah Jobling
- Department of PediatricsDivision of Clinical and Metabolic GeneticsThe Hospital for Sick ChildrenUniversity of TorontoTorontoONCanada
| | - Christian Burns
- Department of Biological SciencesDivision of Natural Sciences and MathematicsUniversity of DenverDenverCOUSA
| | - Paolo Sanza
- Section Cell BiologyCenter for Molecular MedicineInstitute of BiomembranesUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Jan A van der Beek
- Section Cell BiologyCenter for Molecular MedicineInstitute of BiomembranesUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Alfonso Fasano
- Edmond J. Safra Program in Parkinson’s DiseaseMorton and Gloria Shulman Movement Disorders ClinicToronto Western Hospital, UHNTorontoONCanada
- Division of NeurologyUniversity of TorontoTorontoONCanada
- Krembil Brain InstituteTorontoONCanada
- Center for Advancing Neurotechnological Innovation to Application (CRANIA)TorontoONCanada
| | - Lan Chen
- Department of Biological SciencesDivision of Natural Sciences and MathematicsUniversity of DenverDenverCOUSA
| | - Fried J Zwartkruis
- Section Molecular Cancer ResearchCenter for Molecular MedicineUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Susan Zwakenberg
- Section Molecular Cancer ResearchCenter for Molecular MedicineUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Edward F Griffin
- Department of Biological SciencesThe University of AlabamaTuscaloosaALUSA
- Department of NeurologyCenter for Neurodegeneration and Experimental TherapeuticsNathan Shock Center for Basic Research in the Biology of AgingUniversity of Alabama at Birmingham School of MedicineBirminghamALUSA
| | - Corlinda ten Brink
- Section Cell BiologyCenter for Molecular MedicineInstitute of BiomembranesUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Tineke Veenendaal
- Section Cell BiologyCenter for Molecular MedicineInstitute of BiomembranesUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Nalan Liv
- Section Cell BiologyCenter for Molecular MedicineInstitute of BiomembranesUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | | | - Henny H Lemmink
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Rolph Pfundt
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
| | - Susan Blaser
- Department of Diagnostic ImagingHospital for Sick ChildrenTorontoONCanada
| | - Carolina Sepulveda
- Edmond J. Safra Program in Parkinson’s DiseaseMorton and Gloria Shulman Movement Disorders ClinicToronto Western Hospital, UHNTorontoONCanada
- Division of NeurologyUniversity of TorontoTorontoONCanada
| | - Andres M Lozano
- Krembil Brain InstituteTorontoONCanada
- Center for Advancing Neurotechnological Innovation to Application (CRANIA)TorontoONCanada
- Department of NeurosurgeryToronto Western Hospital, UHNTorontoONCanada
- University of TorontoTorontoONCanada
| | - Grace Yoon
- Department of PediatricsDivision of Clinical and Metabolic GeneticsThe Hospital for Sick ChildrenUniversity of TorontoTorontoONCanada
| | | | - Cedric S Asensio
- Department of Biological SciencesDivision of Natural Sciences and MathematicsUniversity of DenverDenverCOUSA
| | - Guy A Caldwell
- Department of Biological SciencesThe University of AlabamaTuscaloosaALUSA
- Department of NeurologyCenter for Neurodegeneration and Experimental TherapeuticsNathan Shock Center for Basic Research in the Biology of AgingUniversity of Alabama at Birmingham School of MedicineBirminghamALUSA
| | - Kim A Caldwell
- Department of Biological SciencesThe University of AlabamaTuscaloosaALUSA
- Department of NeurologyCenter for Neurodegeneration and Experimental TherapeuticsNathan Shock Center for Basic Research in the Biology of AgingUniversity of Alabama at Birmingham School of MedicineBirminghamALUSA
| | - David Chitayat
- Department of PediatricsDivision of Clinical and Metabolic GeneticsThe Hospital for Sick ChildrenUniversity of TorontoTorontoONCanada
- The Prenatal Diagnosis and Medical Genetics ProgramDepartment of Obstetrics and GynecologyUniversity of TorontoTorontoONCanada
| | - Judith Klumperman
- Section Cell BiologyCenter for Molecular MedicineInstitute of BiomembranesUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| |
Collapse
|
19
|
Lane R, Vos Y, Wolters AHG, Kessel LV, Chen SE, Liv N, Klumperman J, Giepmans BNG, Hoogenboom JP. Optimization of negative stage bias potential for faster imaging in large-scale electron microscopy. J Struct Biol X 2021; 5:100046. [PMID: 33763642 PMCID: PMC7973379 DOI: 10.1016/j.yjsbx.2021.100046] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/17/2020] [Accepted: 01/27/2021] [Indexed: 11/24/2022]
Abstract
The use of a negative bias potential was empirically optimized for tissue imaging with SEM. Optimized bias potential leads to a factor 20 increase in imaging speeds as well as an order of magnitude improvement to SNR. SNR increase results from a combination of BSE acceleration and detector response. Similar increases to SNR can be obtained when a magnetic immersion field is combined with a negative bias potential. Stage bias can be applied within an integrated fluorescence and electron microscope allowing for fast correlative imaging of tissue sections.
Large-scale electron microscopy (EM) allows analysis of both tissues and macromolecules in a semi-automated manner, but acquisition rate forms a bottleneck. We reasoned that a negative bias potential may be used to enhance signal collection, allowing shorter dwell times and thus increasing imaging speed. Negative bias potential has previously been used to tune penetration depth in block-face imaging. However, optimization of negative bias potential for application in thin section imaging will be needed prior to routine use and application in large-scale EM. Here, we present negative bias potential optimized through a combination of simulations and empirical measurements. We find that the use of a negative bias potential generally results in improvement of image quality and signal-to-noise ratio (SNR). The extent of these improvements depends on the presence and strength of a magnetic immersion field. Maintaining other imaging conditions and aiming for the same image quality and SNR, the use of a negative stage bias can allow for a 20-fold decrease in dwell time, thus reducing the time for a week long acquisition to less than 8 h. We further show that negative bias potential can be applied in an integrated correlative light electron microscopy (CLEM) application, allowing fast acquisition of a high precision overlaid LM-EM dataset. Application of negative stage bias potential will thus help to solve the current bottleneck of image acquisition of large fields of view at high resolution in large-scale microscopy.
Collapse
Affiliation(s)
- Ryan Lane
- Imaging Physics, Delft University of Technology, The Netherlands
| | - Yoram Vos
- Imaging Physics, Delft University of Technology, The Netherlands
| | - Anouk H G Wolters
- Department of Biomedical Sciences of Cells and Systems, University Groningen, University Medical Center Groningen, The Netherlands
| | - Luc van Kessel
- Imaging Physics, Delft University of Technology, The Netherlands
| | - S Elisa Chen
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
| | - Nalan Liv
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
| | - Judith Klumperman
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
| | - Ben N G Giepmans
- Department of Biomedical Sciences of Cells and Systems, University Groningen, University Medical Center Groningen, The Netherlands
| | | |
Collapse
|
20
|
Ludikhuize MC, Meerlo M, Gallego MP, Xanthakis D, Burgaya Julià M, Nguyen NTB, Brombacher EC, Liv N, Maurice MM, Paik JH, Burgering BMT, Rodriguez Colman MJ. Mitochondria Define Intestinal Stem Cell Differentiation Downstream of a FOXO/Notch Axis. Cell Metab 2020; 32:889-900.e7. [PMID: 33147486 DOI: 10.1016/j.cmet.2020.10.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 05/19/2020] [Accepted: 10/08/2020] [Indexed: 02/08/2023]
Abstract
Differential WNT and Notch signaling regulates differentiation of Lgr5+ crypt-based columnar cells (CBCs) into intestinal cell lineages. Recently we showed that mitochondrial activity supports CBCs, while adjacent Paneth cells (PCs) show reduced mitochondrial activity. This implies that CBC differentiation into PCs involves a metabolic transition toward downregulation of mitochondrial dependency. Here we show that Forkhead box O (FoxO) transcription factors and Notch signaling interact in determining CBC fate. In agreement with the organoid data, Foxo1/3/4 deletion in mouse intestine induces secretory cell differentiation. Importantly, we show that FOXO and Notch signaling converge on regulation of mitochondrial fission, which in turn provokes stem cell differentiation into goblet cells and PCs. Finally, scRNA-seq-based reconstruction of CBC differentiation trajectories supports the role of FOXO, Notch, and mitochondria in secretory differentiation. Together, this points at a new signaling-metabolic axis in CBC differentiation and highlights the importance of mitochondria in determining stem cell fate.
Collapse
Affiliation(s)
- Marlies C Ludikhuize
- Molecular Cancer Research, Center Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CG Utrecht, the Netherlands
| | - Maaike Meerlo
- Molecular Cancer Research, Center Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CG Utrecht, the Netherlands
| | - Marc Pages Gallego
- Molecular Cancer Research, Center Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CG Utrecht, the Netherlands
| | - Despina Xanthakis
- Department of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CG Utrecht, the Netherlands
| | - Mar Burgaya Julià
- Molecular Cancer Research, Center Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CG Utrecht, the Netherlands
| | - Nguyen T B Nguyen
- Molecular Cancer Research, Center Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CG Utrecht, the Netherlands
| | - Eline C Brombacher
- Molecular Cancer Research, Center Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CG Utrecht, the Netherlands; Leids Universitair Medisch Centrum, Department of Parasitology, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Nalan Liv
- Department of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CG Utrecht, the Netherlands
| | - Madelon M Maurice
- Department of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CG Utrecht, the Netherlands; Oncode Institute
| | - Ji-Hye Paik
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Boudewijn M T Burgering
- Molecular Cancer Research, Center Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CG Utrecht, the Netherlands; Oncode Institute
| | - Maria J Rodriguez Colman
- Molecular Cancer Research, Center Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CG Utrecht, the Netherlands.
| |
Collapse
|
21
|
Piperno GM, Naseem A, Silvestrelli G, Amadio R, Caronni N, Cervantes-Luevano KE, Liv N, Klumperman J, Colliva A, Ali H, Graziano F, Benaroch P, Haecker H, Hanna RN, Benvenuti F. Wiskott-Aldrich syndrome protein restricts cGAS/STING activation by dsDNA immune complexes. JCI Insight 2020; 5:132857. [PMID: 32721945 PMCID: PMC7526445 DOI: 10.1172/jci.insight.132857] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 08/21/2019] [Accepted: 07/16/2020] [Indexed: 01/06/2023] Open
Abstract
Dysregulated sensing of self-nucleic acid is a leading cause of autoimmunity in multifactorial and monogenic diseases. Mutations in Wiskott-Aldrich syndrome protein (WASp), a key regulator of cytoskeletal dynamics in immune cells, cause autoimmune manifestations and increased production of type I IFNs by innate cells. Here we show that immune complexes of self-DNA and autoantibodies (DNA-ICs) contribute to elevated IFN levels via activation of the cGAS/STING pathway of cytosolic sensing. Mechanistically, lack of endosomal F-actin nucleation by WASp caused a delay in endolysosomal maturation and prolonged the transit time of ingested DNA-ICs. Stalling in maturation-defective organelles facilitated leakage of DNA-ICs into the cytosol, promoting activation of the TBK1/STING pathway. Genetic deletion of STING and STING and cGAS chemical inhibitors abolished IFN production and rescued systemic activation of IFN-stimulated genes in vivo. These data unveil the contribution of cytosolic self-nucleic acid sensing in WAS and underscore the importance of WASp-mediated endosomal actin remodeling in preventing innate activation.
Collapse
Affiliation(s)
| | - Asma Naseem
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Giulia Silvestrelli
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Roberto Amadio
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Nicoletta Caronni
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center (UMC) Utrecht, Utrecht University, Utrecht, Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center (UMC) Utrecht, Utrecht University, Utrecht, Netherlands
| | - Andrea Colliva
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Hashim Ali
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Francesca Graziano
- Institute Curie Laboratoire Immunité et Cancer - INSERM U932 Transport Intracellulaire et Immunité, Paris, France
| | - Philippe Benaroch
- Institute Curie Laboratoire Immunité et Cancer - INSERM U932 Transport Intracellulaire et Immunité, Paris, France
| | - Hans Haecker
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Richard N Hanna
- Respiratory, Inflammation and Autoimmunity, MedImmune LLC, Gaithersburg, Maryland, USA
| | - Federica Benvenuti
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| |
Collapse
|
22
|
Mohammadian S, Agronskaia AV, Blab GA, van Donselaar EG, de Heus C, Liv N, Klumperman J, Gerritsen HC. Integrated super resolution fluorescence microscopy and transmission electron microscopy. Ultramicroscopy 2020; 215:113007. [PMID: 32470633 DOI: 10.1016/j.ultramic.2020.113007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/14/2020] [Accepted: 04/19/2020] [Indexed: 10/24/2022]
Abstract
In correlative light and electron microscopy (CLEM), the capabilities of fluorescence microscopy (FM) and electron microscopy (EM) are united. FM combines a large field of view with high sensitivity for detecting fluorescence, which makes it an excellent tool for identifying regions of interest. EM has a much smaller field of view but offers superb resolution that allows studying cellular ultrastructure. In CLEM, the potentials of both techniques are combined but a limiting factor is the large difference in resolution between the two imaging modalities. Adding super resolution FM to CLEM reduces the resolution gap between FM and EM; it offers the possibility of identifying multiple targets within the diffraction limit and can increase correlation accuracy. CLEM is usually carried out in two separate setups, which requires transfer of the sample. This may result in distortion and damage of the specimen, which can complicate finding back regions of interest. By integrating the two imaging modalities, such problems can be avoided. Here, an integrated super resolution correlative microscopy approach is presented based on a wide-field super resolution FM integrated in a Transmission Electron Microscope (TEM). Switching imaging modalities is accomplished by rotation of the TEM sample holder. First imaging experiments are presented on sections of Lowicryl embedded Human Umbilical Vein Endothelial Cells labeled for Caveolin both with Protein A-Gold, and Alexa Fluor®647. TEM and FM images were overlaid using fiducial markers visible in both imaging modalities with an overlay accuracy of 28 ± 11 nm. This is close to the optical resolution of ~50 nm.
Collapse
Affiliation(s)
- Sajjad Mohammadian
- Molecular Biophysics, Department of Physics, Faculty of Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands
| | - Alexandra V Agronskaia
- Molecular Biophysics, Department of Physics, Faculty of Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands
| | - Gerhard A Blab
- Molecular Biophysics, Department of Physics, Faculty of Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands
| | - Elly G van Donselaar
- Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Cecilia de Heus
- Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Nalan Liv
- Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Judith Klumperman
- Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Hans C Gerritsen
- Molecular Biophysics, Department of Physics, Faculty of Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands.
| |
Collapse
|
23
|
Jongsma ML, Bakker J, Cabukusta B, Liv N, van Elsland D, Fermie J, Akkermans JL, Kuijl C, van der Zanden SY, Janssen L, Hoogzaad D, van der Kant R, Wijdeven RH, Klumperman J, Berlin I, Neefjes J. SKIP-HOPS recruits TBC1D15 for a Rab7-to-Arl8b identity switch to control late endosome transport. EMBO J 2020; 39:e102301. [PMID: 32080880 PMCID: PMC7073467 DOI: 10.15252/embj.2019102301] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [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: 04/23/2019] [Revised: 01/10/2020] [Accepted: 01/17/2020] [Indexed: 02/06/2023] Open
Abstract
The endolysosomal system fulfils a myriad of cellular functions predicated on regulated membrane identity progressions, collectively termed maturation. Mature or “late” endosomes are designated by small membrane‐bound GTPases Rab7 and Arl8b, which can either operate independently or collaborate to form a joint compartment. Whether, and how, Rab7 and Arl8b resolve this hybrid identity compartment to regain functional autonomy is unknown. Here, we report that Arl8b employs its effector SKIP to instigate inactivation and removal of Rab7 from select membranes. We find that SKIP interacts with Rab7 and functions as its negative effector, delivering the cognate GAP, TBC1D15. Recruitment of TBC1D15 to SKIP occurs via the HOPS complex, whose assembly is facilitated by contacts between Rab7 and the KMI motif of SKIP. Consequently, SKIP mediates reinstatement of single identity Arl8b sub‐compartment through an ordered Rab7‐to‐Arl8b handover, and, together with Rab7's positive effector RILP, enforces spatial, temporal and morphological compartmentalization of endolysosomal organelles.
Collapse
Affiliation(s)
- Marlieke Lm Jongsma
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen Bakker
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Birol Cabukusta
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Daphne van Elsland
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Job Fermie
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jimmy Ll Akkermans
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Coenraad Kuijl
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Sabina Y van der Zanden
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Lennert Janssen
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Denise Hoogzaad
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Rik van der Kant
- Center for Neurogenomics and Cognitive Research, Faculty of Sciences, VU Amsterdam, Amsterdam, The Netherlands
| | - Ruud H Wijdeven
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ilana Berlin
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
24
|
Wijers M, Zanoni P, Liv N, Vos DY, Jäckstein MY, Smit M, Wilbrink S, Wolters JC, van der Veen YT, Huijkman N, Dekker D, Kloosterhuis N, van Dijk TH, Billadeau DD, Kuipers F, Klumperman J, von Eckardstein A, Kuivenhoven JA, van de Sluis B. The hepatic WASH complex is required for efficient plasma LDL and HDL cholesterol clearance. JCI Insight 2019; 4:126462. [PMID: 31167970 DOI: 10.1172/jci.insight.126462] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 12/05/2018] [Accepted: 04/17/2019] [Indexed: 12/21/2022] Open
Abstract
The evolutionary conserved Wiskott-Aldrich syndrome protein and SCAR homolog (WASH) complex is one of the crucial multiprotein complexes that facilitates endosomal recycling of transmembrane proteins. Defects in WASH components have been associated with inherited developmental and neurological disorders in humans. Here, we show that hepatic ablation of the WASH component Washc1 in chow-fed mice increases plasma concentrations of cholesterol in both LDLs and HDLs, without affecting hepatic cholesterol content, hepatic cholesterol synthesis, biliary cholesterol excretion, or hepatic bile acid metabolism. Elevated plasma LDL cholesterol was related to reduced hepatocytic surface levels of the LDL receptor (LDLR) and the LDLR-related protein LRP1. Hepatic WASH ablation also reduced the surface levels of scavenger receptor class B type I and, concomitantly, selective uptake of HDL cholesterol into the liver. Furthermore, we found that WASHC1 deficiency increases LDLR proteolysis by the inducible degrader of LDLR, but does not affect proprotein convertase subtilisin/kexin type 9-mediated LDLR degradation. Remarkably, however, loss of hepatic WASHC1 may sensitize LDLR for proprotein convertase subtilisin/kexin type 9-induced degradation. Altogether, these findings identify the WASH complex as a regulator of LDL as well as HDL metabolism and provide in vivo evidence for endosomal trafficking of scavenger receptor class B type I in hepatocytes.
Collapse
Affiliation(s)
- Melinde Wijers
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Paolo Zanoni
- Institute for Clinical Chemistry, University Hospital Zurich, Zurich, Switzerland; Centre for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Dyonne Y Vos
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Michelle Y Jäckstein
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Marieke Smit
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Sanne Wilbrink
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Justina C Wolters
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ydwine T van der Veen
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Nicolette Huijkman
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Daphne Dekker
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Niels Kloosterhuis
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Theo H van Dijk
- Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Daniel D Billadeau
- Department of Immunology and Biochemistry, Division of Oncology Research, Mayo Clinic, Rochester, New York, USA
| | - Folkert Kuipers
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Arnold von Eckardstein
- Institute for Clinical Chemistry, University Hospital Zurich, Zurich, Switzerland; Centre for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Jan Albert Kuivenhoven
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Bart van de Sluis
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| |
Collapse
|
25
|
van der Beek J, Jonker C, van der Welle R, Liv N, Klumperman J. CORVET, CHEVI and HOPS – multisubunit tethers of the endo-lysosomal system in health and disease. J Cell Sci 2019; 132:132/10/jcs189134. [DOI: 10.1242/jcs.189134] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
ABSTRACT
Multisubunit tethering complexes (MTCs) are multitasking hubs that form a link between membrane fusion, organelle motility and signaling. CORVET, CHEVI and HOPS are MTCs of the endo-lysosomal system. They regulate the major membrane flows required for endocytosis, lysosome biogenesis, autophagy and phagocytosis. In addition, individual subunits control complex-independent transport of specific cargoes and exert functions beyond tethering, such as attachment to microtubules and SNARE activation. Mutations in CHEVI subunits lead to arthrogryposis, renal dysfunction and cholestasis (ARC) syndrome, while defects in CORVET and, particularly, HOPS are associated with neurodegeneration, pigmentation disorders, liver malfunction and various forms of cancer. Diseases and phenotypes, however, vary per affected subunit and a concise overview of MTC protein function and associated human pathologies is currently lacking. Here, we provide an integrated overview on the cellular functions and pathological defects associated with CORVET, CHEVI or HOPS proteins, both with regard to their complexes and as individual subunits. The combination of these data provides novel insights into how mutations in endo-lysosomal proteins lead to human pathologies.
Collapse
Affiliation(s)
- Jan van der Beek
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
| | - Caspar Jonker
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
| | - Reini van der Welle
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
| |
Collapse
|
26
|
Mohammadian S, Fokkema J, Agronskaia AV, Liv N, de Heus C, van Donselaar E, Blab GA, Klumperman J, Gerritsen HC. High accuracy, fiducial marker-based image registration of correlative microscopy images. Sci Rep 2019; 9:3211. [PMID: 30824844 PMCID: PMC6397213 DOI: 10.1038/s41598-019-40098-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 01/28/2019] [Indexed: 12/03/2022] Open
Abstract
Fluorescence microscopy (FM) and electron microscopy (EM) are complementary techniques. FM affords examination of large fields of view and identifying regions of interest but has a low resolution. EM exhibits excellent resolution over a limited field of view. The combination of these two techniques, correlative microscopy, received considerable interest in the past years and has proven its potential in biology and material science. Accurate correlation of FM and EM images is, however, challenging due to the differences in contrast mechanism, size of field of view and resolution. We report an accurate, fast and robust method to correlate FM and EM images using low densities of fiducial markers. Here, 120 nm diameter fiducial markers consisting of fluorescently labelled silica coated gold nanoparticles are used. The method relies on recording FM, low magnification EM and high magnification EM images. Two linear transformation matrices are constructed, FM to low magnification EM and low magnification EM to high magnification EM. Combination of these matrices results in a high accuracy transformation of FM to high magnification EM coordinates. The method was tested using two different transmission electron microscopes and different Tokuyasu and Lowicryl sections. The overall accuracy of the correlation method is high, 5-30 nm.
Collapse
Affiliation(s)
- Sajjad Mohammadian
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Jantina Fokkema
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Alexandra V Agronskaia
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cecilia de Heus
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elly van Donselaar
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gerhard A Blab
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hans C Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
27
|
Ando T, Bhamidimarri SP, Brending N, Colin-York H, Collinson L, De Jonge N, de Pablo PJ, Debroye E, Eggeling C, Franck C, Fritzsche M, Gerritsen H, Giepmans BNG, Grunewald K, Hofkens J, Hoogenboom JP, Janssen KPF, Kaufman R, Klumpermann J, Kurniawan N, Kusch J, Liv N, Parekh V, Peckys DB, Rehfeldt F, Reutens DC, Roeffaers MBJ, Salditt T, Schaap IAT, Schwarz US, Verkade P, Vogel MW, Wagner R, Winterhalter M, Yuan H, Zifarelli G. The 2018 correlative microscopy techniques roadmap. J Phys D Appl Phys 2018; 51:443001. [PMID: 30799880 PMCID: PMC6372154 DOI: 10.1088/1361-6463/aad055] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/14/2018] [Accepted: 07/01/2018] [Indexed: 05/19/2023]
Abstract
Developments in microscopy have been instrumental to progress in the life sciences, and many new techniques have been introduced and led to new discoveries throughout the last century. A wide and diverse range of methodologies is now available, including electron microscopy, atomic force microscopy, magnetic resonance imaging, small-angle x-ray scattering and multiple super-resolution fluorescence techniques, and each of these methods provides valuable read-outs to meet the demands set by the samples under study. Yet, the investigation of cell development requires a multi-parametric approach to address both the structure and spatio-temporal organization of organelles, and also the transduction of chemical signals and forces involved in cell-cell interactions. Although the microscopy technologies for observing each of these characteristics are well developed, none of them can offer read-out of all characteristics simultaneously, which limits the information content of a measurement. For example, while electron microscopy is able to disclose the structural layout of cells and the macromolecular arrangement of proteins, it cannot directly follow dynamics in living cells. The latter can be achieved with fluorescence microscopy which, however, requires labelling and lacks spatial resolution. A remedy is to combine and correlate different readouts from the same specimen, which opens new avenues to understand structure-function relations in biomedical research. At the same time, such correlative approaches pose new challenges concerning sample preparation, instrument stability, region of interest retrieval, and data analysis. Because the field of correlative microscopy is relatively young, the capabilities of the various approaches have yet to be fully explored, and uncertainties remain when considering the best choice of strategy and workflow for the correlative experiment. With this in mind, the Journal of Physics D: Applied Physics presents a special roadmap on the correlative microscopy techniques, giving a comprehensive overview from various leading scientists in this field, via a collection of multiple short viewpoints.
Collapse
Affiliation(s)
- Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | | | | | - H Colin-York
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
| | | | - Niels De Jonge
- INM-Leibniz Institute for New Materials, 66123 Saarbrücken, Germany
- Saarland University, 66123 Saarbrücken, Germany
| | - P J de Pablo
- Dpto. Física de la Materia Condensada Universidad Autónoma de Madrid 28049, Madrid, Spain
- Instituto de Física de la Materia Condensada IFIMAC, Universidad Autónoma de Madrid 28049, Madrid, Spain
| | - Elke Debroye
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
- Institute of Applied Optics, Friedrich-Schiller University, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
| | - Christian Franck
- Department of Mechanical Engineering, University of Wisconsin-Madison, 1513 University Ave, Madison, WI 53706, United States of America
| | - Marco Fritzsche
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Hans Gerritsen
- Debye Institute, Utrecht University, Utrecht, Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Kay Grunewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Centre of Structural Systems Biology Hamburg and University of Hamburg, Hamburg, Germany
- Heinrich-Pette-Institute, Leibniz Institute of Virology, Hamburg, Germany
| | - Johan Hofkens
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | | | | | - Rainer Kaufman
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Centre of Structural Systems Biology Hamburg and University of Hamburg, Hamburg, Germany
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Judith Klumpermann
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584CX Utrecht, Netherlands
| | - Nyoman Kurniawan
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584CX Utrecht, Netherlands
| | - Viha Parekh
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Diana B Peckys
- Faculty of Medicine, Saarland University, 66421 Homburg, Germany
| | - Florian Rehfeldt
- University of Göttingen, Third Institute of Physics-Biophysics, 37077 Göttingen, Germany
| | - David C Reutens
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Tim Salditt
- University of Göttingen, Institute for X-Ray Physics, 37077 Göttingen, Germany
| | - Iwan A T Schaap
- SmarAct GmbH, Schütte-Lanz-Str. 9, D-26135 Oldenburg, Germany
| | - Ulrich S Schwarz
- Institute for Theoretical Physics and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Michael W Vogel
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Richard Wagner
- Department of Life Sciences & Chemistry, Jacobs University, Bremen, Germany
| | | | - Haifeng Yuan
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | - Giovanni Zifarelli
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
28
|
Fokkema J, Fermie J, Liv N, van den Heuvel DJ, Konings TOM, Blab GA, Meijerink A, Klumperman J, Gerritsen HC. Fluorescently Labelled Silica Coated Gold Nanoparticles as Fiducial Markers for Correlative Light and Electron Microscopy. Sci Rep 2018; 8:13625. [PMID: 30206379 PMCID: PMC6133918 DOI: 10.1038/s41598-018-31836-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 05/10/2018] [Accepted: 08/22/2018] [Indexed: 11/09/2022] Open
Abstract
In this work, gold nanoparticles coated with a fluorescently labelled (rhodamine B) silica shell are presented as fiducial markers for correlative light and electron microscopy (CLEM). The synthesis of the particles is optimized to obtain homogeneous, spherical core-shell particles of arbitrary size. Next, particles labelled with different fluorophore densities are characterized to determine under which conditions bright and (photo)stable particles can be obtained. 2 and 3D CLEM examples are presented where optimized particles are used for correlation. In the 2D example, fiducials are added to a cryosection of cells whereas in the 3D example cells are imaged after endocytosis of the fiducials. Both examples demonstrate that the particles are clearly visible in both modalities and can be used for correlation. Additionally, the recognizable core-shell structure of the fiducials proves to be very powerful in electron microscopy: it makes it possible to irrefutably identify the particles and makes it easy to accurately determine the center of the fiducials.
Collapse
Affiliation(s)
- Jantina Fokkema
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Job Fermie
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Dave J van den Heuvel
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Tom O M Konings
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Gerhard A Blab
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Andries Meijerink
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Hans C Gerritsen
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
29
|
Fermie J, Liv N, Ten Brink C, van Donselaar EG, Müller WH, Schieber NL, Schwab Y, Gerritsen HC, Klumperman J. Single organelle dynamics linked to 3D structure by correlative live-cell imaging and 3D electron microscopy. Traffic 2018; 19:354-369. [PMID: 29451726 DOI: 10.1111/tra.12557] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/13/2018] [Accepted: 02/13/2018] [Indexed: 01/05/2023]
Abstract
Live-cell correlative light-electron microscopy (live-cell-CLEM) integrates live movies with the corresponding electron microscopy (EM) image, but a major challenge is to relate the dynamic characteristics of single organelles to their 3-dimensional (3D) ultrastructure. Here, we introduce focused ion beam scanning electron microscopy (FIB-SEM) in a modular live-cell-CLEM pipeline for a single organelle CLEM. We transfected cells with lysosomal-associated membrane protein 1-green fluorescent protein (LAMP-1-GFP), analyzed the dynamics of individual GFP-positive spots, and correlated these to their corresponding fine-architecture and immediate cellular environment. By FIB-SEM we quantitatively assessed morphological characteristics, like number of intraluminal vesicles and contact sites with endoplasmic reticulum and mitochondria. Hence, we present a novel way to integrate multiple parameters of subcellular dynamics and architecture onto a single organelle, which is relevant to address biological questions related to membrane trafficking, organelle biogenesis and positioning. Furthermore, by using CLEM to select regions of interest, our method allows for targeted FIB-SEM, which significantly reduces time required for image acquisition and data processing.
Collapse
Affiliation(s)
- Job Fermie
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Section Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Corlinda Ten Brink
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Elly G van Donselaar
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Wally H Müller
- Section Cryo-EM, Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Nicole L Schieber
- Electron Microscopy Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Yannick Schwab
- Electron Microscopy Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Hans C Gerritsen
- Section Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
30
|
Jonker CTH, Galmes R, Veenendaal T, Ten Brink C, van der Welle REN, Liv N, de Rooij J, Peden AA, van der Sluijs P, Margadant C, Klumperman J. Vps3 and Vps8 control integrin trafficking from early to recycling endosomes and regulate integrin-dependent functions. Nat Commun 2018; 9:792. [PMID: 29476049 PMCID: PMC5824891 DOI: 10.1038/s41467-018-03226-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 07/28/2016] [Accepted: 01/30/2018] [Indexed: 01/09/2023] Open
Abstract
Recycling endosomes maintain plasma membrane homeostasis and are important for cell polarity, migration, and cytokinesis. Yet, the molecular machineries that drive endocytic recycling remain largely unclear. The CORVET complex is a multi-subunit tether required for fusion between early endosomes. Here we show that the CORVET-specific subunits Vps3 and Vps8 also regulate vesicular transport from early to recycling endosomes. Vps3 and Vps8 localise to Rab4-positive recycling vesicles and co-localise with the CHEVI complex on Rab11-positive recycling endosomes. Depletion of Vps3 or Vps8 does not affect transferrin recycling, but delays the delivery of internalised integrins to recycling endosomes and their subsequent return to the plasma membrane. Consequently, Vps3/8 depletion results in defects in integrin-dependent cell adhesion and spreading, focal adhesion formation, and cell migration. These data reveal a role for Vps3 and Vps8 in a specialised recycling pathway important for integrin trafficking.
Collapse
Affiliation(s)
- C T H Jonker
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.,Department of Ophthalmology, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
| | - R Galmes
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.,UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6DD, UK
| | - T Veenendaal
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - C Ten Brink
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - R E N van der Welle
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - N Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - J de Rooij
- Section Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht Universty, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - A A Peden
- Department of Biomedical Science, The University of Sheffield, Sheffield, S10 2TN, UK
| | - P van der Sluijs
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.,Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH Utrecht, The Netherlands
| | - C Margadant
- Department of Molecular Cell Biology, Sanquin Research, Plesmanlaan 125, 1066 CX, Amsterdam, The Netherlands
| | - J Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
| |
Collapse
|
31
|
Vonk LA, van Dooremalen SFJ, Liv N, Klumperman J, Coffer PJ, Saris DB, Lorenowicz MJ. Mesenchymal Stromal/stem Cell-derived Extracellular Vesicles Promote Human Cartilage Regeneration In Vitro. Am J Cancer Res 2018; 8:906-920. [PMID: 29463990 PMCID: PMC5817101 DOI: 10.7150/thno.20746] [Citation(s) in RCA: 219] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 10/08/2017] [Indexed: 12/19/2022] Open
Abstract
Osteoarthritis (OA) is a rheumatic disease leading to chronic pain and disability with no effective treatment available. Recently, allogeneic human mesenchymal stromal/stem cells (MSC) entered clinical trials as a novel therapy for OA. Increasing evidence suggests that therapeutic efficacy of MSC depends on paracrine signalling. Here we investigated the role of extracellular vesicles (EVs) secreted by human bone marrow derived MSC (BMMSC) in human OA cartilage repair. Methods: To test the effect of BMMSC-EVs on OA cartilage inflammation, TNF-alpha-stimulated OA chondrocyte monolayer cultures were treated with BMMSC-EVs and pro-inflammatory gene expression was measured by qRT-PCR after 48 h. To assess the impact of BMMSC-EVs on cartilage regeneration, BMMSC-EVs were added to the regeneration cultures of human OA chondrocytes, which were analyzed after 4 weeks for glycosaminoglycan content by 1,9-dimethylmethylene blue (DMMB) assay. Furthermore, paraffin sections of the regenerated tissue were stained for proteoglycans (safranin-O) and type II collagen (immunostaining). Results: We show that BMMSC-EVs inhibit the adverse effects of inflammatory mediators on cartilage homeostasis. When co-cultured with OA chondrocytes, BMMSC-EVs abrogated the TNF-alpha-mediated upregulation of COX2 and pro-inflammatory interleukins and inhibited TNF-alpha-induced collagenase activity. BMMSC-EVs also promoted cartilage regeneration in vitro. Addition of BMMSC-EVs to cultures of chondrocytes isolated from OA patients stimulated production of proteoglycans and type II collagen by these cells. Conclusion: Our data demonstrate that BMMSC-EVs can be important mediators of cartilage repair and hold great promise as a novel therapeutic for cartilage regeneration and osteoarthritis.
Collapse
|
32
|
Jonker C, de Heus C, Faber L, ten Brink C, Potze L, Fermie J, Liv N, Klumperman J. An adapted protocol to overcome endosomal damage caused by polyethylenimine (PEI) mediated transfections. ACTA ACUST UNITED AC 2017. [DOI: 10.19185/matters.201711000012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
33
|
Yang C, Wu J, de Heus C, Grigoriev I, Liv N, Yao Y, Smal I, Meijering E, Klumperman J, Qi RZ, Akhmanova A. EB1 and EB3 regulate microtubule minus end organization and Golgi morphology. J Cell Biol 2017; 216:3179-3198. [PMID: 28814570 PMCID: PMC5626540 DOI: 10.1083/jcb.201701024] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [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: 01/04/2017] [Revised: 06/08/2017] [Accepted: 07/18/2017] [Indexed: 12/19/2022] Open
Abstract
End-binding proteins regulate the dynamics and function of microtubule plus ends by recruiting a plethora of diverse factors. Yang et al. show that EB1 and EB3 also affect microtubule minus ends by participating in their attachment to Golgi membranes. This function is important for cell polarity and migration. End-binding proteins (EBs) are the core components of microtubule plus end tracking protein complexes, but it is currently unknown whether they are essential for mammalian microtubule organization. Here, by using CRISPR/Cas9-mediated knockout technology, we generated stable cell lines lacking EB2 and EB3 and the C-terminal partner-binding half of EB1. These cell lines show only mild defects in cell division and microtubule polymerization. However, the length of CAMSAP2-decorated stretches at noncentrosomal microtubule minus ends in these cells is reduced, microtubules are detached from Golgi membranes, and the Golgi complex is more compact. Coorganization of microtubules and Golgi membranes depends on the EB1/EB3–myomegalin complex, which acts as membrane–microtubule tether and counteracts tight clustering of individual Golgi stacks. Disruption of EB1 and EB3 also perturbs cell migration, polarity, and the distribution of focal adhesions. EB1 and EB3 thus affect multiple interphase processes and have a major impact on microtubule minus end organization.
Collapse
Affiliation(s)
- Chao Yang
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Jingchao Wu
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Cecilia de Heus
- Department of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ilya Grigoriev
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Nalan Liv
- Department of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Yao Yao
- Department of Medical Informatics, Biomedical Imaging Group Rotterdam, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Radiology, Biomedical Imaging Group Rotterdam, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Ihor Smal
- Department of Medical Informatics, Biomedical Imaging Group Rotterdam, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Radiology, Biomedical Imaging Group Rotterdam, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Erik Meijering
- Department of Medical Informatics, Biomedical Imaging Group Rotterdam, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Radiology, Biomedical Imaging Group Rotterdam, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Judith Klumperman
- Department of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Robert Z Qi
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Anna Akhmanova
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
34
|
Haring MT, Liv N, Zonnevylle AC, Narvaez AC, Voortman LM, Kruit P, Hoogenboom JP. Automated sub-5 nm image registration in integrated correlative fluorescence and electron microscopy using cathodoluminescence pointers. Sci Rep 2017; 7:43621. [PMID: 28252673 PMCID: PMC5333625 DOI: 10.1038/srep43621] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 08/09/2016] [Accepted: 01/26/2017] [Indexed: 11/09/2022] Open
Abstract
In the biological sciences, data from fluorescence and electron microscopy is correlated to allow fluorescence biomolecule identification within the cellular ultrastructure and/or ultrastructural analysis following live-cell imaging. High-accuracy (sub-100 nm) image overlay requires the addition of fiducial markers, which makes overlay accuracy dependent on the number of fiducials present in the region of interest. Here, we report an automated method for light-electron image overlay at high accuracy, i.e. below 5 nm. Our method relies on direct visualization of the electron beam position in the fluorescence detection channel using cathodoluminescence pointers. We show that image overlay using cathodoluminescence pointers corrects for image distortions, is independent of user interpretation, and does not require fiducials, allowing image correlation with molecular precision anywhere on a sample.
Collapse
Affiliation(s)
- Martijn T. Haring
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Nalan Liv
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | | | - Angela C. Narvaez
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | | | - Pieter Kruit
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Jacob P. Hoogenboom
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| |
Collapse
|
35
|
Liv N, van Oosten Slingeland DSB, Baudoin JP, Kruit P, Piston DW, Hoogenboom JP. Electron Microscopy of Living Cells During in Situ Fluorescence Microscopy. ACS Nano 2016; 10:265-73. [PMID: 26580231 PMCID: PMC4729641 DOI: 10.1021/acsnano.5b03970] [Citation(s) in RCA: 10] [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] [Indexed: 05/16/2023]
Abstract
We present an approach toward dynamic nanoimaging: live fluorescence of cells encapsulated in a bionanoreactor is complemented with in situ scanning electron microscopy (SEM) on an integrated microscope. This allows us to take SEM snapshots on-demand, that is, at a specific location in time, at a desired region of interest, guided by the dynamic fluorescence imaging. We show that this approach enables direct visualization, with EM resolution, of the distribution of bioconjugated quantum dots on cellular extensions during uptake and internalization.
Collapse
Affiliation(s)
- Nalan Liv
- Department of Imaging Physics, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | | | - Jean-Pierre Baudoin
- Department of Molecular Physiology and Biophysics, Vanderbilt University, 747 Light Hall, Nashville, Tennessee 37232-0615, United States
| | - Pieter Kruit
- Department of Imaging Physics, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - David W. Piston
- Department of Molecular Physiology and Biophysics, Vanderbilt University, 747 Light Hall, Nashville, Tennessee 37232-0615, United States
| | - Jacob P. Hoogenboom
- Department of Imaging Physics, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
- Corresponding Author:
| |
Collapse
|
36
|
Liv N, Lazić I, Kruit P, Hoogenboom JP. Scanning electron microscopy of individual nanoparticle bio-markers in liquid. Ultramicroscopy 2014; 143:93-9. [DOI: 10.1016/j.ultramic.2013.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/05/2013] [Accepted: 09/10/2013] [Indexed: 11/30/2022]
|
37
|
Voorneveld PW, Kodach LL, Jacobs RJ, Liv N, Zonnevylle AC, Hoogenboom JP, Biemond I, Verspaget HW, Hommes DW, de Rooij K, van Noesel CJM, Morreau H, van Wezel T, Offerhaus GJA, van den Brink GR, Peppelenbosch MP, Ten Dijke P, Hardwick JCH. Loss of SMAD4 alters BMP signaling to promote colorectal cancer cell metastasis via activation of Rho and ROCK. Gastroenterology 2014; 147:196-208.e13. [PMID: 24704720 DOI: 10.1053/j.gastro.2014.03.052] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 03/26/2014] [Accepted: 03/30/2014] [Indexed: 01/22/2023]
Abstract
BACKGROUND & AIMS SMAD4 frequently is lost from colorectal cancers (CRCs), which is associated with the development of metastases and a poor prognosis. SMAD4 loss is believed to alter transforming growth factor β signaling to promote tumor progression. However, SMAD4 is also a central component of the bone morphogenetic protein (BMP) signaling pathway, implicated in CRC pathogenesis by human genetic studies. We investigated the effects of alterations in BMP signaling on the invasive and metastatic abilities of CRC cells and changes in members in this pathway in human tumor samples. METHODS We activated BMP signaling in SMAD4-positive and SMAD4-negative CRC cells (HCT116, HT-29, SW480, and LS174T); SMAD4 was stably expressed or knocked down using lentiviral vectors. We investigated the effects on markers of epithelial-mesenchymal transition and on cell migration, invasion, and formation of invadopodia. We performed kinase activity assays to characterize SMAD4-independent BMP signaling and used an inhibitor screen to identify pathways that regulate CRC cell migration. We investigated the effects of the ROCK inhibitor Y-27632 in immunocompromised (CD-1 Nu) mice with orthotopic metastatic tumors. Immunohistochemistry was used to detect BMPR1a, BMPR1b, BMPR2, and SMAD4 in human colorectal tumors; these were related to patient survival times. RESULTS Activation of BMP signaling in SMAD4-negative cells altered protein and messenger RNA levels of markers of epithelial-mesenchymal transition and increased cell migration, invasion, and formation of invadopodia. Knockdown of the BMP receptor in SMAD4-negative cells reduced their invasive activity in vitro. SMAD4-independent BMP signaling activated Rho signaling via ROCK and LIM domain kinase (LIMK). Pharmacologic inhibition of ROCK reduced metastasis of colorectal xenograft tumors in mice. Loss of SMAD4 from colorectal tumors has been associated with reduced survival time; we found that this association is dependent on the expression of BMP receptors but not transforming growth factor β receptors. CONCLUSIONS Loss of SMAD4 from colorectal cancer cells causes BMP signaling to switch from tumor suppressive to metastasis promoting. Concurrent loss of SMAD4 and normal expression of BMP receptors in colorectal tumors was associated with reduced survival times of patients. Reagents that interfere with SMAD4-independent BMP signaling, such as ROCK inhibitors, might be developed as therapeutics for CRC.
Collapse
Affiliation(s)
- Philip W Voorneveld
- Department of Gastroenterology and Hepatology, Cancer Genomics Centre Netherlands and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Liudmila L Kodach
- Department of Gastroenterology and Hepatology, Cancer Genomics Centre Netherlands and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rutger J Jacobs
- Department of Gastroenterology and Hepatology, Cancer Genomics Centre Netherlands and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Nalan Liv
- Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - A Christiaan Zonnevylle
- Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Jacob P Hoogenboom
- Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Izak Biemond
- Department of Gastroenterology and Hepatology, Cancer Genomics Centre Netherlands and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hein W Verspaget
- Department of Gastroenterology and Hepatology, Cancer Genomics Centre Netherlands and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniel W Hommes
- Department of Gastroenterology and Hepatology, Cancer Genomics Centre Netherlands and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Center for Inflammatory Bowel Diseases, University of California Los Angeles Medical Center, Santa Monica, California
| | - Karien de Rooij
- Department of Radiology, Cancer Genomics Centre Netherlands and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Percuros B.V., Leiden, The Netherlands
| | | | - Hans Morreau
- Department of Pathology, Cancer Genomics Centre Netherlands and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Cancer Genomics Centre Netherlands and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - G Johan A Offerhaus
- Department of Pathology, University Medical Center, Utrecht, The Netherlands
| | - Gijs R van den Brink
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands; Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands
| | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC, Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - Peter Ten Dijke
- Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - James C H Hardwick
- Department of Gastroenterology and Hepatology, Cancer Genomics Centre Netherlands and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
38
|
|
39
|
Narváez AC, Weppelman IGC, Moerland RJ, Liv N, Zonnevylle AC, Kruit P, Hoogenboom JP. Cathodoluminescence Microscopy of nanostructures on glass substrates. Opt Express 2013; 21:29968-29978. [PMID: 24514548 DOI: 10.1364/oe.21.029968] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Cathodoluminescence (CL) microscopy is an emerging analysis technique in the fields of biology and photonics, where it is used for the characterization of nanometer sized structures. For these applications, the use of transparent substrates might be highly preferred, but the detection of CL from nanostructures on glass is challenging because of the strong background generated in these substrates and the relatively weak CL signal from the nanostructures. We present an imaging system for highly efficient CL detection through the substrate using a high numerical aperture objective lens. This system allows for detection of individual nano-phosphors down to thirty nanometer in size as well as the up to ninth order plasmon resonance modes of a gold nanowire on ITO coated glass. We analyze the CL signal-to-background dependence on the primary electron beam energy and discuss different approaches to minimize its influence on the measurement.
Collapse
|
40
|
Liv N, Zonnevylle AC, Narvaez AC, Effting APJ, Voorneveld PW, Lucas MS, Hardwick JC, Wepf RA, Kruit P, Hoogenboom JP. Simultaneous correlative scanning electron and high-NA fluorescence microscopy. PLoS One 2013; 8:e55707. [PMID: 23409024 PMCID: PMC3568124 DOI: 10.1371/journal.pone.0055707] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 12/28/2012] [Indexed: 02/04/2023] Open
Abstract
Correlative light and electron microscopy (CLEM) is a unique method for investigating biological structure-function relations. With CLEM protein distributions visualized in fluorescence can be mapped onto the cellular ultrastructure measured with electron microscopy. Widespread application of correlative microscopy is hampered by elaborate experimental procedures related foremost to retrieving regions of interest in both modalities and/or compromises in integrated approaches. We present a novel approach to correlative microscopy, in which a high numerical aperture epi-fluorescence microscope and a scanning electron microscope illuminate the same area of a sample at the same time. This removes the need for retrieval of regions of interest leading to a drastic reduction of inspection times and the possibility for quantitative investigations of large areas and datasets with correlative microscopy. We demonstrate Simultaneous CLEM (SCLEM) analyzing cell-cell connections and membrane protrusions in whole uncoated colon adenocarcinoma cell line cells stained for actin and cortactin with AlexaFluor488. SCLEM imaging of coverglass-mounted tissue sections with both electron-dense and fluorescence staining is also shown.
Collapse
Affiliation(s)
- Nalan Liv
- Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - A. Christiaan Zonnevylle
- Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Angela C. Narvaez
- Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | | | - Philip W. Voorneveld
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Miriam S. Lucas
- Electron Microscopy ETH Zurich - EMEZ, ETH Zurich, Zurich, Switzerland
| | - James C. Hardwick
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Roger A. Wepf
- Electron Microscopy ETH Zurich - EMEZ, ETH Zurich, Zurich, Switzerland
| | - Pieter Kruit
- Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Jacob P. Hoogenboom
- Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
- * E-mail:
| |
Collapse
|
41
|
Mahran GH, Kadry HA, Thabet CK, El-Olemy MM, Al-Azizi MM, Schiff PL, Wong LK, Liv N. GC/MS Analysis of Volatile Oil of Fruits of Anethum graveolens. ACTA ACUST UNITED AC 2008. [DOI: 10.3109/13880209209053978] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- G. H. Mahran
- Department of Pharmacognosy, Faculties of Pharmacy, Cairo, Egypt
| | - H. A. Kadry
- Department of Pharmacognosy, Faculties of Pharmacy, Al-Azhar University, Egypt
| | - C. K. Thabet
- Department of Pharmacognosy, Faculties of Pharmacy, Cairo, Egypt
| | - M. M. El-Olemy
- College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
| | - M. M. Al-Azizi
- College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
| | - P. L. Schiff
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, PA, 15261
| | - L. K. Wong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, PA, 15261
- G.D. Searle Company, Skokie, IL, 60077, USA
| | - N. Liv
- Department of Pharmacognosy, Faculties of Pharmacy, Al-Azhar University, Egypt
| |
Collapse
|