51
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Wollmann T, Rohr K. Deep Consensus Network: Aggregating predictions to improve object detection in microscopy images. Med Image Anal 2021; 70:102019. [PMID: 33730623 DOI: 10.1016/j.media.2021.102019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/13/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022]
Abstract
Detection of cells and particles in microscopy images is a common and challenging task. In recent years, detection approaches in computer vision achieved remarkable improvements by leveraging deep learning. Microscopy images pose challenges like small and clustered objects, low signal to noise, and complex shape and appearance, for which current approaches still struggle. We introduce Deep Consensus Network, a new deep neural network for object detection in microscopy images based on object centroids. Our network is trainable end-to-end and comprises a Feature Pyramid Network-based feature extractor, a Centroid Proposal Network, and a layer for ensembling detection hypotheses over all image scales and anchors. We suggest an anchor regularization scheme that favours prior anchors over regressed locations. We also propose a novel loss function based on Normalized Mutual Information to cope with strong class imbalance, which we derive within a Bayesian framework. In addition, we introduce an improved algorithm for Non-Maximum Suppression which significantly reduces the algorithmic complexity. Experiments on synthetic data are performed to provide insights into the properties of the proposed loss function and its robustness. We also applied our method to challenging data from the TUPAC16 mitosis detection challenge and the Particle Tracking Challenge, and achieved results competitive or better than state-of-the-art.
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Affiliation(s)
- Thomas Wollmann
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University Im Neuenheimer Feld 267, Heidelberg, Germany.
| | - Karl Rohr
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University Im Neuenheimer Feld 267, Heidelberg, Germany.
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52
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Leroux M, Boutchueng-Djidjou M, Faure R. Insulin's Discovery: New Insights on Its Hundredth Birthday: From Insulin Action and Clearance to Sweet Networks. Int J Mol Sci 2021; 22:ijms22031030. [PMID: 33494161 PMCID: PMC7864324 DOI: 10.3390/ijms22031030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/28/2022] Open
Abstract
In 2021, the 100th anniversary of the isolation of insulin and the rescue of a child with type 1 diabetes from death will be marked. In this review, we highlight advances since the ingenious work of the four discoverers, Frederick Grant Banting, John James Rickard Macleod, James Bertram Collip and Charles Herbert Best. Macleoad closed his Nobel Lecture speech by raising the question of the mechanism of insulin action in the body. This challenge attracted many investigators, and the question remained unanswered until the third part of the 20th century. We summarize what has been learned, from the discovery of cell surface receptors, insulin action, and clearance, to network and precision medicine.
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Lonic A, Gehling F, Belle L, Li X, Schieber NL, Nguyen EV, Goodall GJ, Parton RG, Daly RJ, Khew-Goodall Y. Phosphorylation of PKCδ by FER tips the balance from EGFR degradation to recycling. J Cell Biol 2021; 220:211661. [PMID: 33411917 PMCID: PMC7797899 DOI: 10.1083/jcb.201902073] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/30/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
Receptor degradation terminates signaling by activated receptor tyrosine kinases. Degradation of EGFR occurs in lysosomes and requires the switching of RAB5 for RAB7 on late endosomes to enable their fusion with the lysosome, but what controls this critical switching is poorly understood. We show that the tyrosine kinase FER alters PKCδ function by phosphorylating it on Y374, and that phospho-Y374-PKCδ prevents RAB5 release from nascent late endosomes, thereby inhibiting EGFR degradation and promoting the recycling of endosomal EGFR to the cell surface. The rapid association of phospho-Y374-PKCδ with EGFR-containing endosomes is diminished by PTPN14, which dephosphorylates phospho-Y374-PKCδ. In triple-negative breast cancer cells, the FER-dependent phosphorylation of PKCδ enhances EGFR signaling and promotes anchorage-independent cell growth. Importantly, increased Y374-PKCδ phosphorylation correlating with arrested late endosome maturation was identified in ∼25% of triple-negative breast cancer patients, suggesting that dysregulation of this pathway may contribute to their pathology.
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Affiliation(s)
- Ana Lonic
- Centre for Cancer Biology, An Alliance of SA Pathology and the University of South Australia, Adelaide, South Australia, Australia,The Discipline of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Freya Gehling
- Centre for Cancer Biology, An Alliance of SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Leila Belle
- Centre for Cancer Biology, An Alliance of SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Xiaochun Li
- Centre for Cancer Biology, An Alliance of SA Pathology and the University of South Australia, Adelaide, South Australia, Australia
| | - Nicole L. Schieber
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Elizabeth V. Nguyen
- Cancer Program, Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Gregory J. Goodall
- Centre for Cancer Biology, An Alliance of SA Pathology and the University of South Australia, Adelaide, South Australia, Australia,The Discipline of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia,School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Robert G. Parton
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia,Centre for Microscopy and Microanalysis, The University of Queensland, St. Lucia, Queensland, Australia
| | - Roger J. Daly
- Cancer Program, Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Yeesim Khew-Goodall
- Centre for Cancer Biology, An Alliance of SA Pathology and the University of South Australia, Adelaide, South Australia, Australia,The Discipline of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia,Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia,Correspondence to Yeesim Khew-Goodall:
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54
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Zhang Y, Kong Y, Ma Y, Ni S, Wikerholmen T, Xi K, Zhao F, Zhao Z, Wang J, Huang B, Chen A, Yao Z, Han M, Feng Z, Hu Y, Thorsen F, Wang J, Li X. Loss of COPZ1 induces NCOA4 mediated autophagy and ferroptosis in glioblastoma cell lines. Oncogene 2021; 40:1425-1439. [PMID: 33420375 PMCID: PMC7906905 DOI: 10.1038/s41388-020-01622-3] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 11/25/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023]
Abstract
Dysregulated iron metabolism is a hallmark of many cancers, including glioblastoma (GBM). However, its role in tumor progression remains unclear. Herein, we identified coatomer protein complex subunit zeta 1 (COPZ1) as a therapeutic target candidate which significantly dysregulated iron metabolism in GBM cells. Overexpression of COPZ1 was associated with increasing tumor grade and poor prognosis in glioma patients based on analysis of expression data from the publicly available database The Cancer Genome Atlas (P < 0.001). Protein levels of COPZ1 were significantly increased in GBM compared to non-neoplastic brain tissue samples in immunohistochemistry and western blot analysis. SiRNA knockdown of COPZ1 suppressed proliferation of U87MG, U251 and P3#GBM in vitro. Stable expression of a COPZ1 shRNA construct in U87MG inhibited tumor growth in vivo by ~60% relative to controls at day 21 after implantation (P < 0.001). Kaplan-Meier analysis of the survival data demonstrated that the overall survival of tumor bearing animals increased from 20.8 days (control) to 27.8 days (knockdown, P < 0.05). COPZ1 knockdown also led to the increase in nuclear receptor coactivator 4 (NCOA4), resulting in the degradation of ferritin, and a subsequent increase in the intracellular levels of ferrous iron and ultimately ferroptosis. These data demonstrate that COPZ1 is a critical mediator in iron metabolism. The COPZ1/NCOA4/FTH1 axis is therefore a novel therapeutic target for the treatment of human GBM.
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Affiliation(s)
- Yulin Zhang
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,grid.7914.b0000 0004 1936 7443Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Yang Kong
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,grid.7914.b0000 0004 1936 7443Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Yuan Ma
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China
| | - Shilei Ni
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China
| | - Tobias Wikerholmen
- grid.7914.b0000 0004 1936 7443Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Kaiyan Xi
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China
| | - Feihu Zhao
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China
| | - Zhimin Zhao
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China
| | - Junpeng Wang
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China
| | - Bin Huang
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China
| | - Anjing Chen
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China
| | - Zhong Yao
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China
| | - Mingzhi Han
- grid.7914.b0000 0004 1936 7443Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Zichao Feng
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China
| | - Yaotian Hu
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China
| | - Frits Thorsen
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,grid.7914.b0000 0004 1936 7443Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway ,grid.7914.b0000 0004 1936 7443Molecular Imaging Center, Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Jian Wang
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,grid.7914.b0000 0004 1936 7443Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Xingang Li
- grid.27255.370000 0004 1761 1174Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China ,Shandong Key Laboratory of Brain Function Remodeling, Shandong 107 Wenhua Xi Road, Jinan, 250012 P.R. China
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55
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Veschini L, Sailem H, Malani D, Pietiäinen V, Stojiljkovic A, Wiseman E, Danovi D. High-Content Imaging to Phenotype Human Primary and iPSC-Derived Cells. Methods Mol Biol 2021; 2185:423-445. [PMID: 33165865 DOI: 10.1007/978-1-0716-0810-4_27] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Increasingly powerful microscopy, liquid handling, and computational techniques have enabled cell imaging in high throughput. Microscopy images are quantified using high-content analysis platforms linking object features to cell behavior. This can be attempted on physiologically relevant cell models, including stem cells and primary cells, in complex environments, and conceivably in the presence of perturbations. Recently, substantial focus has been devoted to cell profiling for cell therapy, assays for drug discovery or biomarker identification for clinical decision-making protocols, bringing this wealth of information into translational applications. In this chapter, we focus on two protocols enabling to (1) benchmark human cells, in particular human endothelial cells as a case study and (2) extract cells from blood for follow-up experiments including image-based drug testing. We also present concepts of high-content imaging and discuss the benefits and challenges, with the aim of enabling readers to tailor existing pipelines and bring such approaches closer to translational research and the clinic.
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Affiliation(s)
- Lorenzo Veschini
- Academic Centre of Reconstructive Science, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Heba Sailem
- The Institute of Biomedical Engineering, Oxford, UK
| | - Disha Malani
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute of Life Science-HiLIFE, University of Helsinki, Helsinki, Finland
| | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute of Life Science-HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ana Stojiljkovic
- Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Erika Wiseman
- Stem Cell Hotel, Centre for Stem Cells and Regenerative Medicine, King's College London, London, UK
| | - Davide Danovi
- Stem Cell Hotel, Centre for Stem Cells and Regenerative Medicine, King's College London, London, UK.
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56
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Bhave M, Mino RE, Wang X, Lee J, Grossman HM, Lakoduk AM, Danuser G, Schmid SL, Mettlen M. Functional characterization of 67 endocytic accessory proteins using multiparametric quantitative analysis of CCP dynamics. Proc Natl Acad Sci U S A 2020; 117:31591-31602. [PMID: 33257546 PMCID: PMC7749282 DOI: 10.1073/pnas.2020346117] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Clathrin-mediated endocytosis (CME) begins with the nucleation of clathrin assembly on the plasma membrane, followed by stabilization and growth/maturation of clathrin-coated pits (CCPs) that eventually pinch off and internalize as clathrin-coated vesicles. This highly regulated process involves a myriad of endocytic accessory proteins (EAPs), many of which are multidomain proteins that encode a wide range of biochemical activities. Although domain-specific activities of EAPs have been extensively studied, their precise stage-specific functions have been identified in only a few cases. Using single-guide RNA (sgRNA)/dCas9 and small interfering RNA (siRNA)-mediated protein knockdown, combined with an image-based analysis pipeline, we have determined the phenotypic signature of 67 EAPs throughout the maturation process of CCPs. Based on these data, we show that EAPs can be partitioned into phenotypic clusters, which differentially affect CCP maturation and dynamics. Importantly, these clusters do not correlate with functional modules based on biochemical activities. Furthermore, we discover a critical role for SNARE proteins and their adaptors during early stages of CCP nucleation and stabilization and highlight the importance of GAK throughout CCP maturation that is consistent with GAK's multifunctional domain architecture. Together, these findings provide systematic, mechanistic insights into the plasticity and robustness of CME.
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Affiliation(s)
- Madhura Bhave
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Rosa E Mino
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Xinxin Wang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jeon Lee
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Heather M Grossman
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Ashley M Lakoduk
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Gaudenz Danuser
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sandra L Schmid
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390;
| | - Marcel Mettlen
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390;
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57
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Villari G, Enrico Bena C, Del Giudice M, Gioelli N, Sandri C, Camillo C, Fiorio Pla A, Bosia C, Serini G. Distinct retrograde microtubule motor sets drive early and late endosome transport. EMBO J 2020; 39:e103661. [PMID: 33215754 PMCID: PMC7737607 DOI: 10.15252/embj.2019103661] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/01/2020] [Accepted: 10/14/2020] [Indexed: 11/23/2022] Open
Abstract
Although subcellular positioning of endosomes significantly impacts on their functions, the molecular mechanisms governing the different steady‐state distribution of early endosomes (EEs) and late endosomes (LEs)/lysosomes (LYs) in peripheral and perinuclear eukaryotic cell areas, respectively, are still unsolved. We unveil that such differences arise because, while LE retrograde transport depends on the dynein microtubule (MT) motor only, the one of EEs requires the cooperative antagonism of dynein and kinesin‐14 KIFC1, a MT minus end‐directed motor involved in cancer progression. Mechanistically, the Ser‐x‐Ile‐Pro (SxIP) motif‐mediated interaction of the endoplasmic reticulum transmembrane protein stromal interaction molecule 1 (STIM1) with the MT plus end‐binding protein 1 (EB1) promotes its association with the p150Glued subunit of the dynein activator complex dynactin and the distinct location of EEs and LEs/LYs. The peripheral distribution of EEs requires their p150Glued‐mediated simultaneous engagement with dynein and SxIP motif‐containing KIFC1, via HOOK1 and HOOK3 adaptors, respectively. In sum, we provide evidence that distinct minus end‐directed MT motor systems drive the differential transport and subcellular distribution of EEs and LEs in mammalian cells.
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Affiliation(s)
- Giulia Villari
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
| | - Chiara Enrico Bena
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy.,IIGM - Italian Institute for Genomic Medicine, Candiolo, Italy
| | - Marco Del Giudice
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy.,IIGM - Italian Institute for Genomic Medicine, Candiolo, Italy
| | - Noemi Gioelli
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
| | - Chiara Sandri
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
| | - Chiara Camillo
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
| | - Alessandra Fiorio Pla
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Carla Bosia
- IIGM - Italian Institute for Genomic Medicine, Candiolo, Italy.,Department of Applied Science and Technology, Polytechnic of Torino, Torino, Italy
| | - Guido Serini
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
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58
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Clathrin- and dynamin-dependent endocytosis limits canonical NF-κB signaling triggered by lymphotoxin β receptor. Cell Commun Signal 2020; 18:176. [PMID: 33148272 PMCID: PMC7640449 DOI: 10.1186/s12964-020-00664-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 09/18/2020] [Indexed: 02/08/2023] Open
Abstract
Background Lymphotoxin β receptor (LTβR) is a member of tumor necrosis factor receptor (TNFR) superfamily which regulates the immune response. At the cellular level, upon ligand binding, the receptor activates the pro-inflammatory NF-κB and AP-1 pathways. Yet, the intracellular distribution of LTβR, the routes of its endocytosis and their connection to the signaling activation are not characterized. Here, we investigated the contribution of LTβR internalization to its signaling potential. Methods Intracellular localization of LTβR in unstimulated and stimulated cells was analyzed by confocal microscopy. Endocytosis impairment was achieved through siRNA- or CRISPR/Cas9-mediated depletion, or chemical inhibition of proteins regulating endocytic routes. The activation of LTβR-induced signaling was examined. The levels of effector proteins of the canonical and non-canonical branches of the NF-κB pathway, and the phosphorylation of JNK, Akt, ERK1/2, STAT1 and STAT3 involved in diverse signaling cascades, were measured by Western blotting. A transcriptional response to LTβR stimulation was assessed by qRT-PCR analysis. Results We demonstrated that LTβR was predominantly present on endocytic vesicles and the Golgi apparatus. The ligand-bound pool of the receptor localized to endosomes and was trafficked towards lysosomes for degradation. Depletion of regulators of different endocytic routes (clathrin-mediated, dynamin-dependent or clathrin-independent) resulted in the impairment of LTβR internalization, indicating that this receptor uses multiple entry pathways. Cells deprived of clathrin and dynamins exhibited enhanced activation of canonical NF-κB signaling represented by increased degradation of IκBα inhibitor and elevated expression of LTβR target genes. We also demonstrated that clathrin and dynamin deficiency reduced to some extent LTβR-triggered activation of the non-canonical branch of the NF-κB pathway. Conclusions Our work shows that the impairment of clathrin- and dynamin-dependent internalization amplifies a cellular response to LTβR stimulation. We postulate that receptor internalization restricts responsiveness of the cell to subthreshold stimuli. Video Abstract
Graphical abstract ![]()
Supplementary information Supplementary information accompanies this paper at 10.1186/s12964-020-00664-0.
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59
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Di Natale C, Natale CF, Florio D, Netti PA, Morelli G, Ventre M, Marasco D. Effects of surface nanopatterning on internalization and amyloid aggregation of the fragment 264-277 of Nucleophosmin 1. Colloids Surf B Biointerfaces 2020; 197:111439. [PMID: 33137636 DOI: 10.1016/j.colsurfb.2020.111439] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/06/2020] [Accepted: 10/20/2020] [Indexed: 12/17/2022]
Abstract
The mechanical interpretation of the plethora of factors that governs cellular localization of amyloid aggregates is crucial for planning novel therapeutical interventions in neurodegenerative diseases since these aggregates exert a primary role in the proteostasis machinery. The uptake of Cell Penetrating Peptides (CPPs) conjugated with different amyloid polypeptides occurs via different endocytic processes regulated by cytoskeleton organization and cell morphology. Herein, we deepened the internalization of an amyloid system in cells cultured on nanopatterned surfaces that represent a powerful tool to shape cell and regulate its contractility. We analyzed the behavior of an amyloid model system, employing NPM1264-277 sequence, covalently conjugated to Tat fragment 48-60 as CPP. To investigate its internalization mechanism, we followed the formation of aggregates on two kinds of substrates: a flat and a nanopatterned surface. Herein, investigations during time were carried out by employing both confocal and second harmonic generation (SHG) microscopies. We showed that modifications of cellular environment affect peptide localization, its cytoplasmic translocation and the size of amyloid aggregates.
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Affiliation(s)
- Concetta Di Natale
- Department of Pharmacy, University of Naples "Federico II", Italy; Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano di Tecnologia, Naples, Italy; Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy
| | - Carlo F Natale
- Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy
| | - Daniele Florio
- Department of Pharmacy, University of Naples "Federico II", Italy
| | - Paolo Antonio Netti
- Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano di Tecnologia, Naples, Italy; Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy; Department of Chemical, Materials and Industrial Production Engineering (DICMAPI), University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy
| | | | - Maurizio Ventre
- Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano di Tecnologia, Naples, Italy; Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy; Department of Chemical, Materials and Industrial Production Engineering (DICMAPI), University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", Italy
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60
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Unravelling of Hidden Secrets: The Tumour Suppressor Lethal (2) Giant Discs (Lgd)/CC2D1, Notch Signalling and Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1287:31-46. [PMID: 33034024 DOI: 10.1007/978-3-030-55031-8_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The endosomal pathway plays a pivotal role upon signal transduction in the Notch pathway. Recent work on lethal (2) giant discs (lgd) points to an additional critical role in avoiding uncontrolled ligand-independent signalling during trafficking of the Notch receptor through the endosomal pathway to the lysosome for degradation. In this chapter, we will outline the journey of Notch through the endosomal system and present an overview of the current knowledge about Lgd and its mammalian orthologs Lgd1/CC2D1b and Lgd2/CC2D1a. We will then discuss how Notch is activated in the absence of lgd function in Drosophila and ask whether there is evidence that a similar ligand-independent activation of the Notch pathway can also happen in mammals if the orthologs are inactivated.
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61
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Koseska A, Bastiaens PI. Processing Temporal Growth Factor Patterns by an Epidermal Growth Factor Receptor Network Dynamically Established in Space. Annu Rev Cell Dev Biol 2020; 36:359-383. [DOI: 10.1146/annurev-cellbio-013020-103810] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The proto-oncogenic epidermal growth factor (EGF) receptor (EGFR) is a tyrosine kinase whose sensitivity and response to growth factor signals that vary over time and space determine cellular behavior within a developing tissue. The molecular reorganization of the receptors on the plasma membrane and the enzyme-kinetic mechanisms of phosphorylation are key determinants that couple growth factor binding to EGFR signaling. To enable signal initiation and termination while simultaneously accounting for suppression of aberrant signaling, a coordinated coupling of EGFR kinase and protein tyrosine phosphatase activity is established through space by vesicular dynamics. The dynamical operation mode of this network enables not only time-varying growth factor sensing but also adaptation of the response depending on cellular context. By connecting spatially coupled enzymatic kinase/phosphatase processes and the corresponding dynamical systems description of the EGFR network, we elaborate on the general principles necessary for processing complex growth factor signals.
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Affiliation(s)
- Aneta Koseska
- Lise Meitner Group Cellular Computations and Learning, Centre of Advanced European Studies and Research (caesar), D-53175 Bonn, Germany
| | - Philippe I.H. Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
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62
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Lee MF, Trotman LC. PTEN: Bridging Endocytosis and Signaling. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036103. [PMID: 31818848 DOI: 10.1101/cshperspect.a036103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The transduction of signals in the PTEN/PI3-kinase (PI3K) pathway is built around a phosphoinositide (PIP) lipid messenger, phosphatidylinositol trisphosphate, PI(3,4,5)P3 or PIP3 Another, more ancient role of this family of messengers is the control of endocytosis, where a handful of separate PIPs act like postal codes. Prominent among them is PI(3)P, which helps to ensure that endocytic vesicles, their cargo, and membranes themselves reach their correct destinations. Traditionally, the cancer and the endocytic functions of the PI3K signaling pathway have been studied by cancer and membrane biologists, respectively, with some notable but overall minimal overlap. Modern microscopy has enabled monitoring of the PTEN/PI3K pathway in action. Here, we explore the flurry of groundbreaking concepts emerging from those efforts. The discovery that PTEN contains an autonomous PI(3)P reader domain, fused to the catalytic PIP3 eraser domain has prompted us to explore the relationship between PI3K signaling and endocytosis. This revealed how PTEN can achieve signal termination in a precisely controlled fashion, because endocytosis can package the PIP3 signal into discrete units that PTEN will erase. We explore how PTEN can bridge the worlds of endocytosis and PI3K signaling and discuss progress on how PI3K/AKT signaling can be acting from internal membranes. We discuss how the PTEN/PI3K system for growth control may have emerged from principles of endocytosis, and how this development could have affected the evolution of multicellular organisms.
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Affiliation(s)
- Matthew F Lee
- Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
| | - Lloyd C Trotman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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63
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Chen Z, Schmid SL. Evolving models for assembling and shaping clathrin-coated pits. J Cell Biol 2020; 219:e202005126. [PMID: 32770195 PMCID: PMC7480099 DOI: 10.1083/jcb.202005126] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/13/2020] [Accepted: 07/13/2020] [Indexed: 01/01/2023] Open
Abstract
Clathrin-mediated endocytosis occurs via the assembly of clathrin-coated pits (CCPs) that invaginate and pinch off to form clathrin-coated vesicles (CCVs). It is well known that adaptor protein 2 (AP2) complexes trigger clathrin assembly on the plasma membrane, and biochemical and structural studies have revealed the nature of these interactions. Numerous endocytic accessory proteins collaborate with clathrin and AP2 to drive CCV formation. However, many questions remain as to the molecular events involved in CCP initiation, stabilization, and curvature generation. Indeed, a plethora of recent evidence derived from cell perturbation, correlative light and EM tomography, live-cell imaging, modeling, and high-resolution structural analyses has revealed more complexity and promiscuity in the protein interactions driving CCP maturation than anticipated. After briefly reviewing the evidence supporting prevailing models, we integrate these new lines of evidence to develop a more dynamic and flexible model for how redundant, dynamic, and competing protein interactions can drive endocytic CCV formation and suggest new approaches to test emerging models.
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Affiliation(s)
| | - Sandra L. Schmid
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
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64
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Gubar O, Croisé P, Kropyvko S, Gryaznova T, Tóth P, Blangy A, Vitale N, Rynditch A, Gasman S, Ory S. The atypical Rho GTPase RhoU interacts with intersectin-2 to regulate endosomal recycling pathways. J Cell Sci 2020; 133:jcs234104. [PMID: 32737221 DOI: 10.1242/jcs.234104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/21/2020] [Indexed: 01/22/2023] Open
Abstract
Rho GTPases play a key role in various membrane trafficking processes. RhoU is an atypical small Rho GTPase related to Rac/Cdc42, which possesses unique N- and C-terminal domains that regulate its function and its subcellular localization. RhoU localizes at the plasma membrane, on endosomes and in cell adhesion structures where it governs cell signaling, differentiation and migration. However, despite its endomembrane localization, RhoU function in vesicular trafficking has been unexplored. Here, we identified intersectins (ITSNs) as new binding partners for RhoU and showed that the second PxxP motif at the N terminus of RhoU mediated interactions with the SH3 domains of ITSNs. To evaluate the function of RhoU and ITSNs in vesicular trafficking, we used fluorescent transferrin as a cargo for uptake experiments. We showed that silencing of either RhoU or ITSN2, but not ITSN1, increased transferrin accumulation in early endosomes, resulting from a defect in fast vesicle recycling. Concomitantly, RhoU and ITSN2 colocalized to a subset of Rab4-positive vesicles, suggesting that a RhoU-ITSN2 interaction may occur on fast recycling endosomes to regulate the fate of vesicular cargos.
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Affiliation(s)
- Olga Gubar
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, F-67000 Strasbourg, France
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo Street, Kyiv 03680, Ukraine
| | - Pauline Croisé
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, F-67000 Strasbourg, France
| | - Sergii Kropyvko
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo Street, Kyiv 03680, Ukraine
| | - Tetyana Gryaznova
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo Street, Kyiv 03680, Ukraine
| | - Petra Tóth
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, F-67000 Strasbourg, France
| | - Anne Blangy
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), Univ. Montpellier, CNRS, 34000 Montpellier, France
| | - Nicolas Vitale
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, F-67000 Strasbourg, France
| | - Alla Rynditch
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo Street, Kyiv 03680, Ukraine
| | - Stéphane Gasman
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, F-67000 Strasbourg, France
| | - Stéphane Ory
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, F-67000 Strasbourg, France
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65
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Sharma P, Parveen S, Shah LV, Mukherjee M, Kalaidzidis Y, Kozielski AJ, Rosato R, Chang JC, Datta S. SNX27-retromer assembly recycles MT1-MMP to invadopodia and promotes breast cancer metastasis. J Cell Biol 2020; 219:132732. [PMID: 31820782 PMCID: PMC7039210 DOI: 10.1083/jcb.201812098] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 07/26/2019] [Accepted: 10/21/2019] [Indexed: 12/25/2022] Open
Abstract
Recycling of MT-MMPs to actin-rich membrane-protrusive structures promotes breast cancer invasion. This study shows that SNX27–retromer, an endosomal sorting and recycling machinery, interacts with MT1-MMP and regulates its transport to the cell surface, thus promoting matrix invasive activity of the breast cancer cells. A variety of metastatic cancer cells use actin-rich membrane protrusions, known as invadopodia, for efficient ECM degradation, which involves trafficking of proteases from intracellular compartments to these structures. Here, we demonstrate that in the metastatic breast cancer cell line MDA-MB-231, retromer regulates the matrix invasion activity by recycling matrix metalloprotease, MT1-MMP. We further found that MT2-MMP, another abundantly expressed metalloprotease, is also invadopodia associated. MT1- and MT2-MMP showed a high degree of colocalization but were located on the distinct endosomal domains. Retromer and its associated sorting nexin, SNX27, phenocopied each other in matrix degradation via selectively recycling MT1-MMP but not MT2-MMP. ITC-based studies revealed that both SNX27 and retromer could directly interact with MT1-MMP. Analysis from a publicly available database showed SNX27 to be overexpressed or frequently altered in the patients having invasive breast cancer. In xenograft-based studies, SNX27-depleted cell lines showed prolonged survival of SCID mice, suggesting a possible implication for overexpression of the sorting nexin in tumor samples.
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Affiliation(s)
- Priyanka Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Bhopal, India
| | - Sameena Parveen
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Bhopal, India
| | - Lekha V Shah
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Bhopal, India
| | - Madhumita Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal, Bhopal, India
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | | | | | | | - Sunando Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Bhopal, India
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66
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Franke C, Repnik U, Segeletz S, Brouilly N, Kalaidzidis Y, Verbavatz JM, Zerial M. Correlative single-molecule localization microscopy and electron tomography reveals endosome nanoscale domains. Traffic 2020; 20:601-617. [PMID: 31206952 PMCID: PMC6771687 DOI: 10.1111/tra.12671] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/04/2019] [Accepted: 06/09/2019] [Indexed: 12/12/2022]
Abstract
Many cellular organelles, including endosomes, show compartmentalization into distinct functional domains, which, however, cannot be resolved by diffraction‐limited light microscopy. Single molecule localization microscopy (SMLM) offers nanoscale resolution but data interpretation is often inconclusive when the ultrastructural context is missing. Correlative light electron microscopy (CLEM) combining SMLM with electron microscopy (EM) enables correlation of functional subdomains of organelles in relation to their underlying ultrastructure at nanometer resolution. However, the specific demands for EM sample preparation and the requirements for fluorescent single‐molecule photo‐switching are opposed. Here, we developed a novel superCLEM workflow that combines triple‐color SMLM (dSTORM & PALM) and electron tomography using semi‐thin Tokuyasu thawed cryosections. We applied the superCLEM approach to directly visualize nanoscale compartmentalization of endosomes in HeLa cells. Internalized, fluorescently labeled Transferrin and EGF were resolved into morphologically distinct domains within the same endosome. We found that the small GTPase Rab5 is organized in nanodomains on the globular part of early endosomes. The simultaneous visualization of several proteins in functionally distinct endosomal sub‐compartments demonstrates the potential of superCLEM to link the ultrastructure of organelles with their molecular organization at nanoscale resolution.
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Affiliation(s)
- Christian Franke
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Urska Repnik
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sandra Segeletz
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Nicolas Brouilly
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Instutut de Biologie du Developpement de Marseille-Luminy, Aix-Marseille Universite, Marseille, France
| | - Yannis Kalaidzidis
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Jean-Marc Verbavatz
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Institut Jacques Monod, CNRS, Université Paris-Diderot, Paris, France
| | - Marino Zerial
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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67
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Albumin-conjugated drug is irresistible by single gene mutation of endocytic system: Verification by genome-wide CRISPR-Cas9 loss-of-function screens. J Control Release 2020; 323:311-320. [PMID: 32335155 DOI: 10.1016/j.jconrel.2020.04.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/31/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022]
Abstract
Albumin-conjugated drugs attain KRAS mutant cancer targeting through KRAS-enhanced macropinocytosis and intensified lysosomal degradation due to reduced neonatal Fc receptor (FcRn) expression. The cytosolic delivery of active payloads relies on endocytosis and subsequent intracellular processing of albumin delivery vehicles, wherein complex regulatory mechanisms and molecular machineries are closely involved. Despite the obvious merit of KRAS targeting, could such an endocytic process involving extra molecular regulators also bring about extra vulnerabilities to albumin-conjugated drugs, particularly, unexpected drug resistance? To assess such risks, here we performed an unbiased drug resistance mechanism comparison in pancreatic cancer, between free triptolide (TP, a potent cytotoxin) and albumin-conjugated TP, using genome-wide CRISPR-Cas9 loss-of-function screens. GTF2H5, a subunit of GTF2H transcription factor complex, was the only hit identified regardless of forms of TP treatment. With drug efficacy tests on GTF2H5 knockout clones, we further concluded that GTF2H5 deficiency conferred drug resistance primarily due to the pharmacological mechanism of action (MoA) of TP. In addition, molecules previously considered to be able to affect endocytosis and intracellular processing were not enriched during the screening with albumin-conjugated TP. With the aid of genome-wide CRISPR-Cas9 loss-of-function screens, we conclude that the pharmacological resistance of the active payload, rather than any potential loss-of-function mutations in endocytic molecular machineries, is the solely crucial drug resistance mechanism of albumin-conjugated drugs.
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68
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Huang D, Liu C, Sun X, Sun X, Qu Y, Tang Y, Li G, Tong T. CRL4 DCAF8 and USP11 oppositely regulate the stability of myeloid leukemia factors (MLFs). Biochem Biophys Res Commun 2020; 529:127-132. [PMID: 32703400 DOI: 10.1016/j.bbrc.2020.05.186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 05/25/2020] [Indexed: 01/20/2023]
Abstract
Myeloid leukemia factors (MLF1 and MLF2) are proteins associated with leukemia and several other cancers. However, little is known about the regulatory mechanisms underlying the stability of these proteins. Here, we show that DDB1 and CUL4 associated factor 8 (DCAF8), which can form a functional E3 ligase complex (CRL4DCAF8), has a strong interaction with the MLF2 protein. DCAF8 could promote MLF2 degradation through the ubiquitin-proteasome pathway. In contrast, ubiquitin specific peptidase 11 (USP11) associates with MLF2, thereby increasing its stability. Since MLF1 is highly related to MLF2, we demonstrated that MLF1 also interacts with DCAF8 and USP11, suggesting that CRL4DCAF8 and USP11 may also regulate the expression of MLF1. TCGA analysis revealed that both the myeloid leukemia factors (MLF1 and MLF2) show significant differential expression in various tumors. The results of our study indicate that CRL4DCAF8 and USP11 play opposite roles in the regulation of MLF1 and MLF2, which may, in turn, affect their biological functions in various cancers.
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Affiliation(s)
- Daoyuan Huang
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Cheng Liu
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Xiwen Sun
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Xinpei Sun
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Yanan Qu
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Yunyi Tang
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Guodong Li
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Tanjun Tong
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, 100191, China.
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69
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A New Pathway Promotes Adaptation of Human Glioblastoma Cells to Glucose Starvation. Cells 2020; 9:cells9051249. [PMID: 32443613 PMCID: PMC7290719 DOI: 10.3390/cells9051249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/11/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Adaptation of glioblastoma to caloric restriction induces compensatory changes in tumor metabolism that are incompletely known. Here we show that in human glioblastoma cells maintained in exhausted medium, SHC adaptor protein 3 (SHC3) increases due to down-regulation of SHC3 protein degradation. This effect is reversed by glucose addition and is not present in normal astrocytes. Increased SHC3 levels are associated to increased glucose uptake mediated by changes in membrane trafficking of glucose transporters of the solute carrier 2A superfamily (GLUT/SLC2A). We found that the effects on vesicle trafficking are mediated by SHC3 interactions with adaptor protein complex 1 and 2 (AP), BMP-2-inducible protein kinase and a fraction of poly ADP-ribose polymerase 1 (PARP1) associated to vesicles containing GLUT/SLC2As. In glioblastoma cells, PARP1 inhibitor veliparib mimics glucose starvation in enhancing glucose uptake. Furthermore, cytosol extracted from glioblastoma cells inhibits PARP1 enzymatic activity in vitro while immunodepletion of SHC3 from the cytosol significantly relieves this inhibition. The identification of a new pathway controlling glucose uptake in high grade gliomas represents an opportunity for repositioning existing drugs and designing new ones.
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70
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Morone D, Marazza A, Bergmann TJ, Molinari M. Deep learning approach for quantification of organelles and misfolded polypeptide delivery within degradative compartments. Mol Biol Cell 2020; 31:1512-1524. [PMID: 32401604 PMCID: PMC7359569 DOI: 10.1091/mbc.e20-04-0269] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Endolysosomal compartments maintain cellular fitness by clearing dysfunctional organelles and proteins from cells. Modulation of their activity offers therapeutic opportunities. Quantification of cargo delivery to and/or accumulation within endolysosomes is instrumental for characterizing lysosome-driven pathways at the molecular level and monitoring consequences of genetic or environmental modifications. Here we introduce LysoQuant, a deep learning approach for segmentation and classification of fluorescence images capturing cargo delivery within endolysosomes for clearance. LysoQuant is trained for unbiased and rapid recognition with human-level accuracy, and the pipeline informs on a series of quantitative parameters such as endolysosome number, size, shape, position within cells, and occupancy, which report on activity of lysosome-driven pathways. In our selected examples, LysoQuant successfully determines the magnitude of mechanistically distinct catabolic pathways that ensure lysosomal clearance of a model organelle, the endoplasmic reticulum, and of a model protein, polymerogenic ATZ. It does so with accuracy and velocity compatible with those of high-throughput analyses.
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Affiliation(s)
- Diego Morone
- Università della Svizzera italiana, CH-6900 Lugano, Switzerland.,Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
| | - Alessandro Marazza
- Università della Svizzera italiana, CH-6900 Lugano, Switzerland.,Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3000 Bern, Switzerland
| | - Timothy J Bergmann
- Università della Svizzera italiana, CH-6900 Lugano, Switzerland.,Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
| | - Maurizio Molinari
- Università della Svizzera italiana, CH-6900 Lugano, Switzerland.,Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland.,École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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71
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Tubbesing K, Ward J, Abini-Agbomson R, Malhotra A, Rudkouskaya A, Warren J, Lamar J, Martino N, Adam AP, Barroso M. Complex Rab4-Mediated Regulation of Endosomal Size and EGFR Activation. Mol Cancer Res 2020; 18:757-773. [PMID: 32019812 PMCID: PMC7526990 DOI: 10.1158/1541-7786.mcr-19-0052] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 09/24/2019] [Accepted: 01/30/2020] [Indexed: 11/16/2022]
Abstract
Early sorting endosomes are responsible for the trafficking and function of transferrin receptor (TfR) and EGFR. These receptors play important roles in iron uptake and signaling and are critical for breast cancer development. However, the role of morphology, receptor composition, and signaling of early endosomes in breast cancer remains poorly understood. A novel population of enlarged early endosomes was identified in breast cancer cells and tumor xenografts but not in noncancerous MCF10A cells. Quantitative analysis of endosomal morphology, cargo sorting, EGFR activation, and Rab GTPase regulation was performed using super-resolution and confocal microscopy followed by 3D rendering. MDA-MB-231 breast cancer cells have fewer, but larger EEA1-positive early endosomes compared with MCF10A cells. Live-cell imaging indicated dysregulated cargo sorting, because EGF and Tf traffic together via enlarged endosomes in MDA-MB-231, but not in MCF10A. Large EEA1-positive MDA-MB-231 endosomes exhibited prolonged and increased EGF-induced activation of EGFR upon phosphorylation at tyrosine-1068 (EGFR-p1068). Rab4A overexpression in MCF10A cells produced EEA1-positive enlarged endosomes that displayed prolonged and amplified EGF-induced EGFR-p1068 activation. Knockdown of Rab4A lead to increased endosomal size in MCF10A, but not in MDA-MB-231 cells. Nevertheless, Rab4A knockdown resulted in enhanced EGF-induced activation of EGFR-p1068 in MDA-MB-231 as well as downstream signaling in MCF10A cells. Altogether, this extensive characterization of early endosomes in breast cancer cells has identified a Rab4-modulated enlarged early endosomal compartment as the site of prolonged and increased EGFR activation. IMPLICATIONS: Enlarged early endosomes play a Rab4-modulated role in regulation of EGFR activation in breast cancer cells.
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Affiliation(s)
- Kate Tubbesing
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Jamie Ward
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Raymond Abini-Agbomson
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Aditi Malhotra
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Alena Rudkouskaya
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Janine Warren
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - John Lamar
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Nina Martino
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Alejandro P Adam
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
- Department of Ophthalmology, Albany Medical College, Albany, New York
| | - Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York.
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72
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Wang X, Chen Z, Mettlen M, Noh J, Schmid SL, Danuser G. DASC, a sensitive classifier for measuring discrete early stages in clathrin-mediated endocytosis. eLife 2020; 9:53686. [PMID: 32352376 PMCID: PMC7192580 DOI: 10.7554/elife.53686] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Clathrin-mediated endocytosis (CME) in mammalian cells is driven by resilient machinery that includes >70 endocytic accessory proteins (EAP). Accordingly, perturbation of individual EAPs often results in minor effects on biochemical measurements of CME, thus providing inconclusive/misleading information regarding EAP function. Live-cell imaging can detect earlier roles of EAPs preceding cargo internalization; however, this approach has been limited because unambiguously distinguishing abortive coats (ACs) from bona fide clathrin-coated pits (CCPs) is required but unaccomplished. Here, we develop a thermodynamics-inspired method, “disassembly asymmetry score classification (DASC)”, that resolves ACs from CCPs based on single channel fluorescent movies. After extensive verification, we use DASC-resolved ACs and CCPs to quantify CME progression in 11 EAP knockdown conditions. We show that DASC is a sensitive detector of phenotypic variation in CCP dynamics that is uncorrelated to the variation in biochemical measurements of CME. Thus, DASC is an essential tool for uncovering EAP function.
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Affiliation(s)
- Xinxin Wang
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Zhiming Chen
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Marcel Mettlen
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jungsik Noh
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Sandra L Schmid
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
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73
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Guillen RX, Beckley JR, Chen JS, Gould KL. CRISPR-mediated gene targeting of CK1δ/ε leads to enhanced understanding of their role in endocytosis via phosphoregulation of GAPVD1. Sci Rep 2020; 10:6797. [PMID: 32321936 PMCID: PMC7176688 DOI: 10.1038/s41598-020-63669-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 03/26/2020] [Indexed: 02/05/2023] Open
Abstract
Human casein kinase 1 delta (CK1δ) and epsilon (CK1ε) are members of a conserved family of abundant, ubiquitously expressed serine/threonine kinases that regulate multiple cellular processes including circadian rhythm and endocytosis. Here, we have investigated the localization and interactomes of endogenously tagged CK1δ and CK1ε during interphase and mitosis. CK1δ and CK1ε localize to centrosomes throughout the cell cycle, and in interphase cells to the nucleus, and in both a diffuse and punctate pattern in the cytoplasm. Also, for the first time, they were detected at the midbody during cell division. Mass spectrometry analysis identified a total of 181 proteins co-purifying with a Venus multifunctional (VM)-tagged CK1δ and/or CK1ε. GTPase-activating protein and VPS9 domain-containing protein 1 (GAPVD1), a protein required for efficient endocytosis, was consistently one of the most abundant interacting partners. We demonstrate that GAPVD1 is a substrate of CK1δ/ε with up to 38 phosphorylated residues in vitro and in vivo. Wildtype and a phosphomimetic mutant of GAPVD1, but not a phospho-ablating mutant, were able to rescue defects in transferrin and EGF internalization caused by loss of endogenous GAPVD1. Our results indicate that GAPVD1 is an important interacting partner and substrate of CK1δ/ε for endocytosis.
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Affiliation(s)
- Rodrigo X Guillen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Janel R Beckley
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.,Calico Group LLC, ProteoWorker, Nashville, TN, 32712, USA
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Kathleen L Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
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74
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Saraon P, Snider J, Kalaidzidis Y, Wybenga-Groot LE, Weiss K, Rai A, Radulovich N, Drecun L, Vučković N, Vučetić A, Wong V, Thériault B, Pham NA, Park JH, Datti A, Wang J, Pathmanathan S, Aboualizadeh F, Lyakisheva A, Yao Z, Wang Y, Joseph B, Aman A, Moran MF, Prakesch M, Poda G, Marcellus R, Uehling D, Samaržija M, Jakopović M, Tsao MS, Shepherd FA, Sacher A, Leighl N, Akhmanova A, Al-Awar R, Zerial M, Stagljar I. A drug discovery platform to identify compounds that inhibit EGFR triple mutants. Nat Chem Biol 2020; 16:577-586. [PMID: 32094923 DOI: 10.1038/s41589-020-0484-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/27/2020] [Indexed: 12/21/2022]
Abstract
Receptor tyrosine kinases (RTKs) are transmembrane receptors of great clinical interest due to their role in disease. Historically, therapeutics targeting RTKs have been identified using in vitro kinase assays. Due to frequent development of drug resistance, however, there is a need to identify more diverse compounds that inhibit mutated but not wild-type RTKs. Here, we describe MaMTH-DS (mammalian membrane two-hybrid drug screening), a live-cell platform for high-throughput identification of small molecules targeting functional protein-protein interactions of RTKs. We applied MaMTH-DS to an oncogenic epidermal growth factor receptor (EGFR) mutant resistant to the latest generation of clinically approved tyrosine kinase inhibitors (TKIs). We identified four mutant-specific compounds, including two that would not have been detected by conventional in vitro kinase assays. One of these targets mutant EGFR via a new mechanism of action, distinct from classical TKI inhibition. Our results demonstrate how MaMTH-DS is a powerful complement to traditional drug screening approaches.
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Affiliation(s)
- Punit Saraon
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Konstantin Weiss
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Ankit Rai
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Luka Drecun
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nika Vučković
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Adriana Vučetić
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Victoria Wong
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Brigitte Thériault
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jin H Park
- Department of Pharmacology and Cancer Biology Institute, Yale University, New Haven, CT, USA.,Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Alessandro Datti
- Network Biology Collaborative Centre, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Agriculture, Food, and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Jenny Wang
- Network Biology Collaborative Centre, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Shivanthy Pathmanathan
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Anna Lyakisheva
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Zhong Yao
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Yuhui Wang
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Babu Joseph
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Michael F Moran
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Michael Prakesch
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gennady Poda
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Richard Marcellus
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - David Uehling
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Miroslav Samaržija
- Department for Lung Diseases Jordanovac, Clinical Hospital Centre Zagreb, University of Zagreb, Zagreb, Croatia
| | - Marko Jakopović
- Department for Lung Diseases Jordanovac, Clinical Hospital Centre Zagreb, University of Zagreb, Zagreb, Croatia
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Frances A Shepherd
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Adrian Sacher
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Natasha Leighl
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Anna Akhmanova
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Rima Al-Awar
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada. .,Mediterranean Institute for Life Sciences, Split, Croatia.
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75
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Joseph BB, Wang Y, Edeen P, Lažetić V, Grant BD, Fay DS. Control of clathrin-mediated endocytosis by NIMA family kinases. PLoS Genet 2020; 16:e1008633. [PMID: 32069276 PMCID: PMC7048319 DOI: 10.1371/journal.pgen.1008633] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/28/2020] [Accepted: 01/28/2020] [Indexed: 12/16/2022] Open
Abstract
Endocytosis, the process by which cells internalize plasma membrane and associated cargo, is regulated extensively by posttranslational modifications. Previous studies suggested the potential involvement of scores of protein kinases in endocytic control, of which only a few have been validated in vivo. Here we show that the conserved NIMA-related kinases NEKL-2/NEK8/9 and NEKL-3/NEK6/7 (the NEKLs) control clathrin-mediated endocytosis in C. elegans. Loss of NEKL-2 or NEKL-3 activities leads to penetrant larval molting defects and to the abnormal localization of trafficking markers in arrested larvae. Using an auxin-based degron system, we also find that depletion of NEKLs in adult-stage C. elegans leads to gross clathrin mislocalization and to a dramatic reduction in clathrin mobility at the apical membrane. Using a non-biased genetic screen to identify suppressors of nekl molting defects, we identified several components and regulators of AP2, the major clathrin adapter complex acting at the plasma membrane. Strikingly, reduced AP2 activity rescues both nekl mutant molting defects as well as associated trafficking phenotypes, whereas increased levels of active AP2 exacerbate nekl defects. Moreover, in a unique example of mutual suppression, NEKL inhibition alleviates defects associated with reduced AP2 activity, attesting to the tight link between NEKL and AP2 functions. We also show that NEKLs are required for the clustering and internalization of membrane cargo required for molting. Notably, we find that human NEKs can rescue molting and trafficking defects in nekl mutant worms, suggesting that the control of intracellular trafficking is an evolutionarily conserved function of NEK family kinases. In order to function properly, cells must continually import materials from the outside. This process, termed endocytosis, is necessary for the uptake of nutrients and for interpreting signals coming from the external environment or from within the body. These signals are critical during animal development but also affect many types of cell behaviors throughout life. In our current work, we show that several highly conserved proteins in the nematode Caenorhabditis elegans, NEKL-2 and NEKL-3, regulate endocytosis. The human counterparts of NEKL-2 and NEKL-3 have been implicated in cardiovascular and renal diseases as well as many types of cancers. However, their specific functions within cells is incompletely understood and very little is known about their role in endocytosis or how this role might impact disease processes. Here we use several complementary approaches to characterize the specific functions of C. elegans NEKL-2 and NEKL-3 in endocytosis and show that their human counterparts likely have very similar functions. This work paves the way to a better understanding of fundamental biological processes and to determining the cellular functions of proteins connected to human diseases.
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Affiliation(s)
- Braveen B. Joseph
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Yu Wang
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Phil Edeen
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Vladimir Lažetić
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Barth D. Grant
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - David S. Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
- * E-mail:
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76
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Mattiazzi Usaj M, Sahin N, Friesen H, Pons C, Usaj M, Masinas MPD, Shuteriqi E, Shkurin A, Aloy P, Morris Q, Boone C, Andrews BJ. Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability. Mol Syst Biol 2020; 16:e9243. [PMID: 32064787 PMCID: PMC7025093 DOI: 10.15252/msb.20199243] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/16/2019] [Accepted: 01/15/2020] [Indexed: 12/13/2022] Open
Abstract
Our ability to understand the genotype-to-phenotype relationship is hindered by the lack of detailed understanding of phenotypes at a single-cell level. To systematically assess cell-to-cell phenotypic variability, we combined automated yeast genetics, high-content screening and neural network-based image analysis of single cells, focussing on genes that influence the architecture of four subcellular compartments of the endocytic pathway as a model system. Our unbiased assessment of the morphology of these compartments-endocytic patch, actin patch, late endosome and vacuole-identified 17 distinct mutant phenotypes associated with ~1,600 genes (~30% of all yeast genes). Approximately half of these mutants exhibited multiple phenotypes, highlighting the extent of morphological pleiotropy. Quantitative analysis also revealed that incomplete penetrance was prevalent, with the majority of mutants exhibiting substantial variability in phenotype at the single-cell level. Our single-cell analysis enabled exploration of factors that contribute to incomplete penetrance and cellular heterogeneity, including replicative age, organelle inheritance and response to stress.
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Affiliation(s)
| | - Nil Sahin
- The Donnelly CentreUniversity of TorontoTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | | | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute for Science and TechnologyBarcelona, CataloniaSpain
| | - Matej Usaj
- The Donnelly CentreUniversity of TorontoTorontoONCanada
| | | | | | - Aleksei Shkurin
- The Donnelly CentreUniversity of TorontoTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute for Science and TechnologyBarcelona, CataloniaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)Barcelona, CataloniaSpain
| | - Quaid Morris
- The Donnelly CentreUniversity of TorontoTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
- Computational and Systems Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Charles Boone
- The Donnelly CentreUniversity of TorontoTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
- RIKEN Centre for Sustainable Resource ScienceWakoSaitamaJapan
| | - Brenda J Andrews
- The Donnelly CentreUniversity of TorontoTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
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77
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Desai AS, Hunter MR, Kapustin AN. Using macropinocytosis for intracellular delivery of therapeutic nucleic acids to tumour cells. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180156. [PMID: 30967005 DOI: 10.1098/rstb.2018.0156] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nucleic acids are a rapidly emerging therapeutic modality with the potential to become the third major drug modality alongside antibodies and small molecules. Owing to the unfavourable physico-chemical characteristics of nucleic acids, such as large size and negative charge, intracellular delivery remains a fundamental challenge to realizing this potential. Delivery technologies such as lipids, polymers and peptides have been used to facilitate delivery, with many of the most successful technologies using macropinocytosis to gain cellular entry; mostly by default rather than design. Fundamental knowledge of macropinocytosis is rapidly growing, presenting opportunities to better tailor design strategies to target this pathway. Furthermore, certain types of tumour cells have been observed to have high levels of macropinocytic activity and traffic cargo to favourable destinations within the cell for endosomal release, providing unique opportunities to further use this entry route for drug delivery. In this article, we review the delivery systems reported to be taken up by macropinocytosis and what is known about the mechanisms for regulating macropinocytosis in tumour cells. From this analysis, we identify new opportunities for exploiting this pathway for the intracellular delivery of nucleic acids to tumour cells. This article is part of the Theo Murphy meeting issue 'Macropinocytosis'.
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Affiliation(s)
- Arpan S Desai
- AstraZeneca, IMED Biotech Unit, Pharmaceutical Sciences , Aaron Klug Building, Granta Park, Cambridge CB21 6GH , UK
| | - Morag R Hunter
- AstraZeneca, IMED Biotech Unit, Pharmaceutical Sciences , Aaron Klug Building, Granta Park, Cambridge CB21 6GH , UK
| | - Alexander N Kapustin
- AstraZeneca, IMED Biotech Unit, Pharmaceutical Sciences , Aaron Klug Building, Granta Park, Cambridge CB21 6GH , UK
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78
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Spilger R, Imle A, Lee JY, Muller B, Fackler OT, Bartenschlager R, Rohr K. A Recurrent Neural Network for Particle Tracking in Microscopy Images Using Future Information, Track Hypotheses, and Multiple Detections. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2020; 29:3681-3694. [PMID: 31940539 DOI: 10.1109/tip.2020.2964515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Automatic tracking of particles in time-lapse fluorescence microscopy images is essential for quantifying the dynamic behavior of subcellular structures and virus structures. We introduce a novel particle tracking approach based on a deep recurrent neural network architecture that exploits past and future information in both forward and backward direction. Assignment probabilities are determined jointly across multiple detections, and the probability of missing detections is computed. In addition, existence probabilities are determined by the network to handle track initiation and termination. For correspondence finding, track hypotheses are propagated to future time points so that information at later time points can be used to resolve ambiguities. A handcrafted similarity measure and handcrafted motion features are not necessary. Manually labeled data is not required for network training. We evaluated the performance of our approach using image data of the Particle Tracking Challenge as well as real fluorescence microscopy image sequences of virus structures. It turned out that the proposed approach outperforms previous methods.
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79
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Banach-Orłowska M, Wyszyńska R, Pyrzyńska B, Maksymowicz M, Gołąb J, Miączyńska M. Cholesterol restricts lymphotoxin β receptor-triggered NF-κB signaling. Cell Commun Signal 2019; 17:171. [PMID: 31878945 PMCID: PMC6933913 DOI: 10.1186/s12964-019-0460-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/10/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lymphotoxin β receptor (LTβR) plays important roles in the development of the immune system and immune response. At the cellular level, ligand-bound LTβR activates the pro-inflammatory NF-κB pathway but the detailed mechanisms regulating its signaling remain unknown. Understanding them is of high importance since LTβR and its ligands are promising therapeutic targets. Here, we studied the consequences of perturbed cellular cholesterol content on LTβR-induced NF-κB signaling. METHODS To modulate cholesterol availability and/or level in lung carcinoma A549 and H2228, and endothelial HUVEC cells different treatment regimens with filipin, methyl-β-cyclodextrin and simvastatin were applied. LTβR localization was studied by confocal microscopy. The activity of LTβR-induced NF-κB pathway was assessed by measuring the levels of NF-κB pathway inhibitor IκBα and phosphorylation of RelA transcription factor by Western blotting. The NF-κB transcriptional response, production of chemokines and adhesion molecules were examined by qRT-PCR, ELISA, and Western blotting, respectively. Adherence of different types of primary immune cells to epithelial A549 cells and endothelial HUVECs was measured fluorometrically. Interactions of LTβR with its protein partners were investigated by immunoprecipitation. RESULTS We showed that filipin-mediated sequestration of cholesterol or its depletion from the plasma membrane with methyl-β-cyclodextrin impaired LTβR internalization and potentiated LTβR-dependent activation of the canonical branch of the NF-κB pathway. The latter was manifested by enhanced degradation of IκBα inhibitor, elevated RelA phosphorylation, substantial increase in the expression of NF-κB target genes encoding, among others, cytokines and adhesion molecules known to play important roles in immune response. It was followed by robust secretion of CXCL8 and upregulation of ICAM1, that favored the adhesion of immune cells (NK and T cells, neutrophils) to A549 cells and HUVECs. Mechanistically, we showed that cholesterol depletion stabilized interactions of ligand-stimulated LTβR with modified forms of TRAF2 and NEMO proteins. CONCLUSIONS Our results showed that the reduction of the plasma membrane content of cholesterol or its sequestration strongly potentiated signaling outcome initiated by LTβR. Thus, drugs modulating cholesterol levels could potentially improve efficacy of LTβR-based therapies. Video abstract.
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Affiliation(s)
- Magdalena Banach-Orłowska
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland.
| | - Renata Wyszyńska
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
| | - Beata Pyrzyńska
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Maksymowicz
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
| | - Jakub Gołąb
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Marta Miączyńska
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
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80
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Latcheva NK, Delaney TL, Viveiros JM, Smith RA, Bernard KM, Harsin B, Marenda DR, Liebl FLW. The CHD Protein, Kismet, is Important for the Recycling of Synaptic Vesicles during Endocytosis. Sci Rep 2019; 9:19368. [PMID: 31852969 PMCID: PMC6920434 DOI: 10.1038/s41598-019-55900-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/29/2019] [Indexed: 12/14/2022] Open
Abstract
Chromatin remodeling proteins of the chromodomain DNA-binding protein family, CHD7 and CHD8, mediate early neurodevelopmental events including neural migration and differentiation. As such, mutations in either protein can lead to neurodevelopmental disorders. How chromatin remodeling proteins influence the activity of mature synapses, however, is relatively unexplored. A critical feature of mature neurons is well-regulated endocytosis, which is vital for synaptic function to recycle membrane and synaptic proteins enabling the continued release of synaptic vesicles. Here we show that Kismet, the Drosophila homolog of CHD7 and CHD8, regulates endocytosis. Kismet positively influenced transcript levels and bound to dap160 and endophilin B transcription start sites and promoters in whole nervous systems and influenced the synaptic localization of Dynamin/Shibire. In addition, kismet mutants exhibit reduced VGLUT, a synaptic vesicle marker, at stimulated but not resting synapses and reduced levels of synaptic Rab11. Endocytosis is restored at kismet mutant synapses by pharmacologically inhibiting the function of histone deacetyltransferases (HDACs). These data suggest that HDAC activity may oppose Kismet to promote synaptic vesicle endocytosis. A deeper understanding of how CHD proteins regulate the function of mature neurons will help better understand neurodevelopmental disorders.
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Affiliation(s)
- Nina K Latcheva
- Department of Biology, Drexel University, 3141 Chestnut St., Philadelphia, PA, 19104, USA.,Program in Molecular and Cellular Biology and Genetics, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Taylor L Delaney
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, USA
| | - Jennifer M Viveiros
- Department of Biology, Drexel University, 3141 Chestnut St., Philadelphia, PA, 19104, USA
| | - Rachel A Smith
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, USA
| | - Kelsey M Bernard
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, USA
| | - Benjamin Harsin
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, USA
| | - Daniel R Marenda
- Department of Biology, Drexel University, 3141 Chestnut St., Philadelphia, PA, 19104, USA.,Program in Molecular and Cellular Biology and Genetics, Drexel University College of Medicine, Philadelphia, PA, USA.,Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Faith L W Liebl
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, USA.
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81
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Gilleron J, Bouget G, Ivanov S, Meziat C, Ceppo F, Vergoni B, Djedaini M, Soprani A, Dumas K, Jacquel A, Yvan-Charvet L, Venteclef N, Tanti JF, Cormont M. Rab4b Deficiency in T Cells Promotes Adipose Treg/Th17 Imbalance, Adipose Tissue Dysfunction, and Insulin Resistance. Cell Rep 2019; 25:3329-3341.e5. [PMID: 30566860 DOI: 10.1016/j.celrep.2018.11.083] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 09/04/2018] [Accepted: 11/21/2018] [Indexed: 12/18/2022] Open
Abstract
Obesity modifies T cell populations in adipose tissue, thereby contributing to adipose tissue inflammation and insulin resistance. Here, we show that Rab4b, a small GTPase governing endocytic trafficking, is pivotal in T cells for the development of these pathological events. Rab4b expression is decreased in adipose T cells from mice and patients with obesity. The specific depletion of Rab4b in T cells causes adipocyte hypertrophy and insulin resistance in chow-fed mice and worsens insulin resistance in obese mice. This phenotype is driven by an increase in adipose Th17 and a decrease in adipose Treg due to a cell-autonomous skew of differentiation toward Th17. The Th17/Treg imbalance initiates adipose tissue inflammation and reduces adipogenesis, leading to lipid deposition in liver and muscles. Therefore, we propose that the obesity-induced loss of Rab4b in adipose T cells may contribute to maladaptive white adipose tissue remodeling and insulin resistance by altering adipose T cell fate.
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Affiliation(s)
- Jérôme Gilleron
- INSERM UMR1065, Mediterranean Center of Molecular Medicine C3M, Team "Cellular and Molecular Physiopathology of Obesity and Diabetes," Nice, France; Université Côte d'Azur, Nice, France
| | - Gwennaëlle Bouget
- INSERM UMR1065, Mediterranean Center of Molecular Medicine C3M, Team "Cellular and Molecular Physiopathology of Obesity and Diabetes," Nice, France; Université Côte d'Azur, Nice, France
| | - Stoyan Ivanov
- Université Côte d'Azur, Nice, France; INSERM U1065, Centre Méditerranéen de Médecine Moléculaire C3M, Team "Metabolism and Cancer," Nice, France
| | - Cindy Meziat
- INSERM UMR1065, Mediterranean Center of Molecular Medicine C3M, Team "Cellular and Molecular Physiopathology of Obesity and Diabetes," Nice, France; Université Côte d'Azur, Nice, France
| | - Franck Ceppo
- INSERM UMR1065, Mediterranean Center of Molecular Medicine C3M, Team "Cellular and Molecular Physiopathology of Obesity and Diabetes," Nice, France; Université Côte d'Azur, Nice, France
| | - Bastien Vergoni
- INSERM UMR1065, Mediterranean Center of Molecular Medicine C3M, Team "Cellular and Molecular Physiopathology of Obesity and Diabetes," Nice, France; Université Côte d'Azur, Nice, France
| | - Mansour Djedaini
- INSERM UMR1065, Mediterranean Center of Molecular Medicine C3M, Team "Cellular and Molecular Physiopathology of Obesity and Diabetes," Nice, France; Université Côte d'Azur, Nice, France
| | - Antoine Soprani
- Sorbonne Université, Université Pierre et Marie Curie, INSERM, UMR S_1138 Cordeliers Research Center, Paris, France; Clinique Geoffroy Saint-Hilaire, Ramsey Générale de Santé, Paris, France
| | - Karine Dumas
- INSERM UMR1065, Mediterranean Center of Molecular Medicine C3M, Team "Cellular and Molecular Physiopathology of Obesity and Diabetes," Nice, France; Université Côte d'Azur, Nice, France
| | - Arnaud Jacquel
- Université Côte d'Azur, Nice, France; INSERM U1065, Centre Méditerranéen de Médecine Moléculaire C3M, Team "Cell Death, Differentiation, and Cancer," Nice, France
| | - Laurent Yvan-Charvet
- Université Côte d'Azur, Nice, France; INSERM U1065, Centre Méditerranéen de Médecine Moléculaire C3M, Team "Metabolism and Cancer," Nice, France
| | - Nicolas Venteclef
- Sorbonne Université, Université Pierre et Marie Curie, INSERM, UMR S_1138 Cordeliers Research Center, Paris, France
| | - Jean-François Tanti
- INSERM UMR1065, Mediterranean Center of Molecular Medicine C3M, Team "Cellular and Molecular Physiopathology of Obesity and Diabetes," Nice, France; Université Côte d'Azur, Nice, France
| | - Mireille Cormont
- INSERM UMR1065, Mediterranean Center of Molecular Medicine C3M, Team "Cellular and Molecular Physiopathology of Obesity and Diabetes," Nice, France; Université Côte d'Azur, Nice, France.
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82
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Zhang SF, Yuan CJ, Chen Y, Lin L, Wang DZ. Transcriptomic response to changing ambient phosphorus in the marine dinoflagellate Prorocentrum donghaiense. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 692:1037-1047. [PMID: 31539936 DOI: 10.1016/j.scitotenv.2019.07.291] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 06/10/2023]
Abstract
Dinoflagellates represent major contributors to the harmful algal blooms in the oceans. Phosphorus (P) is an essential macronutrient that limits the growth and proliferation of dinoflagellates. However, the specific molecular mechanisms involved in the P acclimation of dinoflagellates remain poorly understood. Here, the transcriptomes of a dinoflagellate Prorocentrum donghaiense grown under inorganic P-replete, P-deficient, and inorganic- and organic P-resupplied conditions were compared. Genes encoding low- and high-affinity P transporters were significantly down-regulated in the P-deficient cells, while organic P utilization genes were significantly up-regulated, indicating strong ability of P. donghaiense to utilize organic P. Up-regulation of membrane phospholipid catabolism and endocytosis provided intracellular and extracellular organic P for the P-deficient cells. Physiological responses of P. donghaiense to dissolved inorganic P (DIP) or dissolved organic P (DOP) resupply exhibited insignificant differences. However, the corresponding transcriptomic responses significantly differed. Although the expression of multiple genes was significantly altered after DIP resupplementation, few biological processes varied. In contrast, various metabolic processes associated with cell growth, such as translation, transport, nucleotide, carbohydrate and lipid metabolisms, were significantly altered in the DOP-resupplied cells. Our results indicated that P. donghaiense evolved diverse DOP utilization strategies to adapt to low P environments, and that DOPs might play critical roles in the P. donghaiense bloom formation.
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Affiliation(s)
- Shu-Feng Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Chun-Juan Yuan
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Ying Chen
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
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83
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Lauer J, Segeletz S, Cezanne A, Guaitoli G, Raimondi F, Gentzel M, Alva V, Habeck M, Kalaidzidis Y, Ueffing M, Lupas AN, Gloeckner CJ, Zerial M. Auto-regulation of Rab5 GEF activity in Rabex5 by allosteric structural changes, catalytic core dynamics and ubiquitin binding. eLife 2019; 8:46302. [PMID: 31718772 PMCID: PMC6855807 DOI: 10.7554/elife.46302] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 10/22/2019] [Indexed: 02/06/2023] Open
Abstract
Intracellular trafficking depends on the function of Rab GTPases, whose activation is regulated by guanine exchange factors (GEFs). The Rab5 GEF, Rabex5, was previously proposed to be auto-inhibited by its C-terminus. Here, we studied full-length Rabex5 and Rabaptin5 proteins as well as domain deletion Rabex5 mutants using hydrogen deuterium exchange mass spectrometry. We generated a structural model of Rabex5, using chemical cross-linking mass spectrometry and integrative modeling techniques. By correlating structural changes with nucleotide exchange activity for each construct, we uncovered new auto-regulatory roles for the ubiquitin binding domains and the Linker connecting those domains to the catalytic core of Rabex5. We further provide evidence that enhanced dynamics in the catalytic core are linked to catalysis. Our results suggest a more complex auto-regulation mechanism than previously thought and imply that ubiquitin binding serves not only to position Rabex5 but to also control its Rab5 GEF activity through allosteric structural alterations.
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Affiliation(s)
- Janelle Lauer
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sandra Segeletz
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Alice Cezanne
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Francesco Raimondi
- Bioquant, Heidelberg University, Heidelberg, Germany.,Heidelberg University Biochemistry Centre (BZH), Heidelberg, Germany
| | - Marc Gentzel
- Molecular Analysis-Mass Spectrometry Center for Molecular and Cellular Bioengineering, Technical University Dresden, Dresden, Germany
| | - Vikram Alva
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Michael Habeck
- Statistical Inverse Problems in Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of Göttingen, Göttingen, Germany
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marius Ueffing
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Andrei N Lupas
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases, Tübingen, Germany.,Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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84
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Feldman D, Singh A, Schmid-Burgk JL, Carlson RJ, Mezger A, Garrity AJ, Zhang F, Blainey PC. Optical Pooled Screens in Human Cells. Cell 2019; 179:787-799.e17. [PMID: 31626775 PMCID: PMC6886477 DOI: 10.1016/j.cell.2019.09.016] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 07/08/2019] [Accepted: 09/13/2019] [Indexed: 01/06/2023]
Abstract
Genetic screens are critical for the systematic identification of genes underlying cellular phenotypes. Pooling gene perturbations greatly improves scalability but is not compatible with imaging of complex and dynamic cellular phenotypes. Here, we introduce a pooled approach for optical genetic screens in mammalian cells. We use targeted in situ sequencing to demultiplex a library of genetic perturbations following image-based phenotyping. We screened a set of 952 genes across millions of cells for involvement in nuclear factor κB (NF-κB) signaling by imaging the translocation of RelA (p65) to the nucleus. Screening at a single time point across 3 cell lines recovered 15 known pathway components, while repeating the screen with live-cell imaging revealed a role for Mediator complex subunits in regulating the duration of p65 nuclear retention. These results establish a highly multiplexed approach to image-based screens of spatially and temporally defined phenotypes with pooled libraries.
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Affiliation(s)
- David Feldman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Physics, MIT, Cambridge, MA 02142, USA
| | - Avtar Singh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Rebecca J Carlson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Health Sciences and Technology, MIT, Cambridge, MA 02142, USA
| | - Anja Mezger
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | | | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, MIT, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02142, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02142, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, MIT, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA.
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85
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Thottacherry JJ, Sathe M, Prabhakara C, Mayor S. Spoiled for Choice: Diverse Endocytic Pathways Function at the Cell Surface. Annu Rev Cell Dev Biol 2019; 35:55-84. [PMID: 31283376 PMCID: PMC6917507 DOI: 10.1146/annurev-cellbio-100617-062710] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Endocytosis has long been identified as a key cellular process involved in bringing in nutrients, in clearing cellular debris in tissue, in the regulation of signaling, and in maintaining cell membrane compositional homeostasis. While clathrin-mediated endocytosis has been most extensively studied, a number of clathrin-independent endocytic pathways are continuing to be delineated. Here we provide a current survey of the different types of endocytic pathways available at the cell surface and discuss a new classification and plausible molecular mechanisms for some of the less characterized pathways. Along with an evolutionary perspective of the origins of some of these pathways, we provide an appreciation of the distinct roles that these pathways play in various aspects of cellular physiology, including the control of signaling and membrane tension.
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Affiliation(s)
- Joseph Jose Thottacherry
- National Centre for Biological Science, Tata Institute for Fundamental Research, Bangalore 560065, India;
| | - Mugdha Sathe
- National Centre for Biological Science, Tata Institute for Fundamental Research, Bangalore 560065, India;
| | - Chaitra Prabhakara
- National Centre for Biological Science, Tata Institute for Fundamental Research, Bangalore 560065, India;
| | - Satyajit Mayor
- National Centre for Biological Science, Tata Institute for Fundamental Research, Bangalore 560065, India;
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, 560065, India
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86
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Flotillins promote T cell receptor sorting through a fast Rab5-Rab11 endocytic recycling axis. Nat Commun 2019; 10:4392. [PMID: 31558725 PMCID: PMC6763463 DOI: 10.1038/s41467-019-12352-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/28/2019] [Indexed: 12/25/2022] Open
Abstract
The targeted endocytic recycling of the T cell receptor (TCR) to the immunological synapse is essential for T cell activation. Despite this, the mechanisms that underlie the sorting of internalised receptors into recycling endosomes remain poorly understood. To build a comprehensive picture of TCR recycling during T cell activation, we developed a suite of new imaging and quantification tools centred on photoactivation of fluorescent proteins. We show that the membrane-organising proteins, flotillin-1 and -2, are required for TCR to reach Rab5-positive endosomes immediately after endocytosis and for transfer from Rab5- to Rab11a-positive compartments. We further observe that after sorting into in Rab11a-positive vesicles, TCR recycles to the plasma membrane independent of flotillin expression. Our data suggest a mechanism whereby flotillins delineate a fast Rab5-Rab11a endocytic recycling axis and functionally contribute to regulate the spatial organisation of these endosomes. Internalized receptors are recycled back to the cell surface, but their precise mechanisms are unclear. Here, the authors show that the flotillin membrane proteins may regulate the transfer of internalized T cell receptors into Rab5 and Rab11-positive endosomes to support its rapid recycling.
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87
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Boutchueng-Djidjou M, Faure RL. Network medicine-travelling with the insulin receptor: Encounter of the second type. EClinicalMedicine 2019; 13:14-20. [PMID: 31517259 PMCID: PMC6734015 DOI: 10.1016/j.eclinm.2019.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/08/2019] [Accepted: 07/18/2019] [Indexed: 01/21/2023] Open
Abstract
Important progress has been made in understanding many aspects of insulin action in the last 10 years. Attention will be focused here on the physical protein interaction network of the internalized insulin receptor (IR) and its relationships with the genetic architecture of type 2 diabetes mellitus (T2D). The IR recognizes signals from the outside (circulating insulin) and engages the insulin signaling response. Within seconds, the IR is also involved in insulin internalization and its subsequent degradation in endosomes (physiological clearance of insulin). A T2D disease module sharing functional similarities with insulin secretion in pancreatic islets was recently identified in the close neighborhood of the internalized IR in liver. This module brought a new light on the apparent functional heterogeneity of numerous genes at risk to T2D by linking them to a few noncanonical layers of signaling feedback loops. These findings should be translated into a better understanding of the primary mechanisms of the disease and consequently a more precise sub-classification of T2D, ultimately leading to precision medicine and the development of new therapeutical drugs.
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Affiliation(s)
- Martial Boutchueng-Djidjou
- Départment of Pediatrics, Faculty of Medicine, Laval University, CHU de Québec Research Center, Québec City G1V4G2, Canada
| | - Robert L. Faure
- Centre de Recherche du CHU de Québec, Laboratoire de Biologie Cellulaire, local T3-55 2705, Boulevard Laurier Québec, QC, G1V4G2
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88
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Chessel A, Carazo Salas RE. From observing to predicting single-cell structure and function with high-throughput/high-content microscopy. Essays Biochem 2019; 63:197-208. [PMID: 31243141 PMCID: PMC6610450 DOI: 10.1042/ebc20180044] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 02/08/2023]
Abstract
In the past 15 years, cell-based microscopy has evolved its focus from observing cell function to aiming to predict it. In particular-powered by breakthroughs in computer vision, large-scale image analysis and machine learning-high-throughput and high-content microscopy imaging have enabled to uniquely harness single-cell information to systematically discover and annotate genes and regulatory pathways, uncover systems-level interactions and causal links between cellular processes, and begin to clarify and predict causal cellular behaviour and decision making. Here we review these developments, discuss emerging trends in the field, and describe how single-cell 'omics and single-cell microscopy are imminently in an intersecting trajectory. The marriage of these two fields will make possible an unprecedented understanding of cell and tissue behaviour and function.
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Affiliation(s)
- Anatole Chessel
- École polytechnique, Université Paris-Saclay, 91128 Palaiseau Cedex, France
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89
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Bapaume L, Laukamm S, Darbon G, Monney C, Meyenhofer F, Feddermann N, Chen M, Reinhardt D. VAPYRIN Marks an Endosomal Trafficking Compartment Involved in Arbuscular Mycorrhizal Symbiosis. FRONTIERS IN PLANT SCIENCE 2019; 10:666. [PMID: 31231402 PMCID: PMC6558636 DOI: 10.3389/fpls.2019.00666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/02/2019] [Indexed: 05/08/2023]
Abstract
Arbuscular mycorrhiza (AM) is a symbiosis between plants and AM fungi that requires the intracellular accommodation of the fungal partner in the host. For reciprocal nutrient exchange, AM fungi form intracellular arbuscules that are surrounded by the peri-arbuscular membrane. This membrane, together with the fungal plasma membrane, and the space in between, constitute the symbiotic interface, over which nutrients are exchanged. Intracellular establishment of AM fungi requires the VAPYRIN protein which is induced in colonized cells, and which localizes to numerous small mobile structures of unknown identity (Vapyrin-bodies). In order to characterize the identity and function of the Vapyrin-bodies we pursued a dual strategy. First, we co-expressed fluorescently tagged VAPYRIN with a range of subcellular marker proteins, and secondly, we employed biochemical tools to identify interacting partner proteins of VAPYRIN. As an important tool for the quantitative analysis of confocal microscopic data sets from co-expression of fluorescent proteins, we developed a semi-automated image analysis pipeline that allows for precise spatio-temporal quantification of protein co-localization and of the dynamics of organelle association from movies. Taken together, these experiments revealed that Vapyrin-bodies have an endosomal identity with trans-Golgi features, and that VAPYRIN interacts with a symbiotic R-SNARE of the VAMP721 family, that localizes to the same compartment.
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Affiliation(s)
| | | | | | | | | | | | | | - Didier Reinhardt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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90
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The High Mobility Group A1 (HMGA1) Chromatin Architectural Factor Modulates Nuclear Stiffness in Breast Cancer Cells. Int J Mol Sci 2019; 20:ijms20112733. [PMID: 31167352 PMCID: PMC6600462 DOI: 10.3390/ijms20112733] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 12/28/2022] Open
Abstract
Plasticity is an essential condition for cancer cells to invade surrounding tissues. The nucleus is the most rigid cellular organelle and it undergoes substantial deformations to get through environmental constrictions. Nuclear stiffness mostly depends on the nuclear lamina and chromatin, which in turn might be affected by nuclear architectural proteins. Among these is the HMGA1 (High Mobility Group A1) protein, a factor that plays a causal role in neoplastic transformation and that is able to disentangle heterochromatic domains by H1 displacement. Here we made use of atomic force microscopy to analyze the stiffness of breast cancer cellular models in which we modulated HMGA1 expression to investigate its role in regulating nuclear plasticity. Since histone H1 is the main modulator of chromatin structure and HMGA1 is a well-established histone H1 competitor, we correlated HMGA1 expression and cellular stiffness with histone H1 expression level, post-translational modifications, and nuclear distribution. Our results showed that HMGA1 expression level correlates with nuclear stiffness, is associated to histone H1 phosphorylation status, and alters both histone H1 chromatin distribution and expression. These data suggest that HMGA1 might promote chromatin relaxation through a histone H1-mediated mechanism strongly impacting on the invasiveness of cancer cells.
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91
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Larsen MB, Perez Verdaguer M, Schmidt BF, Bruchez MP, Watkins SC, Sorkin A. Generation of endogenous pH-sensitive EGF receptor and its application in high-throughput screening for proteins involved in clathrin-mediated endocytosis. eLife 2019; 8:46135. [PMID: 31066673 PMCID: PMC6533059 DOI: 10.7554/elife.46135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/07/2019] [Indexed: 12/15/2022] Open
Abstract
Previously we used gene-editing to label endogenous EGF receptor (EGFR) with GFP and demonstrate that picomolar concentrations of EGFR ligand drive signaling and endocytosis of EGFR in tumors in vivo (Pinilla-Macua et al., 2017). We now use gene-editing to insert a fluorogen activating protein (FAP) in the EGFR extracellular domain. Binding of the tandem dye pair MG-Bis-SA to FAP-EGFR provides a ratiometric pH-sensitive model with dual fluorescence excitation and a single far-red emission. The excitation ratio of fluorescence intensities was demonstrated to faithfully report the fraction of FAP-EGFR located in acidic endosomal/lysosomal compartments. Coupling native FAP-EGFR expression with the high method sensitivity has allowed development of a high-throughput assay to measure the rates of clathrin-mediated FAP-EGFR endocytosis stimulated with physiological EGF concentrations. The assay was utilized to screen a phosphatase siRNA library. These studies highlight the utility of endogenous pH-sensitive FAP-receptor chimeras in high-throughput analysis of endocytosis.
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Affiliation(s)
- Mads Breum Larsen
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, United States
| | - Mireia Perez Verdaguer
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, United States
| | - Brigitte F Schmidt
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, United States
| | - Marcel P Bruchez
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, United States.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, United States.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, United States.,Sharp Edge Laboratories, Pittsburgh, United States
| | - Simon C Watkins
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, United States
| | - Alexander Sorkin
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, United States
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92
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Iershov A, Nemazanyy I, Alkhoury C, Girard M, Barth E, Cagnard N, Montagner A, Chretien D, Rugarli EI, Guillou H, Pende M, Panasyuk G. The class 3 PI3K coordinates autophagy and mitochondrial lipid catabolism by controlling nuclear receptor PPARα. Nat Commun 2019; 10:1566. [PMID: 30952952 PMCID: PMC6451001 DOI: 10.1038/s41467-019-09598-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 03/20/2019] [Indexed: 12/19/2022] Open
Abstract
The class 3 phosphoinositide 3-kinase (PI3K) is required for lysosomal degradation by autophagy and vesicular trafficking, assuring nutrient availability. Mitochondrial lipid catabolism is another energy source. Autophagy and mitochondrial metabolism are transcriptionally controlled by nutrient sensing nuclear receptors. However, the class 3 PI3K contribution to this regulation is unknown. We show that liver-specific inactivation of Vps15, the essential regulatory subunit of the class 3 PI3K, elicits mitochondrial depletion and failure to oxidize fatty acids. Mechanistically, transcriptional activity of Peroxisome Proliferator Activated Receptor alpha (PPARα), a nuclear receptor orchestrating lipid catabolism, is blunted in Vps15-deficient livers. We find PPARα repressors Histone Deacetylase 3 (Hdac3) and Nuclear receptor co-repressor 1 (NCoR1) accumulated in Vps15-deficient livers due to defective autophagy. Activation of PPARα or inhibition of Hdac3 restored mitochondrial biogenesis and lipid oxidation in Vps15-deficient hepatocytes. These findings reveal roles for the class 3 PI3K and autophagy in transcriptional coordination of mitochondrial metabolism.
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Affiliation(s)
- Anton Iershov
- Institut Necker-Enfants Malades (INEM), 75014, Paris, France
- INSERM U1151/CNRS UMR 8253, 75014, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France
| | - Ivan Nemazanyy
- Institut Necker-Enfants Malades (INEM), 75014, Paris, France
- INSERM U1151/CNRS UMR 8253, 75014, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France
- Platform for Metabolic Analyses, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS 3633, 75014, Paris, France
| | - Chantal Alkhoury
- Institut Necker-Enfants Malades (INEM), 75014, Paris, France
- INSERM U1151/CNRS UMR 8253, 75014, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France
| | - Muriel Girard
- Institut Necker-Enfants Malades (INEM), 75014, Paris, France
- INSERM U1151/CNRS UMR 8253, 75014, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France
- Pediatric Hepatology Unit, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, 75015, France
| | - Esther Barth
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674, Cologne, Germany
| | - Nicolas Cagnard
- Plateforme Bio-informatique, Université Paris Descartes, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS 3633, Paris, 75015, France
| | | | - Dominique Chretien
- INSERM UMR1141, Hôpital Robert Debré, Paris, 75019, France
- Université Paris 7, Faculté de Médecine Denis Diderot, Paris, 75019, France
| | - Elena I Rugarli
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674, Cologne, Germany
| | - Herve Guillou
- Toxalim, Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, 31027, France
| | - Mario Pende
- Institut Necker-Enfants Malades (INEM), 75014, Paris, France
- INSERM U1151/CNRS UMR 8253, 75014, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France
| | - Ganna Panasyuk
- Institut Necker-Enfants Malades (INEM), 75014, Paris, France.
- INSERM U1151/CNRS UMR 8253, 75014, Paris, France.
- Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France.
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93
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Jiao Y, Ahmed U, Sim MFM, Bejar A, Zhang X, Talukder MMU, Rice R, Flannick J, Podgornaia AI, Reilly DF, Engreitz JM, Kost-Alimova M, Hartland K, Mercader JM, Georges S, Wagh V, Tadin-Strapps M, Doench JG, Edwardson JM, Rochford JJ, Rosen ED, Majithia AR. Discovering metabolic disease gene interactions by correlated effects on cellular morphology. Mol Metab 2019; 24:108-119. [PMID: 30940487 PMCID: PMC6531784 DOI: 10.1016/j.molmet.2019.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 12/26/2022] Open
Abstract
Objective Impaired expansion of peripheral fat contributes to the pathogenesis of insulin resistance and Type 2 Diabetes (T2D). We aimed to identify novel disease–gene interactions during adipocyte differentiation. Methods Genes in disease-associated loci for T2D, adiposity and insulin resistance were ranked according to expression in human adipocytes. The top 125 genes were ablated in human pre-adipocytes via CRISPR/CAS9 and the resulting cellular phenotypes quantified during adipocyte differentiation with high-content microscopy and automated image analysis. Morphometric measurements were extracted from all images and used to construct morphologic profiles for each gene. Results Over 107 morphometric measurements were obtained. Clustering of the morphologic profiles accross all genes revealed a group of 14 genes characterized by decreased lipid accumulation, and enriched for known lipodystrophy genes. For two lipodystrophy genes, BSCL2 and AGPAT2, sub-clusters with PLIN1 and CEBPA identifed by morphological similarity were validated by independent experiments as novel protein–protein and gene regulatory interactions. Conclusions A morphometric approach in adipocytes can resolve multiple cellular mechanisms for metabolic disease loci; this approach enables mechanistic interrogation of the hundreds of metabolic disease loci whose function still remains unknown. Loss-of-function genetic screen in human adipocytes for 125 genes selected from metabolic disease-associated loci. Genetic screen read out by cellular morphometry— 77,000 images taken with 400 morphological features extracted per image. Pairwise mechanistic interactions between genes identified by correlations of cellular morphometry—two interactions validated. Novel interaction between BSCL2 and PLIN1 from biophysical association of proteins at lipid droplet surface. Novel interaction between CEBPA and AGPAT2 from CEBPA dependent transcription of AGPAT2.
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Affiliation(s)
- Yang Jiao
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Umer Ahmed
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - M F Michelle Sim
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Andrea Bejar
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xiaolan Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Robert Rice
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason Flannick
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anna I Podgornaia
- Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA 02115, USA
| | - Dermot F Reilly
- Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA 02115, USA
| | | | | | - Kate Hartland
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Sara Georges
- Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA 02115, USA
| | - Vilas Wagh
- Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA 02115, USA
| | | | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Justin J Rochford
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK; Rowett Institute and the Aberdeen Cardiovascular and Diabetes Centre, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Evan D Rosen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Endocrinology, Diabetes and Obesity, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Harvard Medical School, Department of Genetics, Boston, MA 02215, USA
| | - Amit R Majithia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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94
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A gene-based recessive diplotype exome scan discovers FGF6, a novel hepcidin-regulating iron-metabolism gene. Blood 2019; 133:1888-1898. [PMID: 30814063 DOI: 10.1182/blood-2018-10-879585] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/20/2019] [Indexed: 12/14/2022] Open
Abstract
Standard analyses applied to genome-wide association data are well designed to detect additive effects of moderate strength. However, the power for standard genome-wide association study (GWAS) analyses to identify effects from recessive diplotypes is not typically high. We proposed and conducted a gene-based compound heterozygosity test to reveal additional genes underlying complex diseases. With this approach applied to iron overload, a strong association signal was identified between the fibroblast growth factor-encoding gene, FGF6, and hemochromatosis in the central Wisconsin population. Functional validation showed that fibroblast growth factor 6 protein (FGF-6) regulates iron homeostasis and induces transcriptional regulation of hepcidin. Moreover, specific identified FGF6 variants differentially impact iron metabolism. In addition, FGF6 downregulation correlated with iron-metabolism dysfunction in systemic sclerosis and cancer cells. Using the recessive diplotype approach revealed a novel susceptibility hemochromatosis gene and has extended our understanding of the mechanisms involved in iron metabolism.
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95
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Goto-Silva L, McShane MP, Salinas S, Kalaidzidis Y, Schiavo G, Zerial M. Retrograde transport of Akt by a neuronal Rab5-APPL1 endosome. Sci Rep 2019; 9:2433. [PMID: 30792402 PMCID: PMC6385319 DOI: 10.1038/s41598-019-38637-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/27/2018] [Indexed: 01/19/2023] Open
Abstract
Long-distance axonal trafficking plays a critical role in neuronal function and transport defects have been linked to neurodegenerative disorders. Various lines of evidence suggest that the small GTPase Rab5 plays a role in neuronal signaling via early endosomal transport. Here, we characterized the motility of Rab5 endosomes in primary cultures of mouse hippocampal pyramidal cells by live-cell imaging and showed that they exhibit bi-directional long-range motility in axons, with a strong bias toward retrograde transport. Characterization of key Rab5 effectors revealed that endogenous Rabankyrin-5, Rabenosyn-5 and APPL1 are all present in axons. Further analysis of APPL1-positive endosomes showed that, similar to Rab5-endosomes, they display more frequent long-range retrograde than anterograde movement, with the endosomal levels of APPL1 correlated with faster retrograde movement. Interestingly, APPL1-endosomes transport the neurotrophin receptor TrkB and mediate retrograde axonal transport of the kinase Akt1. FRET analysis revealed that APPL1 and Akt1 interact in an endocytosis-dependent manner. We conclude that Rab5-APPL1 endosomes exhibit the hallmarks of axonal signaling endosomes to transport Akt1 in hippocampal pyramidal cells.
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Affiliation(s)
- Livia Goto-Silva
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.,D'Or Institute for Research and Education (IDOR), Rua Diniz Cordeiro, 30, 22281-100, Rio de Janeiro, Brazil
| | - Marisa P McShane
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Sara Salinas
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia.,UMR1058. INSERM/Université de Montpellier/Etablissement Français du Sang Pathogenesis and Control of Chronic Infections, Montpellier, France
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.,Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Giampietro Schiavo
- Molecular NeuroPathobiology Laboratory, Sobell Department of Motor Neuroscience & Movement Disorders, UCL Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.
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96
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Abstract
Basal autophagy is as a compressive catabolic mechanism engaged in the breakdown of damaged macromolecules and organelles leading to the recycling of elementary nutrients. Thought essential to cellular refreshing, little is known about the origin of a constitutional rate of basal autophagy. Here, we found that loss of Drosophila vacuolar peduncle (vap), a presumed GAP enzyme, is associated with enhanced basal autophagy rate and physiological alterations resulting in a wasteful cell energy balance, a hallmark of overactive autophagy. By contrast, starvation-induced autophagy was disrupted in vap mutant conditions, leading to a block of maturation into autolysosomes. This phenotype stem for exacerbated biogenesis of PI(3)P-dependent endomembranes, including autophagosome membranes and ectopic fusions of vesicles. These findings shed new light on the neurodegenerative phenotype found associated to mutant vap adult brains in a former study. A partner of Vap, Sprint (Spri), acting as an endocytic GEF for Rab5, had the converse effect of leading to a reduction in PI(3)P-dependent endomembrane formation in mutants. Spri was conditional to normal basal autophagy and instrumental to the starvation-sensitivity phenotype specific of vap. Rab5 activity itself was essential for PI(3)P and for pre-autophagosome structures formation. We propose that Vap/Spri complexes promote a cell surface-derived flow of endocytic Rab5-containing vesicles, the traffic of which is crucial for the implementation of a basal autophagy rate.
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97
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Starkuviene V, Kallenberger SM, Beil N, Lisauskas T, Schumacher BSS, Bulkescher R, Wajda P, Gunkel M, Beneke J, Erfle H. High-Density Cell Arrays for Genome-Scale Phenotypic Screening. SLAS DISCOVERY 2019; 24:274-283. [PMID: 30682322 DOI: 10.1177/2472555218818757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Due to high associated costs and considerable time investments of cell-based screening, there is a strong demand for new technologies that enable preclinical development and tests of diverse biologicals in a cost-saving and time-efficient manner. For those reasons we developed the high-density cell array (HD-CA) platform, which miniaturizes cell-based screening in the form of preprinted and ready-to-run screening arrays. With the HD-CA technology, up to 24,576 samples can be tested in a single experiment, thereby saving costs and time for microscopy-based screening by 75%. Experiments on the scale of the entire human genome can be addressed in a real parallel manner, with screening campaigns becoming more comfortable and devoid of robotics infrastructure on the user side. The high degree of miniaturization enables working with expensive reagents and rare and difficult-to-obtain cell lines. We have also optimized an automated imaging procedure for HD-CA and demonstrate the applicability of HD-CA to CRISPR-Cas9- and RNAi-mediated phenotypic assessment of the gene function.
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Affiliation(s)
- Vytaute Starkuviene
- 1 BioQuant, Heidelberg University, Heidelberg, Germany.,2 Institute of Biosciences, Vilnius University Life Sciences Center, Vilnius, Lithuania
| | - Stefan M Kallenberger
- 1 BioQuant, Heidelberg University, Heidelberg, Germany.,3 Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nina Beil
- 1 BioQuant, Heidelberg University, Heidelberg, Germany
| | | | | | | | - Piotr Wajda
- 1 BioQuant, Heidelberg University, Heidelberg, Germany
| | - Manuel Gunkel
- 1 BioQuant, Heidelberg University, Heidelberg, Germany
| | - Jürgen Beneke
- 1 BioQuant, Heidelberg University, Heidelberg, Germany
| | - Holger Erfle
- 1 BioQuant, Heidelberg University, Heidelberg, Germany
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98
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Bourdais G, McLachlan DH, Rickett LM, Zhou J, Siwoszek A, Häweker H, Hartley M, Kuhn H, Morris RJ, MacLean D, Robatzek S. The use of quantitative imaging to investigate regulators of membrane trafficking in Arabidopsis stomatal closure. Traffic 2019; 20:168-180. [PMID: 30447039 DOI: 10.1111/tra.12625] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 11/13/2018] [Accepted: 11/13/2018] [Indexed: 12/26/2022]
Abstract
Expansion of gene families facilitates robustness and evolvability of biological processes but impedes functional genetic dissection of signalling pathways. To address this, quantitative analysis of single cell responses can help characterize the redundancy within gene families. We developed high-throughput quantitative imaging of stomatal closure, a response of plant guard cells, and performed a reverse genetic screen in a group of Arabidopsis mutants to five stimuli. Focussing on the intersection between guard cell signalling and the endomembrane system, we identified eight clusters based on the mutant stomatal responses. Mutants generally affected in stomatal closure were mostly in genes encoding SNARE and SCAMP membrane regulators. By contrast, mutants in RAB5 GTPase genes played specific roles in stomatal closure to microbial but not drought stress. Together with timed quantitative imaging of endosomes revealing sequential patterns in FLS2 trafficking, our imaging pipeline can resolve non-redundant functions of the RAB5 GTPase gene family. Finally, we provide a valuable image-based tool to dissect guard cell responses and outline a genetic framework of stomatal closure.
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Affiliation(s)
- Gildas Bourdais
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Deirdre H McLachlan
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.,School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK
| | - Lydia M Rickett
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Ji Zhou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.,The Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Heidrun Häweker
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | | | - Hannah Kuhn
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.,Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | | | - Dan MacLean
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
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99
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Steinauer A, LaRochelle JR, Knox SL, Wissner RF, Berry S, Schepartz A. HOPS-dependent endosomal fusion required for efficient cytosolic delivery of therapeutic peptides and small proteins. Proc Natl Acad Sci U S A 2019; 116:512-521. [PMID: 30610181 PMCID: PMC6329960 DOI: 10.1073/pnas.1812044116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Protein therapeutics represent a significant and growing component of the modern pharmacopeia, but their potential to treat human disease is limited because most proteins fail to traffic across biological membranes. Recently, we discovered a class of cell-permeant miniature proteins (CPMPs) containing a precisely defined, penta-arginine (penta-Arg) motif that traffics readily to the cytosol and nucleus of mammalian cells with efficiencies that rival those of hydrocarbon-stapled peptides active in animals and man. Like many cell-penetrating peptides (CPPs), CPMPs enter the endocytic pathway; the difference is that CPMPs containing a penta-Arg motif are released efficiently from endosomes, while other CPPs are not. Here, we seek to understand how CPMPs traffic from endosomes into the cytosol and what factors contribute to the efficiency of endosomal release. First, using two complementary cell-based assays, we exclude endosomal rupture as the primary means of endosomal escape. Next, using an RNA interference screen, fluorescence correlation spectroscopy, and confocal imaging, we identify VPS39-a gene encoding a subunit of the homotypic fusion and protein-sorting (HOPS) complex-as a critical determinant in the trafficking of CPMPs and hydrocarbon-stapled peptides to the cytosol. Although CPMPs neither inhibit nor activate HOPS function, HOPS activity is essential to efficiently deliver CPMPs to the cytosol. CPMPs localize within the lumen of Rab7+ and Lamp1+ endosomes and their transport requires HOPS activity. Overall, our results identify Lamp1+ late endosomes and lysosomes as portals for passing proteins into the cytosol and suggest that this environment is prerequisite for endosomal escape.
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Affiliation(s)
- Angela Steinauer
- Department of Chemistry, Yale University, New Haven, CT 06520-8107
| | - Jonathan R LaRochelle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103
| | - Susan L Knox
- Department of Chemistry, Yale University, New Haven, CT 06520-8107
| | | | - Samuel Berry
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114
| | - Alanna Schepartz
- Department of Chemistry, Yale University, New Haven, CT 06520-8107;
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103
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100
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Burstein SR, Valsecchi F, Kawamata H, Bourens M, Zeng R, Zuberi A, Milner TA, Cloonan SM, Lutz C, Barrientos A, Manfredi G. In vitro and in vivo studies of the ALS-FTLD protein CHCHD10 reveal novel mitochondrial topology and protein interactions. Hum Mol Genet 2019; 27:160-177. [PMID: 29112723 DOI: 10.1093/hmg/ddx397] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/01/2017] [Indexed: 12/12/2022] Open
Abstract
Mutations in coiled-coil-helix-coiled-coil-helix-domain containing 10 (CHCHD10), a mitochondrial twin CX9C protein whose function is still unknown, cause myopathy, motor neuron disease, frontotemporal dementia, and Parkinson's disease. Here, we investigate CHCHD10 topology and its protein interactome, as well as the effects of CHCHD10 depletion or expression of disease-associated mutations in wild-type cells. We find that CHCHD10 associates with membranes in the mitochondrial intermembrane space, where it interacts with a closely related protein, CHCHD2. Furthermore, both CHCHD10 and CHCHD2 interact with p32/GC1QR, a protein with various intra and extra-mitochondrial functions. CHCHD10 and CHCHD2 have short half-lives, suggesting regulatory rather than structural functions. Cell lines with CHCHD10 knockdown do not display bioenergetic defects, but, unexpectedly, accumulate excessive intramitochondrial iron. In mice, CHCHD10 is expressed in many tissues, most abundantly in heart, skeletal muscle, liver, and in specific CNS regions, notably the dopaminergic neurons of the substantia nigra and spinal cord neurons, which is consistent with the pathology associated with CHCHD10 mutations. Homozygote CHCHD10 knockout mice are viable, have no gross phenotypes, no bioenergetic defects or ultrastructural mitochondrial abnormalities in brain, heart or skeletal muscle, indicating that functional redundancy or compensatory mechanisms for CHCHD10 loss occur in vivo. Instead, cells expressing S59L or R15L mutant versions of CHCHD10, but not WT, have impaired mitochondrial energy metabolism. Taken together, the evidence obtained from our in vitro and in vivo studies suggest that CHCHD10 mutants cause disease through a gain of toxic function mechanism, rather than a loss of function.
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Affiliation(s)
- S R Burstein
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA.,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065, USA
| | - F Valsecchi
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
| | - H Kawamata
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
| | - M Bourens
- Department of Neurology, Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - R Zeng
- Department of Neurology, Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - A Zuberi
- The Jackson Laboratories, ME 04609, USA
| | - T A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA.,Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY 10065, USA
| | - S M Cloonan
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - C Lutz
- The Jackson Laboratories, ME 04609, USA
| | - A Barrientos
- Department of Neurology, Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - G Manfredi
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
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