1
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Dutta T, Vlassakis J. Microscale measurements of protein complexes from single cells. Curr Opin Struct Biol 2024; 87:102860. [PMID: 38848654 DOI: 10.1016/j.sbi.2024.102860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024]
Abstract
Proteins execute numerous cell functions in concert with one another in protein-protein interactions (PPI). While essential in each cell, such interactions are not identical from cell to cell. Instead, PPI heterogeneity contributes to cellular phenotypic heterogeneity in health and diseases such as cancer. Understanding cellular phenotypic heterogeneity thus requires measurements of properties of PPIs such as abundance, stoichiometry, and kinetics at the single-cell level. Here, we review recent, exciting progress in single-cell PPI measurements. Novel technology in this area is enabled by microscale and microfluidic approaches that control analyte concentration in timescales needed to outpace PPI disassembly kinetics. We describe microscale innovations, needed technical capabilities, and methods poised to be adapted for single-cell analysis in the near future.
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Affiliation(s)
- Tanushree Dutta
- Department of Bioengineering, Rice University, Houston, TX 77005, USA. https://twitter.com/duttatanu1717
| | - Julea Vlassakis
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.
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2
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Kageler L, Perr J, Flynn RA. Tools to investigate the cell surface: Proximity as a central concept in glycoRNA biology. Cell Chem Biol 2024; 31:1132-1144. [PMID: 38772372 PMCID: PMC11193615 DOI: 10.1016/j.chembiol.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
Proximity is a fundamental concept in chemistry and biology, referring to the convergence of molecules to facilitate new molecular interactions or reactions. Hybrid biopolymers like glycosylphosphatidylinositol (GPI)-anchored proteins, ubiquitinated proteins, glycosylated RNAs (glycoRNAs), and RNAylated proteins exemplify this by covalent bonding of moieties that are often orthogonally active. Hybrid molecules like glycoRNAs are localized to new physical spaces, generating new interfaces for biological functions. To fully investigate the compositional and spatial features of molecules like glycoRNAs, flexible genetic and chemical tools that encompass different encoding and targeting biopolymers are required. Here we discuss concepts of molecular proximity and explore newer proximity labeling technologies that facilitate applications in RNA biology, cell surface biology, and the interface therein with a particular focus on glycoRNA biology. We review the advantages and disadvantages of methods pertaining to cell surface RNA identification and provide insights into the vast opportunities for method development in this area.
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Affiliation(s)
- Lauren Kageler
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Jonathan Perr
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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3
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Tsutsumi R, Ueberheide B, Liang FX, Neel BG, Sakai R, Saito Y. Endocytic vesicles act as vehicles for glucose uptake in response to growth factor stimulation. Nat Commun 2024; 15:2843. [PMID: 38565573 PMCID: PMC10987504 DOI: 10.1038/s41467-024-46971-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Glycolysis is a fundamental cellular process, yet its regulatory mechanisms remain incompletely understood. Here, we show that a subset of glucose transporter 1 (GLUT1/SLC2A1) co-endocytoses with platelet-derived growth factor (PDGF) receptor (PDGFR) upon PDGF-stimulation. Furthermore, multiple glycolytic enzymes localize to these endocytosed PDGFR/GLUT1-containing vesicles adjacent to mitochondria. Contrary to current models, which emphasize the importance of glucose transporters on the cell surface, we find that PDGF-stimulated glucose uptake depends on receptor/transporter endocytosis. Our results suggest that growth factors generate glucose-loaded endocytic vesicles that deliver glucose to the glycolytic machinery in proximity to mitochondria, and argue for a new layer of regulation for glycolytic control governed by cellular membrane dynamics.
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Affiliation(s)
- Ryouhei Tsutsumi
- Kitasato University School of Medicine, Sagamihara 252-0374, Kanagawa, Japan.
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Miyagi, Japan.
- Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA.
| | - Beatrix Ueberheide
- Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
- Proteomics Laboratory, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
- Department of Neurology, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Feng-Xia Liang
- Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
- Microscopy Laboratory, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Benjamin G Neel
- Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Ryuichi Sakai
- Kitasato University School of Medicine, Sagamihara 252-0374, Kanagawa, Japan
| | - Yoshiro Saito
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Miyagi, Japan
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4
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Nava AA, Arboleda VA. The omics era: a nexus of untapped potential for Mendelian chromatinopathies. Hum Genet 2024; 143:475-495. [PMID: 37115317 PMCID: PMC11078811 DOI: 10.1007/s00439-023-02560-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 04/10/2023] [Indexed: 04/29/2023]
Abstract
The OMICs cascade describes the hierarchical flow of information through biological systems. The epigenome sits at the apex of the cascade, thereby regulating the RNA and protein expression of the human genome and governs cellular identity and function. Genes that regulate the epigenome, termed epigenes, orchestrate complex biological signaling programs that drive human development. The broad expression patterns of epigenes during human development mean that pathogenic germline mutations in epigenes can lead to clinically significant multi-system malformations, developmental delay, intellectual disabilities, and stem cell dysfunction. In this review, we refer to germline developmental disorders caused by epigene mutation as "chromatinopathies". We curated the largest number of human chromatinopathies to date and our expanded approach more than doubled the number of established chromatinopathies to 179 disorders caused by 148 epigenes. Our study revealed that 20.6% (148/720) of epigenes cause at least one chromatinopathy. In this review, we highlight key examples in which OMICs approaches have been applied to chromatinopathy patient biospecimens to identify underlying disease pathogenesis. The rapidly evolving OMICs technologies that couple molecular biology with high-throughput sequencing or proteomics allow us to dissect out the causal mechanisms driving temporal-, cellular-, and tissue-specific expression. Using the full repertoire of data generated by the OMICs cascade to study chromatinopathies will provide invaluable insight into the developmental impact of these epigenes and point toward future precision targets for these rare disorders.
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Affiliation(s)
- Aileen A Nava
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
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5
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Abe T, Kuwahara T, Suenaga S, Sakurai M, Takatori S, Iwatsubo T. Lysosomal stress drives the release of pathogenic α-synuclein from macrophage lineage cells via the LRRK2-Rab10 pathway. iScience 2024; 27:108893. [PMID: 38313055 PMCID: PMC10835446 DOI: 10.1016/j.isci.2024.108893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/26/2023] [Accepted: 01/09/2024] [Indexed: 02/06/2024] Open
Abstract
α-Synuclein and LRRK2 are associated with both familial and sporadic Parkinson's disease (PD), although the mechanistic link between these two proteins has remained elusive. Treating cells with lysosomotropic drugs causes the recruitment of LRRK2 and its substrate Rab10 onto overloaded lysosomes and induces extracellular release of lysosomal contents. Here we show that lysosomal overload elicits the release of insoluble α-synuclein from macrophages and microglia loaded with α-synuclein fibrils. This release occurred specifically in macrophage lineage cells, was dependent on the LRRK2-Rab10 pathway and involved exosomes. Also, the uptake of α-synuclein fibrils enhanced the LRRK2 phosphorylation of Rab10, which was accompanied by an increased recruitment of LRRK2 and Rab10 onto lysosomal surface. Our data collectively suggest that α-synuclein fibrils taken up in lysosomes activate the LRRK2-Rab10 pathway, which in turn upregulates the extracellular release of α-synuclein aggregates, leading to a vicious cycle that could enhance α-synuclein propagation in PD pathology.
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Affiliation(s)
- Tetsuro Abe
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomoki Kuwahara
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shoichi Suenaga
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Maria Sakurai
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sho Takatori
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeshi Iwatsubo
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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6
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Moradi Y, Lee JSH, Armani AM. Detecting Disruption of HER2 Membrane Protein Organization in Cell Membranes with Nanoscale Precision. ACS Sens 2024; 9:52-61. [PMID: 37955934 PMCID: PMC10825864 DOI: 10.1021/acssensors.3c01437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023]
Abstract
The spatiotemporal organization of proteins within the cell membrane can affect numerous biological functions, including cell signaling, communication, and transportation. Deviations from normal spatial arrangements have been observed in various diseases, and a better understanding of this process is a key stepping stone to advancing development of clinical interventions. However, given the nanometer length scales involved, detecting these subtle changes has primarily relied on complex super-resolution and single-molecule imaging methods. In this work, we demonstrate an alternative fluorescent imaging strategy for detecting protein organization based on a material that exhibits a unique photophysical behavior known as aggregation-induced emission (AIE). Organic AIE molecules have an increase in emission signal when they are in close proximity, and the molecular motion is restricted. This property simultaneously addresses the high background noise and low detection signal that limit conventional widefield fluorescent imaging. To demonstrate the potential of this approach, the fluorescent molecule sensor is conjugated to a human epidermal growth factor receptor 2 (HER2)-specific antibody and used to investigate the spatiotemporal behavior of HER2 clustering in the membrane of HER2-overexpressing breast cancer cells. Notably, the disruption of HER2 clusters in response to an FDA-approved monoclonal antibody therapeutic (Trastuzumab) is successfully detected using a simple widefield fluorescent microscope. While the sensor demonstrated here is optimized for sensing HER2 clustering, it is an easily adaptable platform. Moreover, given the compatibility with widefield imaging, the system has the potential to be used with high-throughput imaging techniques, accelerating investigations into membrane protein spatiotemporal organization.
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Affiliation(s)
- Yasaman Moradi
- Mork
Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
- Ellison
Institute of Technology, Los Angeles, California 90064, United States
| | - Jerry S. H. Lee
- Mork
Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
- Ellison
Institute of Technology, Los Angeles, California 90064, United States
- Keck
School of Medicine, University of Southern
California, Los Angeles, California 90089, United States
| | - Andrea M. Armani
- Mork
Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
- Ellison
Institute of Technology, Los Angeles, California 90064, United States
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7
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Evans CG, O'Brien J, Winfree E, Murugan A. Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly. Nature 2024; 625:500-507. [PMID: 38233621 PMCID: PMC10794147 DOI: 10.1038/s41586-023-06890-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/22/2023] [Indexed: 01/19/2024]
Abstract
Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles1-3. Analogous high-dimensional, highly interconnected computational architectures also arise within information-processing molecular systems inside living cells, such as signal transduction cascades and genetic regulatory networks4-7. Might collective modes analogous to neural computation be found more broadly in other physical and chemical processes, even those that ostensibly play non-information-processing roles? Here we examine nucleation during self-assembly of multicomponent structures, showing that high-dimensional patterns of concentrations can be discriminated and classified in a manner similar to neural network computation. Specifically, we design a set of 917 DNA tiles that can self-assemble in three alternative ways such that competitive nucleation depends sensitively on the extent of colocalization of high-concentration tiles within the three structures. The system was trained in silico to classify a set of 18 grayscale 30 × 30 pixel images into three categories. Experimentally, fluorescence and atomic force microscopy measurements during and after a 150 hour anneal established that all trained images were correctly classified, whereas a test set of image variations probed the robustness of the results. Although slow compared to previous biochemical neural networks, our approach is compact, robust and scalable. Our findings suggest that ubiquitous physical phenomena, such as nucleation, may hold powerful information-processing capabilities when they occur within high-dimensional multicomponent systems.
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Affiliation(s)
- Constantine Glen Evans
- California Institute of Technology, Pasadena, CA, USA.
- Evans Foundation for Molecular Medicine, Pasadena, CA, USA.
- Maynooth University, Maynooth, Ireland.
| | | | - Erik Winfree
- California Institute of Technology, Pasadena, CA, USA.
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8
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Ram BM, Dai C. Detection of the DNA binding of transcription factors in situ at the single-cell resolution in cultured cells by proximity ligation assay. STAR Protoc 2023; 4:102692. [PMID: 37917578 PMCID: PMC10651771 DOI: 10.1016/j.xpro.2023.102692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023] Open
Abstract
Transcription factors (TFs) play a pivotal role in gene expression, and their DNA binding is the prerequisite to instigating gene transcription. Here, we present a protocol that exploits the proximity ligation assay technique to measure the DNA-binding activities of TFs in situ at the single-cell resolution. We describe steps for immunostaining with specific antibodies against double-stranded DNA and the TFs of interest, probe incubation, proximity ligation, and signal amplification. We then detail procedures for imaging and image analysis. For complete details on the use and execution of this protocol, please refer to Dai et al. (2015)1 and Xu et al. (2023).2.
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Affiliation(s)
- Babul Moni Ram
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA.
| | - Chengkai Dai
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA.
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9
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Baldrighi M, Doreth C, Li Y, Zhao X, Warner E, Chenoweth H, Kishore K, Umrania Y, Minde DP, Thome S, Yu X, Lu Y, Knapton A, Harrison J, Clarke M, Latz E, de Cárcer G, Malumbres M, Ryffel B, Bryant C, Liu J, Lilley KS, Mallat Z, Li X. PLK1 inhibition dampens NLRP3 inflammasome-elicited response in inflammatory disease models. J Clin Invest 2023; 133:e162129. [PMID: 37698938 PMCID: PMC10617773 DOI: 10.1172/jci162129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/06/2023] [Indexed: 09/14/2023] Open
Abstract
Unabated activation of the NLR family pyrin domain-containing 3 (NLRP3) inflammasome is linked with the pathogenesis of various inflammatory disorders. Polo-like kinase 1 (PLK1) has been widely studied for its role in mitosis. Here, using both pharmacological and genetic approaches, we demonstrate that PLK1 promoted NLRP3 inflammasome activation at cell interphase. Using an unbiased proximity-dependent biotin identification (Bio-ID) screen for the PLK1 interactome in macrophages, we show an enhanced proximal association of NLRP3 with PLK1 upon NLRP3 inflammasome activation. We further confirmed the interaction between PLK1 and NLRP3 and identified the interacting domains. Mechanistically, we show that PLK1 orchestrated the microtubule-organizing center (MTOC) structure and NLRP3 subcellular positioning upon inflammasome activation. Treatment with a selective PLK1 kinase inhibitor suppressed IL-1β production in in vivo inflammatory models, including LPS-induced endotoxemia and monosodium urate-induced peritonitis in mice. Our results uncover a role of PLK1 in regulating NLRP3 inflammasome activation during interphase and identify pharmacological inhibition of PLK1 as a potential therapeutic strategy for inflammatory diseases with excessive NLRP3 inflammasome activation.
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Affiliation(s)
- Marta Baldrighi
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Christian Doreth
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Yang Li
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiaohui Zhao
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Emily Warner
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Hannah Chenoweth
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Yagnesh Umrania
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, United Kingdom
| | - David-Paul Minde
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Thome
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Xian Yu
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Yuning Lu
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Alice Knapton
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - James Harrison
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Murray Clarke
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital, University of Bonn, Bonn, Germany
| | - Guillermo de Cárcer
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Cell Cycle and Cancer Biomarkers Group, “Alberto Sols” Biomedical Research Institute (IIBM-CSIC), Madrid, Spain
| | - Marcos Malumbres
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Bernhard Ryffel
- UMR7355 INEM, Experimental and Molecular Immunology and Neurogenetics CNRS and Université d’Orleans, Orleans, France
| | - Clare Bryant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jinping Liu
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kathryn S. Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, United Kingdom
| | - Ziad Mallat
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Université Paris Cité, PARCC, INSERM, Paris, France
| | - Xuan Li
- The Victor Phillip Dahdaleh Heart and Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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10
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Chen C, Chen M, Wen T, Anderson RA, Cryns VL. Regulation of NRF2 by Phosphoinositides and Small Heat Shock Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564194. [PMID: 37961303 PMCID: PMC10634847 DOI: 10.1101/2023.10.26.564194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Reactive oxygen species (ROS) are generated by aerobic metabolism, and their deleterious effects are buffered by the cellular antioxidant response, which prevents oxidative stress. The nuclear factor erythroid 2-related factor 2 (NRF2) is a master transcriptional regulator of the antioxidant response. Basal levels of NRF2 are kept low by ubiquitin-dependent degradation of NRF2 by E3 ligases, including the Kelch-like ECH-associated protein 1 (KEAP1). Here, we show that the stability and function of NRF2 is regulated by the type I phosphatidylinositol phosphate kinase g (PIPKIg), which binds NRF2 and transfers its product phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P 2 ) to NRF2. PtdIns(4,5)P 2 binding recruits the small heat shock protein HSP27 to the complex. Silencing PIPKIg or HSP27 destabilizes NRF2, reduces expression of its target gene HO-1, and sensitizes cells to oxidative stress. These data demonstrate an unexpected role of phosphoinositides and HSP27 in regulating NRF2 and point to PIPKIg and HSP27 as drug targets to destabilize NRF2 in cancer. In brief Phosphoinositides are coupled to NRF2 by PIPKIγ, and HSP27 is recruited and stabilizes NRF2, promoting stress-resistance.
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11
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Franco CN, Seabrook LJ, Nguyen ST, Yang Y, Campos M, Fan Q, Cicchetto AC, Kong M, Christofk HR, Albrecht LV. Vitamin B 6 is governed by the local compartmentalization of metabolic enzymes during growth. SCIENCE ADVANCES 2023; 9:eadi2232. [PMID: 37682999 PMCID: PMC10491294 DOI: 10.1126/sciadv.adi2232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
Vitamin B6 is a vital micronutrient across cell types and tissues, and dysregulated B6 levels contribute to human disease. Despite its importance, how B6 vitamer levels are regulated is not well understood. Here, we provide evidence that B6 dynamics are rapidly tuned by precise compartmentation of pyridoxal kinase (PDXK), the rate-limiting B6 enzyme. We show that canonical Wnt rapidly led to the accumulation of inactive B6 by shunting cytosolic PDXK into lysosomes. PDXK was modified with methyl-arginine Degron (MrDegron), a protein tag for lysosomes, which enabled delivery via microautophagy. Hyperactive lysosomes resulted in the continuous degradation of PDXK and B6 deficiency that promoted proliferation in Wnt-driven colorectal cancer (CRC) cells. Pharmacological or genetic disruption of the coordinated MrDegron proteolytic pathway was sufficient to reduce CRC survival in cells and organoid models. In sum, this work contributes to the repertoire of micronutrient-regulated processes that enable cancer cell growth and provides insight into the functional impact of B6 deficiencies for survival.
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Affiliation(s)
- Carolina N. Franco
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Laurence J. Seabrook
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, USA
| | - Steven T. Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Ying Yang
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Melissa Campos
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, USA
| | - Qi Fan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Andrew C. Cicchetto
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mei Kong
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Heather R. Christofk
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lauren V. Albrecht
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, USA
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12
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Pierzynska-Mach A, Cainero I, Oneto M, Ferrando-May E, Lanzanò L, Diaspro A. Imaging-based study demonstrates how the DEK nanoscale distribution differentially correlates with epigenetic marks in a breast cancer model. Sci Rep 2023; 13:12749. [PMID: 37550322 PMCID: PMC10406876 DOI: 10.1038/s41598-023-38685-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 07/12/2023] [Indexed: 08/09/2023] Open
Abstract
Epigenetic dysregulation of chromatin is one of the hallmarks of cancer development and progression, and it is continuously investigated as a potential general bio-marker of this complex disease. One of the nuclear factors involved in gene regulation is the unique DEK protein-a histone chaperon modulating chromatin topology. DEK expression levels increase significantly from normal to cancer cells, hence raising the possibility of using DEK as a tumor marker. Although DEK is known to be implicated in epigenetic and transcriptional regulation, the details of these interactions and their relevance in cancer development remain largely elusive. In this work, we investigated the spatial correlation between the nuclear distribution of DEK and chromatin patterns-alongside breast cancer progression-leveraging image cross-correlation spectroscopy (ICCS) coupled with Proximity Ligation Assay (PLA) analysis. We performed our study on the model based on three well-established human breast cell lines to consider this tumor's heterogeneity (MCF10A, MCF7, and MDA-MB-231 cells). Our results show that overexpression of DEK correlates with the overall higher level of spatial proximity between DEK and histone marks corresponding to gene promoters regions (H3K9ac, H3K4me3), although it does not correlate with spatial proximity between DEK and gene enhancers (H3K27ac). Additionally, we observed that colocalizing fractions of DEK and histone marks are lower for the non-invasive cell subtype than for the highly invasive cell line (MDA-MB-231). Thus, this study suggests that the role of DEK on transcriptionally active chromatin regions varies depending on the subtype of the breast cancer cell line.
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Affiliation(s)
| | - Isotta Cainero
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132, Genoa, Italy
| | - Michele Oneto
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
| | - Elisa Ferrando-May
- Department of Biology, University of Konstanz, Konstanz, Germany
- German Cancer Research Center, Heidelberg, Germany
| | - Luca Lanzanò
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
- Department of Physics and Astronomy, University of Catania, Catania, Italy
| | - Alberto Diaspro
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy.
- DIFILAB, Department of Physics, University of Genoa, Genoa, Italy.
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13
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Stahl P, Kollenda S, Sager J, Schmidt L, Schroer MA, Stauber RH, Epple M, Knauer SK. Tuning Nanobodies' Bioactivity: Coupling to Ultrasmall Gold Nanoparticles Allows the Intracellular Interference with Survivin. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300871. [PMID: 37035950 DOI: 10.1002/smll.202300871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Nanobodies are highly affine binders, often used to track disease-relevant proteins inside cells. However, they often fail to interfere with pathobiological functions, required for their clinical exploitation. Here, a nanobody targeting the disease-relevant apoptosis inhibitor and mitosis regulator Survivin (SuN) is utilized. Survivin's multifaceted functions are regulated by an interplay of dynamic cellular localization, dimerization, and protein-protein interactions. However, as Survivin harbors no classical "druggable" binding pocket, one must aim at blocking extended protein surface areas. Comprehensive experimental evidence demonstrates that intracellular expression of SuN allows to track Survivin at low nanomolar concentrations but failed to inhibit its biological functions. Small angle X-ray scattering of the Survivin-SuN complex locates the proposed interaction interface between the C-terminus and the globular domain, as such not blocking any pivotal interaction. By clicking multiple SuN to ultrasmall (2 nm) gold nanoparticles (SuN-N), not only intracellular uptake is enabled, but additionally, Survivin crosslinking and interference with mitotic progression in living cells are also enabled. In sum, it is demonstrated that coupling of nanobodies to nanosized scaffolds can be universally applicable to improve their function and therapeutic applicability.
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Affiliation(s)
- Paul Stahl
- Molecular Biology II, Department of Biology, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Sebastian Kollenda
- Inorganic Chemistry, Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Jonas Sager
- Inorganic Chemistry, Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Laura Schmidt
- Molecular Biology II, Department of Biology, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Martin A Schroer
- Nanoparticle Process Technology, Department of Engineering, University of Duisburg-Essen, Lotharstr. 1, 47057, Duisburg, Germany
| | - Roland H Stauber
- Molecular and Cellular Oncology/ENT, University Medical Center Mainz (UMM), Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Matthias Epple
- Inorganic Chemistry, Department of Chemistry, Center for Nanointegration Duisburg-Essen (CENIDE) and Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Shirley K Knauer
- Molecular Biology II, Department of Biology, Center of Medical Biotechnology (ZMB) and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
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14
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Tsutsumi R, Ueberheide B, Liang FX, Neel BG, Sakai R, Saito Y. Endocytic vesicles act as vehicles for glucose uptake in response to growth factor stimulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.23.550235. [PMID: 37546742 PMCID: PMC10402005 DOI: 10.1101/2023.07.23.550235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Glycolysis is a fundamental cellular process, yet its regulatory mechanisms remain incompletely understood. Here, we show that a subset of glucose transporter 1 (GLUT1/SLC2A1) co-endocytoses with platelet-derived growth factor (PDGF) receptor (PDGFR) upon PDGF-stimulation. Furthermore, multiple glycolytic enzymes localize to these endocytosed PDGFR/GLUT1-containing vesicles adjacent to mitochondria. Contrary to current models, which emphasize the importance of glucose transporters on the cell surface, we find that PDGF-stimulated glucose uptake depends on receptor/transporter endocytosis. Our results suggest that growth factors generate glucose-loaded endocytic vesicles that deliver glucose to the glycolytic machinery in proximity to mitochondria, and argue for a new layer of regulation for glycolytic control governed by cellular membrane dynamics.
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Affiliation(s)
- Ryouhei Tsutsumi
- Kitasato University School of Medicine; Sagamihara 252-0374, Kanagawa, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University; Sendai 980-8578, Miyagi, Japan
- Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health; New York, NY 10016, USA
| | - Beatrix Ueberheide
- Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health; New York, NY 10016, USA
- Proteomics Laboratory, NYU Grossman School of Medicine, NYU Langone Health; New York, NY 10016, USA
- Department of Biochemistry and Molecular Pharmacology and Department of Neurology, NYU Grossman School of Medicine, NYU Langone Health; New York, NY 10016, USA
| | - Feng-Xia Liang
- Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health; New York, NY 10016, USA
- Microscopy Laboratory, NYU Grossman School of Medicine, NYU Langone Health; New York, NY 10016, USA.Paste the full affiliation list here
| | - Benjamin G. Neel
- Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health; New York, NY 10016, USA
| | - Ryuichi Sakai
- Kitasato University School of Medicine; Sagamihara 252-0374, Kanagawa, Japan
| | - Yoshiro Saito
- Graduate School of Pharmaceutical Sciences, Tohoku University; Sendai 980-8578, Miyagi, Japan
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15
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Park YS, Choi S, Jang HJ, Yoo TH. Assay methods based on proximity-enhanced reactions for detecting non-nucleic acid molecules. Front Bioeng Biotechnol 2023; 11:1188313. [PMID: 37456730 PMCID: PMC10343955 DOI: 10.3389/fbioe.2023.1188313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
Accurate and reliable detection of biological molecules such as nucleic acids, proteins, and small molecules is essential for the diagnosis and treatment of diseases. While simple homogeneous assays have been developed and are widely used for detecting nucleic acids, non-nucleic acid molecules such as proteins and small molecules are usually analyzed using methods that require time-consuming procedures and highly trained personnel. Recently, methods using proximity-enhanced reactions (PERs) have been developed for detecting non-nucleic acids. These reactions can be conducted in a homogeneous liquid phase via a single-step procedure. Herein, we review three assays based on PERs for the detection of non-nucleic acid molecules: proximity ligation assay, proximity extension assay, and proximity proteolysis assay.
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Affiliation(s)
- Ye Seop Park
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Sunjoo Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Hee Ju Jang
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, Republic of Korea
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16
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Zhou J, Welinder C, Ekström P. The Phosphoproteome of the Rd1 Mouse Retina, a Model of Inherited Photoreceptor Degeneration, Changes after Protein Kinase G Inhibition. Int J Mol Sci 2023; 24:9836. [PMID: 37372984 DOI: 10.3390/ijms24129836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Retinitis pigmentosa (RP) is a frequent cause of blindness among the working population in industrial countries due to the inheritable death of photoreceptors. Though gene therapy was recently approved for mutations in the RPE65 gene, there is in general no effective treatment presently. Previously, abnormally high levels of cGMP and overactivation of its dependent protein kinase (PKG) have been suggested as causative for the fatal effects on photoreceptors, making it meaningful to explore the cGMP-PKG downstream signaling for more pathological insights and novel therapeutic target development purposes. Here, we manipulated the cGMP-PKG system in degenerating retinas from the rd1 mouse model pharmacologically via adding a PKG inhibitory cGMP-analogue to organotypic retinal explant cultures. A combination of phosphorylated peptide enrichment and mass spectrometry was then applied to study the cGMP-PKG-dependent phosphoproteome. We identified a host of novel potential cGMP-PKG downstream substrates and related kinases using this approach and selected the RAF1 protein, which may act as both a substrate and a kinase, for further validation. This showed that the RAS/RAF1/MAPK/ERK pathway may be involved in retinal degeneration in a yet unclarified mechanism, thus deserving further investigation in the future.
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Affiliation(s)
- Jiaming Zhou
- Ophthalmology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, 221 00 Lund, Sweden
| | - Charlotte Welinder
- Mass Spectrometry, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, 221 00 Lund, Sweden
| | - Per Ekström
- Ophthalmology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, 221 00 Lund, Sweden
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17
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Qian L, Lin X, Gao X, Khan RU, Liao JY, Du S, Ge J, Zeng S, Yao SQ. The Dawn of a New Era: Targeting the "Undruggables" with Antibody-Based Therapeutics. Chem Rev 2023. [PMID: 37186942 DOI: 10.1021/acs.chemrev.2c00915] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The high selectivity and affinity of antibodies toward their antigens have made them a highly valuable tool in disease therapy, diagnosis, and basic research. A plethora of chemical and genetic approaches have been devised to make antibodies accessible to more "undruggable" targets and equipped with new functions of illustrating or regulating biological processes more precisely. In this Review, in addition to introducing how naked antibodies and various antibody conjugates (such as antibody-drug conjugates, antibody-oligonucleotide conjugates, antibody-enzyme conjugates, etc.) work in therapeutic applications, special attention has been paid to how chemistry tools have helped to optimize the therapeutic outcome (i.e., with enhanced efficacy and reduced side effects) or facilitate the multifunctionalization of antibodies, with a focus on emerging fields such as targeted protein degradation, real-time live-cell imaging, catalytic labeling or decaging with spatiotemporal control as well as the engagement of antibodies inside cells. With advances in modern chemistry and biotechnology, well-designed antibodies and their derivatives via size miniaturization or multifunctionalization together with efficient delivery systems have emerged, which have gradually improved our understanding of important biological processes and paved the way to pursue novel targets for potential treatments of various diseases.
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Affiliation(s)
- Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xuefen Lin
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xue Gao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Rizwan Ullah Khan
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jia-Yu Liao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shubo Du
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544
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18
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Zhang H, Xu M, Li H, Mai X, Sun J, Mi L, Ma J, Zhu X, Fei Y. Detection speed optimization of the OI-RD microscope for ultra-high throughput screening. BIOMEDICAL OPTICS EXPRESS 2023; 14:2386-2399. [PMID: 37206144 PMCID: PMC10191655 DOI: 10.1364/boe.487563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/21/2023]
Abstract
The oblique-incidence reflectivity difference (OI-RD) microscope is a label-free detection system for microarrays that has many successful applications in high throughput drug screening. The increase and optimization of the detection speed of the OI-RD microscope will enable it to be a potential ultra-high throughput screening tool. This work presents a series of optimization methods that can significantly reduce the time to scan an OI-RD image. The wait time for the lock-in amplifier was decreased by the proper selection of the time constant and development of a new electronic amplifier. In addition, the time for the software to acquire data and for translation stage movement was also minimized. As a result, the detection speed of the OI-RD microscope is 10 times faster than before, making the OI-RD microscope suitable for ultra-high throughput screening applications.
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Affiliation(s)
- Hang Zhang
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), School of Information Science and Technology,
Fudan University, Shanghai, 200433, China
| | - Mengjing Xu
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), School of Information Science and Technology,
Fudan University, Shanghai, 200433, China
| | - Haofeng Li
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), School of Information Science and Technology,
Fudan University, Shanghai, 200433, China
| | - Xiaohan Mai
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), School of Information Science and Technology,
Fudan University, Shanghai, 200433, China
| | - Jiawei Sun
- Department of Science and Technology, Shanghai Deyu Intelligent Technology Co., Ltd., Shanghai, 201413, China
| | - Lan Mi
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), School of Information Science and Technology,
Fudan University, Shanghai, 200433, China
| | - Jiong Ma
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), School of Information Science and Technology,
Fudan University, Shanghai, 200433, China
| | - Xiangdong Zhu
- Department of Physics, University of California, One Shields Avenue, Davis, California 95616, USA
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), School of Information Science and Technology,
Fudan University, Shanghai, 200433, China
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19
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Quinpirole ameliorates nigral dopaminergic neuron damage in Parkinson's disease mouse model through activating GHS-R1a/D 2R heterodimers. Acta Pharmacol Sin 2023:10.1038/s41401-023-01063-0. [PMID: 36899113 PMCID: PMC10374575 DOI: 10.1038/s41401-023-01063-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/12/2023] [Indexed: 03/12/2023] Open
Abstract
Growth hormone secretagogue receptor 1a (GHS-R1a) is an important G protein-coupled receptor (GPCR) that regulates a variety of functions by binding to ghrelin. It has been shown that the dimerization of GHS-R1a with other receptors also affects ingestion, energy metabolism, learning and memory. Dopamine type 2 receptor (D2R) is a GPCR mainly distributed in the ventral tegmental area (VTA), substantia nigra (SN), striatum and other brain regions. In this study we investigated the existence and function of GHS-R1a/D2R heterodimers in nigral dopaminergic neurons in Parkinson's disease (PD) models in vitro and in vivo. By conducting immunofluorescence staining, FRET and BRET analyses, we confirmed that GHS-R1a and D2R could form heterodimers in PC-12 cells and in the nigral dopaminergic neurons of wild-type mice. This process was inhibited by MPP+ or MPTP treatment. Application of QNP (10 μM) alone significantly increased the viability of MPP+-treated PC-12 cells, and administration of quinpirole (QNP, 1 mg/kg, i.p. once before and twice after MPTP injection) significantly alleviated motor deficits in MPTP-induced PD mice model; the beneficial effects of QNP were abolished by GHS-R1a knockdown. We revealed that the GHS-R1a/D2R heterodimers could increase the protein levels of tyrosine hydroxylase in the SN of MPTP-induced PD mice model through the cAMP response element binding protein (CREB) signaling pathway, ultimately promoting dopamine synthesis and release. These results demonstrate a protective role for GHS-R1a/D2R heterodimers in dopaminergic neurons, providing evidence for the involvement of GHS-R1a in PD pathogenesis independent of ghrelin.
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20
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Zhu Y, Wu J, Zhou Q. Functional DNA sensors integrated with nucleic acid signal amplification strategies for non-nucleic acid targets detection. Biosens Bioelectron 2023; 230:115282. [PMID: 37028002 DOI: 10.1016/j.bios.2023.115282] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
In addition to carrying and transmitting genetic material, some DNA molecules have specific binding ability or catalytic function. DNA with this special function is collectively referred to as functional DNA (fDNA), such as aptamer, DNAzyme and so on. fDNA has the advantages of simple synthetic process, low cost and low toxicity. It also has high chemical stability, recognition specificity and biocompatibility. In recent years, fDNA biosensors have been widely investigated as signal recognition elements and signal transduction elements for the detection of non-nucleic acid targets. However, the main problem of fDNA sensors is their limited sensitivity to trace targets, especially when the affinity of fDNA to the targets is low. To further improve the sensitivity, various nucleic acid signal amplification strategies (NASAS) are explored to improve the limit of detection of fDNA. In this review, we will introduce four NASAS (hybridization chain reaction, entropy-driven catalysis, rolling circle amplification, CRISPR/Cas system) and the corresponding design principles. The principle and application of these fDNA sensors integrated with signal amplification strategies for detection of non-nucleic acid targets are summarized. Finally, the main challenges and application prospects of NASAS integrated fDNA biosensing system are discussed.
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21
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Pelicci S, Furia L, Pelicci PG, Faretta M. Correlative Multi-Modal Microscopy: A Novel Pipeline for Optimizing Fluorescence Microscopy Resolutions in Biological Applications. Cells 2023; 12:cells12030354. [PMID: 36766696 PMCID: PMC9913119 DOI: 10.3390/cells12030354] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
The modern fluorescence microscope is the convergence point of technologies with different performances in terms of statistical sampling, number of simultaneously analyzed signals, and spatial resolution. However, the best results are usually obtained by maximizing only one of these parameters and finding a compromise for the others, a limitation that can become particularly significant when applied to cell biology and that can reduce the spreading of novel optical microscopy tools among research laboratories. Super resolution microscopy and, in particular, molecular localization-based approaches provide a spatial resolution and a molecular localization precision able to explore the scale of macromolecular complexes in situ. However, its use is limited to restricted regions, and consequently few cells, and frequently no more than one or two parameters. Correlative microscopy, obtained by the fusion of different optical technologies, can consequently surpass this barrier by merging results from different spatial scales. We discuss here the use of an acquisition and analysis correlative microscopy pipeline to obtain high statistical sampling, high content, and maximum spatial resolution by combining widefield, confocal, and molecular localization microscopy.
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Affiliation(s)
- Simone Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Laura Furia
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
- Correspondence:
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22
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Oligomerization of the heteromeric γ-aminobutyric acid receptor GABA B in a eukaryotic cell-free system. Sci Rep 2022; 12:20742. [PMID: 36456667 PMCID: PMC9715706 DOI: 10.1038/s41598-022-24885-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
Understanding the assembly mechanism and function of membrane proteins is a fundamental problem in biochemical research. Among the membrane proteins, G protein-coupled receptors (GPCRs) represent the largest class in the human body and have long been considered to function as monomers. Nowadays, the oligomeric assembly of GPCRs is widely accepted, although the functional importance and therapeutic intervention remain largely unexplored. This is partly due to difficulties in the heterologous production of membrane proteins. Cell-free protein synthesis (CFPS) with its endogenous endoplasmic reticulum-derived structures has proven as a technique to address this issue. In this study, we investigate for the first time the conceptual CFPS of a heteromeric GPCR, the γ-aminobutyric acid receptor type B (GABAB), from its protomers BR1 and BR2 using a eukaryotic cell-free lysate. Using a fluorescence-based proximity ligation assay, we provide evidence for colocalization and thus suggesting heterodimerization. We prove the heterodimeric assembly by a bioluminescence resonance energy transfer saturation assay providing the manufacturability of a heterodimeric GPCR by CFPS. Additionally, we show the binding of a fluorescent orthosteric antagonist, demonstrating the feasibility of combining the CFPS of GPCRs with pharmacological applications. These results provide a simple and powerful experimental platform for the synthesis of heteromeric GPCRs and open new perspectives for the modelling of protein-protein interactions. Accordingly, the presented technology enables the targeting of protein assemblies as a new interface for pharmacological intervention in disease-relevant dimers.
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23
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Park JS, Gabel AM, Kassir P, Kang L, Chowdhary PK, Osei-Ntansah A, Tran ND, Viswanathan S, Canales B, Ding P, Lee YS, Brewster R. N-myc downstream regulated gene 1 (ndrg1) functions as a molecular switch for cellular adaptation to hypoxia. eLife 2022; 11:e74031. [PMID: 36214665 PMCID: PMC9550225 DOI: 10.7554/elife.74031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Lack of oxygen (hypoxia and anoxia) is detrimental to cell function and survival and underlies many disease conditions. Hence, metazoans have evolved mechanisms to adapt to low oxygen. One such mechanism, metabolic suppression, decreases the cellular demand for oxygen by downregulating ATP-demanding processes. However, the molecular mechanisms underlying this adaptation are poorly understood. Here, we report on the role of ndrg1a in hypoxia adaptation of the anoxia-tolerant zebrafish embryo. ndrg1a is expressed in the kidney and ionocytes, cell types that use large amounts of ATP to maintain ion homeostasis. ndrg1a mutants are viable and develop normally when raised under normal oxygen. However, their survival and kidney function is reduced relative to WT embryos following exposure to prolonged anoxia. We further demonstrate that Ndrg1a binds to the energy-demanding sodium-potassium ATPase (NKA) pump under anoxia and is required for its degradation, which may preserve ATP in the kidney and ionocytes and contribute to energy homeostasis. Lastly, we show that sodium azide treatment, which increases lactate levels under normoxia, is sufficient to trigger NKA degradation in an Ndrg1a-dependent manner. These findings support a model whereby Ndrg1a is essential for hypoxia adaptation and functions downstream of lactate signaling to induce NKA degradation, a process known to conserve cellular energy.
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Affiliation(s)
- Jong S Park
- Department of Biological Sciences, University of Maryland Baltimore CountyBaltimoreUnited States
| | - Austin M Gabel
- Department of Biological Sciences, University of Maryland Baltimore CountyBaltimoreUnited States
| | - Polina Kassir
- Department of Biological Sciences, University of Maryland Baltimore CountyBaltimoreUnited States
| | - Lois Kang
- Department of Biological Sciences, University of Maryland Baltimore CountyBaltimoreUnited States
| | - Prableen K Chowdhary
- Department of Biological Sciences, University of Maryland Baltimore CountyBaltimoreUnited States
| | - Afia Osei-Ntansah
- Department of Biological Sciences, University of Maryland Baltimore CountyBaltimoreUnited States
| | - Neil D Tran
- Department of Biological Sciences, University of Maryland Baltimore CountyBaltimoreUnited States
| | - Soujanya Viswanathan
- Department of Biological Sciences, University of Maryland Baltimore CountyBaltimoreUnited States
| | - Bryanna Canales
- Department of Biological Sciences, University of Maryland Baltimore CountyBaltimoreUnited States
| | - Pengfei Ding
- Department of Chemistry and Biochemistry, University of Maryland Baltimore CountyBaltimoreUnited States
| | - Young-Sam Lee
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Rachel Brewster
- Department of Biological Sciences, University of Maryland Baltimore CountyBaltimoreUnited States
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24
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Sharanek A, Raco L, Soleimani VD, Jahani-Asl A. In situ detection of protein-protein interaction by proximity ligation assay in patient derived brain tumor stem cells. STAR Protoc 2022; 3:101554. [PMID: 35880130 PMCID: PMC9307678 DOI: 10.1016/j.xpro.2022.101554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Improper or aberrant protein-protein interactions can lead to severe human diseases including cancer. Here, we describe an adapted proximity ligation assay (PLA) protocol for the assessment of galectin-1-HOXA5 interaction in brain tumor stem cells (BTSCs). We detail the steps for culturing and preparation of BTSCs followed by PLA and detection of protein interactions in situ using fluorescent microscopy. This PLA protocol is optimized specifically for BTSCs and includes key controls for effective result analysis. For complete details on the use and execution of this protocol, please refer to Sharanek et al. (2021). Proximity ligation assay to detect protein-protein interaction in BTSCs Optimized plating conditions for BTSC preparation using minute starting material Inclusion of appropriate controls for the PLA to ensure specificity and precision Alternative reagents and buffers to allow user to adapt the protocol to their needs
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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25
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Cheng LC, Zhang X, Abhinav K, Nguyen JA, Baboo S, Martinez-Bartolomé S, Branon TC, Ting AY, Loose E, Yates JR, Gerace L. Shared and Distinctive Neighborhoods of Emerin and Lamin B Receptor Revealed by Proximity Labeling and Quantitative Proteomics. J Proteome Res 2022; 21:2197-2210. [PMID: 35972904 PMCID: PMC9442789 DOI: 10.1021/acs.jproteome.2c00281] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Emerin and lamin B receptor (LBR) are abundant transmembrane
proteins
of the nuclear envelope that are concentrated at the inner nuclear
membrane (INM). Although both proteins interact with chromatin and
nuclear lamins, they have distinctive biochemical and functional properties.
Here, we have deployed proximity labeling using the engineered biotin
ligase TurboID (TbID) and quantitative proteomics to compare the neighborhoods
of emerin and LBR in cultured mouse embryonic fibroblasts. Our analysis
revealed 232 high confidence proximity partners that interact selectively
with emerin and/or LBR, 49 of which are shared by both. These included
previously characterized NE-concentrated proteins, as well as a host
of additional proteins not previously linked to emerin or LBR functions.
Many of these are TM proteins of the ER, including two E3 ubiquitin
ligases. Supporting these results, we found that 11/12 representative
proximity relationships identified by TbID also were detected at the
NE with the proximity ligation assay. Overall, this work presents
methodology that may be used for large-scale mapping of the landscape
of the INM and reveals a group of new proteins with potential functional
connections to emerin and LBR.
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Affiliation(s)
- Li-Chun Cheng
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - Xi Zhang
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - Kanishk Abhinav
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - Julie A Nguyen
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - Sabyasachi Baboo
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - Salvador Martinez-Bartolomé
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - Tess C Branon
- Department of Genetics, Stanford University, Stanford, California 94305, United States
| | - Alice Y Ting
- Department of Genetics, Stanford University, Stanford, California 94305, United States
| | - Esther Loose
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - John R Yates
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
| | - Larry Gerace
- Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla, California 92037, United States
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26
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Gómez-Herranz M, Faktor J, Yébenes Mayordomo M, Pilch M, Nekulova M, Hernychova L, Ball KL, Vojtesek B, Hupp TR, Kote S. Emergent Role of IFITM1/3 towards Splicing Factor (SRSF1) and Antigen-Presenting Molecule (HLA-B) in Cervical Cancer. Biomolecules 2022; 12:1090. [PMID: 36008984 PMCID: PMC9405601 DOI: 10.3390/biom12081090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 11/24/2022] Open
Abstract
The IFITM restriction factors play a role in cancer cell progression through undefined mechanisms. We investigate new protein-protein interactions for IFITM1/3 in the context of cancer that would shed some light on how IFITM1/3 attenuate the expression of targeted proteins such as HLA-B. SBP-tagged IFITM1 protein was used to identify an association of IFITM1 protein with the SRSF1 splicing factor and transporter of mRNA to the ribosome. Using in situ proximity ligation assays, we confirmed a predominant cytosolic protein-protein association for SRSF1 and IFITM1/3. Accordingly, IFITM1/3 interacted with HLA-B mRNA in response to IFNγ stimulation using RNA-protein proximity ligation assays. In addition, RT-qPCR assays in IFITM1/IFITM3 null cells and wt-SiHa cells indicated that HLA-B gene expression at the mRNA level does not account for lowered HLA-B protein synthesis in response to IFNγ. Complementary, shotgun RNA sequencing did not show major transcript differences between IFITM1/IFITM3 null cells and wt-SiHa cells. Furthermore, ribosome profiling using sucrose gradient sedimentation identified a reduction in 80S ribosomal fraction an IFITM1/IFITM3 null cells compared to wild type. It was partially reverted by IFITM1/3 complementation. Our data link IFITM1/3 proteins to HLA-B mRNA and SRSF1 and, all together, our results begin to elucidate how IFITM1/3 catalyze the synthesis of target proteins. IFITMs are widely studied for their role in inhibiting viruses, and multiple studies have associated IFITMs with cancer progression. Our study has identified new proteins associated with IFITMs which support their role in mediating protein expression; a pivotal function that is highly relevant for viral infection and cancer progression. Our results suggest that IFITM1/3 affect the expression of targeted proteins; among them, we identified HLA-B. Changes in HLA-B expression could impact the presentation and recognition of oncogenic antigens on the cell surface by cytotoxic T cells and, ultimately, limit tumor cell eradication. In addition, the role of IFITMs in mediating protein abundance is relevant, as it has the potential for regulating the expression of viral and oncogenic proteins.
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Affiliation(s)
- Maria Gómez-Herranz
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- International Centre for Cancer Vaccine Science, University of Gdańsk, 80-822 Gdańsk, Poland
| | - Jakub Faktor
- International Centre for Cancer Vaccine Science, University of Gdańsk, 80-822 Gdańsk, Poland
- Masaryk Memorial Cancer Institute, Research Centre for Applied Molecular Oncology, 65653 Brno, Czech Republic
| | - Marcos Yébenes Mayordomo
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- International Centre for Cancer Vaccine Science, University of Gdańsk, 80-822 Gdańsk, Poland
| | - Magdalena Pilch
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- International Centre for Cancer Vaccine Science, University of Gdańsk, 80-822 Gdańsk, Poland
| | - Marta Nekulova
- Masaryk Memorial Cancer Institute, Research Centre for Applied Molecular Oncology, 65653 Brno, Czech Republic
| | - Lenka Hernychova
- Masaryk Memorial Cancer Institute, Research Centre for Applied Molecular Oncology, 65653 Brno, Czech Republic
| | - Kathryn L. Ball
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Borivoj Vojtesek
- Masaryk Memorial Cancer Institute, Research Centre for Applied Molecular Oncology, 65653 Brno, Czech Republic
| | - Ted R. Hupp
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- International Centre for Cancer Vaccine Science, University of Gdańsk, 80-822 Gdańsk, Poland
- Masaryk Memorial Cancer Institute, Research Centre for Applied Molecular Oncology, 65653 Brno, Czech Republic
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdańsk, 80-822 Gdańsk, Poland
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27
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Oxidative Stress in Type 2 Diabetes: The Case for Future Pediatric Redoxomics Studies. Antioxidants (Basel) 2022; 11:antiox11071336. [PMID: 35883827 PMCID: PMC9312244 DOI: 10.3390/antiox11071336] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 01/27/2023] Open
Abstract
Considerable evidence supports the role of oxidative stress in adult type 2 diabetes (T2D). Due to increasing rates of pediatric obesity, lack of physical activity, and consumption of excess food calories, it is projected that the number of children living with insulin resistance, prediabetes, and T2D will markedly increase with enormous worldwide economic costs. Understanding the factors contributing to oxidative stress and T2D risk may help develop optimal early intervention strategies. Evidence suggests that oxidative stress, triggered by excess dietary fat consumption, causes excess mitochondrial hydrogen peroxide emission in skeletal muscle, alters redox status, and promotes insulin resistance leading to T2D. The pathophysiological events arising from excess calorie-induced mitochondrial reactive oxygen species production are complex and not yet investigated in children. Systems medicine is an integrative approach leveraging conventional medical information and environmental factors with data obtained from “omics” technologies such as genomics, proteomics, and metabolomics. In adults with T2D, systems medicine shows promise in risk assessment and predicting drug response. Redoxomics is a branch of systems medicine focusing on “omics” data related to redox status. Systems medicine with a complementary emphasis on redoxomics can potentially optimize future healthcare strategies for adults and children with T2D.
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28
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Exploring solid-phase proximity ligation assay for survivin detection in urine. PLoS One 2022; 17:e0270535. [PMID: 35767525 PMCID: PMC9242480 DOI: 10.1371/journal.pone.0270535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/11/2022] [Indexed: 11/19/2022] Open
Abstract
Urine-based biomarkers are a rational and promising approach for the detection of bladder cancer due to the proximity of urine to the location of the tumor site and the non-invasive nature of its sampling. A well-known and highly investigated biomarker for bladder cancer is survivin. For detection of very small amounts of urinary survivin protein a highly sensitive assay was developed. The assay is based on the immuno-PCR technology, more precisely a solid-phase proximity ligation assay (spPLA). The limit of detection for the survivin spPLA was 1.45 pg/mL, resulting in an improvement of the limit of detection by a factor of approximately 23 compared to the previously in-house developed survivin ELISA. A key step in development was the initial isolation of survivin by a molecular fishing rod based on magnetic beads. Interfering matrix compounds pose a special challenge for further analytical application, but can be overcome by this isolation step. The assay is designed to work with only 500 μL of voided urine. The survivin spPLA showed a sensitivity of 30% and specificity of 89% for bladder cancer detection in this study of 110 bladder cancer cases and 133 clinical controls. Moreover, the results demonstrated again that survivin is a useful complementary marker in combination with UBC® Rapid by increasing the overall sensitivity to 70% with a specificity of 86%. Although the performance for detection of bladder cancer was rather low, the herein developed assay might serve as a new tool for survivin biomarker research in diverse human fluids, even if the biological matrix is complex or survivin is only present in small amounts.
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29
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Cao Q, Tartaglia G, Alexander M, Park PH, Poojan S, Farshchian M, Fuentes I, Chen M, McGrath JA, Palisson F, Salas-Alanis J, South AP. A role for Collagen VII in matrix protein secretion. Matrix Biol 2022; 111:226-244. [PMID: 35779741 DOI: 10.1016/j.matbio.2022.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 11/28/2022]
Abstract
Lack of type VII collagen (C7) disrupts cellular proteostasis yet the mechanism remains undescribed. By studying the relationship between C7 and the extracellular matrix (ECM)-associated proteins thrombospondin-1 (TSP1), type XII collagen (C12) and tissue transglutaminase (TGM2) in primary human dermal fibroblasts from multiple donors with or without the genetic disease recessive dystrophic epidermolysis bullosa (RDEB) (n=31), we demonstrate that secretion of each of these proteins is increased in the presence of C7. In dermal fibroblasts isolated from patients with RDEB, where C7 is absent or defective, association with the COPII outer coat protein SEC31 and ultimately secretion of each of these ECM-associated proteins is reduced and intracellular levels are increased. In RDEB fibroblasts, overall collagen secretion (as determined by the levels of hydroxyproline in the media) is unchanged while traffic from the ER to Golgi of TSP1, C12 and TGM2 occurs in a type I collagen (C1) dependent manner. In normal fibroblasts association of TSP1, C12 and TGM2 with the ER exit site transmembrane protein Transport ANd Golgi Organization-1 (TANGO1) as determined by proximity ligation assays, requires C7. In the absence of wild-type C7, or when ECM-associated proteins are overexpressed, C1 proximity and intracellular levels increase resulting in elevated cellular stress responses and elevated TGFβ signaling. Collectively, these data demonstrate a role for C7 in loading COPII vesicle cargo and provides a mechanism for disrupted proteostasis, elevated cellular stress and increased TGFβ signaling in patients with RDEB. Furthermore, our data point to a threshold of cargo loading that can be exceeded with increased protein levels leading to pathological outcomes in otherwise normal cells.
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Affiliation(s)
- Qingqing Cao
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA
| | - Grace Tartaglia
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA
| | - Michael Alexander
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA
| | - Pyung Hung Park
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA
| | - Shiv Poojan
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA
| | - Mehdi Farshchian
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA
| | - Ignacia Fuentes
- DEBRA Chile, Santiago, Chile; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana, Universidad de Desarrollo, Santiago, Chile
| | - Mei Chen
- Department of Dermatology, The Keck School of Medicine at the University of Southern California, Los Angeles, CA
| | - John A McGrath
- St. John's Institute of Dermatology, King's College London (Guy's Campus), UK
| | - Francis Palisson
- DEBRA Chile, Santiago, Chile; Facultad de Medicina Clínica Alemana, Universidad de Desarrollo, Santiago, Chile
| | | | - Andrew P South
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA; The Joan and Joel Rosenbloom Research Center for Fibrotic Diseases, Thomas Jefferson University, Philadelphia, PA; Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA.
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30
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Novel Tools to Measure Single Molecules Colocalization in Fluorescence Nanoscopy by Image Cross Correlation Spectroscopy. NANOMATERIALS 2022; 12:nano12040686. [PMID: 35215014 PMCID: PMC8875509 DOI: 10.3390/nano12040686] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 01/27/2023]
Abstract
Super Resolution Microscopy revolutionized the approach to the study of molecular interactions by providing new quantitative tools to describe the scale below 100 nanometers. Single Molecule Localization Microscopy (SMLM) reaches a spatial resolution less than 50 nm with a precision in calculating molecule coordinates between 10 and 20 nanometers. However new procedures are required to analyze data from the list of molecular coordinates created by SMLM. We propose new tools based on Image Cross Correlation Spectroscopy (ICCS) to quantify the colocalization of fluorescent signals at single molecule level. These analysis procedures have been inserted into an experimental pipeline to optimize the produced results. We show that Fluorescent NanoDiamonds targeted to an intracellular compartment can be employed (i) to correct spatial drift to maximize the localization precision and (ii) to register confocal and SMLM images in correlative multiresolution, multimodal imaging. We validated the ICCS based approach on defined biological control samples and showed its ability to quantitatively map area of interactions inside the cell. The produced results show that the ICCS analysis is an efficient tool to measure relative spatial distribution of different molecular species at the nanoscale.
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31
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Suraritdechachai S, Lakkanasirorat B, Uttamapinant C. Molecular probes for cellular imaging of post-translational proteoforms. RSC Chem Biol 2022; 3:201-219. [PMID: 35360891 PMCID: PMC8826509 DOI: 10.1039/d1cb00190f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/04/2022] [Indexed: 12/29/2022] Open
Abstract
Specific post-translational modification (PTM) states of a protein affect its property and function; understanding their dynamics in cells would provide deep insight into diverse signaling pathways and biological processes. However, it is not trivial to visualize post-translational modifications in a protein- and site-specific manner, especially in a living-cell context. Herein, we review recent advances in the development of molecular imaging tools to detect diverse classes of post-translational proteoforms in individual cells, and their applications in studying precise roles of PTMs in regulating the function of cellular proteins.
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Affiliation(s)
- Surased Suraritdechachai
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Benya Lakkanasirorat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
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32
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Dale NC, Johnstone EKM, Pfleger KDG. GPCR heteromers: An overview of their classification, function and physiological relevance. Front Endocrinol (Lausanne) 2022; 13:931573. [PMID: 36111299 PMCID: PMC9468249 DOI: 10.3389/fendo.2022.931573] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are capable of interacting to form higher order structures such as homomers and heteromers. Heteromerisation in particular has implications for receptor function, with research showing receptors can attain unique expression, ligand binding, signalling and intracellular trafficking upon heteromerisation. As such, GPCR heteromers represent novel drug targets with extensive therapeutic potential. Changes to ligand affinity, efficacy and G protein coupling have all been described, with alterations to these pharmacological aspects now well accepted as common traits for heteromeric complexes. Changes in internalisation and trafficking kinetics, as well as β-arrestin interactions are also becoming more apparent, however, few studies to date have explicitly looked at the implications these factors have upon the signalling profile of a heteromer. Development of ligands to target GPCR heteromers both experimentally and therapeutically has been mostly concentrated on bivalent ligands due to difficulties in identifying and developing heteromer-specific ligands. Improving our understanding of the pharmacology and physiology of GPCR heteromers will enable further development of heteromer-specific ligands with potential to provide therapeutics with increased efficacy and decreased side effects.
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Affiliation(s)
- Natasha C. Dale
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, WA, Australia
- Australian Research Council Centre for Personalised Therapeutics Technologies, Perth, WA, Australia
| | - Elizabeth K. M. Johnstone
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, WA, Australia
- Australian Research Council Centre for Personalised Therapeutics Technologies, Perth, WA, Australia
- School of Biomedical Sciences, The University of Western Australia, Nedlands, WA, Australia
- *Correspondence: Kevin D. G. Pfleger, ; Elizabeth K. M. Johnstone,
| | - Kevin D. G. Pfleger
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, WA, Australia
- Australian Research Council Centre for Personalised Therapeutics Technologies, Perth, WA, Australia
- Dimerix Limited, Nedlands, Australia
- *Correspondence: Kevin D. G. Pfleger, ; Elizabeth K. M. Johnstone,
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33
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Chen L, Liang J. A proximity ligation assay (PLA) based sensing platform for the ultrasensitive detection of P53 protein-specific SUMOylation. Process Biochem 2022. [DOI: 10.1016/j.procbio.2021.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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34
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Peng W, Li W, Han H, Liu H, Liu P, Gong X, Chang J. Development of chromogenic detection for biomolecular analysis. VIEW 2022. [DOI: 10.1002/viw.20200191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Weipan Peng
- School of Life Sciences Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures Tianjin University Tianjin China
| | - Wenna Li
- School of Life Sciences Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures Tianjin University Tianjin China
| | - Houyu Han
- School of Life Sciences Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures Tianjin University Tianjin China
| | - Hao Liu
- Tianjin Stomatological Hospital, Nankai University Tianjin China
| | - Ping Liu
- Tianjin Enterprise Key Laboratory of Chemiluminescence and POCT Diagnostic Technology Tianjin China
| | - Xiaoqun Gong
- School of Life Sciences Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures Tianjin University Tianjin China
| | - Jin Chang
- School of Life Sciences Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures Tianjin University Tianjin China
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35
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Gao YP, Huang KJ, Wang FT, Hou YY, Xu J, Li G. Recent advances in biological detection with rolling circle amplification: design strategy, biosensing mechanism, and practical applications. Analyst 2022; 147:3396-3414. [DOI: 10.1039/d2an00556e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rolling circle amplification (RCA) is a simple and isothermal DNA amplification technique that is used to generate thousands of repeating DNA sequences using circular templates under the catalysis of DNA polymerase.
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Affiliation(s)
- Yong-ping Gao
- International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, School of Physics and Electronics, Henan University, Kaifeng, 475004, PR China
- Analysis and Testing Center, Xinyang College, Xinyang 464000, PR China
| | - Ke-Jing Huang
- Key Laboratory of Guangxi Colleges and Universities for Food Safety and Pharmaceutical Analytical Chemistry, School of Chemistry and Chemical and Engineering, Guangxi Minzu University, Nanning 530008, PR China
| | - Fu-Ting Wang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Yang-Yang Hou
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Jing Xu
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Guoqiang Li
- International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, School of Physics and Electronics, Henan University, Kaifeng, 475004, PR China
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36
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Bonagura TW, Babischkin JS, Pepe GJ, Albrecht ED. Quantification of Protein Expression by Proximity Ligation Assay in the Nonhuman Primate in Response to Estrogen. Methods Mol Biol 2022; 2418:77-93. [PMID: 35119661 PMCID: PMC9818029 DOI: 10.1007/978-1-0716-1920-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In the field of protein biology, immunology-based techniques are continuously evolving for the detection and quantification of individual protein levels, protein-protein interaction, and protein modifications in cells and tissues. The proximity ligation assay (PLA), a method of detection that combines immunologic and PCR-based approaches, was developed to overcome some of the drawbacks that are inherent with other detection methods. The PLA allows for very sensitive and discretely quantifiable measures of unmodified, native protein levels and protein-protein interaction/modification complexes in situ in both fixed tissues and cultured cells. We describe herein the PLA method and its applicability to quantify the effects of estrogen on expression of angioregulatory factors, e.g., endothelial nitric oxide synthase (eNOS) in the vasculature, vascular endothelial growth factor (VEGF) in the placenta, and melanocortin 2 receptor (MC2R)/accessory protein (MRAP) in the fetal adrenal of the nonhuman primate.
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Affiliation(s)
| | - Jeffery S Babischkin
- Department of Obstetrics and Gynecology, Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Gerald J Pepe
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Eugene D Albrecht
- Department of Obstetrics and Gynecology, Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
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37
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Benhammouda S, Vishwakarma A, Gatti P, Germain M. Mitochondria Endoplasmic Reticulum Contact Sites (MERCs): Proximity Ligation Assay as a Tool to Study Organelle Interaction. Front Cell Dev Biol 2021; 9:789959. [PMID: 34926468 PMCID: PMC8678465 DOI: 10.3389/fcell.2021.789959] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/18/2021] [Indexed: 01/17/2023] Open
Abstract
Organelles cooperate with each other to regulate vital cellular homoeostatic functions. This occurs through the formation of close connections through membrane contact sites. Mitochondria-Endoplasmic-Reticulum (ER) contact sites (MERCS) are one of such contact sites that regulate numerous biological processes by controlling calcium and metabolic homeostasis. However, the extent to which contact sites shape cellular biology and the underlying mechanisms remain to be fully elucidated. A number of biochemical and imaging approaches have been established to address these questions, resulting in the identification of a number of molecular tethers between mitochondria and the ER. Among these techniques, fluorescence-based imaging is widely used, including analysing signal overlap between two organelles and more selective techniques such as in-situ proximity ligation assay (PLA). While these two techniques allow the detection of endogenous proteins, preventing some problems associated with techniques relying on overexpression (FRET, split fluorescence probes), they come with their own issues. In addition, proper image analysis is required to minimise potential artefacts associated with these methods. In this review, we discuss the protocols and outline the limitations of fluorescence-based approaches used to assess MERCs using endogenous proteins.
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Affiliation(s)
- Sara Benhammouda
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
| | - Anjali Vishwakarma
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
| | - Priya Gatti
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
| | - Marc Germain
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
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Distributed synthesis of sarcolemmal and sarcoplasmic reticulum membrane proteins in cardiac myocytes. Basic Res Cardiol 2021; 116:63. [PMID: 34713358 PMCID: PMC8553722 DOI: 10.1007/s00395-021-00895-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/30/2021] [Accepted: 09/11/2021] [Indexed: 02/05/2023]
Abstract
It is widely assumed that synthesis of membrane proteins, particularly in the heart, follows the classical secretory pathway with mRNA translation occurring in perinuclear regions followed by protein trafficking to sites of deployment. However, this view is based on studies conducted in less-specialized cells, and has not been experimentally addressed in cardiac myocytes. Therefore, we undertook direct experimental investigation of protein synthesis in cardiac tissue and isolated myocytes using single-molecule visualization techniques and a novel proximity-ligated in situ hybridization approach for visualizing ribosome-associated mRNA molecules for a specific protein species, indicative of translation sites. We identify here, for the first time, that the molecular machinery for membrane protein synthesis occurs throughout the cardiac myocyte, and enables distributed synthesis of membrane proteins within sub-cellular niches where the synthesized protein functions using local mRNA pools trafficked, in part, by microtubules. We also observed cell-wide distribution of membrane protein mRNA in myocardial tissue from both non-failing and hypertrophied (failing) human hearts, demonstrating an evolutionarily conserved distributed mechanism from mouse to human. Our results identify previously unanticipated aspects of local control of cardiac myocyte biology and highlight local protein synthesis in cardiac myocytes as an important potential determinant of the heart’s biology in health and disease.
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Keeney MT, Hoffman EK, Greenamyre TJ, Di Maio R. Measurement of LRRK2 Kinase Activity by Proximity Ligation Assay. Bio Protoc 2021; 11:e4140. [PMID: 34604446 PMCID: PMC8443460 DOI: 10.21769/bioprotoc.4140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/06/2021] [Accepted: 05/12/2021] [Indexed: 11/02/2022] Open
Abstract
Missense mutations in leucine rich-repeat kinase 2 (LRRK2) cause forms of familial Parkinson's disease and have been linked to 'idiopathic' Parkinson's disease. Assessment of LRRK2 kinase activity has been very challenging due to its size, complex structure, and relatively low abundance. A standard in the field to assess LRRK2 kinase activity is to measure the level of substrate phosphorylation (pThr73-Rab10) or autophosphorylation of serine 1292 (i.e., phosphoserine 1292; pS1292). The levels of pS1292 have typically been assessed by western blotting, which limits cellular and anatomical resolution. Here, we describe the method for a novel proximity ligation assay (PLA) that can detect endogenous LRRK2 kinase activity (PLA LRRK2) in situ at cellular and subcellular resolutions. PLA is a fluorescence- or chromogen-based assay that can be used to either (1) detect protein-protein interactions or (2) detect and amplify post-translational modifications on proteins. We used PLA for in situ detection and amplification of LRRK2 autophosphorylation levels at serine 1292. Our findings demonstrate that PLA LRRK2 is a highly sensitive and specific assay that can be used for assessing kinase activity in cultured cells and postmortem tissues.
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Affiliation(s)
- Matthew T. Keeney
- Pittsburgh Institute for Neurodegenerative Diseases, Pittsburgh, PA, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eric K. Hoffman
- Pittsburgh Institute for Neurodegenerative Diseases, Pittsburgh, PA, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy J. Greenamyre
- Pittsburgh Institute for Neurodegenerative Diseases, Pittsburgh, PA, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Roberto Di Maio
- Pittsburgh Institute for Neurodegenerative Diseases, Pittsburgh, PA, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
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Pereira PHS, Garcia CRS, Bouvier M. Identifying Plasmodium falciparum receptor activation using bioluminescence resonance energy transfer (BRET)-based biosensors in HEK293 cells. Methods Cell Biol 2021; 166:223-233. [PMID: 34752334 DOI: 10.1016/bs.mcb.2021.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Throughout evolution the need for unicellular organisms to associate and form a single cluster of cells had several evolutionary advantages. G protein coupled receptors (GPCRs) are responsible for a large part of the senses that allow this clustering to succeed, playing a fundamental role in the perception of cell's external environment, enabling the interaction and coordinated development between each cell of a multicellular organism. GPCRs are not exclusive to complex multicellular organisms. In single-celled organisms, GPCRs are also present and have a similar function of detecting changes in the external environment and transforming them into a biological response. There are no reports of GPCRs in parasitic protozoa, such as the Plasmodium genus, and the identification of a protein of this family in P. falciparum would have a significant impact both on the understanding of the basic biology of the parasite and on the history of the evolution of GPCRs. The protocol described here was successfully applied to study a GPCR candidate in P. falciparum for the first time, and we hope that it helps other groups to use the same approach to study this deadly parasite.
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Affiliation(s)
- Pedro H S Pereira
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Celia R S Garcia
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
| | - Michel Bouvier
- Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
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Mendes T, Herledan A, Leroux F, Deprez B, Lambert JC, Kilinc D. High-Content Screening for Protein-Protein Interaction Modulators Using Proximity Ligation Assay in Primary Neurons. ACTA ACUST UNITED AC 2021; 86:e100. [PMID: 31876395 DOI: 10.1002/cpcb.100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The proximity ligation assay (PLA) allows the detection and subcellular localization of protein-protein interactions with high specificity. We recently developed a high-content screening model based on primary hippocampal neurons cultured in 384-well plates and screened a library of ∼1100 compounds using a PLA between tau and bridging integrator 1, a genetic risk factor for Alzheimer's disease. We developed image-segmentation and spot-detection algorithms to delineate PLA signals in the axonal network, but not in cell bodies, from confocal images acquired via a high-throughput microscope. To compare data generated from different plates and through different experiments, we developed a computational routine to optimize the image analysis parameters for each plate and devised a range of quality-control measures to ultimately identify compounds that consistently increase or decrease our read-out. We provide the following protocols. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Routine culture of rat postnatal hippocampal neurons in 384-well plates Basic Protocol 2: Compound incubation using the high-content screening platform Support Protocol 1: Preparation of intermediate plates for compound screening Support Protocol 2: Preparation of intermediate plates for hit validation (dose-response curves) Basic Protocol 3: Proximity ligation assay in 384-well plates Basic Protocol 4: Image acquisition and analysis Support Protocol 3: Optimization of analysis parameters Basic Protocol 5: Identification of hits Basic Protocol 6: Validation of hits based on dose-response curves.
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Affiliation(s)
- Tiago Mendes
- Université de Lille, INSERM U1167, Institut Pasteur de Lille, Lille, France
| | - Adrien Herledan
- Université de Lille, EGID, INSERM U1177, Institut Pasteur de Lille, Lille, France
| | - Florence Leroux
- Université de Lille, EGID, INSERM U1177, Institut Pasteur de Lille, Lille, France
| | - Benoit Deprez
- Université de Lille, EGID, INSERM U1177, Institut Pasteur de Lille, Lille, France
| | | | - Devrim Kilinc
- Université de Lille, INSERM U1167, Institut Pasteur de Lille, Lille, France
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Xu L, Zhou Z, Gou X, Shi W, Gong Y, Yi M, Cheng W, Song F. Light up multiple protein dimers on cell surface based on proximity-induced fluorescence activation of DNA-templated sliver nanoclusters. Biosens Bioelectron 2021; 179:113064. [DOI: 10.1016/j.bios.2021.113064] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/27/2021] [Accepted: 01/31/2021] [Indexed: 02/07/2023]
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Hogea A, Shah S, Jones F, Carver CM, Hao H, Liang C, Huang D, Du X, Gamper N. Junctophilin-4 facilitates inflammatory signalling at plasma membrane-endoplasmic reticulum junctions in sensory neurons. J Physiol 2021; 599:2103-2123. [PMID: 33569781 DOI: 10.1113/jp281331] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/02/2021] [Indexed: 12/21/2022] Open
Abstract
KEY POINTS Rat somatosensory neurons express a junctional protein, junctophilin-4 (JPH4) JPH4 is necessary for the formation of store operated Ca2+ entry (SOCE) complex at the junctions between plasma membrane and endoplasmic reticulum in these neurons. Knockdown of JPH4 impairs endoplasmic reticulum Ca2+ store refill and junctional Ca2+ signalling in sensory neurons. In vivo knockdown of JPH4 in the dorsal root ganglion (DRG) sensory neurons significantly attenuated experimentally induced inflammatory pain in rats. Junctional nanodomain Ca2+ signalling maintained by JPH4 is an important contributor to the inflammatory pain mechanisms. ABSTRACT Junctions of endoplasmic reticulum and plasma membrane (ER-PM junctions) form signalling nanodomains in eukaryotic cells. ER-PM junctions are present in peripheral sensory neurons and are important for the fidelity of G protein coupled receptor (GPCR) signalling. Yet little is known about the assembly, maintenance and physiological role of these junctions in somatosensory transduction. Using fluorescence imaging, proximity ligation, super-resolution microscopy, in vitro and in vivo gene knockdown we demonstrate that a member of the junctophilin protein family, junctophilin-4 (JPH4), is necessary for the formation of store operated Ca2+ entry (SOCE) complex at the ER-PM junctions in rat somatosensory neurons. Thus we show that JPH4 localises to the ER-PM junctional areas and co-clusters with SOCE proteins STIM1 and Orai1 upon ER Ca2+ store depletion. Knockdown of JPH4 impairs SOCE and ER Ca2+ store refill in sensory neurons. Furthermore, we demonstrate a key role of the JPH4 and junctional nanodomain Ca2+ signalling in the pain-like response induced by the inflammatory mediator bradykinin. Indeed, an in vivo knockdown of JPH4 in the dorsal root ganglion (DRG) sensory neurons significantly shortened the duration of nocifensive behaviour induced by hindpaw injection of bradykinin in rats. Since the ER supplies Ca2+ for the excitatory action of multiple inflammatory mediators, we suggest that junctional nanodomain Ca2+ signalling maintained by JPH4 is an important contributor to the inflammatory pain mechanisms.
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Affiliation(s)
- Alexandra Hogea
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Shihab Shah
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Frederick Jones
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Chase M Carver
- Department of Cellular and Integrative Physiology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Han Hao
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Ce Liang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Dongyang Huang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Xiaona Du
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Nikita Gamper
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Department of Pharmacology, Hebei Medical University, Shijiazhuang, China
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Abstract
In vitro, the differentiation of megakaryocytes (MKs) is improved by aryl-hydrocarbon receptor (AHR) antagonists such as StemRegenin 1 (SR1), an effect physiologically recapitulated by the presence of stromal mesenchymal cells (MSC). This inhibition promotes the amplification of a CD34+CD41low population able to mature as MKs with a high capacity for platelet production. In this short report, we showed that the emergence of the thrombocytogenic precursors and the enhancement of platelet production triggered by SR1 involved IKAROS. The downregulation/inhibition of IKAROS (shRNA or lenalidomide) significantly reduced the emergence of SR1-induced thrombocytogenic population, suggesting a crosstalk between AHR and IKAROS. Interestingly, using a proximity ligation assay, we could demonstrate a physical interaction between AHR and IKAROS. This interaction was also observed in the megakaryocytic cells differentiated in the presence of MSCs. In conclusion, our study revealed a previously unknown AHR/ IKAROS -dependent pathway which prompted the expansion of the thrombocytogenic precursors. This AHR- IKAROS dependent checkpoint controlling MK maturation opens new perspectives to platelet production engineering.
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45
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Wang H, Hou W, Perera A, Bettler C, Beach JR, Ding X, Li J, Denning MF, Dhanarajan A, Cotler SJ, Joyce C, Yin J, Ahmed F, Roberts LR, Qiu W. Targeting EphA2 suppresses hepatocellular carcinoma initiation and progression by dual inhibition of JAK1/STAT3 and AKT signaling. Cell Rep 2021; 34:108765. [PMID: 33626345 PMCID: PMC7954228 DOI: 10.1016/j.celrep.2021.108765] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 12/07/2020] [Accepted: 01/28/2021] [Indexed: 02/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) remains one of the deadliest malignancies worldwide. One major obstacle to treatment is a lack of effective molecular-targeted therapies. In this study, we find that EphA2 expression and signaling are enriched in human HCC and associated with poor prognosis. Loss of EphA2 suppresses the initiation and growth of HCC both in vitro and in vivo. Furthermore, CRISPR/CAS9-mediated EphA2 inhibition significantly delays tumor development in a genetically engineered murine model of HCC. Mechanistically, we discover that targeting EphA2 suppresses both AKT and JAK1/STAT3 signaling, two separate oncogenic pathways in HCC. We also identify a small molecule kinase inhibitor of EphA2 that suppresses tumor progression in a murine HCC model. Together, our results suggest EphA2 as a promising therapeutic target for HCC.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Benzamides/pharmacology
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/enzymology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Cell Line, Tumor
- Databases, Genetic
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Janus Kinase 1/genetics
- Janus Kinase 1/metabolism
- Liver Neoplasms/drug therapy
- Liver Neoplasms/enzymology
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Male
- Mice, Inbred C57BL
- Molecular Targeted Therapy
- Niacinamide/analogs & derivatives
- Niacinamide/pharmacology
- Phosphorylation
- Proto-Oncogene Proteins c-akt/metabolism
- Receptor, EphA2/antagonists & inhibitors
- Receptor, EphA2/genetics
- Receptor, EphA2/metabolism
- Retrospective Studies
- STAT3 Transcription Factor/genetics
- STAT3 Transcription Factor/metabolism
- Signal Transduction
- Tumor Burden/drug effects
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Hao Wang
- Department of Surgery, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA; Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Wei Hou
- Department of Surgery, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA; Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Aldeb Perera
- Department of Surgery, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA; Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Carlee Bettler
- Department of Surgery, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA; Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Jordan R Beach
- Department of Cell and Molecular Physiology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Xianzhong Ding
- Department of Pathology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Jun Li
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN, USA
| | - Mitchell F Denning
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Asha Dhanarajan
- Department of Medicine, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Scott J Cotler
- Department of Medicine, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Cara Joyce
- Department of Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Jun Yin
- Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Fowsiyo Ahmed
- Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Wei Qiu
- Department of Surgery, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA; Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA.
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Jung YS, Stratton SA, Lee SH, Kim MJ, Jun S, Zhang J, Zheng B, Cervantes CL, Cha JH, Barton MC, Park JI. TMEM9-v-ATPase Activates Wnt/β-Catenin Signaling Via APC Lysosomal Degradation for Liver Regeneration and Tumorigenesis. Hepatology 2021; 73:776-794. [PMID: 32380568 PMCID: PMC7647947 DOI: 10.1002/hep.31305] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS How Wnt signaling is orchestrated in liver regeneration and tumorigenesis remains elusive. Recently, we identified transmembrane protein 9 (TMEM9) as a Wnt signaling amplifier. APPROACH AND RESULTS TMEM9 facilitates v-ATPase assembly for vesicular acidification and lysosomal protein degradation. TMEM9 is highly expressed in regenerating liver and hepatocellular carcinoma (HCC) cells. TMEM9 expression is enriched in the hepatocytes around the central vein and acutely induced by injury. In mice, Tmem9 knockout impairs hepatic regeneration with aberrantly increased adenomatosis polyposis coli (Apc) and reduced Wnt signaling. Mechanistically, TMEM9 down-regulates APC through lysosomal protein degradation through v-ATPase. In HCC, TMEM9 is overexpressed and necessary to maintain β-catenin hyperactivation. TMEM9-up-regulated APC binds to and inhibits nuclear translocation of β-catenin, independent of HCC-associated β-catenin mutations. Pharmacological blockade of TMEM9-v-ATPase or lysosomal degradation suppresses Wnt/β-catenin through APC stabilization and β-catenin cytosolic retention. CONCLUSIONS Our results reveal that TMEM9 hyperactivates Wnt signaling for liver regeneration and tumorigenesis through lysosomal degradation of APC.
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Affiliation(s)
- Youn-Sang Jung
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX.,Department of Life ScienceChung-Ang UniversitySeoulSouth Korea
| | - Sabrina A Stratton
- Department of Epigenetics and Molecular CarcinogenesisThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Sung Ho Lee
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Moon-Jong Kim
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Sohee Jun
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Jie Zhang
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Biyun Zheng
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Christopher L Cervantes
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Jong-Ho Cha
- Department of Biomedical SciencesCollege of MedicineInha UniversityIncheonSouth Korea
| | - Michelle C Barton
- Department of Epigenetics and Molecular CarcinogenesisThe University of Texas MD Anderson Cancer CenterHoustonTX.,Graduate School of Biomedical SciencesThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Jae-Il Park
- Department of Experimental Radiation OncologyDivision of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX.,Graduate School of Biomedical SciencesThe University of Texas MD Anderson Cancer CenterHoustonTX.,Program in Genetics and EpigeneticsThe University of Texas MD Anderson Cancer CenterHoustonTX
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47
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Proximity Ligation Assay Detection of Protein-DNA Interactions-Is There a Link between Heme Oxygenase-1 and G-quadruplexes? Antioxidants (Basel) 2021; 10:antiox10010094. [PMID: 33445471 PMCID: PMC7827836 DOI: 10.3390/antiox10010094] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 01/12/2023] Open
Abstract
G-quadruplexes (G4) are stacked nucleic acid structures that are stabilized by heme. In cells, they affect DNA replication and gene transcription. They are unwound by several helicases but the composition of the repair complex and its heme sensitivity are unclear. We found that the accumulation of G-quadruplexes is affected by heme oxygenase-1 (Hmox1) expression, but in a cell-type-specific manner: hematopoietic stem cells (HSCs) from Hmox1−/− mice have upregulated expressions of G4-unwinding helicases (e.g., Brip1, Pif1) and show weaker staining for G-quadruplexes, whereas Hmox1-deficient murine induced pluripotent stem cells (iPSCs), despite the upregulation of helicases, have more G-quadruplexes, especially after exposure to exogenous heme. Using iPSCs expressing only nuclear or only cytoplasmic forms of Hmox1, we found that nuclear localization promotes G4 removal. We demonstrated that the proximity ligation assay (PLA) can detect cellular co-localization of G-quadruplexes with helicases, as well as with HMOX1, suggesting the potential role of HMOX1 in G4 modifications. However, this colocalization does not mean a direct interaction was detectable using the immunoprecipitation assay. Therefore, we concluded that HMOX1 influences G4 accumulation, but rather as one of the proteins regulating the heme availability, not as a rate-limiting factor. It is noteworthy that cellular G4–protein colocalizations can be quantitatively analyzed using PLA, even in rare cells.
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Proximity ligation assay: an ultrasensitive method for protein quantification and its applications in pathogen detection. Appl Microbiol Biotechnol 2021; 105:923-935. [PMID: 33427935 DOI: 10.1007/s00253-020-11049-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/27/2020] [Accepted: 12/09/2020] [Indexed: 01/08/2023]
Abstract
It is of great significance to establish sensitive and accurate pathogen detection methods, considering the continuous emergence or re-emergence of infectious diseases seriously influences the safety of human and animals. Proximity ligation assay (PLA) is developed for the sensitive protein detection and also can be used for the detection of pathogens. PLA employs aptamer or monoclonal/polyclonal antibody-nucleic acid complexes as proximity probes. When the paired proximity probes bind to the same target protein or protein complex, they will be adjacent to each other and form an amplifiable DNA sequence through ligation. Combining the specificity of enzyme-linked immunosorbent assay (ELISA) and sensitivity of polymerase chain reaction (PCR), PLA transforms the detection of protein into the detection of DNA nucleic acid sequence. Therefore, as an ultrasensitive protein assay, PLA has great potential for quantification, localization of protein, and clinical diagnostics. In this review, we summarize the basic principles of PLA and its applications in pathogen detection. KEY POINTS: • Different forms of proximity ligation assay are introduced. • Applications of proximity ligation assay in pathogen detection are summarized. • Proximity ligation assay is an ultrasensitive method to quantify protein and pathogen.
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49
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Benhammouda S, Vishwakarma A, Gatti P, Germain M. Mitochondria Endoplasmic Reticulum Contact Sites (MERCs): Proximity Ligation Assay as a Tool to Study Organelle Interaction. Front Cell Dev Biol 2021. [PMID: 34926468 DOI: 10.3389/fcell.2021.789959.ecollection2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
Organelles cooperate with each other to regulate vital cellular homoeostatic functions. This occurs through the formation of close connections through membrane contact sites. Mitochondria-Endoplasmic-Reticulum (ER) contact sites (MERCS) are one of such contact sites that regulate numerous biological processes by controlling calcium and metabolic homeostasis. However, the extent to which contact sites shape cellular biology and the underlying mechanisms remain to be fully elucidated. A number of biochemical and imaging approaches have been established to address these questions, resulting in the identification of a number of molecular tethers between mitochondria and the ER. Among these techniques, fluorescence-based imaging is widely used, including analysing signal overlap between two organelles and more selective techniques such as in-situ proximity ligation assay (PLA). While these two techniques allow the detection of endogenous proteins, preventing some problems associated with techniques relying on overexpression (FRET, split fluorescence probes), they come with their own issues. In addition, proper image analysis is required to minimise potential artefacts associated with these methods. In this review, we discuss the protocols and outline the limitations of fluorescence-based approaches used to assess MERCs using endogenous proteins.
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Affiliation(s)
- Sara Benhammouda
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
| | - Anjali Vishwakarma
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
| | - Priya Gatti
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
| | - Marc Germain
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université Du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre D'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montréal, QC, Canada
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Chen M, Horn HT, Wen T, Cryns VL, Anderson RA. Assessing In Situ Phosphoinositide-Protein Interactions Through Fluorescence Proximity Ligation Assay in Cultured Cells. Methods Mol Biol 2021; 2251:133-142. [PMID: 33481236 PMCID: PMC9789737 DOI: 10.1007/978-1-0716-1142-5_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Proximity ligation assay (PLA) is a well-established method for detecting in situ interactions between two epitopes with high resolution and specificity. Notably, PLA is not only a robust method for studying protein-protein interaction but also an efficient approach to characterize and validate protein posttranslational modifications (PTM) using one antibody against the core protein and one against the PTM residue. Therefore, it could be applied as a powerful approach to detect specific interactions of endogenous phosphoinositides and their binding proteins within cells. Importantly, we have specifically detected the PLA signal between PtdIns(4,5)P2 and its binding effector p53 in the nucleus. This cutting-edge method fully complements other conventional approaches for studying phosphoinositide-protein interactions and provides important localization signals and robust quantitation of the detected interactions. Here, we present the PLA fluorescence protocol for detecting in situ phosphoinositide-protein interactions in cultured cells and is semiquantitative for interactions that are regulated by cellular signaling.
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Affiliation(s)
- Mo Chen
- University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Hudson T. Horn
- University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Tianmu Wen
- University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Vincent L. Cryns
- Department of Medicine, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, School of Medicine and Public Health, 1111 Highland Avenue, Madison, WI 53705, USA
| | - Richard A. Anderson
- University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA,Correspondence to: Richard A. Anderson, 3750 Medical Sciences Center, 1300 University Avenue, Madison, WI 53706. Phone: 608-262-3753; Fax: 608-262-1257;
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