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Wu Y, Xie Q, Wu L, Li Z, Li X, Zhang L, Zhang B. Identification of activating transcription factor 6 (ATF6) as a novel prognostic biomarker and potential target in oral squamous cell carcinoma. Gene 2024; 915:148436. [PMID: 38579904 DOI: 10.1016/j.gene.2024.148436] [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: 01/12/2024] [Revised: 03/08/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND Oral squamous cell carcinoma (OSCC) is originating from oral mucosal epithelial cells. Autophagy plays a crucial role in cancer treatment by promoting cellular self-degradation and eliminating damaged components, thereby enhancing therapeutic efficacy. In this study, we aim to identify a novel autophagy-related biomarker to improve OSCC therapy. METHODS We firstly utilized Cox and Lasso analyses to identify that ATF6 is associated with OSCC prognosis, and validated the results by Kaplan-Meier survival analysis. We further identified the downstream pathways and related genes by enrichment analysis and WGCNA analysis. Subsequently, we used short interfering RNA to investigate the effects of ATF6 knockdown on proliferation, migration, apoptosis, and autophagy in SCC-9 and SCC-15 cells through cell viability assay, transwell assay, EdU incorporation assay, flow cytometry analysis, western blot analysis and immunofluorescence analysis, etc. RESULTS: Bioinformatics analyses showed that ATF6 overexpression was associated with prognosis and detrimental to survival. In vitro studies verified that ATF6 knockdown reduced OSCC cell proliferation and migration. Mechanistically, ATF6 knockdown could promote cellular autophagy and apoptosis. CONCLUSION We propose that ATF6 holds potential as a prognostic biomarker linked to autophagy in OSCC. This study provides valuable clues for further exploration of targeted therapy against OSCC.
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Affiliation(s)
- Yan Wu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, China
| | - Qiang Xie
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lifeng Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhijia Li
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Xiaojing Li
- CHN ENERGY Digital Intelligence Technology Development (Beijing) Co., Ltd., Beijing 100011, China
| | - Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - Bin Zhang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, China.
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2
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Perego E, Zappone S, Castagnetti F, Mariani D, Vitiello E, Rupert J, Zacco E, Tartaglia GG, Bozzoni I, Slenders E, Vicidomini G. Single-photon microscopy to study biomolecular condensates. Nat Commun 2023; 14:8224. [PMID: 38086853 PMCID: PMC10716487 DOI: 10.1038/s41467-023-43969-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Biomolecular condensates serve as membrane-less compartments within cells, concentrating proteins and nucleic acids to facilitate precise spatial and temporal orchestration of various biological processes. The diversity of these processes and the substantial variability in condensate characteristics present a formidable challenge for quantifying their molecular dynamics, surpassing the capabilities of conventional microscopy. Here, we show that our single-photon microscope provides a comprehensive live-cell spectroscopy and imaging framework for investigating biomolecular condensation. Leveraging a single-photon detector array, single-photon microscopy enhances the potential of quantitative confocal microscopy by providing access to fluorescence signals at the single-photon level. Our platform incorporates photon spatiotemporal tagging, which allowed us to perform time-lapse super-resolved imaging for molecular sub-diffraction environment organization with simultaneous monitoring of molecular mobility, interactions, and nano-environment properties through fluorescence lifetime fluctuation spectroscopy. This integrated correlative study reveals the dynamics and interactions of RNA-binding proteins involved in forming stress granules, a specific type of biomolecular condensates, across a wide range of spatial and temporal scales. Our versatile framework opens up avenues for exploring a broad spectrum of biomolecular processes beyond the formation of membrane-less organelles.
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Affiliation(s)
- Eleonora Perego
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Sabrina Zappone
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
- Dipartimento di Informatica, Bioingegneria, Robotica e Ingegneria dei Sistemi, University of Genoa, Genoa, Italy
| | - Francesco Castagnetti
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Davide Mariani
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Erika Vitiello
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Jakob Rupert
- RNA Systems Biology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Biology and Biotechnologies 'C. Darwin', Sapienza University of Rome, Rome, Italy
| | - Elsa Zacco
- RNA Systems Biology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Gian Gaetano Tartaglia
- RNA Systems Biology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Biology and Biotechnologies 'C. Darwin', Sapienza University of Rome, Rome, Italy
| | - Irene Bozzoni
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Biology and Biotechnologies 'C. Darwin', Sapienza University of Rome, Rome, Italy
| | - Eli Slenders
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy.
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Pabba MK, Ritter C, Chagin VO, Meyer J, Celikay K, Stear JH, Loerke D, Kolobynina K, Prorok P, Schmid AK, Leonhardt H, Rohr K, Cardoso MC. Replisome loading reduces chromatin motion independent of DNA synthesis. eLife 2023; 12:RP87572. [PMID: 37906089 PMCID: PMC10617993 DOI: 10.7554/elife.87572] [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: 11/02/2023] Open
Abstract
Chromatin has been shown to undergo diffusional motion, which is affected during gene transcription by RNA polymerase activity. However, the relationship between chromatin mobility and other genomic processes remains unclear. Hence, we set out to label the DNA directly in a sequence unbiased manner and followed labeled chromatin dynamics in interphase human cells expressing GFP-tagged proliferating cell nuclear antigen (PCNA), a cell cycle marker and core component of the DNA replication machinery. We detected decreased chromatin mobility during the S-phase compared to G1 and G2 phases in tumor as well as normal diploid cells using automated particle tracking. To gain insight into the dynamical organization of the genome during DNA replication, we determined labeled chromatin domain sizes and analyzed their motion in replicating cells. By correlating chromatin mobility proximal to the active sites of DNA synthesis, we showed that chromatin motion was locally constrained at the sites of DNA replication. Furthermore, inhibiting DNA synthesis led to increased loading of DNA polymerases. This was accompanied by accumulation of the single-stranded DNA binding protein on the chromatin and activation of DNA helicases further restricting local chromatin motion. We, therefore, propose that it is the loading of replisomes but not their catalytic activity that reduces the dynamics of replicating chromatin segments in the S-phase as well as their accessibility and probability of interactions with other genomic regions.
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Affiliation(s)
| | - Christian Ritter
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - Vadim O Chagin
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
- Institute of Cytology RASSt. PetersburgRussian Federation
| | - Janis Meyer
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - Kerem Celikay
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - Jeffrey H Stear
- EMBL Australia Node in Single Molecule Science, University of New South WalesSydneyAustralia
| | - Dinah Loerke
- Department of Physics & Astronomy, University of DenverDenverUnited States
| | - Ksenia Kolobynina
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
| | - Paulina Prorok
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
| | - Alice Kristin Schmid
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | | | - Karl Rohr
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - M Cristina Cardoso
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
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4
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Yang CF, Liao CC, Hsu HW, Liang JJ, Chang CS, Ko HY, Chang RH, Tang WC, Chang MH, Wang IH, Lin YL. Human ACE2 protein is a molecular switch controlling the mode of SARS-CoV-2 transmission. J Biomed Sci 2023; 30:87. [PMID: 37828601 PMCID: PMC10571257 DOI: 10.1186/s12929-023-00980-w] [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: 05/15/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND Human angiotensin-converting enzyme 2 (hACE2) is the receptor mediating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. hACE2 expression is low in the lungs and is upregulated after SARS-CoV-2 infection. How such a hACE2-limited pulmonary environment supports efficient virus transmission and how dynamic hACE2 expression affects SARS-CoV-2 infection are unclear. METHODS We generated stable cell lines with different expression levels of hACE2 to evaluate how the hACE2 expression level can affect SARS-CoV-2 transmission. RESULTS We demonstrated that the hACE2 expression level controls the mode of SARS-CoV-2 transmission. The hACE2-limited cells have an advantage for SARS-CoV-2 shedding, which leads to cell-free transmission. By contrast, enhanced hACE2 expression facilitates the SARS-CoV-2 cell-to-cell transmission. Furthermore, this cell-to-cell transmission is likely facilitated by hACE2-containing vesicles, which accommodate numerous SARS-CoV-2 virions and transport them to neighboring cells through intercellular extensions. CONCLUSIONS This hACE2-mediated switch between cell-free and cell-to-cell transmission routes provides SARS-CoV-2 with advantages for either viral spread or evasion of humoral immunity, thereby contributing to the COVID-19 pandemic and pathogenesis.
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Affiliation(s)
- Chao-Fu Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.
| | - Chun-Che Liao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Hung-Wei Hsu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Jian-Jong Liang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Chih-Shin Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Hui-Ying Ko
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Rue-Hsin Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Wei-Chun Tang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Ming-Hao Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - I-Hsuan Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11529, Taiwan.
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5
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Sankaran J, Wohland T. Current capabilities and future perspectives of FCS: super-resolution microscopy, machine learning, and in vivo applications. Commun Biol 2023; 6:699. [PMID: 37419967 PMCID: PMC10328937 DOI: 10.1038/s42003-023-05069-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is a single molecule sensitive tool for the quantitative measurement of biomolecular dynamics and interactions. Improvements in biology, computation, and detection technology enable real-time FCS experiments with multiplexed detection even in vivo. These new imaging modalities of FCS generate data at the rate of hundreds of MB/s requiring efficient data processing tools to extract information. Here, we briefly review FCS's capabilities and limitations before discussing recent directions that address these limitations with a focus on imaging modalities of FCS, their combinations with super-resolution microscopy, new evaluation strategies, especially machine learning, and applications in vivo.
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Affiliation(s)
- Jagadish Sankaran
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138632, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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6
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Schüssele DS, Haller PK, Haas ML, Hunter C, Sporbeck K, Proikas-Cezanne T. Autophagy profiling in single cells with open source CellProfiler-based image analysis. Autophagy 2023; 19:338-351. [PMID: 35435815 PMCID: PMC9809960 DOI: 10.1080/15548627.2022.2065617] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Single cell-based analysis of macroautophagy/autophagy is largely achieved through the use of fluorescence microscopy to detect autophagy-related proteins that associate with autophagic membranes and therefore can be quantified as fluorescent puncta. In this context, an automated analysis of the number and size of recognized puncta is preferable to a manual count, because more reliable results can be generated in a short time. Here we present a method for open source CellProfiler software-based analysis for quantitative autophagy assessments using GFP-tagged WIPI1 (WD repeat domain, phosphoinositide interacting 1) images acquired with Airyscan or confocal laser-scanning microscopy. The CellProfiler protocol is provided as a ready-to-use software pipeline, and the creation of this pipeline is detailed in both text and video formats. In addition, we provide CellProfiler pipelines for endogenous SQSTM1/p62 (sequestosome 1) or intracellular lipid droplet (LD) analysis, suitable to assess forms of selective autophagy. All protocols and software pipelines can be quickly and easily adapted for the use of alternative autophagy markers or cell types, and can also be used for high-throughput purposes.Abbreviations: AF Alexa Fluor ATG autophagy related BafA1 bafilomycin A1 BSA bovine serum albumin DAPI 4,6-diamidino-2-phenylindole DMEM Dulbecco's modified Eagle's medium DMSO dimethyl sulfoxide EDTA ethylenediaminetetraacetic acid EBSS Earle's balanced salt solution FBS fetal bovine serum GFP green fluorescent protein LD lipid droplet LSM laser scanning microscope MAP1LC3B microtubule associated protein 1 light chain 3 beta MTOR mechanistic target of rapamycin kinase PBS phosphate-buffered saline PIK3C3/VPS34 phosphatidylinositol 3-kinase catalytic subunit type 3 SQSTM1 sequestosome 1 TIFF tagged image file format U2OS U-2 OS cell line WIPI WD repeat domain, phosphoinositide interacting.
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Affiliation(s)
- David S. Schüssele
- Interfaculty Institute of Cell Biology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Patricia K. Haller
- Interfaculty Institute of Cell Biology, Eberhard Karls University Tübingen, Tübingen, Germany,International Max Planck Research School ‘From Molecules to Organisms’, Max Planck Institute for Developmental Biology and Eberhard Karls University Tübingen, Tübingen, Germany
| | - Maximilian L. Haas
- Interfaculty Institute of Cell Biology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Catherine Hunter
- Interfaculty Institute of Cell Biology, Eberhard Karls University Tübingen, Tübingen, Germany,International Max Planck Research School ‘From Molecules to Organisms’, Max Planck Institute for Developmental Biology and Eberhard Karls University Tübingen, Tübingen, Germany
| | - Katharina Sporbeck
- Interfaculty Institute of Cell Biology, Eberhard Karls University Tübingen, Tübingen, Germany,International Max Planck Research School ‘From Molecules to Organisms’, Max Planck Institute for Developmental Biology and Eberhard Karls University Tübingen, Tübingen, Germany
| | - Tassula Proikas-Cezanne
- Interfaculty Institute of Cell Biology, Eberhard Karls University Tübingen, Tübingen, Germany,International Max Planck Research School ‘From Molecules to Organisms’, Max Planck Institute for Developmental Biology and Eberhard Karls University Tübingen, Tübingen, Germany,CONTACT Tassula Proikas-Cezanne Interfaculty Institute of Cell Biology, Eberhard Karls University Tübingen, D-72076Tübingen, Germany
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7
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The BrightEyes-TTM as an open-source time-tagging module for democratising single-photon microscopy. Nat Commun 2022; 13:7406. [PMID: 36456575 PMCID: PMC9715684 DOI: 10.1038/s41467-022-35064-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
Fluorescence laser-scanning microscopy (LSM) is experiencing a revolution thanks to new single-photon (SP) array detectors, which give access to an entirely new set of single-photon information. Together with the blooming of new SP LSM techniques and the development of tailored SP array detectors, there is a growing need for (i) DAQ systems capable of handling the high-throughput and high-resolution photon information generated by these detectors, and (ii) incorporating these DAQ protocols in existing fluorescence LSMs. We developed an open-source, low-cost, multi-channel time-tagging module (TTM) based on a field-programmable gate array that can tag in parallel multiple single-photon events, with 30 ps precision, and multiple synchronisation events, with 4 ns precision. We use the TTM to demonstrate live-cell super-resolved fluorescence lifetime image scanning microscopy and fluorescence lifetime fluctuation spectroscopy. We expect that our BrightEyes-TTM will support the microscopy community in spreading SP-LSM in many life science laboratories.
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Das A, Madeshiya AK, Biswas N, Ghosh N, Gorain M, Rawat A, Mahajan SP, Khanna S, Sen CK, Roy S. Oncostatin M Improves Cutaneous Wound Re-Epithelialization and Is Deficient under Diabetic Conditions. J Invest Dermatol 2022; 142:679-691.e3. [PMID: 34534575 PMCID: PMC8860865 DOI: 10.1016/j.jid.2021.04.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/03/2021] [Accepted: 04/12/2021] [Indexed: 11/29/2022]
Abstract
Impaired re-epithelialization characterized by hyperkeratotic nonmigratory wound epithelium is a hallmark of nonhealing diabetic wounds. In chronic wounds, the copious release of oncostatin M (OSM) from wound macrophages is evident. OSM is a potent keratinocyte (KC) activator. This work sought to understand the signal transduction pathway responsible for wound re-epithelialization, the primary mechanism underlying wound closure. Daily topical treatment of full-thickness excisional wounds of C57BL/6 mice with recombinant murine OSM improved wound re-epithelialization and accelerated wound closure by bolstering KC proliferation and migration. OSM activated the Jak-signal transducer and activator of transcription pathway as manifested by signal transducer and activator of transcription 3 phosphorylation. Such signal transduction in the human KC induced TP63, the master regulator of KC function. Elevated TP63 induced ITGB1, a known effector of KC migration. In diabetic wounds, OSM was more abundant than the level in nondiabetic wounds. However, in diabetic wounds, OSM activity was compromised by glycation. Aminoguanidine, a deglycation agent, rescued the compromised KC migration caused by glycated OSM. Finally, topical application of recombinant OSM improved KC migration and accelerated wound closure in db/db mice. This work recognizes that despite its abundance at the wound site, OSM is inactivated by glycation, and topical delivery of exogenous OSM is likely to be productive in accelerating diabetic wound closure.
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Affiliation(s)
- Amitava Das
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Amit K. Madeshiya
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Nirupam Biswas
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Nandini Ghosh
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Mahadeo Gorain
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Atul Rawat
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Sanskruti P. Mahajan
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Savita Khanna
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Chandan K. Sen
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Sashwati Roy
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, Indiana, USA.
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9
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Ghosh N, Das A, Biswas N, Mahajan SP, Madeshiya AK, Khanna S, Sen CK, Roy S. MYO-Inositol In Fermented Sugar Matrix Improves Human Macrophage Function. Mol Nutr Food Res 2022; 66:e2100852. [PMID: 35073444 PMCID: PMC9420542 DOI: 10.1002/mnfr.202100852] [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: 09/14/2021] [Revised: 12/07/2021] [Indexed: 11/07/2022]
Abstract
SCOPE Reactive oxygen species production by innate immune cells plays a central role in host defense against invading pathogens at wound-site. A weakened hos-defense results in persistent infection leading to wound chronicity. Fermented Papaya Preparation (FPP), a complex sugar matrix, bolstered respiratory burst activity and improved wound healing outcomes in chronic wound patients. The objective of the current study was to identify underlying molecular factor/s responsible for augmenting macrophage host defense mechanisms following FPP supplementation. METHODS AND RESULTS In depth LC-MS/MS analysis of cells supplemented with FPP led to identification of myo-inositol as a key determinant of FPP activity towards improving macrophage function. Myo-inositol, in quantities that is present in FPP, significantly improved macrophage respiratory burst and phagocytosis via de novo synthesis pathway of ISYNA1. Additionally, myo-inositol transporters, HMIT and SMIT1, played a significant role in such activity. Blocking these pathways using siRNA attenuated FPP-induced improved macrophage host defense activities. FPP supplementation emerges as a novel approach to increase intracellular myo-inositol levels. Such supplementation also modified wound microenvironment in chronic wound patients to augment myo-inositol levels in wound fluid. CONCLUSION These observations indicate that myo-inositol in FPP influences multiple aspects of macrophage function critical for host defense against invading pathogens. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Nandini Ghosh
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Amitava Das
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Nirupam Biswas
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Sanskruti P Mahajan
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Amit K Madeshiya
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Savita Khanna
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Chandan K Sen
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Sashwati Roy
- Department of Surgery, IU Health Comprehensive Wound Center, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, 46202
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10
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Slenders E, Perego E, Buttafava M, Tortarolo G, Conca E, Zappone S, Pierzynska-Mach A, Villa F, Petrini EM, Barberis A, Tosi A, Vicidomini G. Cooled SPAD array detector for low light-dose fluorescence laser scanning microscopy. BIOPHYSICAL REPORTS 2021; 1:None. [PMID: 34939046 PMCID: PMC8651514 DOI: 10.1016/j.bpr.2021.100025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/14/2021] [Indexed: 11/30/2022]
Abstract
The single-photon timing and sensitivity performance and the imaging ability of asynchronous-readout single-photon avalanche diode (SPAD) array detectors have opened up enormous perspectives in fluorescence (lifetime) laser scanning microscopy (FLSM), such as super-resolution image scanning microscopy and high-information content fluorescence fluctuation spectroscopy. However, the strengths of these FLSM techniques depend on the many different characteristics of the detector, such as dark noise, photon-detection efficiency, after-pulsing probability, and optical cross talk, whose overall optimization is typically a trade-off between these characteristics. To mitigate this trade-off, we present, to our knowledge, a novel SPAD array detector with an active cooling system that substantially reduces the dark noise without significantly deteriorating any other detector characteristics. In particular, we show that lowering the temperature of the sensor to −15°C significantly improves the signal/noise ratio due to a 10-fold decrease in the dark count rate compared with room temperature. As a result, for imaging, the laser power can be decreased by more than a factor of three, which is particularly beneficial for live-cell super-resolution imaging, as demonstrated in fixed and living cells expressing green-fluorescent-protein-tagged proteins. For fluorescence fluctuation spectroscopy, together with the benefit of the reduced laser power, we show that cooling the detector is necessary to remove artifacts in the correlation function, such as spurious negative correlations observed in the hot elements of the detector, i.e., elements for which dark noise is substantially higher than the median value. Overall, this detector represents a further step toward the integration of SPAD array detectors in any FLSM system.
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11
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The Development of Microscopy for Super-Resolution: Confocal Microscopy, and Image Scanning Microscopy. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11198981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Optical methods of super-resolution microscopy, such as confocal microscopy, structured illumination, nonlinear microscopy, and image scanning microscopy are reviewed. These methods avoid strong invasive interaction with a sample, allowing the observation of delicate biological samples. The meaning of resolution and the basic principles and different approaches to superresolution are discussed.
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12
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Zhang J, Bai Z, Ouyang M, Xu X, Xiong H, Wang Q, Grimm B, Rochaix JD, Zhang L. The DnaJ proteins DJA6 and DJA5 are essential for chloroplast iron-sulfur cluster biogenesis. EMBO J 2021; 40:e106742. [PMID: 33855718 DOI: 10.15252/embj.2020106742] [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] [Received: 09/10/2020] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/21/2022] Open
Abstract
Fe-S clusters are ancient, ubiquitous and highly essential prosthetic groups for numerous fundamental processes of life. The biogenesis of Fe-S clusters is a multistep process including iron acquisition, sulfur mobilization, and cluster formation. Extensive studies have provided deep insights into the mechanism of the latter two assembly steps. However, the mechanism of iron utilization during chloroplast Fe-S cluster biogenesis is still unknown. Here we identified two Arabidopsis DnaJ proteins, DJA6 and DJA5, that can bind iron through their conserved cysteine residues and facilitate iron incorporation into Fe-S clusters by interactions with the SUF (sulfur utilization factor) apparatus through their J domain. Loss of these two proteins causes severe defects in the accumulation of chloroplast Fe-S proteins, a dysfunction of photosynthesis, and a significant intracellular iron overload. Evolutionary analyses revealed that DJA6 and DJA5 are highly conserved in photosynthetic organisms ranging from cyanobacteria to higher plants and share a strong evolutionary relationship with SUFE1, SUFC, and SUFD throughout the green lineage. Thus, our work uncovers a conserved mechanism of iron utilization for chloroplast Fe-S cluster biogenesis.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Photobiology, Institute of Botany, Photosynthesis Research Center, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Crop Stress Adaption and Improvement, School of Life Sciences, Henan University, Kaifeng, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zechen Bai
- Key Laboratory of Photobiology, Institute of Botany, Photosynthesis Research Center, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Min Ouyang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Xiumei Xu
- State Key Laboratory of Crop Stress Adaption and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Haibo Xiong
- Key Laboratory of Photobiology, Institute of Botany, Photosynthesis Research Center, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaption and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Bernhard Grimm
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jean-David Rochaix
- Departments of Molecular Biology and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Lixin Zhang
- State Key Laboratory of Crop Stress Adaption and Improvement, School of Life Sciences, Henan University, Kaifeng, China
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13
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Fluorescence Fluctuation Spectroscopy enables quantification of potassium channel subunit dynamics and stoichiometry. Sci Rep 2021; 11:10719. [PMID: 34021177 PMCID: PMC8140153 DOI: 10.1038/s41598-021-90002-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/15/2021] [Indexed: 11/08/2022] Open
Abstract
Voltage-gated potassium (Kv) channels are a family of membrane proteins that facilitate K+ ion diffusion across the plasma membrane, regulating both resting and action potentials. Kv channels comprise four pore-forming α subunits, each with a voltage sensing domain, and they are regulated by interaction with β subunits such as those belonging to the KCNE family. Here we conducted a comprehensive biophysical characterization of stoichiometry and protein diffusion across the plasma membrane of the epithelial KCNQ1-KCNE2 complex, combining total internal reflection fluorescence (TIRF) microscopy and a series of complementary Fluorescence Fluctuation Spectroscopy (FFS) techniques. Using this approach, we found that KCNQ1-KCNE2 has a predominant 4:4 stoichiometry, while non-bound KCNE2 subunits are mostly present as dimers in the plasma membrane. At the same time, we identified unique spatio-temporal diffusion modalities and nano-environment organization for each channel subunit. These findings improve our understanding of KCNQ1-KCNE2 channel function and suggest strategies for elucidating the subunit stoichiometry and forces directing localization and diffusion of ion channel complexes in general.
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14
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Slenders E, Castello M, Buttafava M, Villa F, Tosi A, Lanzanò L, Koho SV, Vicidomini G. Confocal-based fluorescence fluctuation spectroscopy with a SPAD array detector. LIGHT, SCIENCE & APPLICATIONS 2021; 10:31. [PMID: 33542179 PMCID: PMC7862647 DOI: 10.1038/s41377-021-00475-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/17/2020] [Accepted: 01/14/2021] [Indexed: 05/13/2023]
Abstract
The combination of confocal laser-scanning microscopy (CLSM) and fluorescence fluctuation spectroscopy (FFS) is a powerful tool in studying fast, sub-resolution biomolecular processes in living cells. A detector array can further enhance CLSM-based FFS techniques, as it allows the simultaneous acquisition of several samples-essentially images-of the CLSM detection volume. However, the detector arrays that have previously been proposed for this purpose require tedious data corrections and preclude the combination of FFS with single-photon techniques, such as fluorescence lifetime imaging. Here, we solve these limitations by integrating a novel single-photon-avalanche-diode (SPAD) array detector in a CLSM system. We validate this new implementation on a series of FFS analyses: spot-variation fluorescence correlation spectroscopy, pair-correlation function analysis, and image-derived mean squared displacement analysis. We predict that the unique combination of spatial and temporal information provided by our detector will make the proposed architecture the method of choice for CLSM-based FFS.
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Affiliation(s)
- Eli Slenders
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Marco Castello
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Mauro Buttafava
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Federica Villa
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Alberto Tosi
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Luca Lanzanò
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
- Dipartimento di Fisica e Astronomia, Università di Catania, Catania, Italy
| | - Sami Valtteri Koho
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy.
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15
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DeDreu J, Walker JL, Menko AS. Dynamics of the lens basement membrane capsule and its interaction with connective tissue-like extracapsular matrix proteins. Matrix Biol 2021; 96:18-46. [PMID: 33383103 PMCID: PMC7902460 DOI: 10.1016/j.matbio.2020.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/24/2020] [Accepted: 12/24/2020] [Indexed: 12/11/2022]
Abstract
The lens, suspended in the middle of the eye by tendon-like ciliary zonule fibers and facing three different compartments of the eye, is enclosed in what has been described as the thickest basement membrane in the body. While the protein components of the capsule have been a subject of study for many years, the dynamics of capsule formation, and the region-specific relationship of its basement membrane components to one another as well as to other matrix molecules remains to be explored. Through high resolution confocal and super-resolution imaging of the lens capsule and 3D surface renderings of acquired z-stacks, our studies revealed that each of its basement membrane proteins, laminin, collagen IV, nidogen and perlecan, has unique structure, organization, and distribution specific both to the region of the lens that the capsule is located in and the position of the capsule within the eye. We provide evidence of basal membrane gradients across the depth of the capsule as well as the synthesis of distinct basement membrane lamella within the capsule. These distinctions are most prominent in the equatorial capsule zone where collagen IV and nidogen span the capsule depth, while laminin and perlecan are located in two separate lamellae located at the innermost and outermost capsule domains. We discovered that an extracapsular matrix compartment rich in the connective tissue-like matrix molecules fibronectin, tenascin-C, and fibrillin is integrated with the superficial surface of the lens capsule. Each matrix protein in this extracapsular zone also exhibits region-specific distribution with fibrils of fibrillin, the matrix protein that forms the backbone of the ciliary zonules, inserting within the laminin/perlecan lamella at the surface of the equatorial lens capsule.
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Affiliation(s)
- JodiRae DeDreu
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, 564 Jefferson Alumni Hall, 1020 Locust Street, Philadelphia, PA 19107, United States.
| | - Janice L Walker
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, 564 Jefferson Alumni Hall, 1020 Locust Street, Philadelphia, PA 19107, United States.
| | - A Sue Menko
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, 564 Jefferson Alumni Hall, 1020 Locust Street, Philadelphia, PA 19107, United States.
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16
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Pemberton JG, Kim YJ, Humpolickova J, Eisenreichova A, Sengupta N, Toth DJ, Boura E, Balla T. Defining the subcellular distribution and metabolic channeling of phosphatidylinositol. J Cell Biol 2020; 219:133809. [PMID: 32211894 PMCID: PMC7054996 DOI: 10.1083/jcb.201906130] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/08/2019] [Accepted: 12/23/2019] [Indexed: 02/06/2023] Open
Abstract
Phosphatidylinositol (PI) is an essential structural component of eukaryotic membranes that also serves as the common precursor for polyphosphoinositide (PPIn) lipids. Despite the recognized importance of PPIn species for signal transduction and membrane homeostasis, there is still a limited understanding of the relationship between PI availability and the turnover of subcellular PPIn pools. To address these shortcomings, we established a molecular toolbox for investigations of PI distribution within intact cells by exploiting the properties of a bacterial enzyme, PI-specific PLC (PI-PLC). Using these tools, we find a minor presence of PI in membranes of the ER, as well as a general enrichment within the cytosolic leaflets of the Golgi complex, peroxisomes, and outer mitochondrial membrane, but only detect very low steady-state levels of PI within the plasma membrane (PM) and endosomes. Kinetic studies also demonstrate the requirement for sustained PI supply from the ER for the maintenance of monophosphorylated PPIn species within the PM, Golgi complex, and endosomal compartments.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Yeun Ju Kim
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Jana Humpolickova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Andrea Eisenreichova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Nivedita Sengupta
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Daniel J Toth
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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17
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Experience-dependent plasticity in an innate social behavior is mediated by hypothalamic LTP. Proc Natl Acad Sci U S A 2020; 117:25789-25799. [PMID: 32973099 PMCID: PMC7568289 DOI: 10.1073/pnas.2011782117] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Modification of instinctive behaviors occurs through experience, yet the mechanisms through which this happens have remained largely unknown. Recent studies have shown that potentiation of aggression, an innate behavior, can occur through repeated winning of aggressive encounters. Here, we show that synaptic plasticity at a specific excitatory input to a hypothalamic cell population is correlated with, and required for, the expression of increasingly higher levels of aggressive behavior following aggressive experience. We additionally show that the amplitude and persistence of long-term potentiation at this synapse are influenced by serum testosterone, administration of which can normalize individual differences in the expression of intermale aggression among genetically identical mice. All animals can perform certain survival behaviors without prior experience, suggesting a “hard wiring” of underlying neural circuits. Experience, however, can alter the expression of innate behaviors. Where in the brain and how such plasticity occurs remains largely unknown. Previous studies have established the phenomenon of “aggression training,” in which the repeated experience of winning successive aggressive encounters across multiple days leads to increased aggressiveness. Here, we show that this procedure also leads to long-term potentiation (LTP) at an excitatory synapse, derived from the posteromedial part of the amygdalohippocampal area (AHiPM), onto estrogen receptor 1-expressing (Esr1+) neurons in the ventrolateral subdivision of the ventromedial hypothalamus (VMHvl). We demonstrate further that the optogenetic induction of such LTP in vivo facilitates, while optogenetic long-term depression (LTD) diminishes, the behavioral effect of aggression training, implying a causal role for potentiation at AHiPM→VMHvlEsr1 synapses in mediating the effect of this training. Interestingly, ∼25% of inbred C57BL/6 mice fail to respond to aggression training. We show that these individual differences are correlated both with lower levels of testosterone, relative to mice that respond to such training, and with a failure to exhibit LTP after aggression training. Administration of exogenous testosterone to such nonaggressive mice restores both behavioral and physiological plasticity. Together, these findings reveal that LTP at a hypothalamic circuit node mediates a form of experience-dependent plasticity in an innate social behavior, and a potential hormone-dependent basis for individual differences in such plasticity among genetically identical mice.
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18
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Song Y, Zhang X, Shen Z, Yang W, Wei J, Li S, Wang X, Li X, He Q, Zhang S, Zhang Q, Gao B. Improving Brightness and Stability of Si-Rhodamine for Super-Resolution Imaging of Mitochondria in Living Cells. Anal Chem 2020; 92:12137-12144. [PMID: 32844652 DOI: 10.1021/acs.analchem.9b04926] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Photostable and bright organic dyes emitting in the near-infrared region are highly desirable for long-term dynamic bioimaging. Herein, we report a synthetic approach to build novel methoxy modified Si-rhodamine (SiRMO) dyes by introducing the methoxybenzene on the xanthene moiety. The brightness of SiRMO increased from 2300 M-1 cm-1 (SiRMO-0) to 49000 M-1 cm-1 (SiRMO-2) when the substituent 2,5-dimethoxybenzene was replaced with 2,6-dimethoxybenzene. Moreover, the stability of SiRMO-2 was significantly improved due to the steric hindrance protection of the two methoxy groups on the ninth carbon atom of the xanthene. After fast cellular uptake, the SiRMO dyes selectively stained the mitochondria with a low background in live cultured cells and primary neurons. The high brightness and stability of SiRMO-2 significantly improved the capability of monitoring mitochondria dynamic processes in living cells under super-resolution conditions. Moreover, with the fluorescence nanoscopy techniques, we observed the structure of mitochondrial cristae and mitochondria fission, fusion, and apoptosis with a high temporal resolution. Under two-photon illumination, SiRMO-2 showed also enhanced two-photon brightness and stability, which are important for imaging in thick tissue.
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Affiliation(s)
- Yifang Song
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Xue Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Zixin Shen
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Wei Yang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Juandi Wei
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Shiyi Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Xu Wang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Xinwei Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Qihua He
- Peking University Health Science Center, Beijing 100191, China
| | - Shuchen Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Qisheng Zhang
- Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Baoxiang Gao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), and Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
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19
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Ohata H, Shiokawa D, Obata Y, Sato A, Sakai H, Fukami M, Hara W, Taniguchi H, Ono M, Nakagama H, Okamoto K. NOX1-Dependent mTORC1 Activation via S100A9 Oxidation in Cancer Stem-like Cells Leads to Colon Cancer Progression. Cell Rep 2020; 28:1282-1295.e8. [PMID: 31365870 DOI: 10.1016/j.celrep.2019.06.085] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 02/15/2019] [Accepted: 06/22/2019] [Indexed: 12/28/2022] Open
Abstract
Cancer stem cells (CSCs) are associated with the refractory nature of cancer, and elucidating the targetable pathways for CSCs is crucial for devising innovative antitumor therapies. We find that the proliferation of CSC-enriched colon spheroids from clinical specimen is dependent on mTORC1 kinase, which is activated by reactive oxygen species (ROS) produced by NOX1, an NADPH oxidase. In the spheroid-derived xenograft tumors, NOX1 is preferentially expressed in LGR5-positive cells. Dependence on NOX1 expression or mTOR kinase activity is corroborated in the xenograft tumors and mouse colon cancer-derived organoids. NOX1 co-localizes with mTORC1 in VPS41-/VPS39-positive lysosomes, where mTORC1 binds to S100A9, a member of S100 calcium binding proteins, in a NOX1-produced ROS-dependent manner. S100A9 is oxidized by NOX1-produced ROS, which facilitates binding to mTORC1 and its activation. We propose that NOX1-dependent mTORC1 activation via S100A9 oxidation in VPS41-/VPS39-positive lysosomes is crucial for colon CSC proliferation and colon cancer progression.
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Affiliation(s)
- Hirokazu Ohata
- Division of Cancer Differentiation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Daisuke Shiokawa
- Division of Cancer Differentiation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Yuuki Obata
- Division of Cancer Differentiation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Ai Sato
- Division of Cancer Differentiation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Hiroaki Sakai
- Division of Cancer Differentiation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Mayu Fukami
- Division of Cancer Differentiation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Wakako Hara
- Division of Cancer Differentiation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Hirokazu Taniguchi
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Masaya Ono
- Department of Clinical Proteomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Hitoshi Nakagama
- National Cancer Center, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Koji Okamoto
- Division of Cancer Differentiation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
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20
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Wen L, Fan Z, Mikulski Z, Ley K. Imaging of the immune system - towards a subcellular and molecular understanding. J Cell Sci 2020; 133:133/5/jcs234922. [PMID: 32139598 DOI: 10.1242/jcs.234922] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Immune responses involve many types of leukocytes that traffic to the site of injury, recognize the insult and respond appropriately. Imaging of the immune system involves a set of methods and analytical tools that are used to visualize immune responses at the cellular and molecular level as they occur in real time. We will review recent and emerging technological advances in optical imaging, and their application to understanding the molecular and cellular responses of neutrophils, macrophages and lymphocytes. Optical live-cell imaging provides deep mechanistic insights at the molecular, cellular, tissue and organism levels. Live-cell imaging can capture quantitative information in real time at subcellular resolution with minimal phototoxicity and repeatedly in the same living cells or in accessible tissues of the living organism. Advanced FRET probes allow tracking signaling events in live cells. Light-sheet microscopy allows for deeper tissue penetration in optically clear samples, enriching our understanding of the higher-level organization of the immune response. Super-resolution microscopy offers insights into compartmentalized signaling at a resolution beyond the diffraction limit, approaching single-molecule resolution. This Review provides a current perspective on live-cell imaging in vitro and in vivo with a focus on the assessment of the immune system.
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Affiliation(s)
- Lai Wen
- Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
| | - Zhichao Fan
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Zbigniew Mikulski
- Microscopy Core Facility, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
| | - Klaus Ley
- Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA .,Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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21
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Li YB, Xu R, Liu C, Shen N, Han LB, Tang D. Magnaporthe oryzae fimbrin organizes actin networks in the hyphal tip during polar growth and pathogenesis. PLoS Pathog 2020; 16:e1008437. [PMID: 32176741 PMCID: PMC7098657 DOI: 10.1371/journal.ppat.1008437] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 03/26/2020] [Accepted: 02/26/2020] [Indexed: 01/19/2023] Open
Abstract
Magnaporthe oryzae causes rice blast disease, but little is known about the dynamic restructuring of the actin cytoskeleton during its polarized tip growth and pathogenesis. Here, we used super-resolution live-cell imaging to investigate the dynamic organization of the actin cytoskeleton in M. oryzae during hyphal tip growth and pathogenesis. We observed a dense actin network at the apical region of the hyphae and actin filaments originating from the Spitzenkörper (Spk, the organizing center for hyphal growth and development) that formed branched actin bundles radiating to the cell membrane. The actin cross-linking protein Fimbrin (MoFim1) helps organize this actin distribution. MoFim1 localizes to the actin at the subapical collar, the actin bundles, and actin at the Spk. Knockout of MoFim1 resulted in impaired Spk maintenance and reduced actin bundle formation, preventing polar growth, vesicle transport, and the expansion of hyphae in plant cells. Finally, transgenic rice (Oryza sativa) expressing RNA hairpins targeting MoFim1 exhibited improved resistance to M. oryzae infection, indicating that MoFim1 represents an excellent candidate for M. oryzae control. These results reveal the dynamics of actin assembly in M. oryzae during hyphal tip development and pathogenesis, and they suggest a mechanism in which MoFim1 organizes such actin networks.
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Affiliation(s)
- Yuan-Bao Li
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Rui Xu
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chengyu Liu
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ningning Shen
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Li-Bo Han
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Dingzhong Tang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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22
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Deroubaix A, Moahla B, Penny C. Monitoring of intracellular localization of Hepatitis B virus P22 protein using Laser Scanning Confocal Microscopy and Airyscan. Microsc Res Tech 2020; 83:499-506. [PMID: 31926041 DOI: 10.1002/jemt.23438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/03/2019] [Accepted: 12/27/2019] [Indexed: 11/09/2022]
Abstract
The aim of this study was to assess nucleo-cytoplasmic protein localization to better understand the exact intracellular localization of viral proteins involved with infections. Having determined the general protein localization of hepatitis B virus P22 precore protein, the aim was to more specifically resolve its intracellular organization. This was done using both laser scanning microscopy and Airyscan techniques. Using a 63× objective, the resolution obtained with Airyscan was increased by 1.5-fold as compared to confocal microscopy (p value <.00001).
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Affiliation(s)
- Aurélie Deroubaix
- Life Sciences Imaging Facility, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,HVDRU, School of Clinical Medicine, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bongani Moahla
- HVDRU, School of Clinical Medicine, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Clement Penny
- Life Sciences Imaging Facility, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Oncology Division, School of Clinical Medicine, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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23
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Lindquist NC, de Albuquerque CDL, Sobral-Filho RG, Paci I, Brolo AG. High-speed imaging of surface-enhanced Raman scattering fluctuations from individual nanoparticles. NATURE NANOTECHNOLOGY 2019; 14:981-987. [PMID: 31527841 DOI: 10.1038/s41565-019-0535-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/23/2019] [Indexed: 05/06/2023]
Abstract
The concept of plasmonic hotspots is central to the interpretation of the surface-enhanced Raman scattering (SERS) effect. Although plasmonic hotspots are generally portrayed as static features, single-molecule SERS (SM-SERS) is marked by characteristic time-dependent fluctuations in signal intensity. The origin of those fluctuations can be assigned to a variety of dynamic and complex processes, including molecular adsorption or desorption, surface diffusion, molecular reorientation and metal surface reconstruction. Since each of these mechanisms simultaneously contributes to a fluctuating SERS signal, probing their relative impact in SM-SERS remains an experimental challenge. Here, we introduce a super-resolution imaging technique with an acquisition rate of 800,000 frames per second to probe the spatial and temporal features of the SM-SERS fluctuations from single silver nanoshells. The technique has a spatial resolution of ~7 nm. The images reveal short ~10 µs scattering events localized in various regions on a single nanoparticle. Remarkably, even a fully functionalized nanoparticle was 'dark' more than 98% of the time. The sporadic SERS emission suggests a transient hotspot formation mechanism driven by a random reconstruction of the metallic surface, an effect that dominates over any plasmonic resonance of the particle itself. Our results provide the SERS community with a high-speed experimental approach to study the fast dynamic properties of SM-SERS hotspots in typical room-temperature experimental conditions, with possible implications in catalysis and sensing.
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Affiliation(s)
- Nathan C Lindquist
- Department of Physics and Engineering, Bethel University, St Paul, MN, USA
| | - Carlos Diego L de Albuquerque
- Department of Chemistry, University of Victoria, Victoria, British Columbia, Canada
- Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, Victoria, British Columbia, Canada
| | - Regivaldo G Sobral-Filho
- Department of Chemistry, University of Victoria, Victoria, British Columbia, Canada
- Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, Victoria, British Columbia, Canada
| | - Irina Paci
- Department of Chemistry, University of Victoria, Victoria, British Columbia, Canada
- Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, Victoria, British Columbia, Canada
| | - Alexandre G Brolo
- Department of Chemistry, University of Victoria, Victoria, British Columbia, Canada.
- Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, Victoria, British Columbia, Canada.
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24
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Trivedi P, Palomba F, Niedzialkowska E, Digman MA, Gratton E, Stukenberg PT. The inner centromere is a biomolecular condensate scaffolded by the chromosomal passenger complex. Nat Cell Biol 2019; 21:1127-1137. [PMID: 31481798 DOI: 10.1038/s41556-019-0376-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 07/19/2019] [Indexed: 12/19/2022]
Abstract
The inner centromere is a region on every mitotic chromosome that enables specific biochemical reactions that underlie properties, such as the maintenance of cohesion, the regulation of kinetochores and the assembly of specialized chromatin, that can resist microtubule pulling forces. The chromosomal passenger complex (CPC) is abundantly localized to the inner centromeres and it is unclear whether it is involved in non-kinase activities that contribute to the generation of these unique chromatin properties. We find that the borealin subunit of the CPC drives phase separation of the CPC in vitro at concentrations that are below those found on the inner centromere. We also provide strong evidence that the CPC exists in a phase-separated state at the inner centromere. CPC phase separation is required for its inner-centromere localization and function during mitosis. We suggest that the CPC combines phase separation, kinase and histone code-reading activities to enable the formation of a chromatin body with unique biochemical activities at the inner centromere.
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Affiliation(s)
- Prasad Trivedi
- Department of Cell Biology, University of Virginia, School of Medicine, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, USA
| | - Francesco Palomba
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Ewa Niedzialkowska
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, USA
| | - Michelle A Digman
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Enrico Gratton
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - P Todd Stukenberg
- Department of Cell Biology, University of Virginia, School of Medicine, Charlottesville, VA, USA. .,Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, USA.
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25
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Fluorescence fluctuation spectroscopy: an invaluable microscopy tool for uncovering the biophysical rules for navigating the nuclear landscape. Biochem Soc Trans 2019; 47:1117-1129. [DOI: 10.1042/bst20180604] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Nuclear architecture is fundamental to the manner by which molecules traverse the nucleus. The nucleoplasm is a crowded environment where dynamic rearrangements in local chromatin compaction locally redefine the space accessible toward nuclear protein diffusion. Here, we review a suite of methods based on fluorescence fluctuation spectroscopy (FFS) and how they have been employed to interrogate chromatin organization, as well as the impact this structural framework has on nuclear protein target search. From first focusing on a set of studies that apply FFS to an inert fluorescent tracer diffusing inside the nucleus of a living cell, we demonstrate the capacity of this technology to measure the accessibility of the nucleoplasm. Then with a baseline understanding of the exploration volume available to nuclear proteins during target search, we review direct applications of FFS to fluorescently labeled transcription factors (TFs). FFS can detect changes in TF mobility due to DNA binding, as well as the formation of TF complexes via changes in brightness due to oligomerization. Collectively, we find that FFS-based methods can uncover how nuclear proteins in general navigate the nuclear landscape.
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