1
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Strickland MR, Rau MJ, Summers B, Basore K, Wulf J, Jiang H, Chen Y, Ulrich JD, Randolph GJ, Zhang R, Fitzpatrick JAJ, Cashikar AG, Holtzman DM. Apolipoprotein E secreted by astrocytes forms antiparallel dimers in discoidal lipoproteins. Neuron 2024; 112:1100-1109.e5. [PMID: 38266643 PMCID: PMC10994765 DOI: 10.1016/j.neuron.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/24/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The Apolipoprotein E gene (APOE) is of great interest due to its role as a risk factor for late-onset Alzheimer's disease. ApoE is secreted by astrocytes in the central nervous system in high-density lipoprotein (HDL)-like lipoproteins. Structural models of lipidated ApoE of high resolution could aid in a mechanistic understanding of how ApoE functions in health and disease. Using monoclonal Fab and F(ab')2 fragments, we characterize the structure of lipidated ApoE on astrocyte-secreted lipoproteins. Our results provide support for the "double-belt" model of ApoE in nascent discoidal HDL-like lipoproteins, where two ApoE proteins wrap around the nanodisc in an antiparallel conformation. We further show that lipidated, recombinant ApoE accurately models astrocyte-secreted ApoE lipoproteins. Cryogenic electron microscopy of recombinant lipidated ApoE further supports ApoE adopting antiparallel dimers in nascent discoidal lipoproteins.
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Affiliation(s)
| | - Michael J Rau
- Washington University Center for Cellular Imaging, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Brock Summers
- Washington University Center for Cellular Imaging, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Katherine Basore
- Washington University Center for Cellular Imaging, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - John Wulf
- Washington University Center for Cellular Imaging, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Hong Jiang
- Department of Neurology, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Yun Chen
- Department of Neurology, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Department of Pathology and Immunology, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Jason D Ulrich
- Department of Neurology, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Knight Alzheimer's Disease Research Center, 4488 Forest Park Ave., St. Louis, MO 63108, USA
| | - Gwendalyn J Randolph
- Department of Pathology and Immunology, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Anil G Cashikar
- Hope Center for Neurological Disorders, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Department of Psychiatry, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Taylor Family institute for Innovative Psychiatric Research, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - David M Holtzman
- Department of Neurology, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Knight Alzheimer's Disease Research Center, 4488 Forest Park Ave., St. Louis, MO 63108, USA.
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2
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Dhavale DD, Barclay AM, Borcik CG, Basore K, Berthold DA, Gordon IR, Liu J, Milchberg MH, O'Shea JY, Rau MJ, Smith Z, Sen S, Summers B, Smith J, Warmuth OA, Perrin RJ, Perlmutter JS, Chen Q, Fitzpatrick JAJ, Schwieters CD, Tajkhorshid E, Rienstra CM, Kotzbauer PT. Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue. Nat Commun 2024; 15:2750. [PMID: 38553463 PMCID: PMC10980826 DOI: 10.1038/s41467-024-46832-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
The defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation of alpha-synuclein (Asyn) fibrils in Lewy bodies and Lewy neurites. Here we develop and validate a method to amplify Asyn fibrils extracted from LBD postmortem tissue samples and use solid state nuclear magnetic resonance (SSNMR) studies to determine atomic resolution structure. Amplified LBD Asyn fibrils comprise a mixture of single protofilament and two protofilament fibrils with very low twist. The protofilament fold is highly similar to the fold determined by a recent cryo-electron microscopy study for a minority population of twisted single protofilament fibrils extracted from LBD tissue. These results expand the structural characterization of LBD Asyn fibrils and approaches for studying disease mechanisms, imaging agents and therapeutics targeting Asyn.
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Affiliation(s)
- Dhruva D Dhavale
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Alexander M Barclay
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Collin G Borcik
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Katherine Basore
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Deborah A Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Isabelle R Gordon
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jialu Liu
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Moses H Milchberg
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jennifer Y O'Shea
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Michael J Rau
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Zachary Smith
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Soumyo Sen
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Brock Summers
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John Smith
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Owen A Warmuth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Richard J Perrin
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joel S Perlmutter
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Radiology, Neuroscience, Physical Therapy and Occupational Therapy, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - James A J Fitzpatrick
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Charles D Schwieters
- Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Chad M Rienstra
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Paul T Kotzbauer
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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Li J, Moretti F, Hidvegi T, Sviben S, Fitzpatrick JAJ, Sundaramoorthi H, Pak SC, Silverman GA, Knapp B, Filipuzzi I, Alford J, Reece-Hoyes J, Nigsch F, Murphy LO, Nyfeler B, Perlmutter DH. Multiple Genes Core to ERAD, Macroautophagy and Lysosomal Degradation Pathways Participate in the Proteostasis Response in α1-Antitrypsin Deficiency. Cell Mol Gastroenterol Hepatol 2024; 17:1007-1024. [PMID: 38336172 PMCID: PMC11053228 DOI: 10.1016/j.jcmgh.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND & AIMS In the classic form of α1-antitrypsin deficiency (ATD), the misfolded α1-antitrypsin Z (ATZ) variant accumulates in the endoplasmic reticulum (ER) of liver cells. A gain-of-function proteotoxic mechanism is responsible for chronic liver disease in a subgroup of homozygotes. Proteostatic response pathways, including conventional endoplasmic reticulum-associated degradation and autophagy, have been proposed as the mechanisms that allow cellular adaptation and presumably protection from the liver disease phenotype. Recent studies have concluded that a distinct lysosomal pathway called endoplasmic reticulum-to-lysosome completely supplants the role of the conventional macroautophagy pathway in degradation of ATZ. Here, we used several state-of-the-art approaches to characterize the proteostatic responses more fully in cellular systems that model ATD. METHODS We used clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing coupled to a cell selection step by fluorescence-activated cell sorter to perform screening for proteostasis genes that regulate ATZ accumulation and combined that with selective genome editing in 2 other model systems. RESULTS Endoplasmic reticulum-associated degradation genes are key early regulators and multiple autophagy genes, from classic as well as from ER-to-lysosome and other newly described ER-phagy pathways, participate in degradation of ATZ in a manner that is temporally regulated and evolves as ATZ accumulation persists. Time-dependent changes in gene expression are accompanied by specific ultrastructural changes including dilation of the ER, formation of globular inclusions, budding of autophagic vesicles, and alterations in the overall shape and component parts of mitochondria. CONCLUSIONS Macroautophagy is a critical component of the proteostasis response to cellular ATZ accumulation and it becomes more important over time as ATZ synthesis continues unabated. Multiple subtypes of macroautophagy and nonautophagic lysosomal degradative pathways are needed to respond to the high concentrations of misfolded protein that characterizes ATD and these pathways are attractive candidates for genetic variants that predispose to the hepatic phenotype.
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Affiliation(s)
- Jie Li
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | | | - Tunda Hidvegi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Sanja Sviben
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, Missouri
| | - James A J Fitzpatrick
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, Missouri; Department of Cell Biology, Washington University School of Medicine, St. Louis, Missouri; Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri
| | | | - Stephen C Pak
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Gary A Silverman
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Britta Knapp
- Novartis Biomedical Research, Basel, Switzerland
| | | | - John Alford
- Novartis Biomedical Research, Cambridge, Massachusetts
| | | | | | - Leon O Murphy
- Novartis Biomedical Research, Cambridge, Massachusetts
| | - Beat Nyfeler
- Novartis Biomedical Research, Basel, Switzerland
| | - David H Perlmutter
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri.
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4
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Dalal V, Arcario MJ, Petroff JT, Tan BK, Dietzen NM, Rau MJ, Fitzpatrick JAJ, Brannigan G, Cheng WWL. Lipid nanodisc scaffold and size alter the structure of a pentameric ligand-gated ion channel. Nat Commun 2024; 15:25. [PMID: 38167383 PMCID: PMC10762164 DOI: 10.1038/s41467-023-44366-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Lipid nanodiscs have become a standard tool for studying membrane proteins, including using single particle cryo-electron microscopy (cryo-EM). We find that reconstituting the pentameric ligand-gated ion channel (pLGIC), Erwinia ligand-gated ion channel (ELIC), in different nanodiscs produces distinct structures by cryo-EM. The effect of the nanodisc on ELIC structure extends to the extracellular domain and agonist binding site. Additionally, molecular dynamic simulations indicate that nanodiscs of different size impact ELIC structure and that the nanodisc scaffold directly interacts with ELIC. These findings suggest that the nanodisc plays a crucial role in determining the structure of pLGICs, and that reconstitution of ion channels in larger nanodiscs may better approximate a lipid membrane environment.
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Affiliation(s)
- Vikram Dalal
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Mark J Arcario
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - John T Petroff
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Brandon K Tan
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Noah M Dietzen
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Michael J Rau
- Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, USA
| | - James A J Fitzpatrick
- Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, USA
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
- Department of Physics, Rutgers University, Camden, NJ, USA
| | - Wayland W L Cheng
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.
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5
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Deveryshetty J, Chadda R, Mattice JR, Karunakaran S, Rau MJ, Basore K, Pokhrel N, Englander N, Fitzpatrick JAJ, Bothner B, Antony E. Yeast Rad52 is a homodecamer and possesses BRCA2-like bipartite Rad51 binding modes. Nat Commun 2023; 14:6215. [PMID: 37798272 PMCID: PMC10556141 DOI: 10.1038/s41467-023-41993-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
Homologous recombination (HR) is an essential double-stranded DNA break repair pathway. In HR, Rad52 facilitates the formation of Rad51 nucleoprotein filaments on RPA-coated ssDNA. Here, we decipher how Rad52 functions using single-particle cryo-electron microscopy and biophysical approaches. We report that Rad52 is a homodecameric ring and each subunit possesses an ordered N-terminal and disordered C-terminal half. An intrinsic structural asymmetry is observed where a few of the C-terminal halves interact with the ordered ring. We describe two conserved charged patches in the C-terminal half that harbor Rad51 and RPA interacting motifs. Interactions between these patches regulate ssDNA binding. Surprisingly, Rad51 interacts with Rad52 at two different bindings sites: one within the positive patch in the disordered C-terminus and the other in the ordered ring. We propose that these features drive Rad51 nucleation onto a single position on the DNA to promote formation of uniform pre-synaptic Rad51 filaments in HR.
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Affiliation(s)
- Jaigeeth Deveryshetty
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Rahul Chadda
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Jenna R Mattice
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Simrithaa Karunakaran
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Michael J Rau
- Center for Cellular Imaging, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Katherine Basore
- Center for Cellular Imaging, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
- Aera Therapeutics, Boston, MA, USA
| | - Noah Englander
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - James A J Fitzpatrick
- Center for Cellular Imaging, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA.
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6
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Leid J, Gray R, Rakita P, Koenig AL, Tripathy R, Fitzpatrick JAJ, Kaufman C, Solnica-Krezel L, Lavine KJ. Deletion of taf1 and taf5 in zebrafish capitulate cardiac and craniofacial abnormalities associated with TAFopathies through perturbations in metabolism. Biol Open 2023; 12:bio059905. [PMID: 37746814 PMCID: PMC10354717 DOI: 10.1242/bio.059905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/16/2023] [Indexed: 09/26/2023] Open
Abstract
Intellectual disability is a neurodevelopmental disorder that affects 2-3% of the general population. Syndromic forms of intellectual disability frequently have a genetic basis and are often accompanied by additional developmental anomalies. Pathogenic variants in components of TATA-binding protein associated factors (TAFs) have recently been identified in a subset of patients with intellectual disability, craniofacial hypoplasia, and congenital heart disease. This syndrome has been termed as a TAFopathy and includes mutations in TATA binding protein (TBP), TAF1, TAF2, and TAF6. The underlying mechanism by which TAFopathies give rise to neurodevelopmental, craniofacial, and cardiac abnormalities remains to be defined. Through a forward genetic screen in zebrafish, we have recovered a recessive mutant phenotype characterized by craniofacial hypoplasia, ventricular hypoplasia, heart failure at 96 h post-fertilization and lethality, and show it is caused by a nonsense mutation in taf5. CRISPR/CAS9 mediated gene editing revealed that these defects where phenocopied by mutations in taf1 and taf5. Mechanistically, taf5-/- zebrafish displayed misregulation in metabolic gene expression and metabolism as evidenced by RNA sequencing, respiration assays, and metabolite studies. Collectively, these findings suggest that the TAF complex may contribute to neurologic, craniofacial, and cardiac development through regulation of metabolism.
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Affiliation(s)
- Jamison Leid
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ryan Gray
- Departments of Nutritional Sciences, Dell Pediatrics Research Institute, University of Texas at Austin, Austin, TX 78723, USA
| | - Peter Rakita
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew L. Koenig
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rohan Tripathy
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James A. J. Fitzpatrick
- Departments of Neuroscience and Cell Biology, Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Charles Kaufman
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kory J. Lavine
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Immunology and Pathology, Washington University School of Medicine, St. Louis, MO 63110, USA
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7
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Sun Z, Kwon JS, Ren Y, Chen S, Cates K, Lu X, Walker CK, Karahan H, Sviben S, Fitzpatrick JAJ, Valdez C, Houlden H, Karch CM, Bateman RJ, Sato C, Mennerick SJ, Diamond MI, Kim J, Tanzi RE, Holtzman DM, Yoo AS. Endogenous recapitulation of Alzheimer's disease neuropathology through human 3D direct neuronal reprogramming. bioRxiv 2023:2023.05.24.542155. [PMID: 37292658 PMCID: PMC10245934 DOI: 10.1101/2023.05.24.542155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder that primarily affects elderly individuals, and is characterized by hallmark neuronal pathologies including extracellular amyloid-β (Aβ) plaque deposition, intracellular tau tangles, and neuronal death. However, recapitulating these age-associated neuronal pathologies in patient-derived neurons has remained a significant challenge, especially for late-onset AD (LOAD), the most common form of the disorder. Here, we applied the high efficiency microRNA-mediated direct neuronal reprogramming of fibroblasts from AD patients to generate cortical neurons in three-dimensional (3D) Matrigel and self-assembled neuronal spheroids. Our findings indicate that neurons and spheroids reprogrammed from both autosomal dominant AD (ADAD) and LOAD patients exhibited AD-like phenotypes linked to neurons, including extracellular Aβ deposition, dystrophic neurites with hyperphosphorylated, K63-ubiquitin-positive, seed-competent tau, and spontaneous neuronal death in culture. Moreover, treatment with β- or γ-secretase inhibitors in LOAD patient-derived neurons and spheroids before Aβ deposit formation significantly lowered Aβ deposition, as well as tauopathy and neurodegeneration. However, the same treatment after the cells already formed Aβ deposits only had a mild effect. Additionally, inhibiting the synthesis of age-associated retrotransposable elements (RTEs) by treating LOAD neurons and spheroids with the reverse transcriptase inhibitor, lamivudine, alleviated AD neuropathology. Overall, our results demonstrate that direct neuronal reprogramming of AD patient fibroblasts in a 3D environment can capture age-related neuropathology and reflect the interplay between Aβ accumulation, tau dysregulation, and neuronal death. Moreover, miRNA-based 3D neuronal conversion provides a human-relevant AD model that can be used to identify compounds that can potentially ameliorate AD-associated pathologies and neurodegeneration.
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8
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Hou J, Zhou Y, Cai Z, Terekhova M, Swain A, Andhey PS, Guimaraes RM, Ulezko Antonova A, Qiu T, Sviben S, Strout G, Fitzpatrick JAJ, Chen Y, Gilfillan S, Kim DH, Van Dyken SJ, Artyomov MN, Colonna M. Transcriptomic atlas and interaction networks of brain cells in mouse CNS demyelination and remyelination. Cell Rep 2023; 42:112293. [PMID: 36952346 PMCID: PMC10511667 DOI: 10.1016/j.celrep.2023.112293] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/04/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
Demyelination is a hallmark of multiple sclerosis, leukoencephalopathies, cerebral vasculopathies, and several neurodegenerative diseases. The cuprizone mouse model is widely used to simulate demyelination and remyelination occurring in these diseases. Here, we present a high-resolution single-nucleus RNA sequencing (snRNA-seq) analysis of gene expression changes across all brain cells in this model. We define demyelination-associated oligodendrocytes (DOLs) and remyelination-associated MAFBhi microglia, as well as astrocytes and vascular cells with signatures of altered metabolism, oxidative stress, and interferon response. Furthermore, snRNA-seq provides insights into how brain cell types connect and interact, defining complex circuitries that impact demyelination and remyelination. As an explicative example, perturbation of microglia caused by TREM2 deficiency indirectly impairs the induction of DOLs. Altogether, this study provides a rich resource for future studies investigating mechanisms underlying demyelinating diseases.
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Affiliation(s)
- Jinchao Hou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yingyue Zhou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zhangying Cai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marina Terekhova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amanda Swain
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Prabhakar S Andhey
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rafaela M Guimaraes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Ribeirão Preto Medical School, University of São Paulo - Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Alina Ulezko Antonova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tian Qiu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sanja Sviben
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gregory Strout
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA; Departments of Cell Biology and Physiology and Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Yun Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan Gilfillan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Do-Hyun Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven J Van Dyken
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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9
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He Z, Zhao Y, Rau MJ, Fitzpatrick JAJ, Sah R, Hu H, Yuan P. Structural and functional analysis of human pannexin 2 channel. Nat Commun 2023; 14:1712. [PMID: 36973289 PMCID: PMC10043284 DOI: 10.1038/s41467-023-37413-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
The pannexin 2 channel (PANX2) participates in multiple physiological processes including skin homeostasis, neuronal development, and ischemia-induced brain injury. However, the molecular basis of PANX2 channel function remains largely unknown. Here, we present a cryo-electron microscopy structure of human PANX2, which reveals pore properties contrasting with those of the intensely studied paralog PANX1. The extracellular selectivity filter, defined by a ring of basic residues, more closely resembles that of the distantly related volume-regulated anion channel (VRAC) LRRC8A, rather than PANX1. Furthermore, we show that PANX2 displays a similar anion permeability sequence as VRAC, and that PANX2 channel activity is inhibited by a commonly used VRAC inhibitor, DCPIB. Thus, the shared channel properties between PANX2 and VRAC may complicate dissection of their cellular functions through pharmacological manipulation. Collectively, our structural and functional analysis provides a framework for development of PANX2-specific reagents that are needed for better understanding of channel physiology and pathophysiology.
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Affiliation(s)
- Zhihui He
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
| | - Yonghui Zhao
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, Saint Louis, MO, USA
| | - Michael J Rau
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, USA
| | - James A J Fitzpatrick
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Biomedical Engineering, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Rajan Sah
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Internal Medicine, Cardiovascular Division, Washington University School of Medicine, Saint Louis, MO, USA
| | - Hongzhen Hu
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.
- Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA.
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA.
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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10
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Pan S, Yang PH, DeFreitas D, Ramagiri S, Bayguinov PO, Hacker CD, Snyder AZ, Wilborn J, Huang H, Koller GM, Raval DK, Halupnik GL, Sviben S, Achilefu S, Tang R, Haller G, Quirk JD, Fitzpatrick JAJ, Esakky P, Strahle JM. Gold nanoparticle-enhanced X-ray microtomography of the rodent reveals region-specific cerebrospinal fluid circulation in the brain. Nat Commun 2023; 14:453. [PMID: 36707519 PMCID: PMC9883388 DOI: 10.1038/s41467-023-36083-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/12/2023] [Indexed: 01/28/2023] Open
Abstract
Cerebrospinal fluid (CSF) is essential for the development and function of the central nervous system (CNS). However, the brain and its interstitium have largely been thought of as a single entity through which CSF circulates, and it is not known whether specific cell populations within the CNS preferentially interact with the CSF. Here, we develop a technique for CSF tracking, gold nanoparticle-enhanced X-ray microtomography, to achieve micrometer-scale resolution visualization of CSF circulation patterns during development. Using this method and subsequent histological analysis in rodents, we identify previously uncharacterized CSF pathways from the subarachnoid space (particularly the basal cisterns) that mediate CSF-parenchymal interactions involving 24 functional-anatomic cell groupings in the brain and spinal cord. CSF distribution to these areas is largely restricted to early development and is altered in posthemorrhagic hydrocephalus. Our study also presents particle size-dependent CSF circulation patterns through the CNS including interaction between neurons and small CSF tracers, but not large CSF tracers. These findings have implications for understanding the biological basis of normal brain development and the pathogenesis of a broad range of disease states, including hydrocephalus.
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Affiliation(s)
- Shelei Pan
- Department of Neurosurgery, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Peter H Yang
- Department of Neurosurgery, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Dakota DeFreitas
- Department of Neurosurgery, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Sruthi Ramagiri
- Department of Neurosurgery, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Peter O Bayguinov
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Carl D Hacker
- Department of Neurosurgery, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Abraham Z Snyder
- Department of Radiology, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Neurology, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Jackson Wilborn
- Department of Neurosurgery, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Hengbo Huang
- Department of Radiology, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Gretchen M Koller
- Department of Neurosurgery, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Dhvanii K Raval
- Department of Neurosurgery, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Grace L Halupnik
- Department of Neurosurgery, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Sanja Sviben
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Samuel Achilefu
- Department of Biomedical Engineering, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Rui Tang
- Department of Radiology, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Gabriel Haller
- Department of Neurosurgery, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Neurology, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - James D Quirk
- Department of Radiology, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Neuroscience, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Prabagaran Esakky
- Department of Neurosurgery, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Jennifer M Strahle
- Department of Neurosurgery, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA.
- Department of Orthopedic Surgery, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA.
- Department of Pediatrics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA.
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11
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Dhavale DD, Barclay AM, Borcik CG, Basore K, Gordon IR, Liu J, Milchberg MH, O’shea J, Rau MJ, Smith Z, Sen S, Summers B, Smith J, Warmuth OA, Chen Q, Fitzpatrick JAJ, Schwieters CD, Tajkhorshid E, Rienstra CM, Kotzbauer PT. Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue. bioRxiv 2023:2023.01.09.523303. [PMID: 36711931 PMCID: PMC9882085 DOI: 10.1101/2023.01.09.523303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation of alpha-synuclein (Asyn) fibrils in Lewy bodies and Lewy neurites. We developed and validated a novel method to amplify Asyn fibrils extracted from LBD postmortem tissue samples and used solid state nuclear magnetic resonance (SSNMR) studies to determine atomic resolution structure. Amplified LBD Asyn fibrils comprise two protofilaments with pseudo-21 helical screw symmetry, very low twist and an interface formed by antiparallel beta strands of residues 85-93. The fold is highly similar to the fold determined by a recent cryo-electron microscopy study for a minority population of twisted single protofilament fibrils extracted from LBD tissue. These results expand the structural landscape of LBD Asyn fibrils and inform further studies of disease mechanisms, imaging agents and therapeutics targeting Asyn.
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Affiliation(s)
- Dhruva D. Dhavale
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alexander M. Barclay
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Collin G. Borcik
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Katherine Basore
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Isabelle R. Gordon
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jialu Liu
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Moses H. Milchberg
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jennifer O’shea
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J. Rau
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zachary Smith
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Soumyo Sen
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Brock Summers
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John Smith
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Owen A. Warmuth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - James A. J. Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Charles D. Schwieters
- Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chad M. Rienstra
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53706 USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul T. Kotzbauer
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
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12
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Mount J, Maksaev G, Summers BT, Fitzpatrick JAJ, Yuan P. Structural basis for mechanotransduction in a potassium-dependent mechanosensitive ion channel. Nat Commun 2022; 13:6904. [PMID: 36371466 PMCID: PMC9653487 DOI: 10.1038/s41467-022-34737-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022] Open
Abstract
Mechanosensitive channels of small conductance, found in many living organisms, open under elevated membrane tension and thus play crucial roles in biological response to mechanical stress. Amongst these channels, MscK is unique in that its activation also requires external potassium ions. To better understand this dual gating mechanism by force and ligand, we elucidate distinct structures of MscK along the gating cycle using cryo-electron microscopy. The heptameric channel comprises three layers: a cytoplasmic domain, a periplasmic gating ring, and a markedly curved transmembrane domain that flattens and expands upon channel opening, which is accompanied by dilation of the periplasmic ring. Furthermore, our results support a potentially unifying mechanotransduction mechanism in ion channels depicted as flattening and expansion of the transmembrane domain.
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Affiliation(s)
- Jonathan Mount
- grid.4367.60000 0001 2355 7002Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO USA ,grid.4367.60000 0001 2355 7002Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO USA
| | - Grigory Maksaev
- grid.4367.60000 0001 2355 7002Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO USA ,grid.4367.60000 0001 2355 7002Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO USA
| | - Brock T. Summers
- grid.4367.60000 0001 2355 7002Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO USA
| | - James A. J. Fitzpatrick
- grid.4367.60000 0001 2355 7002Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO USA ,grid.4367.60000 0001 2355 7002Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Biomedical Engineering, Washington University in Saint Louis, Saint Louis, MO USA
| | - Peng Yuan
- grid.4367.60000 0001 2355 7002Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO USA ,grid.4367.60000 0001 2355 7002Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO USA
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13
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Bhadra AK, Rau MJ, Daw JA, Fitzpatrick JAJ, Weihl CC, True HL. Disease-associated mutations within the yeast DNAJB6 homolog Sis1 slow conformer-specific substrate processing and can be corrected by the modulation of nucleotide exchange factors. Nat Commun 2022; 13:4570. [PMID: 35931773 PMCID: PMC9355953 DOI: 10.1038/s41467-022-32318-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Molecular chaperones, or heat shock proteins (HSPs), protect against the toxic misfolding and aggregation of proteins. As such, mutations or deficiencies within the chaperone network can lead to disease. Dominant mutations within DNAJB6 (Hsp40)—an Hsp70 co-chaperone—lead to a protein aggregation-linked myopathy termed Limb-Girdle Muscular Dystrophy Type D1 (LGMDD1). Here, we used the yeast prion model client in conjunction with in vitro chaperone activity assays to gain mechanistic insights into the molecular basis of LGMDD1. Here, we show how mutations analogous to those found in LGMDD1 affect Sis1 (a functional homolog of human DNAJB6) function by altering the structure of client protein aggregates, interfering with the Hsp70 ATPase cycle, dimerization and substrate processing; poisoning the function of wild-type protein. These results uncover the mechanisms through which LGMDD1-associated mutations alter chaperone activity, and provide insights relevant to potential therapeutic interventions. Here the authors describe mechanisms through which analogous LGMDD1 (Limb-Girdle Muscular Dystrophy Type D1) mutations affect Sis1 (a yeast functional homolog of human DNAJB6) chaperone activity and poison the function of wild-type protein; potentially uncovering a new therapeutic route to explore.
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Affiliation(s)
- Ankan K Bhadra
- Department of Cell Biology and Physiology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA
| | - Michael J Rau
- Washington University Center for Cellular Imaging (WUCCI), Washington University School of Medicine, St. Louis, MO, USA
| | - Jil A Daw
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - James A J Fitzpatrick
- Department of Cell Biology and Physiology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA.,Washington University Center for Cellular Imaging (WUCCI), Washington University School of Medicine, St. Louis, MO, USA.,Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Conrad C Weihl
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Heather L True
- Department of Cell Biology and Physiology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA.
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14
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Feng J, Zhao Y, Xie Z, Zang K, Sviben S, Hu X, Fitzpatrick JAJ, Wen L, Liu Y, Wang T, Lawson K, Liu Q, Yan Y, Dong X, Han L, Wu GF, Kim BS, Hu H. Miswiring of Merkel cell and pruriceptive C fiber drives the itch-scratch cycle. Sci Transl Med 2022; 14:eabn4819. [PMID: 35857641 PMCID: PMC9888006 DOI: 10.1126/scitranslmed.abn4819] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Itch sensation provokes the scratch reflex to protect us from harmful stimuli in the skin. Although scratching transiently relieves acute itch through activation of mechanoreceptors, it propagates the vicious itch-scratch cycle in chronic itch by further aggravating itch over time. Although well recognized clinically, the peripheral mechanisms underlying the itch-scratch cycle remain poorly understood. Here, we show that mechanical stimulation of the skin results in activation of the Piezo2 channels on Merkel cells that pathologically promotes spontaneous itch in experimental dry skin. Three-dimensional reconstruction and immunoelectron microscopy revealed structural alteration of MRGPRA3+ pruriceptor nerve endings directed toward Merkel cells in the setting of dry skin. Our results uncover a functional miswiring mechanism under pathologic conditions, resulting in touch receptors triggering the firing of pruriceptors in the skin to drive the itch-scratch cycle.
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Affiliation(s)
- Jing Feng
- Department of Anesthesiology, The Center for the Study of Itch & Sensory Disorders, Washington University School of Medicine; Saint Louis, MO, 63110, USA.,Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, 201203, China.,Corresponding author: and
| | - Yonghui Zhao
- Department of Anesthesiology, The Center for the Study of Itch & Sensory Disorders, Washington University School of Medicine; Saint Louis, MO, 63110, USA
| | - Zili Xie
- Department of Anesthesiology, The Center for the Study of Itch & Sensory Disorders, Washington University School of Medicine; Saint Louis, MO, 63110, USA
| | - Kaikai Zang
- Department of Anesthesiology, The Center for the Study of Itch & Sensory Disorders, Washington University School of Medicine; Saint Louis, MO, 63110, USA
| | - Sanja Sviben
- Washington University Center for Cellular Imaging, Washington University School of Medicine; Saint Louis, MO, 63110, USA
| | - Xueming Hu
- Department of Anesthesiology, The Center for the Study of Itch & Sensory Disorders, Washington University School of Medicine; Saint Louis, MO, 63110, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine; Saint Louis, MO, 63110, USA
| | - Lu Wen
- Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, 201203, China
| | - Yifei Liu
- Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, 201203, China
| | - Ting Wang
- Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, 201203, China
| | - Katy Lawson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Qin Liu
- Department of Anesthesiology, The Center for the Study of Itch & Sensory Disorders, Washington University School of Medicine; Saint Louis, MO, 63110, USA
| | - Yan Yan
- Department of Surgery, Washington University School of Medicine; Saint Louis, MO, 63110, USA
| | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Liang Han
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gregory F Wu
- Department of Neurology, Washington University School of Medicine; Saint Louis, MO, 63110, USA
| | - Brian S Kim
- Department of Anesthesiology, The Center for the Study of Itch & Sensory Disorders, Washington University School of Medicine; Saint Louis, MO, 63110, USA.,Division of Dermatology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Hongzhen Hu
- Department of Anesthesiology, The Center for the Study of Itch & Sensory Disorders, Washington University School of Medicine; Saint Louis, MO, 63110, USA.,Corresponding author: and
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15
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Ruben EA, Summers B, Rau MJ, Fitzpatrick JAJ, Di Cera E. Cryo-EM structure of the prothrombin-prothrombinase complex. Blood 2022; 139:3463-3473. [PMID: 35427420 PMCID: PMC9203702 DOI: 10.1182/blood.2022015807] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/30/2022] [Indexed: 11/23/2022] Open
Abstract
The intrinsic and extrinsic pathways of the coagulation cascade converge to a common step where the prothrombinase complex, comprising the enzyme factor Xa (fXa), the cofactor fVa, Ca2+ and phospholipids, activates the zymogen prothrombin to the protease thrombin. The reaction entails cleavage at 2 sites, R271 and R320, generating the intermediates prethrombin 2 and meizothrombin, respectively. The molecular basis of these interactions that are central to hemostasis remains elusive. We solved 2 cryogenic electron microscopy (cryo-EM) structures of the fVa-fXa complex, 1 free on nanodiscs at 5.3-Å resolution and the other bound to prothrombin at near atomic 4.1-Å resolution. In the prothrombin-fVa-fXa complex, the Gla domains of fXa and prothrombin align on a plane with the C1 and C2 domains of fVa for interaction with membranes. Prothrombin and fXa emerge from this plane in curved conformations that bring their protease domains in contact with each other against the A2 domain of fVa. The 672ESTVMATRKMHDRLEPEDEE691 segment of the A2 domain closes on the protease domain of fXa like a lid to fix orientation of the active site. The 696YDYQNRL702 segment binds to prothrombin and establishes the pathway of activation by sequestering R271 against D697 and directing R320 toward the active site of fXa. The cryo-EM structure provides a molecular view of prothrombin activation along the meizothrombin pathway and suggests a mechanism for cleavage at the alternative R271 site. The findings advance our basic knowledge of a key step of coagulation and bear broad relevance to other interactions in the blood.
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Affiliation(s)
- Eliza A Ruben
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | | | | | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging
- Department of Cell Biology and Physiology, and
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO; and
- Department of Biomedical Engineering, Washington University in Saint Louis, St. Louis, MO
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
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16
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Mulenga C, Sviben S, Chandwe K, Amadi B, Kayamba V, Fitzpatrick JAJ, Mudenda V, Kelly P. Epithelial Abnormalities in the Small Intestine of Zambian Children With Stunting. Front Med (Lausanne) 2022; 9:849677. [PMID: 35372420 PMCID: PMC8966729 DOI: 10.3389/fmed.2022.849677] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/22/2022] [Indexed: 01/17/2023] Open
Abstract
Background Environmental enteropathy (EE) contributes to impaired linear growth (stunting), in millions of children worldwide. We have previously reported that confocal laser endomicroscopy (CLE) shows fluorescein leaking from blood to gut lumen in vivo in adults and children with EE. We set out to identify epithelial lesions which might explain this phenomenon in Zambian children with stunting non-responsive to nutritional support. Methods We performed confocal laser endomicroscopy (CLE) in 75 children and collected intestinal biopsies for histology in 91 children. CLE videos were evaluated, employing the Watson score to determine severity of leakiness. Morphometry was carried out on well-orientated mucosa and 3 biopsies were examined by electron microscopy. Results Confocal laser endomicroscopy demonstrated substantial leakage from circulation to gut lumen in 73 (97%) children. Histology consistently showed characteristic changes of EE: villus blunting, lamina propria and epithelial inflammation, and depletion of secretory cells (Paneth cells and goblet cells). Epithelial abnormalities included marked variability in epithelial height, disorganised and shortened microvilli, dilated intercellular spaces, pseudostratification, formation of synechiae between epithelium on adjacent villi, crypt destruction, and abundant destructive lesions which may correspond to the microerosions identified on CLE. Conclusion Epithelial abnormalities were almost universal in Zambian children with non-responsive stunting, including epithelial microerosions, cell-cell adhesion anomalies, and defects in secretory cells which may all contribute to impairment of mucosal barrier function and microbial translocation.
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Affiliation(s)
- Chola Mulenga
- Tropical Gastroenterology and Nutrition Group, University of Zambia School of Medicine, Lusaka, Zambia
| | - Sanja Sviben
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, United States
| | - Kanta Chandwe
- Tropical Gastroenterology and Nutrition Group, University of Zambia School of Medicine, Lusaka, Zambia
| | - Beatrice Amadi
- Tropical Gastroenterology and Nutrition Group, University of Zambia School of Medicine, Lusaka, Zambia
| | - Violet Kayamba
- Tropical Gastroenterology and Nutrition Group, University of Zambia School of Medicine, Lusaka, Zambia
| | - James A. J. Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, United States
- Departments of Cell Biology & Physiology and Neuroscience, Washington University School of Medicine, St. Louis, MO, United States
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, United States
| | - Victor Mudenda
- Department of Pathology and Microbiology, University of Zambia School of Medicine, Lusaka, Zambia
| | - Paul Kelly
- Tropical Gastroenterology and Nutrition Group, University of Zambia School of Medicine, Lusaka, Zambia
- Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, United Kingdom
- *Correspondence: Paul Kelly,
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17
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Fisher KE, Krishnamoorthy P, Joens MS, Chory J, Fitzpatrick JAJ, Woodson JD. Singlet Oxygen Leads to Structural Changes to Chloroplasts during their Degradation in the Arabidopsis thaliana plastid ferrochelatase two Mutant. Plant Cell Physiol 2022; 63:248-264. [PMID: 34850209 DOI: 10.1093/pcp/pcab167] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/01/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
During stress, chloroplasts produce large amounts of reactive oxygen species (ROS). Chloroplasts also contain many nutrients, including 80% of a leaf's nitrogen supply. Therefore, to protect cells from photo-oxidative damage and to redistribute nutrients to sink tissues, chloroplasts are prime targets for degradation. Multiple chloroplast degradation pathways are induced by photo-oxidative stress or nutrient starvation, but the mechanisms by which damaged or senescing chloroplasts are identified, transported to the central vacuole and degraded are poorly defined. Here, we investigated the structures involved with degrading chloroplasts induced by the ROS singlet oxygen (1O2) in the Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant. Under mild 1O2 stress, most fc2 chloroplasts appeared normal, but had reduced starch content. A subset of chloroplasts was degrading, and some protruded into the central vacuole via 'blebbing' structures. A 3D electron microscopy analysis demonstrated that up to 35% of degrading chloroplasts contained such structures. While the location of a chloroplast within a cell did not affect the likelihood of its degradation, chloroplasts in spongy mesophyll cells were degraded at a higher rate than those in palisade mesophyll cells. To determine if degrading chloroplasts have unique structural characteristics, allowing them to be distinguished from healthy chloroplasts, we analyzed fc2 seedlings grown under different levels of photo-oxidative stress. A correlation was observed among chloroplast swelling, 1O2 signaling and the state of degradation. Finally, plastoglobule (PG) enzymes involved in chloroplast disassembly were upregulated while PGs increased their association with the thylakoid grana, implicating an interaction between 1O2-induced chloroplast degradation and senescence pathways.
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Affiliation(s)
- Karen E Fisher
- The School of Plant Sciences, University of Arizona, 1140 E South Campus Dr., Tucson, AZ 85721, USA
| | - Praveen Krishnamoorthy
- Washington University Center for Cellular Imaging, Washington University School of Medicine, 660 W. Euclid Avenue, St. Louis, MO 63110, USA
| | | | - Joanne Chory
- Plant Biology Laboratory and the Howard Hughes Medical Institute, The Salk Institute, 10010 N Torrey Pines Rd., La Jolla, CA 92037, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, 660 W. Euclid Avenue, St. Louis, MO 63110, USA
- Departments of Cell Biology & Physiology and Neuroscience, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - Jesse D Woodson
- The School of Plant Sciences, University of Arizona, 1140 E South Campus Dr., Tucson, AZ 85721, USA
- Washington University Center for Cellular Imaging, Washington University School of Medicine, 660 W. Euclid Avenue, St. Louis, MO 63110, USA
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18
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Luke CJ, Markovina S, Good M, Wight IE, Thomas BJ, Linneman JM, Lanik WE, Koroleva O, Coffman MR, Miedel MT, Gong Q, Andress A, Campos Guerrero M, Wang S, Chen L, Beatty WL, Hausmann KN, White FV, Fitzpatrick JAJ, Orvedahl A, Pak SC, Silverman GA. Lysoptosis is an evolutionarily conserved cell death pathway moderated by intracellular serpins. Commun Biol 2022; 5:47. [PMID: 35022507 PMCID: PMC8755814 DOI: 10.1038/s42003-021-02953-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/07/2021] [Indexed: 01/02/2023] Open
Abstract
Lysosomal membrane permeabilization (LMP) and cathepsin release typifies lysosome-dependent cell death (LDCD). However, LMP occurs in most regulated cell death programs suggesting LDCD is not an independent cell death pathway, but is conscripted to facilitate the final cellular demise by other cell death routines. Previously, we demonstrated that Caenorhabditis elegans (C. elegans) null for a cysteine protease inhibitor, srp-6, undergo a specific LDCD pathway characterized by LMP and cathepsin-dependent cytoplasmic proteolysis. We designated this cell death routine, lysoptosis, to distinguish it from other pathways employing LMP. In this study, mouse and human epithelial cells lacking srp-6 homologues, mSerpinb3a and SERPINB3, respectively, demonstrated a lysoptosis phenotype distinct from other cell death pathways. Like in C. elegans, this pathway depended on LMP and released cathepsins, predominantly cathepsin L. These studies suggested that lysoptosis is an evolutionarily-conserved eukaryotic LDCD that predominates in the absence of neutralizing endogenous inhibitors. Cliff Luke et al. report that lysoptosis is a eukaryotic stand-alone regulated cell death pathway. They identify that this new cell death modality predominates in the absence of neutralizing endogenous inhibitors.
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Affiliation(s)
- Cliff J Luke
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA. .,Siteman Cancer Center, and Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA.
| | - Stephanie Markovina
- Siteman Cancer Center, and Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA.,Radiation Oncology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Misty Good
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Ira E Wight
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Brian J Thomas
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - John M Linneman
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Wyatt E Lanik
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Olga Koroleva
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Maggie R Coffman
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Mark T Miedel
- Department of Computational and Systems biology, Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Qingqing Gong
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Arlise Andress
- Radiation Oncology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Marlene Campos Guerrero
- Radiation Oncology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Songyan Wang
- Radiation Oncology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - LiYun Chen
- Radiation Oncology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Wandy L Beatty
- Molecular Microbiology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Kelsey N Hausmann
- Molecular Microbiology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Frances V White
- Department of Pathology and Immunology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - James A J Fitzpatrick
- Cell Biology and Physiology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA.,Neuroscience, and Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Anthony Orvedahl
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Stephen C Pak
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Gary A Silverman
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA. .,Siteman Cancer Center, and Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA. .,Cell Biology and Physiology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA. .,Genetics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA.
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19
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Errico JM, Zhao H, Chen RE, Liu Z, Case JB, Ma M, Schmitz AJ, Rau MJ, Fitzpatrick JAJ, Shi PY, Diamond MS, Whelan SPJ, Ellebedy AH, Fremont DH. Structural mechanism of SARS-CoV-2 neutralization by two murine antibodies targeting the RBD. Cell Rep 2021; 37:109881. [PMID: 34655519 PMCID: PMC8498651 DOI: 10.1016/j.celrep.2021.109881] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/11/2021] [Accepted: 10/04/2021] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has necessitated the rapid development of antibody-based therapies and vaccines as countermeasures. Here, we use cryoelectron microscopy (cryo-EM) to characterize two protective anti-SARS-CoV-2 murine monoclonal antibodies (mAbs) in complex with the spike protein, revealing similarities between epitopes targeted by human and murine B cells. The more neutralizing mAb, 2B04, binds the receptor-binding motif (RBM) of the receptor-binding domain (RBD) and competes with angiotensin-converting enzyme 2 (ACE2). By contrast, 2H04 binds adjacent to the RBM and does not compete for ACE2 binding. Naturally occurring sequence variants of SARS-CoV-2 and corresponding neutralization escape variants selected in vitro map to our structurally defined epitopes, suggesting that SARS-CoV-2 might evade therapeutic antibodies with a limited set of mutations, underscoring the importance of combination mAb therapeutics. Finally, we show that 2B04 neutralizes SARS-CoV-2 infection by preventing ACE2 engagement, whereas 2H04 reduces host cell attachment without directly disrupting ACE2-RBM interactions, providing distinct inhibitory mechanisms used by RBD-specific mAbs.
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MESH Headings
- Angiotensin-Converting Enzyme 2/metabolism
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- COVID-19/immunology
- Cryoelectron Microscopy
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/immunology
- Humans
- Mice
- Protein Interaction Domains and Motifs/immunology
- Protein Structure, Quaternary
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- John M Errico
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Haiyan Zhao
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rita E Chen
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Meisheng Ma
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Aaron J Schmitz
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael J Rau
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA; Departments of Neuroscience and Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Michael S Diamond
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ali H Ellebedy
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Daved H Fremont
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA; Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
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20
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Reddy NC, Majidi SP, Kong L, Nemera M, Ferguson CJ, Moore M, Goncalves TM, Liu HK, Fitzpatrick JAJ, Zhao G, Yamada T, Bonni A, Gabel HW. CHARGE syndrome protein CHD7 regulates epigenomic activation of enhancers in granule cell precursors and gyrification of the cerebellum. Nat Commun 2021; 12:5702. [PMID: 34588434 PMCID: PMC8481233 DOI: 10.1038/s41467-021-25846-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 09/01/2021] [Indexed: 12/16/2022] Open
Abstract
Regulation of chromatin plays fundamental roles in the development of the brain. Haploinsufficiency of the chromatin remodeling enzyme CHD7 causes CHARGE syndrome, a genetic disorder that affects the development of the cerebellum. However, how CHD7 controls chromatin states in the cerebellum remains incompletely understood. Using conditional knockout of CHD7 in granule cell precursors in the mouse cerebellum, we find that CHD7 robustly promotes chromatin accessibility, active histone modifications, and RNA polymerase recruitment at enhancers. In vivo profiling of genome architecture reveals that CHD7 concordantly regulates epigenomic modifications associated with enhancer activation and gene expression of topologically-interacting genes. Genome and gene ontology studies show that CHD7-regulated enhancers are associated with genes that control brain tissue morphogenesis. Accordingly, conditional knockout of CHD7 triggers a striking phenotype of cerebellar polymicrogyria, which we have also found in a case of CHARGE syndrome. Finally, we uncover a CHD7-dependent switch in the preferred orientation of granule cell precursor division in the developing cerebellum, providing a potential cellular basis for the cerebellar polymicrogyria phenotype upon loss of CHD7. Collectively, our findings define epigenomic regulation by CHD7 in granule cell precursors and identify abnormal cerebellar patterning upon CHD7 depletion, with potential implications for our understanding of CHARGE syndrome. CHARGE syndrome that affects cerebellar development can be caused by haploinsufficiency of the chromatin remodeling enzyme CHD7; however the precise role of CHD7 remains unknown. Here the authors show CHD7 promotes chromatin accessibility and enhancer activity in granule cell precursors and regulates morphogenesis of the cerebellar cortex, where loss of CHD7 triggers cerebellar polymicrogyria.
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Affiliation(s)
- Naveen C Reddy
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Shahriyar P Majidi
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA.,MD-PhD Program, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Lingchun Kong
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Mati Nemera
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Cole J Ferguson
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Michael Moore
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tassia M Goncalves
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hai-Kun Liu
- Division of Molecular Neurogenetics, DKFZ-ZMBH Alliance, German Cancer Research Center Im Neunheimer Feld 280, 69120, Heidelberg, Germany
| | - James A J Fitzpatrick
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Guoyan Zhao
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tomoko Yamada
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Neurobiology, Northwestern University, Evanston, IL, 60201, USA
| | - Azad Bonni
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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21
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Wong NR, Mohan J, Kopecky BJ, Guo S, Du L, Leid J, Feng G, Lokshina I, Dmytrenko O, Luehmann H, Bajpai G, Ewald L, Bell L, Patel N, Bredemeyer A, Weinheimer CJ, Nigro JM, Kovacs A, Morimoto S, Bayguinov PO, Fisher MR, Stump WT, Greenberg M, Fitzpatrick JAJ, Epelman S, Kreisel D, Sah R, Liu Y, Hu H, Lavine KJ. Resident cardiac macrophages mediate adaptive myocardial remodeling. Immunity 2021; 54:2072-2088.e7. [PMID: 34320366 DOI: 10.1016/j.immuni.2021.07.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/04/2021] [Accepted: 07/07/2021] [Indexed: 12/17/2022]
Abstract
Cardiac macrophages represent a heterogeneous cell population with distinct origins, dynamics, and functions. Recent studies have revealed that C-C Chemokine Receptor 2 positive (CCR2+) macrophages derived from infiltrating monocytes regulate myocardial inflammation and heart failure pathogenesis. Comparatively little is known about the functions of tissue resident (CCR2-) macrophages. Herein, we identified an essential role for CCR2- macrophages in the chronically failing heart. Depletion of CCR2- macrophages in mice with dilated cardiomyopathy accelerated mortality and impaired ventricular remodeling and coronary angiogenesis, adaptive changes necessary to maintain cardiac output in the setting of reduced cardiac contractility. Mechanistically, CCR2- macrophages interacted with neighboring cardiomyocytes via focal adhesion complexes and were activated in response to mechanical stretch through a transient receptor potential vanilloid 4 (TRPV4)-dependent pathway that controlled growth factor expression. These findings establish a role for tissue-resident macrophages in adaptive cardiac remodeling and implicate mechanical sensing in cardiac macrophage activation.
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Affiliation(s)
- Nicole R Wong
- Departmental of Medicine, Washington University School of Medicine
| | - Jay Mohan
- Departmental of Medicine, Washington University School of Medicine
| | | | - Shuchi Guo
- Departmental of Medicine, Washington University School of Medicine
| | - Lixia Du
- Department of Anesthesiology, Washington University School of Medicine
| | - Jamison Leid
- Departmental of Medicine, Washington University School of Medicine
| | - Guoshuai Feng
- Departmental of Medicine, Washington University School of Medicine
| | - Inessa Lokshina
- Departmental of Medicine, Washington University School of Medicine
| | | | - Hannah Luehmann
- Department of Radiology, Washington University School of Medicine
| | - Geetika Bajpai
- Departmental of Medicine, Washington University School of Medicine
| | - Laura Ewald
- Departmental of Medicine, Washington University School of Medicine
| | - Lauren Bell
- Departmental of Medicine, Washington University School of Medicine
| | - Nikhil Patel
- Departmental of Genetics, Washington University School of Medicine
| | | | | | - Jessica M Nigro
- Departmental of Medicine, Washington University School of Medicine
| | - Attila Kovacs
- Departmental of Medicine, Washington University School of Medicine
| | - Sachio Morimoto
- Department of Physical Therapy, International University of Health and Welfare, Japan
| | - Peter O Bayguinov
- Department of Biochemistry, Washington University School of Medicine
| | - Max R Fisher
- Department of Biochemistry, Washington University School of Medicine
| | - W Tom Stump
- Department of Biochemistry, Washington University School of Medicine
| | - Michael Greenberg
- Department of Biochemistry, Washington University School of Medicine
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine; Departments of Neuroscience, Cell Biology & Physiology, and Biomedical Engineering, Washington University School of Medicine
| | - Slava Epelman
- Toronto General Hospital Research Institute, University Health Network
| | - Daniel Kreisel
- Department of Pathology and Immunology, Washington University School of Medicine; Department of Surgery, Washington University School of Medicine
| | - Rajan Sah
- Departmental of Medicine, Washington University School of Medicine
| | - Yongjian Liu
- Department of Radiology, Washington University School of Medicine
| | - Hongzhen Hu
- Department of Anesthesiology, Washington University School of Medicine
| | - Kory J Lavine
- Departmental of Medicine, Washington University School of Medicine; Department of Pathology and Immunology, Washington University School of Medicine; Department of Developmental Biology, Washington University School of Medicine.
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22
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Payne SA, Joens MS, Chung H, Skigen N, Frank A, Gattani S, Vaughn K, Schwed A, Nester M, Bhattacharyya A, Iyer G, Davis B, Carlquist J, Patel H, Fitzpatrick JAJ, Rutherford MA. Maturation of Heterogeneity in Afferent Synapse Ultrastructure in the Mouse Cochlea. Front Synaptic Neurosci 2021; 13:678575. [PMID: 34220482 PMCID: PMC8248813 DOI: 10.3389/fnsyn.2021.678575] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/11/2021] [Indexed: 12/11/2022] Open
Abstract
Auditory nerve fibers (ANFs) innervating the same inner hair cell (IHC) may have identical frequency tuning but different sound response properties. In cat and guinea pig, ANF response properties correlate with afferent synapse morphology and position on the IHC, suggesting a causal structure-function relationship. In mice, this relationship has not been fully characterized. Here we measured the emergence of synaptic morphological heterogeneities during maturation of the C57BL/6J mouse cochlea by comparing postnatal day 17 (p17, ∼3 days after hearing onset) with p34, when the mouse cochlea is mature. Using serial block face scanning electron microscopy and three-dimensional reconstruction we measured the size, shape, vesicle content, and position of 70 ribbon synapses from the mid-cochlea. Several features matured over late postnatal development. From p17 to p34, presynaptic densities (PDs) and post-synaptic densities (PSDs) became smaller on average (PDs: 0.75 to 0.33; PSDs: 0.58 to 0.31 μm2) and less round as their short axes shortened predominantly on the modiolar side, from 770 to 360 nm. Membrane-associated synaptic vesicles decreased in number from 53 to 30 per synapse from p17 to p34. Anatomical coupling, measured as PSD to ribbon distance, tightened predominantly on the pillar side. Ribbons became less spherical as long-axes lengthened only on the modiolar side of the IHC, from 372 to 541 nm. A decreasing gradient of synaptic ribbon size along the modiolar-pillar axis was detected only at p34 after aligning synapses of adjacent IHCs to a common reference frame (median volumes in nm3 × 106: modiolar 4.87; pillar 2.38). The number of ribbon-associated synaptic vesicles scaled with ribbon size (range 67 to 346 per synapse at p34), thus acquiring a modiolar-pillar gradient at p34, but overall medians were similar at p17 (120) and p34 (127), like ribbon surface area (0.36 vs. 0.34 μm2). PD and PSD morphologies were tightly correlated to each other at individual synapses, more so at p34 than p17, but not to ribbon morphology. These observations suggest that PDs and PSDs mature according to different cues than ribbons, and that ribbon size may be more influenced by cues from the IHC than the surrounding tissue.
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Affiliation(s)
- Shelby A Payne
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO, United States
| | - Matthew S Joens
- Center for Cellular Imaging, Washington University in St. Louis, St. Louis, MO, United States.,TESCAN USA, Inc., Warrendale, PA, United States
| | - Heather Chung
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO, United States.,Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Natalie Skigen
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Adam Frank
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Sonali Gattani
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Kya Vaughn
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Allison Schwed
- Graduate Program in Audiology and Communications Sciences, Washington University School of Medicine, St. Louis, MO, United States
| | - Matt Nester
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Atri Bhattacharyya
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO, United States.,Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Guhan Iyer
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Bethany Davis
- Graduate Program in Audiology and Communications Sciences, Washington University School of Medicine, St. Louis, MO, United States
| | - Jason Carlquist
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO, United States.,Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Honey Patel
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - James A J Fitzpatrick
- Center for Cellular Imaging, Washington University in St. Louis, St. Louis, MO, United States.,Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, United States.,Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States.,Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO, United States
| | - Mark A Rutherford
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO, United States
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23
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Brioschi S, Wang WL, Peng V, Wang M, Shchukina I, Greenberg ZJ, Bando JK, Jaeger N, Czepielewski RS, Swain A, Mogilenko DA, Beatty WL, Bayguinov P, Fitzpatrick JAJ, Schuettpelz LG, Fronick CC, Smirnov I, Kipnis J, Shapiro VS, Wu GF, Gilfillan S, Cella M, Artyomov MN, Kleinstein SH, Colonna M. Heterogeneity of meningeal B cells reveals a lymphopoietic niche at the CNS borders. Science 2021; 373:science.abf9277. [PMID: 34083450 DOI: 10.1126/science.abf9277] [Citation(s) in RCA: 199] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/01/2021] [Accepted: 05/24/2021] [Indexed: 12/11/2022]
Abstract
The meninges contain adaptive immune cells that provide immunosurveillance of the central nervous system (CNS). These cells are thought to derive from the systemic circulation. Through single-cell analyses, confocal imaging, bone marrow chimeras, and parabiosis experiments, we show that meningeal B cells derive locally from the calvaria, which harbors a bone marrow niche for hematopoiesis. B cells reach the meninges from the calvaria through specialized vascular connections. This calvarial-meningeal path of B cell development may provide the CNS with a constant supply of B cells educated by CNS antigens. Conversely, we show that a subset of antigen-experienced B cells that populate the meninges in aging mice are blood-borne. These results identify a private source for meningeal B cells, which may help maintain immune privilege within the CNS.
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Affiliation(s)
- Simone Brioschi
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Wei-Le Wang
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Vincent Peng
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Meng Wang
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Irina Shchukina
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Zev J Greenberg
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jennifer K Bando
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Natalia Jaeger
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Rafael S Czepielewski
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Amanda Swain
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Denis A Mogilenko
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Wandy L Beatty
- Department of Molecular Microbiology, Center for Infectious Disease Research, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Peter Bayguinov
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO 63110, USA.,Departments of Cell Biology and Physiology and Neuroscience, Washington University School of Medicine, Saint Louis, MO 63110, USA.,Department of Biomedical Engineering, Washington University in Saint Louis, Saint Louis, MO 63130, USA
| | - Laura G Schuettpelz
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Catrina C Fronick
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Igor Smirnov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jonathan Kipnis
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | | | - Gregory F Wu
- Department of Neurology, Washington University in Saint Louis, Saint Louis, MO 63110, USA
| | - Susan Gilfillan
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA.,Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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24
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Abstract
Coagulation factor V (fV) is the precursor of fVa, which, together with fXa, Ca2+, and phospholipids, defines the prothrombinase complex and activates prothrombin in the penultimate step of the coagulation cascade. We solved the cryogenic electron microscopy (cryo-EM) structures of human fV and fVa at atomic (3.3 Å) and near-atomic (4.4 Å) resolution, respectively. The structure of fV reveals the entire A1-A2-B-A3-C1-C2 assembly, but with a surprisingly disordered B domain. The C1 and C2 domains provide a platform for interaction with phospholipid membranes and support the A1 and A3 domains, with the A2 domain sitting on top of them. The B domain is highly dynamic and visible only for short segments connecting to the A2 and A3 domains. The A2 domain reveals all sites of proteolytic processing by thrombin and activated protein C, a partially buried epitope for binding fXa, and fully exposed epitopes for binding activated protein C and prothrombin. Removal of the B domain and activation to fVa exposes the sites of cleavage by activated protein C at R306 and R506 and produces increased disorder in the A1-A2-A3-C1-C2 assembly, especially in the C-terminal acidic portion of the A2 domain that is responsible for prothrombin binding. Ordering of this region and full exposure of the fXa epitope emerge as necessary steps in the assembly of the prothrombin-prothrombinase complex. These structures offer molecular context for the function of fV and fVa and pioneer the analysis of coagulation factors by cryo-EM.
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Affiliation(s)
- Eliza A Ruben
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | | | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging
- Department of Cell Biology and Physiology, and
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO; and
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
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25
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Newberry EP, Strout GW, Fitzpatrick JAJ, Davidson NO. Liver-specific deletion of Mttp versus Tm6sf2 reveals distinct defects in stepwise VLDL assembly. J Lipid Res 2021; 62:100080. [PMID: 33915141 PMCID: PMC8170145 DOI: 10.1016/j.jlr.2021.100080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Elizabeth P Newberry
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Gregory W Strout
- Washington University Center for Cellular Imaging, St. Louis, MO, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, St. Louis, MO, USA; Departments of Cell Biology & Physiology and Neuroscience, Washington University School of Medicine, St. Louis, MO, USA; Department of Biomedical Engineering, Washington University in Saint Louis, St. Louis, MO, USA
| | - Nicholas O Davidson
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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26
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Fox GC, Su X, Davis JL, Xu Y, Kwakwa KA, Ross MH, Fontana F, Xiang J, Esser AK, Cordell E, Pagliai K, Dang HX, Sivapackiam J, Stewart SA, Maher CA, Bakewell SJ, Fitzpatrick JAJ, Sharma V, Achilefu S, Veis DJ, Lanza GM, Weilbaecher KN. Targeted Therapy to β3 Integrin Reduces Chemoresistance in Breast Cancer Bone Metastases. Mol Cancer Ther 2021; 20:1183-1198. [PMID: 33785647 DOI: 10.1158/1535-7163.mct-20-0931] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/04/2021] [Accepted: 03/11/2021] [Indexed: 11/16/2022]
Abstract
Breast cancer bone metastases are common and incurable. Tumoral integrin β3 (β3) expression is induced through interaction with the bone microenvironment. Although β3 is known to promote bone colonization, its functional role during therapy of established bone metastases is not known. We found increased numbers of β3+ tumor cells in murine bone metastases after docetaxel chemotherapy. β3+ tumor cells were present in 97% of post-neoadjuvant chemotherapy triple-negative breast cancer patient samples (n = 38). High tumoral β3 expression was associated with worse outcomes in both pre- and postchemotherapy triple-negative breast cancer groups. Genetic deletion of tumoral β3 had minimal effect in vitro, but significantly enhanced in vivo docetaxel activity, particularly in the bone. Rescue experiments confirmed that this effect required intact β3 signaling. Ultrastructural, transcriptomic, and functional analyses revealed an alternative metabolic response to chemotherapy in β3-expressing cells characterized by enhanced oxygen consumption, reactive oxygen species generation, and protein production. We identified mTORC1 as a candidate for therapeutic targeting of this β3-mediated, chemotherapy-induced metabolic response. mTORC1 inhibition in combination with docetaxel synergistically attenuated murine bone metastases. Furthermore, micelle nanoparticle delivery of mTORC1 inhibitor to cells expressing activated αvβ3 integrins enhanced docetaxel efficacy in bone metastases. Taken together, we show that β3 integrin induction by the bone microenvironment promotes resistance to chemotherapy through an altered metabolic response that can be defused by combination with αvβ3-targeted mTORC1 inhibitor nanotherapy. Our work demonstrates the importance of the metastatic microenvironment when designing treatments and presents new, bone-specific strategies for enhancing chemotherapeutic efficacy.
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Affiliation(s)
- Gregory C Fox
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Xinming Su
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Jennifer L Davis
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Yalin Xu
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Kristin A Kwakwa
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Michael H Ross
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Francesca Fontana
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri.,Department of Medicine, Division of Cardiology, Washington University School of Medicine, St. Louis, Missouri
| | - Jingyu Xiang
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Alison K Esser
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Elizabeth Cordell
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Kristen Pagliai
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Ha X Dang
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Jothilingam Sivapackiam
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri.,ICCE Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Sheila A Stewart
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.,ICCE Institute, Washington University School of Medicine, St. Louis, Missouri.,Department of Medicine, Washington University School of Medicine, St. Louis, Missouri.,Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri
| | - Christopher A Maher
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri.,Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri
| | - Suzanne J Bakewell
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - James A J Fitzpatrick
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri.,Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri.,Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri
| | - Vijay Sharma
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri.,ICCE Institute, Washington University School of Medicine, St. Louis, Missouri.,Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri.,Deparment of Neurology, Washington University School of Medicine, St. Louis, Missouri
| | - Samuel Achilefu
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.,Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri.,Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Deborah J Veis
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri.,Musculoskeletal Research Center, Histology and Morphometry Core, Washington University School of Medicine, St. Louis, Missouri.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Gregory M Lanza
- Department of Medicine, Division of Cardiology, Washington University School of Medicine, St. Louis, Missouri
| | - Katherine N Weilbaecher
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri. .,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.,Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
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27
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Pandey KK, Bera S, Shi K, Rau MJ, Oleru AV, Fitzpatrick JAJ, Engelman AN, Aihara H, Grandgenett DP. Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome. Commun Biol 2021; 4:330. [PMID: 33712691 PMCID: PMC7955051 DOI: 10.1038/s42003-021-01855-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/12/2021] [Indexed: 12/14/2022] Open
Abstract
Despite conserved catalytic integration mechanisms, retroviral intasomes composed of integrase (IN) and viral DNA possess diverse structures with variable numbers of IN subunits. To investigate intasome assembly mechanisms, we employed the Rous sarcoma virus (RSV) IN dimer that assembles a precursor tetrameric structure in transit to the mature octameric intasome. We determined the structure of RSV octameric intasome stabilized by a HIV-1 IN strand transfer inhibitor using single particle cryo-electron microscopy. The structure revealed significant flexibility of the two non-catalytic distal IN dimers along with previously unrecognized movement of the conserved intasome core, suggesting ordered conformational transitions between intermediates that may be important to capture the target DNA. Single amino acid substitutions within the IN C-terminal domain affected intasome assembly and function in vitro and infectivity of pseudotyped RSV virions. Unexpectedly, 17 C-terminal amino acids of IN were dispensable for virus infection despite regulating the transition of the tetrameric intasome to the octameric form in vitro. We speculate that this region may regulate the binding of highly flexible distal IN dimers to the intasome core to form the octameric complex. Our studies reveal key steps in the assembly of RSV intasomes. Pandey, Bera, Shi et al. report the cryo-electron microscopy structure of the Rous sarcoma virus octameric intasome complex stabilized by a HIV-1 integrase strand transfer inhibitor. This new structure highlights the intrinsic flexibility of the distal integrase subunits and suggests that ordered conformational transitions occur within the conserved intasome core during the assembly process.
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Affiliation(s)
- Krishan K Pandey
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St. Louis, MO, USA.
| | - Sibes Bera
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St. Louis, MO, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Michael J Rau
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA
| | - Amarachi V Oleru
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA.,Departments of Cell Biology & Physiology and Neuroscience, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
| | - Duane P Grandgenett
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St. Louis, MO, USA.
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28
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Burns CH, Yau B, Rodriguez A, Triplett J, Maslar D, An YS, van der Welle REN, Kossina RG, Fisher MR, Strout GW, Bayguinov PO, Veenendaal T, Chitayat D, Fitzpatrick JAJ, Klumperman J, Kebede MA, Asensio CS. Pancreatic β-Cell-Specific Deletion of VPS41 Causes Diabetes Due to Defects in Insulin Secretion. Diabetes 2021; 70:436-448. [PMID: 33168621 PMCID: PMC7881869 DOI: 10.2337/db20-0454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022]
Abstract
Insulin secretory granules (SGs) mediate the regulated secretion of insulin, which is essential for glucose homeostasis. The basic machinery responsible for this regulated exocytosis consists of specific proteins present both at the plasma membrane and on insulin SGs. The protein composition of insulin SGs thus dictates their release properties, yet the mechanisms controlling insulin SG formation, which determine this molecular composition, remain poorly understood. VPS41, a component of the endolysosomal tethering homotypic fusion and vacuole protein sorting (HOPS) complex, was recently identified as a cytosolic factor involved in the formation of neuroendocrine and neuronal granules. We now find that VPS41 is required for insulin SG biogenesis and regulated insulin secretion. Loss of VPS41 in pancreatic β-cells leads to a reduction in insulin SG number, changes in their transmembrane protein composition, and defects in granule-regulated exocytosis. Exploring a human point mutation, identified in patients with neurological but no endocrine defects, we show that the effect on SG formation is independent of HOPS complex formation. Finally, we report that mice with a deletion of VPS41 specifically in β-cells develop diabetes due to severe depletion of insulin SG content and a defect in insulin secretion. In sum, our data demonstrate that VPS41 contributes to glucose homeostasis and metabolism.
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Affiliation(s)
| | - Belinda Yau
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia
| | | | - Jenna Triplett
- Department of Biological Sciences, University of Denver, Denver, CO
| | - Drew Maslar
- Department of Biological Sciences, University of Denver, Denver, CO
| | - You Sun An
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia
| | - Reini E N van der Welle
- Section of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ross G Kossina
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO
| | - Max R Fisher
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO
| | - Gregory W Strout
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO
| | - Peter O Bayguinov
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO
| | - Tineke Veenendaal
- Section of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO
- Departments of Neuroscience and Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO
| | - Judith Klumperman
- Section of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Melkam A Kebede
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia
| | - Cedric S Asensio
- Department of Biological Sciences, University of Denver, Denver, CO
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29
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Deng Z, Zhao Y, Feng J, Zhang J, Zhao H, Rau MJ, Fitzpatrick JAJ, Hu H, Yuan P. Cryo-EM structure of a proton-activated chloride channel TMEM206. Sci Adv 2021; 7:7/9/eabe5983. [PMID: 33627432 PMCID: PMC7904269 DOI: 10.1126/sciadv.abe5983] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/08/2021] [Indexed: 05/12/2023]
Abstract
TMEM206 has been recently identified as an evolutionarily conserved chloride channel that underlies ubiquitously expressed, proton-activated, outwardly rectifying anion currents. Here, we report the cryo-electron microscopy structure of pufferfish TMEM206, which forms a trimeric channel, with each subunit comprising two transmembrane segments and a large extracellular domain. An ample vestibule in the extracellular region is accessible laterally from the three side portals. The central pore contains multiple constrictions. A conserved lysine residue near the cytoplasmic end of the inner helix forms the presumed chloride ion selectivity filter. Unprecedentedly, the core structure and assembly closely resemble those of the epithelial sodium channel/degenerin family of sodium channels that are unrelated in amino acid sequence and conduct cations instead of anions. Together with electrophysiology, this work provides insights into ion conduction and gating for a new class of chloride channels that is architecturally distinct from previously characterized chloride channel families.
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Affiliation(s)
- Zengqin Deng
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Yonghui Zhao
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jing Feng
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jingying Zhang
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Haiyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michael J Rau
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - James A J Fitzpatrick
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in Saint Louis, Saint Louis, MO 63130, USA
| | - Hongzhen Hu
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO 63110, USA
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30
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Bayguinov PO, Fisher MR, Fitzpatrick JAJ. Assaying three-dimensional cellular architecture using X-ray tomographic and correlated imaging approaches. J Biol Chem 2020; 295:15782-15793. [PMID: 32938716 PMCID: PMC7667966 DOI: 10.1074/jbc.rev120.009633] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/15/2020] [Indexed: 12/16/2022] Open
Abstract
Much of our understanding of the spatial organization of and interactions between cellular organelles and macromolecular complexes has been the result of imaging studies utilizing either light- or electron-based microscopic analyses. These classical approaches, while insightful, are nonetheless limited either by restrictions in resolution or by the sheer complexity of generating multidimensional data. Recent advances in the use and application of X-rays to acquire micro- and nanotomographic data sets offer an alternative methodology to visualize cellular architecture at the nanoscale. These new approaches allow for the subcellular analyses of unstained vitrified cells and three-dimensional localization of specific protein targets and have served as an essential tool in bridging light and electron correlative microscopy experiments. Here, we review the theory, instrumentation details, acquisition principles, and applications of both soft X-ray tomography and X-ray microscopy and how the use of these techniques offers a succinct means of analyzing three-dimensional cellular architecture. We discuss some of the recent work that has taken advantage of these approaches and detail how they have become integral in correlative microscopy workflows.
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Affiliation(s)
- Peter O Bayguinov
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Max R Fisher
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, Missouri, USA; Departments of Cell Biology and Physiology and Neuroscience, Washington University School of Medicine, Saint Louis, Missouri, USA; Department of Biomedical Engineering, Washington University in Saint Louis, Saint Louis, Missouri, USA.
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31
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Deng Z, Maksaev G, Schlegel AM, Zhang J, Rau M, Fitzpatrick JAJ, Haswell ES, Yuan P. Structural mechanism for gating of a eukaryotic mechanosensitive channel of small conductance. Nat Commun 2020; 11:3690. [PMID: 32704140 PMCID: PMC7378837 DOI: 10.1038/s41467-020-17538-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 07/07/2020] [Indexed: 01/21/2023] Open
Abstract
Mechanosensitive ion channels transduce physical force into electrochemical signaling that underlies an array of fundamental physiological processes, including hearing, touch, proprioception, osmoregulation, and morphogenesis. The mechanosensitive channels of small conductance (MscS) constitute a remarkably diverse superfamily of channels critical for management of osmotic pressure. Here, we present cryo-electron microscopy structures of a MscS homolog from Arabidopsis thaliana, MSL1, presumably in both the closed and open states. The heptameric MSL1 channel contains an unusual bowl-shaped transmembrane region, which is reminiscent of the evolutionarily and architecturally unrelated mechanosensitive Piezo channels. Upon channel opening, the curved transmembrane domain of MSL1 flattens and expands. Our structures, in combination with functional analyses, delineate a structural mechanism by which mechanosensitive channels open under increased membrane tension. Further, the shared structural feature between unrelated channels suggests the possibility of a unified mechanical gating mechanism stemming from membrane deformation induced by a non-planar transmembrane domain. Mechanosensitive channels transduce physical force into electrochemical signaling in processes such as hearing, touch, proprioception, osmoregulation, and morphogenesis. Here, authors use cryo-electron microscopy to provide structural insights into the mechanical gating mechanism.
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Affiliation(s)
- Zengqin Deng
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA.,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Grigory Maksaev
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA.,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Angela M Schlegel
- Department of Biology, Washington University in Saint Louis, Saint Louis, MO, 63130, USA.,NSF Center for Engineering Mechanobiology, Washington University in Saint Louis, Saint Louis, MO, 63130, USA
| | - Jingying Zhang
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA.,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Michael Rau
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - James A J Fitzpatrick
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA.,Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, 63110, USA.,Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, 63110, USA.,Department of Biomedical Engineering, Washington University in Saint Louis, Saint Louis, MO, 63130, USA
| | - Elizabeth S Haswell
- Department of Biology, Washington University in Saint Louis, Saint Louis, MO, 63130, USA.,NSF Center for Engineering Mechanobiology, Washington University in Saint Louis, Saint Louis, MO, 63130, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA. .,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
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32
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Hervas R, Rau MJ, Park Y, Zhang W, Murzin AG, Fitzpatrick JAJ, Scheres SHW, Si K. Cryo-EM structure of a neuronal functional amyloid implicated in memory persistence in Drosophila. Science 2020; 367:1230-1234. [PMID: 32165583 DOI: 10.1126/science.aba3526] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/18/2020] [Indexed: 12/14/2022]
Abstract
How long-lived memories withstand molecular turnover is a fundamental question. Aggregates of a prion-like RNA-binding protein, cytoplasmic polyadenylation element-binding (CPEB) protein, is a putative substrate of long-lasting memories. We isolated aggregated Drosophila CPEB, Orb2, from adult heads and determined its activity and atomic structure, at 2.6-angstrom resolution, using cryo-electron microscopy. Orb2 formed ~75-nanometer-long threefold-symmetric amyloid filaments. Filament formation transformed Orb2 from a translation repressor to an activator and "seed" for further translationally active aggregation. The 31-amino acid protofilament core adopted a cross-β unit with a single hydrophilic hairpin stabilized through interdigitated glutamine packing. Unlike the hydrophobic core of pathogenic amyloids, the hydrophilic core of Orb2 filaments suggests how some neuronal amyloids could be a stable yet regulatable substrate of memory.
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Affiliation(s)
- Ruben Hervas
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Michael J Rau
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Younshim Park
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Wenjuan Zhang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alexey G Murzin
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA.,Departments of Neuroscience and Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kausik Si
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA. .,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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33
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Deng Z, He Z, Maksaev G, Bitter RM, Rau M, Fitzpatrick JAJ, Yuan P. Cryo-EM structures of the ATP release channel pannexin 1. Nat Struct Mol Biol 2020; 27:373-381. [PMID: 32231289 DOI: 10.1038/s41594-020-0401-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 02/25/2020] [Indexed: 12/15/2022]
Abstract
The plasma membrane adenosine triphosphate (ATP) release channel pannexin 1 (PANX1) has been implicated in many physiological and pathophysiological processes associated with purinergic signaling, including cancer progression, apoptotic cell clearance, inflammation, blood pressure regulation, oocyte development, epilepsy and neuropathic pain. Here we present near-atomic-resolution structures of human and frog PANX1 determined by cryo-electron microscopy that revealed a heptameric channel architecture. Compatible with ATP permeation, the transmembrane pore and cytoplasmic vestibule were exceptionally wide. An extracellular tryptophan ring located at the outer pore created a constriction site, potentially functioning as a molecular sieve that restricts the size of permeable substrates. The amino and carboxyl termini, not resolved in the density map, appeared to be structurally dynamic and might contribute to narrowing of the pore during channel gating. In combination with functional characterization, this work elucidates the previously unknown architecture of pannexin channels and establishes a foundation for understanding their unique channel properties.
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Affiliation(s)
- Zengqin Deng
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Zhihui He
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Grigory Maksaev
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Ryan M Bitter
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael Rau
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA
| | - James A J Fitzpatrick
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.,Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA.,Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA.,Department of Biomedical Engineering, Washington University in Saint Louis, St. Louis, MO, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA. .,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA.
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34
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Guang Y, McGrath TM, Klug NR, Nims RJ, Shih CC, Bayguinov PO, Guilak F, Pham CTN, Fitzpatrick JAJ, Setton LA. Combined Experimental Approach and Finite Element Modeling of Small Molecule Transport Through Joint Synovium to Measure Effective Diffusivity. J Biomech Eng 2019; 142:975688. [PMID: 31536113 DOI: 10.1115/1.4044892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Indexed: 11/08/2022]
Abstract
Trans-synovial solute transport plays a critical role in the clearance of intra-articularly (IA) delivered drugs. In this study, we present a computational finite element model (FEM) of solute transport through the synovium validated by experiments on synovial explants. Unsteady diffusion of urea, a small uncharged molecule, was measured through devitalized porcine and human synovium using custom-built diffusion chambers. A multiphasic computational model was constructed and optimized with the experimental data to extract effective diffusivity for urea within the synovium. A monotonic decrease in urea concentration was observed in the donor bath over time, with an effective diffusivity found to be an order of magnitude lower in synovium versus that measured in free solution. Parametric studies incorporating an intimal cell layer with varying thickness and varying effective diffusivities were performed, revealing a dependence of drug clearance kinetics on both parameters. The findings of this study indicate that the synovial matrix impedes urea solute transport out of the joint with little retention of the solute in the matrix.
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Affiliation(s)
- Young Guang
- Department of Biomedical Engineering, Washington University in St. Louis, Whitaker Hall, 1 Brookings Dr., St. Louis, MO 63130
| | - Tom M McGrath
- Department of Biomedical Engineering, Washington University in St. Louis, Whitaker Hall, 1 Brookings Dr., St. Louis, MO 63130
| | - Natalie R Klug
- Department of Biomedical Engineering, Washington University in St. Louis, Whitaker Hall, 1 Brookings Dr., St. Louis, MO 63130
| | - Robert J Nims
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO 63110
| | - Chien-Cheng Shih
- Center for Cellular Imaging, Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110
| | - Peter O Bayguinov
- Center for Cellular Imaging, Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO 63110
| | - Christine T N Pham
- Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110
| | - James A J Fitzpatrick
- Scientific Director Center for Cellular Imaging, Department of Neuroscience, Department Cell Biology & Physiology and Neuroscience, Washington University School of Medicine, St. Louis, MO 63110; Department of Biomedical Engineering, Washington University in St. Louis, Whitaker Hall, 1 Brookings Dr., St. Louis, MO 63130
| | - Lori A Setton
- Department of Biomedical Engineering, Washington University in St. Louis, Whitaker Hall, 1 Brookings Dr., St. Louis, MO 63130
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35
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Yang Z, Yan H, Dai W, Jing J, Yang Y, Mahajan S, Zhou Y, Li W, Macaubas C, Mellins ED, Shih CC, Fitzpatrick JAJ, Faccio R. Tmem178 negatively regulates store-operated calcium entry in myeloid cells via association with STIM1. J Autoimmun 2019; 101:94-108. [PMID: 31018906 DOI: 10.1016/j.jaut.2019.04.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/09/2019] [Accepted: 04/12/2019] [Indexed: 12/27/2022]
Abstract
Store-operated calcium entry (SOCE) modulates cytosolic calcium in multiple cells. Endoplasmic reticulum (ER)-localized STIM1 and plasma membrane (PM)-localized ORAI1 are two main components of SOCE. STIM1:ORAI1 association requires STIM1 oligomerization, its re-distribution to ER-PM junctions, and puncta formation. However, little is known about the negative regulation of these steps to prevent calcium overload. Here, we identified Tmem178 as a negative modulator of STIM1 puncta formation in myeloid cells. Using site-directed mutagenesis, co-immunoprecipitation assays and FRET imaging, we determined that Tmem178:STIM1 association occurs via their transmembrane motifs. Mutants that increase Tmem178:STIM1 association reduce STIM1 puncta formation, SOCE activation, impair inflammatory cytokine production in macrophages and osteoclastogenesis. Mutants that reduce Tmem178:STIM1 association reverse these effects. Furthermore, exposure to plasma from arthritic patients decreases Tmem178 expression, enhances SOCE activation and cytoplasmic calcium. In conclusion, Tmem178 modulates the rate-limiting step of STIM1 puncta formation and therefore controls SOCE in inflammatory conditions.
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Affiliation(s)
- Zhengfeng Yang
- Department of Orthopaedics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hui Yan
- Department of Orthopaedics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Wentao Dai
- Shanghai Center for Bioinformation Technology & Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, China
| | - Ji Jing
- Institute of Biosciences and Technology, Texas A&M University College of Medicine, Houston, TX 77030, USA
| | - Yihu Yang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Sahil Mahajan
- Department of Orthopaedics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yubin Zhou
- Institute of Biosciences and Technology, Texas A&M University College of Medicine, Houston, TX 77030, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Claudia Macaubas
- Department of Pediatrics, Program in Immunology, Stanford University, Stanford, CA 94305, USA
| | - Elizabeth D Mellins
- Department of Pediatrics, Program in Immunology, Stanford University, Stanford, CA 94305, USA
| | - Chien-Cheng Shih
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA; Department of Biomedical Engineering, Washington University, St. Louis, MO, USA
| | - Roberta Faccio
- Department of Orthopaedics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Shriners Hospitals for Children, St. Louis MO, USA.
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36
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Robles H, Park S, Joens MS, Fitzpatrick JAJ, Craft CS, Scheller EL. Characterization of the bone marrow adipocyte niche with three-dimensional electron microscopy. Bone 2019; 118:89-98. [PMID: 29366839 PMCID: PMC6063802 DOI: 10.1016/j.bone.2018.01.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 01/10/2023]
Abstract
Unlike white and brown adipose tissues, the bone marrow adipocyte (BMA) exists in a microenvironment containing unique populations of hematopoietic and skeletal cells. To study this microenvironment at the sub-cellular level, we performed a three-dimensional analysis of the ultrastructure of the BMA niche with focused ion beam scanning electron microscopy (FIB-SEM). This revealed that BMAs display hallmarks of metabolically active cells including polarized lipid deposits, a dense mitochondrial network, and areas of endoplasmic reticulum. The distinct orientations of the triacylglycerol droplets suggest that fatty acids are taken up and/or released in three key areas - at the endothelial interface, into the hematopoietic milieu, and at the bone surface. Near the sinusoidal vasculature, endothelial cells send finger-like projections into the surface of the BMA which terminate near regions of lipid within the BMA cytoplasm. In some regions, perivascular cells encase the BMA with their flattened cellular projections, limiting contacts with other cells in the niche. In the hematopoietic milieu, BMAT adipocytes of the proximal tibia interact extensively with maturing cells of the myeloid/granulocyte lineage. Associations with erythroblast islands are also prominent. At the bone surface, the BMA extends organelle and lipid-rich cytoplasmic regions toward areas of active osteoblasts. This suggests that the BMA may serve to partition nutrient utilization between diverse cellular compartments, serving as an energy-rich hub of the stromal-reticular network. Lastly, though immuno-EM, we've identified a subset of bone marrow adipocytes that are innervated by the sympathetic nervous system, providing an additional mechanism for regulation of the BMA. In summary, this work reveals that the bone marrow adipocyte is a dynamic cell with substantial capacity for interactions with the diverse components of its surrounding microenvironment. These local interactions likely contribute to its unique regulation relative to peripheral adipose tissues.
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Affiliation(s)
- Hero Robles
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University, St. Louis, MO, USA.
| | - SungJae Park
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University, St. Louis, MO, USA.
| | - Matthew S Joens
- Center for Cellular Imaging, Washington University, St. Louis, MO, USA.
| | - James A J Fitzpatrick
- Department of Cell Biology & Physiology, Washington University, St. Louis, MO, USA; Department of Neuroscience, Washington University, St. Louis, MO, USA; Center for Cellular Imaging, Washington University, St. Louis, MO, USA; Department of Biomedical Engineering, Washington University, St. Louis, MO, USA.
| | - Clarissa S Craft
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University, St. Louis, MO, USA; Department of Cell Biology & Physiology, Washington University, St. Louis, MO, USA.
| | - Erica L Scheller
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University, St. Louis, MO, USA; Department of Cell Biology & Physiology, Washington University, St. Louis, MO, USA.
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37
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Rogers SC, Dosier LB, McMahon TJ, Zhu H, Timm D, Zhang H, Herbert J, Atallah J, Palmer GM, Cook A, Ernst M, Prakash J, Terng M, Towfighi P, Doctor R, Said A, Joens MS, Fitzpatrick JAJ, Hanna G, Lin X, Reisz JA, Nemkov T, D’Alessandro A, Doctor A. Red blood cell phenotype fidelity following glycerol cryopreservation optimized for research purposes. PLoS One 2018; 13:e0209201. [PMID: 30576340 PMCID: PMC6303082 DOI: 10.1371/journal.pone.0209201] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/01/2018] [Indexed: 12/20/2022] Open
Abstract
Intact red blood cells (RBCs) are required for phenotypic analyses. In order to allow separation (time and location) between subject encounter and sample analysis, we developed a research-specific RBC cryopreservation protocol and assessed its impact on data fidelity for key biochemical and physiological assays. RBCs drawn from healthy volunteers were aliquotted for immediate analysis or following glycerol-based cryopreservation, thawing, and deglycerolization. RBC phenotype was assessed by (1) scanning electron microscopy (SEM) imaging and standard morphometric RBC indices, (2) osmotic fragility, (3) deformability, (4) endothelial adhesion, (5) oxygen (O2) affinity, (6) ability to regulate hypoxic vasodilation, (7) nitric oxide (NO) content, (8) metabolomic phenotyping (at steady state, tracing with [1,2,3-13C3]glucose ± oxidative challenge with superoxide thermal source; SOTS-1), as well as in vivo quantification (following human to mouse RBC xenotransfusion) of (9) blood oxygenation content mapping and flow dynamics (velocity and adhesion). Our revised glycerolization protocol (40% v/v final) resulted in >98.5% RBC recovery following freezing (-80°C) and thawing (37°C), with no difference compared to the standard reported method (40% w/v final). Full deglycerolization (>99.9% glycerol removal) of 40% v/v final samples resulted in total cumulative lysis of ~8%, compared to ~12-15% with the standard method. The post cryopreservation/deglycerolization RBC phenotype was indistinguishable from that for fresh RBCs with regard to physical RBC parameters (morphology, volume, and density), osmotic fragility, deformability, endothelial adhesivity, O2 affinity, vasoregulation, metabolomics, and flow dynamics. These results indicate that RBC cryopreservation/deglycerolization in 40% v/v glycerol final does not significantly impact RBC phenotype (compared to fresh cells).
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Affiliation(s)
- Stephen C. Rogers
- Department of Pediatrics, Divisions of Critical Care Medicine, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
- Department of Biochemistry & Molecular Biophysics, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
| | - Laura B. Dosier
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, United States of America
| | - Timothy J. McMahon
- Department Medicine, Duke University School of Medicine, Durham, NC, United States of America
- Departments of Medicine, Durham VA Medical Center, Durham, NC, United States of America
| | - Hongmei Zhu
- Department Medicine, Duke University School of Medicine, Durham, NC, United States of America
- Departments of Medicine, Durham VA Medical Center, Durham, NC, United States of America
| | - David Timm
- Department of Pediatrics, Divisions of Critical Care Medicine, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
| | - Hengtao Zhang
- Department of Radiation Oncology, Duke Univ. School of Medicine, Durham, NC, United States of America
| | - Joseph Herbert
- Department of Radiation Oncology, Duke Univ. School of Medicine, Durham, NC, United States of America
| | - Jacqueline Atallah
- Department Medicine, Duke University School of Medicine, Durham, NC, United States of America
| | - Gregory M. Palmer
- Department of Radiation Oncology, Duke Univ. School of Medicine, Durham, NC, United States of America
| | - Asa Cook
- Department of Pediatrics, Divisions of Critical Care Medicine, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
| | - Melanie Ernst
- Department of Pediatrics, Divisions of Critical Care Medicine, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
| | - Jaya Prakash
- Department of Pediatrics, Divisions of Critical Care Medicine, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
| | - Mark Terng
- Department of Pediatrics, Divisions of Critical Care Medicine, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
| | - Parhom Towfighi
- Department of Pediatrics, Divisions of Critical Care Medicine, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
| | - Reid Doctor
- Department of Pediatrics, Divisions of Critical Care Medicine, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
| | - Ahmed Said
- Department of Pediatrics, Divisions of Critical Care Medicine, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
| | - Matthew S. Joens
- Washington University Center for Cellular Imaging, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
| | - James A. J. Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
- Departments of Neuroscience and Cell Biology & Physiology, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
| | - Gabi Hanna
- Department of Radiation Oncology, Duke Univ. School of Medicine, Durham, NC, United States of America
| | - Xue Lin
- Department of Pediatrics, Divisions of Critical Care Medicine, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
| | - Julie A. Reisz
- Department of Biochemistry, University of Colorado Denver—Aurora, CO, United States of America
| | - Travis Nemkov
- Department of Biochemistry, University of Colorado Denver—Aurora, CO, United States of America
| | - Angelo D’Alessandro
- Department of Biochemistry, University of Colorado Denver—Aurora, CO, United States of America
| | - Allan Doctor
- Department of Pediatrics, Divisions of Critical Care Medicine, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
- Department of Biochemistry & Molecular Biophysics, Washington University in Saint Louis, School of Medicine, Saint Louis, MO, United States of America
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Cheruiyot A, Li S, Nickless A, Roth R, Fitzpatrick JAJ, You Z. Compound C inhibits nonsense-mediated RNA decay independently of AMPK. PLoS One 2018; 13:e0204978. [PMID: 30289931 PMCID: PMC6173407 DOI: 10.1371/journal.pone.0204978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/18/2018] [Indexed: 12/26/2022] Open
Abstract
The nonsense mediated RNA decay (NMD) pathway safeguards the integrity of the transcriptome by targeting mRNAs with premature translation termination codons (PTCs) for degradation. It also regulates gene expression by degrading a large number of non-mutant RNAs (including mRNAs and noncoding RNAs) that bear NMD-inducing features. Consequently, NMD has been shown to influence development, cellular response to stress, and clinical outcome of many genetic diseases. Small molecules that can modulate NMD activity provide critical tools for understanding the mechanism and physiological functions of NMD, and they also offer potential means for treating certain genetic diseases and cancer. Therefore, there is an intense interest in identifying small-molecule NMD inhibitors or enhancers. It was previously reported that both inhibition of NMD and treatment with the AMPK-selective inhibitor Compound C (CC) induce autophagy in human cells, raising the possibility that CC may be capable of inhibiting NMD. Here we show that CC indeed has a NMD-inhibitory activity. Inhibition of NMD by CC is, however, independent of AMPK activity. As a competitive ATP analog, CC does not affect the kinase activity of SMG1, an essential NMD factor and the only known kinase in the NMD pathway. However, CC treatment down-regulates the protein levels of several NMD factors. The induction of autophagy by CC treatment is independent of ATF4, a NMD target that has been shown to promote autophagy in response to NMD inhibition. Our results reveal a new activity of CC as a NMD inhibitor, which has implications for its use in basic research and drug development.
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Affiliation(s)
- Abigael Cheruiyot
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Shan Li
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Andrew Nickless
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Robyn Roth
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - James A. J. Fitzpatrick
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Biomedical Engineering Washington University, St. Louis, Missouri, United States of America
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Zhongsheng You
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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Strubberg AM, Veronese Paniagua DA, Zhao T, Dublin L, Pritchard T, Bayguinov PO, Fitzpatrick JAJ, Madison BB. The Zinc Finger Transcription Factor PLAGL2 Enhances Stem Cell Fate and Activates Expression of ASCL2 in Intestinal Epithelial Cells. Stem Cell Reports 2018; 11:410-424. [PMID: 30017821 PMCID: PMC6092695 DOI: 10.1016/j.stemcr.2018.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 06/11/2018] [Accepted: 06/12/2018] [Indexed: 01/02/2023] Open
Abstract
Intestinal epithelial stem cell (IESC) fate is promoted by two major transcriptional regulators, the TCF4/β-catenin complex and ASCL2, which drive expression of IESC-specific factors, including Lgr5, Ephb2, and Rnf43. Canonical Wnt signaling via TCF4/β-catenin directly transactivates Ascl2, which in turn auto-regulates its own expression. Conversely, Let-7 microRNAs antagonize the IESC lineage by repressing specific mRNA targets. Here, we identify the zinc finger transcription factor PLAGL2 as a Let-7 target that regulates IESC fate. PLAGL2 drives an IESC expression signature, activates Wnt gene expression, and enhances a TCF/LEF reporter in intestinal organoids. In parallel, via cell-autonomous mechanisms, PLAGL2 is required for lineage clonal expansion and directly enhances expression of ASCL2. PLAGL2 also supports enteroid growth and survival in the context of Wnt ligand depletion. PLAGL2 expression is strongly associated with an IESC signature in colorectal cancer and may be responsible for contributing to the aberrant activation of an immature phenotype.
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Affiliation(s)
- Ashlee M Strubberg
- Department of Medicine, Division of Gastroenterology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus Box 8124, CSRB NT 923, Saint Louis, MO 63110, USA
| | - Daniel A Veronese Paniagua
- Department of Medicine, Division of Gastroenterology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus Box 8124, CSRB NT 923, Saint Louis, MO 63110, USA
| | - Tingting Zhao
- Department of Breast Surgery, First Hospital of China Medical University, Shenyang 110001, China
| | - Leeran Dublin
- Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Thomas Pritchard
- Department of Medicine, Division of Gastroenterology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus Box 8124, CSRB NT 923, Saint Louis, MO 63110, USA
| | - Peter O Bayguinov
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO 63110, USA; Departments of Cell Biology & Physiology and Neuroscience, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO 63105, USA
| | - Blair B Madison
- Department of Medicine, Division of Gastroenterology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus Box 8124, CSRB NT 923, Saint Louis, MO 63110, USA.
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Abstract
Since its commercialization in the late 1980's, confocal laser scanning microscopy (CLSM) has since become one of the most prevalent fluorescence microscopy techniques for three-dimensional structural studies of biological cells and tissues. The flexibility of the approach has enabled its application in a diverse array of studies, from the fast imaging of dynamic processes in living cells, to meticulous morphological analyses of tissues, and co-localization of protein expression patterns. In this chapter, we introduce the principles of confocal microscopy and discuss how the approach has become a mainstay in the biological sciences. We describe the components of a CLSM system and assess how modern implementations of the approach have further expanded the use of the technique. Finally, we briefly outline some practical considerations to take into account when acquiring data using a CLSM system. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Peter O Bayguinov
- Center for Cellular Imaging, Washington University in St. Louis, St. Louis, Missouri
| | - Dennis M Oakley
- Center for Cellular Imaging, Washington University in St. Louis, St. Louis, Missouri
| | - Chien-Cheng Shih
- Center for Cellular Imaging, Washington University in St. Louis, St. Louis, Missouri
| | - Daniel J Geanon
- Center for Cellular Imaging, Washington University in St. Louis, St. Louis, Missouri
| | - Matthew S Joens
- Center for Cellular Imaging, Washington University in St. Louis, St. Louis, Missouri
| | - James A J Fitzpatrick
- Center for Cellular Imaging, Washington University in St. Louis, St. Louis, Missouri.,Departments of Cell Biology & Physiology and Neuroscience, Washington University School of Medicine, St. Louis, Missouri.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri
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41
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Hoshi M, Reginensi A, Joens MS, Fitzpatrick JAJ, McNeill H, Jain S. Reciprocal Spatiotemporally Controlled Apoptosis Regulates Wolffian Duct Cloaca Fusion. J Am Soc Nephrol 2018; 29:775-783. [PMID: 29326158 DOI: 10.1681/asn.2017040380] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 12/04/2017] [Indexed: 01/04/2023] Open
Abstract
The epithelial Wolffian duct (WD) inserts into the cloaca (primitive bladder) before metanephric kidney development, thereby establishing the initial plumbing for eventual joining of the ureters and bladder. Defects in this process cause common anomalies in the spectrum of congenital anomalies of the kidney and urinary tract (CAKUT). However, developmental, cellular, and molecular mechanisms of WD-cloaca fusion are poorly understood. Through systematic analysis of early WD tip development in mice, we discovered that a novel process of spatiotemporally regulated apoptosis in WD and cloaca was necessary for WD-cloaca fusion. Aberrant RET tyrosine kinase signaling through tyrosine (Y) 1062, to which PI3K- or ERK-activating proteins dock, or Y1015, to which PLCγ docks, has been shown to cause CAKUT-like defects. Cloacal apoptosis did not occur in RetY1062F mutants, in which WDs did not reach the cloaca, or in RetY1015F mutants, in which WD tips reached the cloaca but did not fuse. Moreover, inhibition of ERK or apoptosis prevented WD-cloaca fusion in cultures, and WD-specific genetic deletion of YAP attenuated cloacal apoptosis and WD-cloacal fusion in vivo Thus, cloacal apoptosis requires direct contact and signals from the WD tip and is necessary for WD-cloacal fusion. These findings may explain the mechanisms of many CAKUT.
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Affiliation(s)
- Masato Hoshi
- Division of Nephrology, Department of Internal Medicine
| | - Antoine Reginensi
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - James A J Fitzpatrick
- Center for Cellular Imaging.,Department of Cell Biology and Physiology.,Department of Neuroscience, and
| | - Helen McNeill
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sanjay Jain
- Division of Nephrology, Department of Internal Medicine, .,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri; and
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42
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Hummer BH, de Leeuw NF, Burns C, Chen L, Joens MS, Hosford B, Fitzpatrick JAJ, Asensio CS. HID-1 controls formation of large dense core vesicles by influencing cargo sorting and trans-Golgi network acidification. Mol Biol Cell 2017; 28:3870-3880. [PMID: 29074564 PMCID: PMC5739301 DOI: 10.1091/mbc.e17-08-0491] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/05/2017] [Accepted: 10/16/2017] [Indexed: 12/19/2022] Open
Abstract
The peripheral membrane protein HID-1 localizes to the trans-Golgi network, where it contributes to the formation of large dense core vesicles of neuroendocrine cells by influencing cargo sorting and trans-Golgi network acidification. Large dense core vesicles (LDCVs) mediate the regulated release of neuropeptides and peptide hormones. They form at the trans-Golgi network (TGN), where their soluble content aggregates to form a dense core, but the mechanisms controlling biogenesis are still not completely understood. Recent studies have implicated the peripheral membrane protein HID-1 in neuropeptide sorting and insulin secretion. Using CRISPR/Cas9, we generated HID-1 KO rat neuroendocrine cells, and we show that the absence of HID-1 results in specific defects in peptide hormone and monoamine storage and regulated secretion. Loss of HID-1 causes a reduction in the number of LDCVs and affects their morphology and biochemical properties, due to impaired cargo sorting and dense core formation. HID-1 KO cells also exhibit defects in TGN acidification together with mislocalization of the Golgi-enriched vacuolar H+-ATPase subunit isoform a2. We propose that HID-1 influences early steps in LDCV formation by controlling dense core formation at the TGN.
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Affiliation(s)
- Blake H Hummer
- Department of Biological Sciences, University of Denver, Denver, CO 80210
| | - Noah F de Leeuw
- Department of Biological Sciences, University of Denver, Denver, CO 80210
| | - Christian Burns
- Department of Biological Sciences, University of Denver, Denver, CO 80210
| | - Lan Chen
- Department of Biological Sciences, University of Denver, Denver, CO 80210
| | - Matthew S Joens
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110
| | - Bethany Hosford
- Department of Biological Sciences, University of Denver, Denver, CO 80210
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110
| | - Cedric S Asensio
- Department of Biological Sciences, University of Denver, Denver, CO 80210
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43
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Ross MH, Esser AK, Fox GC, Schmieder AH, Yang X, Hu G, Pan D, Su X, Xu Y, Novack DV, Walsh T, Colditz GA, Lukaszewicz GH, Cordell E, Novack J, Fitzpatrick JAJ, Waning DL, Mohammad KS, Guise TA, Lanza GM, Weilbaecher KN. Bone-Induced Expression of Integrin β3 Enables Targeted Nanotherapy of Breast Cancer Metastases. Cancer Res 2017; 77:6299-6312. [PMID: 28855208 DOI: 10.1158/0008-5472.can-17-1225] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 07/26/2017] [Accepted: 08/24/2017] [Indexed: 11/16/2022]
Abstract
Bone metastases occur in approximately 70% of metastatic breast cancer patients, often leading to skeletal injuries. Current treatments are mainly palliative and underscore the unmet clinical need for improved therapies. In this study, we provide preclinical evidence for an antimetastatic therapy based on targeting integrin β3 (β3), which is selectively induced on breast cancer cells in bone by the local bone microenvironment. In a preclinical model of breast cancer, β3 was strongly expressed on bone metastatic cancer cells, but not primary mammary tumors or visceral metastases. In tumor tissue from breast cancer patients, β3 was significantly elevated on bone metastases relative to primary tumors from the same patient (n = 42). Mechanistic investigations revealed that TGFβ signaling through SMAD2/SMAD3 was necessary for breast cancer induction of β3 within the bone. Using a micelle-based nanoparticle therapy that recognizes integrin αvβ3 (αvβ3-MPs of ∼12.5 nm), we demonstrated specific localization to breast cancer bone metastases in mice. Using this system for targeted delivery of the chemotherapeutic docetaxel, we showed that bone tumor burden could be reduced significantly with less bone destruction and less hepatotoxicity compared with equimolar doses of free docetaxel. Furthermore, mice treated with αvβ3-MP-docetaxel exhibited a significant decrease in bone-residing tumor cell proliferation compared with free docetaxel. Taken together, our results offer preclinical proof of concept for a method to enhance delivery of chemotherapeutics to breast cancer cells within the bone by exploiting their selective expression of integrin αvβ3 at that metastatic site. Cancer Res; 77(22); 6299-312. ©2017 AACR.
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Affiliation(s)
- Michael H Ross
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Alison K Esser
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Gregory C Fox
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Anne H Schmieder
- Department of Medicine, Division of Cardiology, Washington University School of Medicine, St. Louis, Missouri
| | - Xiaoxia Yang
- Department of Medicine, Division of Cardiology, Washington University School of Medicine, St. Louis, Missouri
| | - Grace Hu
- Department of Medicine, Division of Cardiology, Washington University School of Medicine, St. Louis, Missouri
| | - Dipanjan Pan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois
| | - Xinming Su
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Yalin Xu
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Deborah V Novack
- Department of Medicine, Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, Missouri
- Department of Pathology, Washington University School of Medicine, St. Louis, Missouri
| | - Thomas Walsh
- Department of Surgery, Division of Public Health Sciences, St. Louis Breast Tissue Registry, Washington University School of Medicine, St. Louis, Missouri
| | - Graham A Colditz
- Department of Surgery, Division of Public Health Sciences, St. Louis Breast Tissue Registry, Washington University School of Medicine, St. Louis, Missouri
| | - Gabriel H Lukaszewicz
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Elizabeth Cordell
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Joshua Novack
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - James A J Fitzpatrick
- Departments of Cell Biology & Physiology and Neuroscience, Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, Missouri
| | - David L Waning
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Khalid S Mohammad
- Department of Medicine, Division of Endocrinology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Theresa A Guise
- Department of Medicine, Division of Endocrinology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Gregory M Lanza
- Department of Medicine, Division of Cardiology, Washington University School of Medicine, St. Louis, Missouri
| | - Katherine N Weilbaecher
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri.
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Kerman BE, Kim HJ, Padmanabhan K, Mei A, Georges S, Joens MS, Fitzpatrick JAJ, Jappelli R, Chandross KJ, August P, Gage FH. In vitro myelin formation using embryonic stem cells. Development 2015; 142:2213-25. [PMID: 26015546 DOI: 10.1242/dev.116517] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 04/21/2015] [Indexed: 01/21/2023]
Abstract
Myelination in the central nervous system is the process by which oligodendrocytes form myelin sheaths around the axons of neurons. Myelination enables neurons to transmit information more quickly and more efficiently and allows for more complex brain functions; yet, remarkably, the underlying mechanism by which myelination occurs is still not fully understood. A reliable in vitro assay is essential to dissect oligodendrocyte and myelin biology. Hence, we developed a protocol to generate myelinating oligodendrocytes from mouse embryonic stem cells and established a myelin formation assay with embryonic stem cell-derived neurons in microfluidic devices. Myelin formation was quantified using a custom semi-automated method that is suitable for larger scale analysis. Finally, early myelination was followed in real time over several days and the results have led us to propose a new model for myelin formation.
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Affiliation(s)
- Bilal E Kerman
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hyung Joon Kim
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Krishnan Padmanabhan
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA Computational Neuroscience Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA Crick Jacobs Center for Theoretical and Computational Biology, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Arianna Mei
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Shereen Georges
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Matthew S Joens
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - James A J Fitzpatrick
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Roberto Jappelli
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Karen J Chandross
- Sanofi US, R&D, Genzyme MS/Neurology, 55 Corporate Drive, Bridgewater, NJ 08807, USA
| | - Paul August
- Sanofi US, R&D, Early to Candidate Unit, Tucson Innovation Center, 2090 E. Innovation Park Drive, Tucson, AZ 85755, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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Abstract
The development of confocal microscopy techniques introduced the ability to optically section fluorescent samples in the axial dimension, perpendicular to the image plane. These approaches, via the placement of a pinhole in the conjugate image plane, provided superior resolution in the axial (z) dimension resulting in nearly isotropic optical sections. However, increased axial resolution, via pinhole optics, comes at the cost of both speed and excitation efficiency. Light sheet fluorescent microscopy (LSFM), a century-old idea made possible with modern developments in both excitation and detection optics, provides sub-cellular resolution and optical sectioning capabilities without compromising speed or excitation efficiency. Over the past decade, several variations of LSFM have been implemented each with its own benefits and deficiencies. Here we discuss LSFM fundamentals and outline the basic principles of several major light-sheet-based imaging modalities (SPIM, inverted SPIM, multi-view SPIM, Bessel beam SPIM, and stimulated emission depletion SPIM) while considering their biological relevance in terms of intrusiveness, temporal resolution, and sample requirements.
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Affiliation(s)
- Michael W Adams
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California
| | - Andrew F Loftus
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California
| | - Sarah E Dunn
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California
| | - Matthew S Joens
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California
| | - James A J Fitzpatrick
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California
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46
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Contreras H, Joens MS, McMath LM, Le VP, Tullius MV, Kimmey JM, Bionghi N, Horwitz MA, Fitzpatrick JAJ, Goulding CW. Characterization of a Mycobacterium tuberculosis nanocompartment and its potential cargo proteins. J Biol Chem 2014; 289:18279-89. [PMID: 24855650 PMCID: PMC4140288 DOI: 10.1074/jbc.m114.570119] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/19/2014] [Indexed: 01/24/2023] Open
Abstract
Mycobacterium tuberculosis has evolved various mechanisms by which the bacterium can maintain homeostasis under numerous environmental assaults generated by the host immune response. M. tuberculosis harbors enzymes involved in the oxidative stress response that aid in survival during the production of reactive oxygen species in activated macrophages. Previous studies have shown that a dye-decolorizing peroxidase (DyP) is encapsulated by a bacterial nanocompartment, encapsulin (Enc), whereby packaged DyP interacts with Enc via a unique C-terminal extension. M. tuberculosis also harbors an encapsulin homolog (CFP-29, Mt-Enc), within an operon with M. tuberculosis DyP (Mt-DyP), which contains a C-terminal extension. Together these observations suggest that Mt-DyP interacts with Mt-Enc. Furthermore, it has been suggested that DyPs may function as either a heme-dependent peroxidase or a deferrochelatase. Like Mt-DyP, M. tuberculosis iron storage ferritin protein, Mt-BfrB, and an M. tuberculosis protein involved in folate biosynthesis, 7,8-dihydroneopterin aldolase (Mt-FolB), have C-terminal tails that could also interact with Mt-Enc. For the first time, we show by co-purification and electron microscopy that mycobacteria via Mt-Enc can encapsulate Mt-DyP, Mt-BfrB, and Mt-FolB. Functional studies of free or encapsulated proteins demonstrate that they retain their enzymatic activity within the Mt-Enc nanocompartment. Mt-DyP, Mt-FolB, and Mt-BfrB all have antioxidant properties, suggesting that if these proteins are encapsulated by Mt-Enc, then this nanocage may play a role in the M. tuberculosis oxidative stress response. This report provides initial structural and biochemical clues regarding the molecular mechanisms that utilize compartmentalization by which the mycobacterial cell may aid in detoxification of the local environment to ensure long term survival.
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Affiliation(s)
- Heidi Contreras
- From the Departments of Molecular Biology and Biochemistry and
| | - Matthew S Joens
- the Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California 92037, and
| | - Lisa M McMath
- From the Departments of Molecular Biology and Biochemistry and
| | - Vincent P Le
- From the Departments of Molecular Biology and Biochemistry and
| | - Michael V Tullius
- the Division of Infectious Diseases, Department of Medicine, School of Medicine, UCLA, Los Angeles, California 90095
| | - Jaqueline M Kimmey
- the Division of Infectious Diseases, Department of Medicine, School of Medicine, UCLA, Los Angeles, California 90095
| | - Neda Bionghi
- the Division of Infectious Diseases, Department of Medicine, School of Medicine, UCLA, Los Angeles, California 90095
| | - Marcus A Horwitz
- the Division of Infectious Diseases, Department of Medicine, School of Medicine, UCLA, Los Angeles, California 90095
| | - James A J Fitzpatrick
- the Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California 92037, and
| | - Celia W Goulding
- From the Departments of Molecular Biology and Biochemistry and Pharmaceutical Sciences, University of California, Irvine, California 92697,
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Fitzpatrick JAJ, Inouye Y, Manley S, Moerner WE. From “There′s Plenty of Room at the Bottom” to Seeing What is Actually There. Chemphyschem 2014; 15:547-9. [DOI: 10.1002/cphc.201400097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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48
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Joens MS, Huynh C, Kasuboski JM, Ferranti D, Sigal YJ, Zeitvogel F, Obst M, Burkhardt CJ, Curran KP, Chalasani SH, Stern LA, Goetze B, Fitzpatrick JAJ. Helium Ion Microscopy (HIM) for the imaging of biological samples at sub-nanometer resolution. Sci Rep 2013; 3:3514. [PMID: 24343236 PMCID: PMC3865489 DOI: 10.1038/srep03514] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/26/2013] [Indexed: 11/08/2022] Open
Abstract
Scanning Electron Microscopy (SEM) has long been the standard in imaging the sub-micrometer surface ultrastructure of both hard and soft materials. In the case of biological samples, it has provided great insights into their physical architecture. However, three of the fundamental challenges in the SEM imaging of soft materials are that of limited imaging resolution at high magnification, charging caused by the insulating properties of most biological samples and the loss of subtle surface features by heavy metal coating. These challenges have recently been overcome with the development of the Helium Ion Microscope (HIM), which boasts advances in charge reduction, minimized sample damage, high surface contrast without the need for metal coating, increased depth of field, and 5 angstrom imaging resolution. We demonstrate the advantages of HIM for imaging biological surfaces as well as compare and contrast the effects of sample preparation techniques and their consequences on sub-nanometer ultrastructure.
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Affiliation(s)
- Matthew S. Joens
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Chuong Huynh
- Ion Microscopy Innovation Center, Carl Zeiss Microscopy LLC, One Corporation Way, Peabody, MA 01960, USA
| | - James M. Kasuboski
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - David Ferranti
- Ion Microscopy Innovation Center, Carl Zeiss Microscopy LLC, One Corporation Way, Peabody, MA 01960, USA
| | - Yury J. Sigal
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Fabian Zeitvogel
- Center for Applied Geosciences, University Tübingen, Hoelderlinstr. 12, 72074 Tuebingen, Germany
| | - Martin Obst
- Center for Applied Geosciences, University Tübingen, Hoelderlinstr. 12, 72074 Tuebingen, Germany
| | - Claus J. Burkhardt
- NMI Natural and Medical Sciences Institute, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Kevin P. Curran
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sreekanth H. Chalasani
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lewis A. Stern
- Ion Microscopy Innovation Center, Carl Zeiss Microscopy LLC, One Corporation Way, Peabody, MA 01960, USA
| | - Bernhard Goetze
- Ion Microscopy Innovation Center, Carl Zeiss Microscopy LLC, One Corporation Way, Peabody, MA 01960, USA
| | - James A. J. Fitzpatrick
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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Hu YS, Zhu Q, Elkins K, Tse K, Li Y, Fitzpatrick JAJ, Verma IM, Cang H. Light-sheet Bayesian microscopy enables deep-cell super-resolution imaging of heterochromatin in live human embryonic stem cells. ACTA ACUST UNITED AC 2013; 2. [PMID: 27795878 PMCID: PMC5082751 DOI: 10.1186/2192-2853-2-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Background Heterochromatin in the nucleus of human embryonic cells plays an important role in the epigenetic regulation of gene expression. The architecture of heterochromatin and its dynamic organization remain elusive because of the lack of fast and high-resolution deep-cell imaging tools. We enable this task by advancing instrumental and algorithmic implementation of the localization-based super-resolution technique. Results We present light-sheet Bayesian super-resolution microscopy (LSBM). We adapt light-sheet illumination for super-resolution imaging by using a novel prism-coupled condenser design to illuminate a thin slice of the nucleus with high signal-to-noise ratio. Coupled with a Bayesian algorithm that resolves overlapping fluorophores from high-density areas, we show, for the first time, nanoscopic features of the heterochromatin structure in both fixed and live human embryonic stem cells. The enhanced temporal resolution allows capturing the dynamic change of heterochromatin with a lateral resolution of 50–60 nm on a time scale of 2.3 s. Conclusion Light-sheet Bayesian microscopy opens up broad new possibilities of probing nanometer-scale nuclear structures and real-time sub-cellular processes and other previously difficult-to-access intracellular regions of living cells at the single-molecule, and single cell level.
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Affiliation(s)
- Ying S Hu
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Quan Zhu
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Keri Elkins
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kevin Tse
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Yu Li
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - James A J Fitzpatrick
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Inder M Verma
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Hu Cang
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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Chien YH, Werner ME, Stubbs J, Joens MS, Li J, Chien S, Fitzpatrick JAJ, Mitchell BJ, Kintner C. Bbof1 is required to maintain cilia orientation. Development 2013; 140:3468-77. [PMID: 23900544 DOI: 10.1242/dev.096727] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Multiciliate cells (MCCs) are highly specialized epithelial cells that employ hundreds of motile cilia to produce a vigorous directed flow in a variety of organ systems. The production of this flow requires the establishment of planar cell polarity (PCP) whereby MCCs align hundreds of beating cilia along a common planar axis. The planar axis of cilia in MCCs is known to be established via the PCP pathway and hydrodynamic cues, but the downstream steps required for cilia orientation remain poorly defined. Here, we describe a new component of cilia orientation, based on the phenotypic analysis of an uncharacterized coiled-coil protein, called bbof1. We show that the expression of bbof1 is induced during the early phases of MCC differentiation by the master regulator foxj1. MCC differentiation and ciliogenesis occurs normally in embryos where bbof1 activity is reduced, but cilia orientation is severely disrupted. We show that cilia in bbof1 mutants can still respond to patterning and hydrodynamic cues, but lack the ability to maintain their precise orientation. Misexpression of bbof1 promotes cilia alignment, even in the absence of flow or in embryos where microtubules and actin filaments are disrupted. Bbof1 appears to mediate cilia alignment by localizing to a polar structure adjacent to the basal body. Together, these results suggest that bbof1 is a basal body component required in MCCs to align and maintain cilia orientation in response to flow.
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Affiliation(s)
- Yuan-Hung Chien
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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