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  1. Article: Constitutive Endolysosomal Perforation in Neurons allows Induction of α-Synuclein Aggregation by Internalized Pre-Formed Fibrils.

    Sanyal, Anwesha / Scanavachi, Gustavo / Somerville, Elliott / Saminathan, Anand / Nair, Athul / Oikonomou, Athanasios / Hatzakis, Nikos S / Kirchhausen, Tom

    bioRxiv : the preprint server for biology

    2024  

    Abstract: The endocytic pathway is both an essential route of molecular uptake in cells and a potential entry point for pathology-inducing cargo. The cell-to-cell spread of cytotoxic aggregates, such as those of α-synuclein (α-syn) in Parkinson's Disease (PD), ... ...

    Abstract The endocytic pathway is both an essential route of molecular uptake in cells and a potential entry point for pathology-inducing cargo. The cell-to-cell spread of cytotoxic aggregates, such as those of α-synuclein (α-syn) in Parkinson's Disease (PD), exemplifies this duality. Here we used a human iPSC-derived induced neuronal model (iNs) prone to death mediated by aggregation in late endosomes and lysosomes of endogenous α-syn, seeded by internalized pre-formed fibrils of α-syn (PFFs). This PFF-mediated death was not observed with parental iPSCs or other non-neuronal cells. Using live-cell optical microscopy to visualize the read out of biosensors reporting endo-lysosome wounding, we discovered that up to about 10% of late endosomes and lysosomes in iNs exhibited spontaneous constitutive perforations, regardless of the presence of internalized PFFs. This wounding, absent in parental iPSCs and non-neuronal cells, corresponded to partial damage by nanopores in the limiting membranes of a subset of endolysosomes directly observed by volumetric focused ion beam scanning electron microscopy (FIB-SEM) in iNs and in CA1 pyramidal neurons from mouse brain, and not found in iPSCs or in other non-neuronal cells in culture or in mouse liver and skin. We suggest that the compromised limiting membranes in iNs and neurons in general are the primary conduit for cytosolic α-syn to access PFFs entrapped within endo-lysosomal lumens, initiating PFF-mediated α-syn aggregation. Significantly, eradicating the intrinsic endolysosomal perforations in iNs by inhibiting the endosomal Phosphatidylinositol-3-Phosphate/Phosphatidylinositol 5-Kinase (PIKfyve kinase) using Apilimod or Vacuolin-1 markedly reduced PFF-induced α-syn aggregation, despite PFFs continuing to enter the endolysosomal compartment. Crucially, this intervention also diminished iN death associated with PFF incubation. Our results reveal the surprising presence of intrinsically perforated endo-lysosomes in neurons, underscoring their crucial early involvement in the genesis of toxic α-syn aggregates induced by internalized PFFs. This discovery offers a basis for employing PIKfyve kinase inhibition as a potential therapeutic strategy to counteract synucleinopathies.
    Language English
    Publishing date 2024-01-01
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.12.30.573738
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Bending membranes.

    Kirchhausen, Tom

    Nature cell biology

    2012  Volume 14, Issue 9, Page(s) 906–908

    Abstract: It is widely assumed that peripheral membrane proteins induce intracellular membrane curvature by the asymmetric insertion of a protein segment into the lipid bilayer, or by imposing shape by adhesion of a curved protein domain to the membrane surface. ... ...

    Abstract It is widely assumed that peripheral membrane proteins induce intracellular membrane curvature by the asymmetric insertion of a protein segment into the lipid bilayer, or by imposing shape by adhesion of a curved protein domain to the membrane surface. Two papers now provide convincing evidence challenging these views. The first shows that specific assembly of a clathrin protein scaffold, coupled to the membrane, seems to be the most prevalent mechanism for bending a lipid bilayer in a cell. The second reports that membrane crowding, driven by protein-protein interactions, can also drive membrane bending, even in the absence of any protein insertion into the bilayer.
    MeSH term(s) Cell Membrane/metabolism ; Clathrin/metabolism ; Clathrin-Coated Vesicles/metabolism ; Coated Vesicles/metabolism ; Membrane Proteins/metabolism
    Chemical Substances Clathrin ; Membrane Proteins
    Language English
    Publishing date 2012-09-04
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 1474722-4
    ISSN 1476-4679 ; 1465-7392
    ISSN (online) 1476-4679
    ISSN 1465-7392
    DOI 10.1038/ncb2570
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Temporal dynamics and stoichiometry in human Notch signaling from Notch synaptic complex formation to nuclear entry of the Notch intracellular domain.

    Tveriakhina, Lena / Scanavachi, Gustavo / Egan, Emily D / Da Cunha Correia, Ricardo Bango / Martin, Alexandre P / Rogers, Julia M / Yodh, Jeremy S / Aster, Jon C / Kirchhausen, Tom / Blacklow, Stephen C

    Developmental cell

    2024  

    Abstract: Mammalian Notch signaling occurs when the binding of Delta or Jagged to Notch stimulates the proteolytic release of the Notch intracellular domain (NICD), which enters the nucleus to control target gene expression. To determine the temporal dynamics of ... ...

    Abstract Mammalian Notch signaling occurs when the binding of Delta or Jagged to Notch stimulates the proteolytic release of the Notch intracellular domain (NICD), which enters the nucleus to control target gene expression. To determine the temporal dynamics of events associated with Notch signaling under native conditions, we fluorescently tagged Notch and Delta at their endogenous genomic loci and visualized them upon pairing of receiver (Notch) and sender (Delta) cells as a function of time after cell contact. At contact sites, Notch and Delta immediately accumulated at 1:1 stoichiometry in synapses, which resolved by 15-20 min after contact. Synapse formation preceded the entrance of the Notch extracellular domain into the sender cell and accumulation of NICD in the nucleus of the receiver cell, which approached a maximum after ∼45 min and was prevented by chemical and genetic inhibitors of signaling. These findings directly link Notch-Delta synapse dynamics to NICD production with spatiotemporal precision.
    Language English
    Publishing date 2024-03-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2054967-2
    ISSN 1878-1551 ; 1534-5807
    ISSN (online) 1878-1551
    ISSN 1534-5807
    DOI 10.1016/j.devcel.2024.03.021
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Imaging endocytic clathrin structures in living cells.

    Kirchhausen, Tom

    Trends in cell biology

    2009  Volume 19, Issue 11, Page(s) 596–605

    Abstract: Our understanding of the clathrin-dependent endocytic pathway owes much to new visualization techniques. Budding coated pits and clathrin-coated structures are transient molecular machines with distinctive morphological characteristics, and fluorescently ...

    Abstract Our understanding of the clathrin-dependent endocytic pathway owes much to new visualization techniques. Budding coated pits and clathrin-coated structures are transient molecular machines with distinctive morphological characteristics, and fluorescently labeled versions of a variety of marker proteins have given us a tantalizing glimpse of the dynamics of the system in living cells. Recent live-cell imaging studies have revealed unexpected modes of coat assembly, with distinct kinetics, distinct recruitment of associated proteins, distinct requirements for the participation of actin and its accessory proteins, and apparently distinct mechanisms of membrane deformation. A crucial issue is to connect the events detected by light microscopy with the structures and properties of the molecular constituents. Here, I outline descriptions of coat assembly in different circumstances that are consistent with what is known from X-ray crystallography and electron microscopy.
    MeSH term(s) Animals ; Cell Survival ; Clathrin/chemistry ; Clathrin/ultrastructure ; Crystallography, X-Ray ; Endocytosis ; Humans ; Microscopy, Electron
    Chemical Substances Clathrin
    Language English
    Publishing date 2009-10-17
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 30122-x
    ISSN 1879-3088 ; 0962-8924
    ISSN (online) 1879-3088
    ISSN 0962-8924
    DOI 10.1016/j.tcb.2009.09.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Deep learning assisted single particle tracking for automated correlation between diffusion and function.

    Kæstel-Hansen, Jacob / de Sautu, Marilina / Saminathan, Anand / Scanavachi, Gustavo / Da Cunha Correia, Ricardo F Bango / Nielsen, Annette Juma / Bleshøy, Sara Vogt / Boomsma, Wouter / Kirchhausen, Tom / Hatzakis, Nikos S

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Sub-cellular diffusion in living systems reflects cellular processes and interactions. Recent advances in optical microscopy allow the tracking of this nanoscale diffusion of individual objects with an unprecedented level of precision. However, the ... ...

    Abstract Sub-cellular diffusion in living systems reflects cellular processes and interactions. Recent advances in optical microscopy allow the tracking of this nanoscale diffusion of individual objects with an unprecedented level of precision. However, the agnostic and automated extraction of functional information from the diffusion of molecules and organelles within the sub-cellular environment, is labor-intensive and poses a significant challenge. Here we introduce DeepSPT, a deep learning framework to interpret the diffusional 2D or 3D temporal behavior of objects in a rapid and efficient manner, agnostically. Demonstrating its versatility, we have applied DeepSPT to automated mapping of the early events of viral infections, identifying distinct types of endosomal organelles, and clathrin-coated pits and vesicles with up to 95% accuracy and within seconds instead of weeks. The fact that DeepSPT effectively extracts biological information from diffusion alone indicates that besides structure, motion encodes function at the molecular and subcellular level.
    Language English
    Publishing date 2023-11-17
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.11.16.567393
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Temporal Dynamics and Stoichiometry in Notch Signaling - from Notch Synaptic Complex Formation to NICD Nuclear Entry.

    Tveriakhina, Lena / Scanavachi, Gustavo / Egan, Emily D / Correia, Ricardo Bango Da Cunha / Martin, Alexandre P / Rogers, Julia M / Yodh, Jeremy S / Aster, Jon C / Kirchhausen, Tom / Blacklow, Stephen C

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Mammalian Notch signaling occurs when binding of Delta or Jagged to Notch stimulates proteolytic release of the Notch intracellular domain (NICD), which enters the nucleus to regulate target gene expression. To determine the temporal dynamics of events ... ...

    Abstract Mammalian Notch signaling occurs when binding of Delta or Jagged to Notch stimulates proteolytic release of the Notch intracellular domain (NICD), which enters the nucleus to regulate target gene expression. To determine the temporal dynamics of events associated with Notch signaling under native conditions, we fluorescently tagged Notch and Delta at their endogenous genomic loci and visualized them upon pairing of receiver (Notch) and sender (Delta) cells as a function of time after cell contact. At contact sites, Notch and Delta immediately accumulated at 1:1 stoichiometry in synapses, which resolved by 15-20 min after contact. Synapse formation preceded entrance of the Notch extracellular domain into the sender cell and accumulation of NICD in the nucleus of the receiver cell, which approached a maximum after ∼45 min and was prevented by chemical and genetic inhibitors of signaling. These findings directly link Notch-Delta synapse dynamics to NICD production with unprecedented spatiotemporal precision.
    Language English
    Publishing date 2023-09-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.27.559780
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: A spatiotemporal Notch interaction map from plasma membrane to nucleus.

    Martin, Alexandre P / Bradshaw, Gary A / Eisert, Robyn J / Egan, Emily D / Tveriakhina, Lena / Rogers, Julia M / Dates, Andrew N / Scanavachi, Gustavo / Aster, Jon C / Kirchhausen, Tom / Kalocsay, Marian / Blacklow, Stephen C

    Science signaling

    2023  Volume 16, Issue 796, Page(s) eadg6474

    Abstract: Notch signaling relies on ligand-induced proteolysis of the transmembrane receptor Notch to liberate a nuclear effector that drives cell fate decisions. Upon ligand binding, sequential cleavage of Notch by the transmembrane protease ADAM10 and the ... ...

    Abstract Notch signaling relies on ligand-induced proteolysis of the transmembrane receptor Notch to liberate a nuclear effector that drives cell fate decisions. Upon ligand binding, sequential cleavage of Notch by the transmembrane protease ADAM10 and the intracellular protease γ-secretase releases the Notch intracellular domain (NICD), which translocates to the nucleus and forms a complex that induces target gene transcription. To map the location and timing of the individual steps required for the proteolysis and movement of Notch from the plasma membrane to the nucleus, we used proximity labeling with quantitative, multiplexed mass spectrometry to monitor the interaction partners of endogenous NOTCH2 after ligand stimulation in the presence of a γ-secretase inhibitor and as a function of time after inhibitor removal. Our studies showed that γ-secretase-mediated cleavage of NOTCH2 occurred in an intracellular compartment and that formation of nuclear complexes and recruitment of chromatin-modifying enzymes occurred within 45 min of inhibitor washout. These findings provide a detailed spatiotemporal map tracking the path of Notch from the plasma membrane to the nucleus and identify signaling events that are potential targets for modulating Notch activity.
    MeSH term(s) Amyloid Precursor Protein Secretases/genetics ; Amyloid Precursor Protein Secretases/metabolism ; Ligands ; Receptors, Notch/genetics ; Receptors, Notch/metabolism ; Cell Membrane/metabolism ; Signal Transduction ; Receptor, Notch1/genetics
    Chemical Substances Amyloid Precursor Protein Secretases (EC 3.4.-) ; Ligands ; Receptors, Notch ; Receptor, Notch1
    Language English
    Publishing date 2023-08-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2417226-1
    ISSN 1937-9145 ; 1945-0877
    ISSN (online) 1937-9145
    ISSN 1945-0877
    DOI 10.1126/scisignal.adg6474
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Complete Protection from SARS-CoV-2 Lung Infection in Mice Through Combined Intranasal Delivery of PIKfyve Kinase and TMPRSS2 Protease Inhibitors.

    Kant, Ravi / Kareinen, Lauri / Ojha, Ravi / Strandin, Tomas / Saber, Saber Hassan / Lesnikova, Angelina / Kuivanen, Suvi / Sirnonen, Tarja / Joensuu, Merja / Vapalahti, Olli / Kirchhausen, Tom / Kipar, Anja / Balistreri, Giuseppe

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Emerging variants of concern of SARS-CoV-2 can significantly reduce the prophylactic and therapeutic efficacy of vaccines and neutralizing antibodies due to mutations in the viral genome. Targeting cell host factors required for infection provides a ... ...

    Abstract Emerging variants of concern of SARS-CoV-2 can significantly reduce the prophylactic and therapeutic efficacy of vaccines and neutralizing antibodies due to mutations in the viral genome. Targeting cell host factors required for infection provides a complementary strategy to overcome this problem since the host genome is less susceptible to variation during the life span of infection. The enzymatic activities of the endosomal PIKfyve phosphoinositide kinase and the serine protease TMPRSS2 are essential to meditate infection in two complementary viral entry pathways. Simultaneous inhibition in cultured cells of their enzymatic activities with the small molecule inhibitors apilimod dimesylate and nafamostat mesylate synergistically prevent viral entry and infection of native SARS-CoV-2 and vesicular stomatitis virus (VSV)-SARS-CoV-2 chimeras expressing the SARS-CoV-2 surface spike (S) protein and of variants of concern. We now report prophylactic prevention of lung infection in mice intranasally infected with SARS-CoV-2 beta by combined intranasal delivery of very low doses of apilimod dimesylate and nafamostat mesylate, in a formulation that is stable for over 3 months at room temperature. Administration of these drugs up to 6 hours post infection did not inhibit infection of the lungs but substantially reduced death of infected airway epithelial cells. The efficiency and simplicity of formulation of the drug combination suggests its suitability as prophylactic or therapeutic treatment against SARS-CoV-2 infection in households, point of care facilities, and under conditions where refrigeration would not be readily available.
    Language English
    Publishing date 2023-07-20
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.07.19.549731
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Synergistic block of SARS-CoV-2 infection by combined drug inhibition of the host entry factors PIKfyve kinase and TMPRSS2 protease.

    Kreutzberger, Alex J B / Sanyal, Anwesha / Ojha, Ravi / Pyle, Jesse D / Vapalahti, Olli / Balistreri, Giuseppe / Kirchhausen, Tom

    bioRxiv : the preprint server for biology

    2021  

    Abstract: Repurposing FDA-approved inhibitors able to prevent infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could provide a rapid path to establish new therapeutic options to mitigate the effects of coronavirus disease 2019 (COVID-19). ... ...

    Abstract Repurposing FDA-approved inhibitors able to prevent infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could provide a rapid path to establish new therapeutic options to mitigate the effects of coronavirus disease 2019 (COVID-19). Proteolytic cleavages of the spike S protein of SARS-CoV-2, mediated by the host cell proteases cathepsin and TMPRSS2, alone or in combination, are key early activation steps required for efficient infection. The PIKfyve kinase inhibitor apilimod interferes with late endosomal viral traffic, and through an ill-defined mechanism prevents
    Language English
    Publishing date 2021-08-12
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.06.01.446623
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Synergistic Block of SARS-CoV-2 Infection by Combined Drug Inhibition of the Host Entry Factors PIKfyve Kinase and TMPRSS2 Protease.

    Kreutzberger, Alex J B / Sanyal, Anwesha / Ojha, Ravi / Pyle, Jesse D / Vapalahti, Olli / Balistreri, Giuseppe / Kirchhausen, Tom

    Journal of virology

    2021  Volume 95, Issue 21, Page(s) e0097521

    Abstract: Repurposing FDA-approved inhibitors able to prevent infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could provide a rapid path to establish new therapeutic options to mitigate the effects of coronavirus disease 2019 (COVID-19). ... ...

    Abstract Repurposing FDA-approved inhibitors able to prevent infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could provide a rapid path to establish new therapeutic options to mitigate the effects of coronavirus disease 2019 (COVID-19). Proteolytic cleavages of the spike (S) protein of SARS-CoV-2, mediated by the host cell proteases cathepsin and TMPRSS2, alone or in combination, are key early activation steps required for efficient infection. The PIKfyve kinase inhibitor apilimod interferes with late endosomal viral traffic and through an ill-defined mechanism prevents
    MeSH term(s) Animals ; Antiviral Agents/pharmacology ; Benzamidines/pharmacology ; COVID-19/drug therapy ; Cell Line, Tumor ; Chlorocebus aethiops ; Drug Synergism ; Esters/pharmacology ; Guanidines/pharmacology ; Humans ; Hydrazones/pharmacology ; Morpholines/pharmacology ; Phosphatidylinositol 3-Kinases/metabolism ; Phosphoinositide-3 Kinase Inhibitors/pharmacology ; Protease Inhibitors/pharmacology ; Pyrimidines/pharmacology ; SARS-CoV-2/drug effects ; SARS-CoV-2/physiology ; Serine Endopeptidases/metabolism ; Vero Cells ; Virus Internalization
    Chemical Substances Antiviral Agents ; Benzamidines ; Esters ; Guanidines ; Hydrazones ; Morpholines ; Phosphoinositide-3 Kinase Inhibitors ; Protease Inhibitors ; Pyrimidines ; camostat (0FD207WKDU) ; PIKFYVE protein, human (EC 2.7.1.137) ; Serine Endopeptidases (EC 3.4.21.-) ; TMPRSS2 protein, human (EC 3.4.21.-) ; apilimod (GFW2K84S4L) ; nafamostat (Y25LQ0H97D)
    Language English
    Publishing date 2021-08-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 80174-4
    ISSN 1098-5514 ; 0022-538X
    ISSN (online) 1098-5514
    ISSN 0022-538X
    DOI 10.1128/JVI.00975-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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