1
|
Choi JE, Qiao Y, Kryczek I, Yu J, Gurkan J, Bao Y, Gondal M, Tien JCY, Maj T, Yazdani S, Parolia A, Xia H, Zhou J, Wei S, Grove S, Vatan L, Lin H, Li G, Zheng Y, Zhang Y, Cao X, Su F, Wang R, He T, Cieslik M, Green MD, Zou W, Chinnaiyan AM. PIKfyve controls dendritic cell function and tumor immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582543. [PMID: 38464258 PMCID: PMC10925294 DOI: 10.1101/2024.02.28.582543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The modern armamentarium for cancer treatment includes immunotherapy and targeted therapy, such as protein kinase inhibitors. However, the mechanisms that allow cancer-targeting drugs to effectively mobilize dendritic cells (DCs) and affect immunotherapy are poorly understood. Here, we report that among shared gene targets of clinically relevant protein kinase inhibitors, high PIKFYVE expression was least predictive of complete response in patients who received immune checkpoint blockade (ICB). In immune cells, high PIKFYVE expression in DCs was associated with worse response to ICB. Genetic and pharmacological studies demonstrated that PIKfyve ablation enhanced DC function via selectively altering the alternate/non-canonical NF-κB pathway. Both loss of Pikfyve in DCs and treatment with apilimod, a potent and specific PIKfyve inhibitor, restrained tumor growth, enhanced DC-dependent T cell immunity, and potentiated ICB efficacy in tumor-bearing mouse models. Furthermore, the combination of a vaccine adjuvant and apilimod reduced tumor progression in vivo . Thus, PIKfyve negatively controls DCs, and PIKfyve inhibition has promise for cancer immunotherapy and vaccine treatment strategies.
Collapse
|
2
|
Tanaka Y, Kozuma L, Hino H, Takeya K, Eto M. Abemaciclib and Vacuolin-1 decrease aggregate-prone TDP-43 accumulation by accelerating autophagic flux. Biochem Biophys Rep 2024; 38:101705. [PMID: 38596406 PMCID: PMC11001778 DOI: 10.1016/j.bbrep.2024.101705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/14/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024] Open
Abstract
(Macro)autophagy is a cellular degradation system for unnecessary materials, such as aggregate-prone TDP-43, a central molecule in neurodegenerative diseases including amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Abemaciclib (Abe) and vacuolin-1 (Vac) treatments are known to induce vacuoles characterized by an autophagosome and a lysosome component, suggesting that they facilitate autophagosome-lysosome fusion. However, it remains unknown whether Abe and Vac suppress the accumulation of aggregate-prone TDP-43 by accelerating autophagic flux. In the present study, the Abe and Vac treatment dose-dependently reduced the GFP/RFP ratio in SH-SY5Y neuroblastoma cells stably expressing the autophagic flux marker GFP-LC3-RFP-LC3ΔG. Abe and Vac also increased the omegasome marker GFP-ATG13 signal and the autophagosome marker mCherry-LC3 localized to the lysosome marker LAMP1-GFP. The Abe and Vac treatment decreased the intracellular level of the lysosome marker LAMP1-GFP in SH-SY5Y cells stably expressing LAMP1-GFP, but did not increase the levels of LAMP1-GFP, the autophagosome marker LC3-II, or the multivesicular body marker TSG101 in the extracellular vesicle-enriched fraction. Moreover, Abe and Vac treatment autophagy-dependently inhibited GFP-tagged aggregate-prone TDP-43 accumulation. The results of a PI(3)P reporter assay using the fluorescent protein tagged-2 × FYVE and LAMP1-GFP indicated that Abe and Vac increased the intensity of the PI(3)P signal on lysosomes. A treatment with the VPS34 inhibitor wortmannin (WM) suppressed Abe-/Vac-facilitated autophagic flux and the degradation of GFP-tagged aggregate-prone TDP-43. Collectively, these results suggest that Abe and Vac degrade aggregate-prone TDP-43 by accelerating autophagosome formation and autophagosome-lysosome fusion through the formation of PI(3)P.
Collapse
Affiliation(s)
- Yoshinori Tanaka
- Biochemistry Unit, Faculty of Veterinary Medicine, Okayama University of Science, Imabari-shi, Ehime, Japan
| | - Lina Kozuma
- Biochemistry Unit, Faculty of Veterinary Medicine, Okayama University of Science, Imabari-shi, Ehime, Japan
| | - Hirotsugu Hino
- Division of Anatomical Science, Department of Functional Morphology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Kosuke Takeya
- Biochemistry Unit, Faculty of Veterinary Medicine, Okayama University of Science, Imabari-shi, Ehime, Japan
| | - Masumi Eto
- Biochemistry Unit, Faculty of Veterinary Medicine, Okayama University of Science, Imabari-shi, Ehime, Japan
| |
Collapse
|
3
|
Choi JE, Qiao Y, Kryczek I, Yu J, Gurkan J, Bao Y, Gondal M, Tien JCY, Maj T, Yazdani S, Parolia A, Xia H, Zhou J, Wei S, Grove S, Vatan L, Lin H, Li G, Zheng Y, Zhang Y, Cao X, Su F, Wang R, He T, Cieslik M, Green MD, Zou W, Chinnaiyan AM. PIKfyve, expressed by CD11c-positive cells, controls tumor immunity. Nat Commun 2024; 15:5487. [PMID: 38942798 PMCID: PMC11213953 DOI: 10.1038/s41467-024-48931-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 05/15/2024] [Indexed: 06/30/2024] Open
Abstract
Cancer treatment continues to shift from utilizing traditional therapies to targeted ones, such as protein kinase inhibitors and immunotherapy. Mobilizing dendritic cells (DC) and other myeloid cells with antigen presenting and cancer cell killing capacities is an attractive but not fully exploited approach. Here, we show that PIKFYVE is a shared gene target of clinically relevant protein kinase inhibitors and high expression of this gene in DCs is associated with poor patient response to immune checkpoint blockade (ICB) therapy. Genetic and pharmacological studies demonstrate that PIKfyve ablation enhances the function of CD11c+ cells (predominantly dendritic cells) via selectively altering the non-canonical NF-κB pathway. Both loss of Pikfyve in CD11c+ cells and treatment with apilimod, a potent and specific PIKfyve inhibitor, restrained tumor growth, enhanced DC-dependent T cell immunity, and potentiated ICB efficacy in tumor-bearing mouse models. Furthermore, the combination of a vaccine adjuvant and apilimod reduced tumor progression in vivo. Thus, PIKfyve negatively regulates the function of CD11c+ cells, and PIKfyve inhibition has promise for cancer immunotherapy and vaccine treatment strategies.
Collapse
Affiliation(s)
- Jae Eun Choi
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Yuanyuan Qiao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Ilona Kryczek
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Jiali Yu
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Gurkan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yi Bao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Mahnoor Gondal
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jean Ching-Yi Tien
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Tomasz Maj
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Sahr Yazdani
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Abhijit Parolia
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Houjun Xia
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - JiaJia Zhou
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Shuang Wei
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Sara Grove
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Linda Vatan
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Heng Lin
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Gaopeng Li
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zheng
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xuhong Cao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rui Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Tongchen He
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Marcin Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Michael D Green
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Department of Radiation Oncology Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Weiping Zou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA.
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI, USA.
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
4
|
Gopaldass N, Mayer A. PROPPINs and membrane fission in the endo-lysosomal system. Biochem Soc Trans 2024; 52:1233-1241. [PMID: 38747700 DOI: 10.1042/bst20230897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 06/27/2024]
Abstract
PROPPINs constitute a conserved protein family with multiple members being expressed in many eukaryotes. PROPPINs have mainly been investigated for their role in autophagy, where they co-operate with several core factors for autophagosome formation. Recently, novel functions of these proteins on endo-lysosomal compartments have emerged. PROPPINs support the division of these organelles and the formation of tubulo-vesicular cargo carriers that mediate protein exit from them, such as those generated by the Retromer coat. In both cases, PROPPINs provide membrane fission activity. Integrating information from yeast and human cells this review summarizes the most important molecular features that allow these proteins to facilitate membrane fission and thus provide a critical element to endo-lysosomal protein traffic.
Collapse
Affiliation(s)
- Navin Gopaldass
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Andreas Mayer
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| |
Collapse
|
5
|
Boesch DJ, Singla A, Han Y, Kramer DA, Liu Q, Suzuki K, Juneja P, Zhao X, Long X, Medlyn MJ, Billadeau DD, Chen Z, Chen B, Burstein E. Structural organization of the retriever-CCC endosomal recycling complex. Nat Struct Mol Biol 2024; 31:910-924. [PMID: 38062209 DOI: 10.1038/s41594-023-01184-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
The recycling of membrane proteins from endosomes to the cell surface is vital for cell signaling and survival. Retriever, a trimeric complex of vacuolar protein-sorting-associated protein (VPS)35L, VPS26C and VPS29, together with the CCC complex comprising coiled-coil domain-containing (CCDC)22, CCDC93 and copper metabolism domain-containing (COMMD) proteins, plays a crucial role in this process. The precise mechanisms underlying retriever assembly and its interaction with CCC have remained elusive. Here, we present a high-resolution structure of retriever in humans determined using cryogenic electron microscopy. The structure reveals a unique assembly mechanism, distinguishing it from its remotely related paralog retromer. By combining AlphaFold predictions and biochemical, cellular and proteomic analyses, we further elucidate the structural organization of the entire retriever-CCC complex across evolution and uncover how cancer-associated mutations in humans disrupt complex formation and impair membrane protein homeostasis. These findings provide a fundamental framework for understanding the biological and pathological implications associated with retriever-CCC-mediated endosomal recycling.
Collapse
Affiliation(s)
- Daniel J Boesch
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Amika Singla
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Han
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Daniel A Kramer
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Qi Liu
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kohei Suzuki
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Puneet Juneja
- Cryo-EM Facility, Office of Biotechnology, Iowa State University, Ames, IA, USA
| | - Xuefeng Zhao
- Information Technology Services, Iowa State University, Ames, IA, USA
| | - Xin Long
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael J Medlyn
- Division of Oncology Research, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Daniel D Billadeau
- Division of Oncology Research, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Baoyu Chen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.
| | - Ezra Burstein
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
6
|
Chadwick SR, Barreda D, Wu JZ, Ye G, Yusuf B, Ren D, Freeman SA. Two-pore channels regulate endomembrane tension to enable remodeling and resolution of phagolysosomes. Proc Natl Acad Sci U S A 2024; 121:e2309465121. [PMID: 38354262 PMCID: PMC10895354 DOI: 10.1073/pnas.2309465121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/21/2023] [Indexed: 02/16/2024] Open
Abstract
Phagocytes promptly resolve ingested targets to replenish lysosomes and maintain their responsiveness. The resolution process requires that degradative hydrolases, solute transporters, and proteins involved in lipid traffic are delivered and made active in phagolysosomes. It also involves extensive membrane remodeling. We report that cation channels that localize to phagolysosomes were essential for resolution. Specifically, the conductance of Na+ by two-pore channels (TPCs) and the presence of a Na+ gradient between the phagolysosome lumen and the cytosol were critical for the controlled release of membrane tension that permits deformation of the limiting phagolysosome membrane. In turn, membrane deformation was a necessary step to efficiently transport the cholesterol extracted from cellular targets, permeabilizing them to hydrolases. These results place TPCs as regulators of endomembrane remodeling events that precede target degradation in cases when the target is bound by a cholesterol-containing membrane. The findings may help to explain lipid metabolism dysfunction and autophagic flux impairment reported in TPC KO mice and establish stepwise regulation to the resolution process that begins with lysis of the target.
Collapse
Affiliation(s)
- Sarah R Chadwick
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Dante Barreda
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jing Ze Wu
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gang Ye
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Bushra Yusuf
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Dejian Ren
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Spencer A Freeman
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| |
Collapse
|
7
|
Rizalar FS, Lucht MT, Petzoldt A, Kong S, Sun J, Vines JH, Telugu NS, Diecke S, Kaas T, Bullmann T, Schmied C, Löwe D, King JS, Cho W, Hallermann S, Puchkov D, Sigrist SJ, Haucke V. Phosphatidylinositol 3,5-bisphosphate facilitates axonal vesicle transport and presynapse assembly. Science 2023; 382:223-230. [PMID: 37824668 PMCID: PMC10938084 DOI: 10.1126/science.adg1075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 08/16/2023] [Indexed: 10/14/2023]
Abstract
Neurons relay information via specialized presynaptic compartments for neurotransmission. Unlike conventional organelles, the specialized apparatus characterizing the neuronal presynapse must form de novo. How the components for presynaptic neurotransmission are transported and assembled is poorly understood. Our results show that the rare late endosomal signaling lipid phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2] directs the axonal cotransport of synaptic vesicle and active zone proteins in precursor vesicles in human neurons. Precursor vesicles are distinct from conventional secretory organelles, endosomes, and degradative lysosomes and are transported by coincident detection of PI(3,5)P2 and active ARL8 via kinesin KIF1A to the presynaptic compartment. Our findings identify a crucial mechanism that mediates the delivery of synaptic vesicle and active zone proteins to developing synapses.
Collapse
Affiliation(s)
- Filiz Sila Rizalar
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Max T. Lucht
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Astrid Petzoldt
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Shuhan Kong
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Jiachen Sun
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - James H. Vines
- School of Biosciences, University of Sheffield, Firth Court Western Bank, Sheffield S10 2TN, UK
| | - Narasimha Swamy Telugu
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Technology Platform Pluripotent Stem Cells, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Sebastian Diecke
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Technology Platform Pluripotent Stem Cells, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Thomas Kaas
- Leipzig University, Carl-Ludwig-Institute of Physiology, Faculty of Medicine, 04103 Leipzig, Germany
| | - Torsten Bullmann
- Leipzig University, Carl-Ludwig-Institute of Physiology, Faculty of Medicine, 04103 Leipzig, Germany
| | - Christopher Schmied
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Delia Löwe
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Jason S. King
- School of Biosciences, University of Sheffield, Firth Court Western Bank, Sheffield S10 2TN, UK
| | - Wonhwa Cho
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Stefan Hallermann
- Leipzig University, Carl-Ludwig-Institute of Physiology, Faculty of Medicine, 04103 Leipzig, Germany
| | - Dmytro Puchkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Stephan J. Sigrist
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
- Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| |
Collapse
|
8
|
Weckerly CC, Hammond GR. Molding a PI(3,5)P2 biosensor. J Cell Biol 2023; 222:e202308004. [PMID: 37578524 PMCID: PMC10424508 DOI: 10.1083/jcb.202308004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
The lipid phosphatidylinositol 3,5-bisphosphate-PI(3,5)P2-is known to be a key regulator of cellular traffic in health and disease, but its cellular localization was somewhat enigmatic until now, with the discovery of a new PI(3,5)P2 biosensor reported in this issue of JCB by Vines et al. (2023. J. Cell Biol.https://doi.org/10.1083/jcb.202209077).
Collapse
Affiliation(s)
- Claire C. Weckerly
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Gerald R.V. Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| |
Collapse
|
9
|
Rivero-Ríos P, Tsukahara T, Uygun T, Chen A, Chavis GD, Giridharan SSP, Iwase S, Sutton MA, Weisman LS. Recruitment of the SNX17-Retriever recycling pathway regulates synaptic function and plasticity. J Cell Biol 2023; 222:e202207025. [PMID: 37141105 PMCID: PMC10165670 DOI: 10.1083/jcb.202207025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 03/10/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
Trafficking of cell-surface proteins from endosomes to the plasma membrane is a key mechanism to regulate synaptic function. In non-neuronal cells, proteins recycle to the plasma membrane either via the SNX27-Retromer-WASH pathway or via the recently discovered SNX17-Retriever-CCC-WASH pathway. While SNX27 is responsible for the recycling of key neuronal receptors, the roles of SNX17 in neurons are less understood. Here, using cultured hippocampal neurons, we demonstrate that the SNX17 pathway regulates synaptic function and plasticity. Disruption of this pathway results in a loss of excitatory synapses and prevents structural plasticity during chemical long-term potentiation (cLTP). cLTP drives SNX17 recruitment to synapses, where its roles are in part mediated by regulating the surface expression of β1-integrin. SNX17 recruitment relies on NMDAR activation, CaMKII signaling, and requires binding to the Retriever and PI(3)P. Together, these findings provide molecular insights into the regulation of SNX17 at synapses and define key roles for SNX17 in synaptic maintenance and in regulating enduring forms of synaptic plasticity.
Collapse
Affiliation(s)
- Pilar Rivero-Ríos
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Takao Tsukahara
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tunahan Uygun
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Alex Chen
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Garrett D. Chavis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
- Molecular and Integrative Physiology Graduate Program, University, Ann Arbor, MI, USA
| | - Sai Srinivas Panapakkam Giridharan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Michael A. Sutton
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Molecular and Integrative Physiology Graduate Program, University, Ann Arbor, MI, USA
| | - Lois S. Weisman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
10
|
Boesch DJ, Singla A, Han Y, Kramer DA, Liu Q, Suzuki K, Juneja P, Zhao X, Long X, Medlyn MJ, Billadeau DD, Chen Z, Chen B, Burstein E. Structural Organization of the Retriever-CCC Endosomal Recycling Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543888. [PMID: 37333304 PMCID: PMC10274727 DOI: 10.1101/2023.06.06.543888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The recycling of membrane proteins from endosomes to the cell surface is vital for cell signaling and survival. Retriever, a trimeric complex of VPS35L, VPS26C and VPS29, together with the CCC complex comprising CCDC22, CCDC93, and COMMD proteins, plays a crucial role in this process. The precise mechanisms underlying Retriever assembly and its interaction with CCC have remained elusive. Here, we present the first high-resolution structure of Retriever determined using cryogenic electron microscopy. The structure reveals a unique assembly mechanism, distinguishing it from its remotely related paralog, Retromer. By combining AlphaFold predictions and biochemical, cellular, and proteomic analyses, we further elucidate the structural organization of the entire Retriever-CCC complex and uncover how cancer-associated mutations disrupt complex formation and impair membrane protein homeostasis. These findings provide a fundamental framework for understanding the biological and pathological implications associated with Retriever-CCC-mediated endosomal recycling.
Collapse
Affiliation(s)
- Daniel J. Boesch
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Amika Singla
- Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Yan Han
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Daniel A. Kramer
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Qi Liu
- Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Kohei Suzuki
- Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Puneet Juneja
- Cryo-EM facility, Office of Biotechnology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Xuefeng Zhao
- Research IT, College of Liberal Arts and Sciences, Iowa State University, 2415 Osborn Dr, Ames, IA 50011, USA
| | - Xin Long
- Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Michael J. Medlyn
- Division of Oncology Research, College of Medicine, Mayo Clinic, Rochester MN, 55905, USA
| | - Daniel D. Billadeau
- Division of Oncology Research, College of Medicine, Mayo Clinic, Rochester MN, 55905, USA
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Baoyu Chen
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Ezra Burstein
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| |
Collapse
|
11
|
Dostál V, Humhalová T, Beránková P, Pácalt O, Libusová L. SWIP mediates retromer-independent membrane recruitment of the WASH complex. Traffic 2023; 24:216-230. [PMID: 36995008 DOI: 10.1111/tra.12884] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/28/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
The pentameric WASH complex facilitates endosomal protein sorting by activating Arp2/3, which in turn leads to the formation of F-actin patches specifically on the endosomal surface. It is generally accepted that WASH complex attaches to the endosomal membrane via the interaction of its subunit FAM21 with the retromer subunit VPS35. However, we observe the WASH complex and F-actin present on endosomes even in the absence of VPS35. We show that the WASH complex binds to the endosomal surface in both a retromer-dependent and a retromer-independent manner. The retromer-independent membrane anchor is directly mediated by the subunit SWIP. Furthermore, SWIP can interact with a number of phosphoinositide species. Of those, our data suggest that the interaction with phosphatidylinositol-3,5-bisphosphate (PI(3,5)P2 ) is crucial to the endosomal binding of SWIP. Overall, this study reveals a new role of the WASH complex subunit SWIP and highlights the WASH complex as an independent, self-sufficient trafficking regulator.
Collapse
Affiliation(s)
- Vojtěch Dostál
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Tereza Humhalová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Pavla Beránková
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Ondřej Pácalt
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Lenka Libusová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| |
Collapse
|
12
|
Dellin M, Rohrbeck I, Asrani P, Schreiber JA, Ritter N, Glorius F, Wünsch B, Budde T, Temme L, Strünker T, Stallmeyer B, Tüttelmann F, Meuth SG, Spehr M, Matschke J, Steinbicker A, Gatsogiannis C, Stoll R, Strutz-Seebohm N, Seebohm G. The second PI(3,5)P 2 binding site in the S0 helix of KCNQ1 stabilizes PIP 2-at the primary PI1 site with potential consequences on intermediate-to-open state transition. Biol Chem 2023; 404:241-254. [PMID: 36809224 DOI: 10.1515/hsz-2022-0247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/13/2022] [Indexed: 02/23/2023]
Abstract
The Phosphatidylinositol 3-phosphate 5-kinase Type III PIKfyve is the main source for selectively generated phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2), a known regulator of membrane protein trafficking. PI(3,5)P2 facilitates the cardiac KCNQ1/KCNE1 channel plasma membrane abundance and therewith increases the macroscopic current amplitude. Functional-physical interaction of PI(3,5)P2 with membrane proteins and its structural impact is not sufficiently understood. This study aimed to identify molecular interaction sites and stimulatory mechanisms of the KCNQ1/KCNE1 channel via the PIKfyve-PI(3,5)P2 axis. Mutational scanning at the intracellular membrane leaflet and nuclear magnetic resonance (NMR) spectroscopy identified two PI(3,5)P2 binding sites, the known PIP2 site PS1 and the newly identified N-terminal α-helix S0 as relevant for functional PIKfyve effects. Cd2+ coordination to engineered cysteines and molecular modeling suggest that repositioning of S0 stabilizes the channel s open state, an effect strictly dependent on parallel binding of PI(3,5)P2 to both sites.
Collapse
Affiliation(s)
- Maurice Dellin
- IfGH-Cellular Electrophysiology, Department of Cardiology and Angiology, University Hospital of Münster, Robert-Koch Str. 45, D-48149, Münster, Germany
| | - Ina Rohrbeck
- IfGH-Cellular Electrophysiology, Department of Cardiology and Angiology, University Hospital of Münster, Robert-Koch Str. 45, D-48149, Münster, Germany
| | - Purva Asrani
- Faculty of Chemistry and Biochemistry, Biomolecular NMR Spectroscopy and RUBiospek|NMR, Ruhr University of Bochum, Universitätsstraße 150, D-44780, Bochum, Germany
| | - Julian A Schreiber
- IfGH-Cellular Electrophysiology, Department of Cardiology and Angiology, University Hospital of Münster, Robert-Koch Str. 45, D-48149, Münster, Germany
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149, Münster, Germany
| | - Nadine Ritter
- IfGH-Cellular Electrophysiology, Department of Cardiology and Angiology, University Hospital of Münster, Robert-Koch Str. 45, D-48149, Münster, Germany
- GRK 2515, Chemical biology of ion channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Frank Glorius
- GRK 2515, Chemical biology of ion channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, D-48149, Münster, Germany
| | - Bernhard Wünsch
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149, Münster, Germany
- GRK 2515, Chemical biology of ion channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Thomas Budde
- GRK 2515, Chemical biology of ion channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany
- Institute of Physiology I, Westfälische Wilhelms-Universität, Robert-Koch-Str. 27a, D-48149, Münster, Germany
| | - Louisa Temme
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149, Münster, Germany
- GRK 2515, Chemical biology of ion channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Timo Strünker
- GRK 2515, Chemical biology of ion channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, University of Münster, Domagkstraße 11, D-48149, Münster, Germany
- Cells in Motion Interfaculty Centre, University of Münster, Münster, Germany
| | - Birgit Stallmeyer
- Institute of Reproductive Genetics, University of Münster, Vesaliusweg 12-14, D-48149, Münster, Germany
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Vesaliusweg 12-14, D-48149, Münster, Germany
| | - Sven G Meuth
- Department of Neurology, Heinrich Heine University Düsseldorf, Moorenstraße 5, D-40225, Düsseldorf, Germany
| | - Marc Spehr
- Department of Chemosensation, Institute for Biology II, RWTH Aachen University, Worringerweg 3, D-52074, Aachen, Germany
| | - Johann Matschke
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, D-45147, Essen, Germany
| | - Andrea Steinbicker
- Goethe University Frankfurt and University Hospital Frankfurt, Theodor-Stern-Kai 7, D-60590, Frankfurt, Germany
| | - Christos Gatsogiannis
- Institute for Medical Physics and Biophysics and Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, Münster, Busso-Peus Strasse 10, D-48149, Germany
| | - Raphael Stoll
- Faculty of Chemistry and Biochemistry, Biomolecular NMR Spectroscopy and RUBiospek|NMR, Ruhr University of Bochum, Universitätsstraße 150, D-44780, Bochum, Germany
| | - Nathalie Strutz-Seebohm
- IfGH-Cellular Electrophysiology, Department of Cardiology and Angiology, University Hospital of Münster, Robert-Koch Str. 45, D-48149, Münster, Germany
| | - Guiscard Seebohm
- IfGH-Cellular Electrophysiology, Department of Cardiology and Angiology, University Hospital of Münster, Robert-Koch Str. 45, D-48149, Münster, Germany
- GRK 2515, Chemical biology of ion channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany
| |
Collapse
|
13
|
Placidi G, Mattu C, Ciardelli G, Campa CC. Small molecules targeting endocytic uptake and recycling pathways. Front Cell Dev Biol 2023; 11:1125801. [PMID: 36968200 PMCID: PMC10036367 DOI: 10.3389/fcell.2023.1125801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/23/2023] [Indexed: 03/12/2023] Open
Abstract
Over the past years a growing number of studies highlighted the pivotal role of intracellular trafficking in cell physiology. Among the distinct transport itineraries connecting the endocytic system, both internalization (endocytosis) and recycling (endocytic recycling) pathways were found fundamental to ensure cellular sensing, cell-to-cell communication, cellular division, and collective cell migration in tissue specific-contexts. Consistently, the dysregulation of endocytic trafficking pathways is correlated with several human diseases including both cancers and neurodegeneration. Aimed at suppress specific intracellular trafficking routes involved in disease onset and progression, huge efforts have been made to identify small molecule inhibitors with suitable pharmacological properties for in vivo administration. Here, we review most used drugs and recently discovered small molecules able to block endocytosis and endocytic recycling pathways. We characterize such pharmacological inhibitors by emphasizing their target specificity, molecular affinity, biological activity and efficacy in both in vitro and in vivo experimental models.
Collapse
Affiliation(s)
- Giampaolo Placidi
- Italian Institute for Genomic Medicine, Candiolo, Italy
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Clara Mattu
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Gianluca Ciardelli
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
- Chemical-Physical Processes, National Research Council (CNR-IPCF), Pisa, Italy
| | - Carlo C. Campa
- Italian Institute for Genomic Medicine, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| |
Collapse
|
14
|
Finicle B, Eckenstein K, Revenko A, Anderson B, Wan W, McCracken A, Gil D, Fruman D, Hanessian S, Seth P, Edinger A. Simultaneous inhibition of endocytic recycling and lysosomal fusion sensitizes cells and tissues to oligonucleotide therapeutics. Nucleic Acids Res 2023; 51:1583-1599. [PMID: 36727438 PMCID: PMC9976930 DOI: 10.1093/nar/gkad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/03/2023] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
Inefficient endosomal escape remains the primary barrier to the broad application of oligonucleotide therapeutics. Liver uptake after systemic administration is sufficiently robust that a therapeutic effect can be achieved but targeting extrahepatic tissues remains challenging. Prior attempts to improve oligonucleotide activity using small molecules that increase the leakiness of endosomes have failed due to unacceptable toxicity. Here, we show that the well-tolerated and orally bioavailable synthetic sphingolipid analog, SH-BC-893, increases the activity of antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs) up to 200-fold in vitro without permeabilizing endosomes. SH-BC-893 treatment trapped endocytosed oligonucleotides within extra-lysosomal compartments thought to be more permeable due to frequent membrane fission and fusion events. Simultaneous disruption of ARF6-dependent endocytic recycling and PIKfyve-dependent lysosomal fusion was necessary and sufficient for SH-BC-893 to increase non-lysosomal oligonucleotide levels and enhance their activity. In mice, oral administration of SH-BC-893 increased ASO potency in the liver by 15-fold without toxicity. More importantly, SH-BC-893 enabled target RNA knockdown in the CNS and lungs of mice treated subcutaneously with cholesterol-functionalized duplexed oligonucleotides or unmodified ASOs, respectively. Together, these results establish the feasibility of using a small molecule that disrupts endolysosomal trafficking to improve the activity of oligonucleotides in extrahepatic tissues.
Collapse
Affiliation(s)
- Brendan T Finicle
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Kazumi H Eckenstein
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | | | | | - W Brad Wan
- Ionis Pharmaceuticals, Carlsbad, CA, USA
| | | | | | - David A Fruman
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, Montréal, QC, Canada
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
| | | | - Aimee L Edinger
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| |
Collapse
|
15
|
Llorente A, Arora GK, Grenier SF, Emerling BM. PIP kinases: A versatile family that demands further therapeutic attention. Adv Biol Regul 2023; 87:100939. [PMID: 36517396 PMCID: PMC9992244 DOI: 10.1016/j.jbior.2022.100939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Phosphoinositides are membrane-localized phospholipids that regulate a plethora of essential cellular processes. These lipid signaling molecules are critical for cell homeostasis and therefore their levels are strictly regulated by the coordinated action of several families of lipid kinases and phosphatases. In this review, we provide a focused perspective on the phosphatidylinositol phosphate kinase (PIPK) family and the three subfamilies that compose it: Type I PIPKs or phosphatidylinositol-4-phosphate 5-kinases (PI4P5Ks), Type II PIPKs or phosphatidylinositol-5-phosphate 4-kinases (PI5P4Ks), and Type III PIPKs or phosphatidylinositol-3-phosphate 5-kinases (PIKfyve). Each subfamily is responsible for catalyzing a hydroxyl phosphorylation on specific phosphoinositide species to generate a double phosphorylated lipid, therefore regulating the levels of both substrate and product. Here, we summarize our current knowledge about the functions and regulation of each PIPK subfamily. Further, we highlight the roles of these kinases in various in vivo genetic models and give an overview of their involvement in multiple pathological conditions. The phosphoinositide field has been long focused on targeting PI3K signaling, but growing evidence suggests that it is time to draw attention to the other phosphoinositide kinases. The discovery of the involvement of PIPKs in the pathogenesis of multiple diseases has prompted substantial efforts to turn these enzymes into pharmacological targets. An increasingly refined knowledge of the biology of PIPKs in a variety of in vitro and in vivo models will facilitate the development of effective approaches for therapeutic intervention with the potential to translate into meaningful clinical benefits for patients suffering from cancer, immunological and infectious diseases, and neurodegenerative disorders.
Collapse
Affiliation(s)
- Alicia Llorente
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Gurpreet K Arora
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Shea F Grenier
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Brooke M Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA.
| |
Collapse
|
16
|
Integrin receptor trafficking in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 196:271-302. [PMID: 36813362 DOI: 10.1016/bs.pmbts.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Integrins are a family of 24 different heterodimers that are indispensable for multicellular life. Cell polarity, adhesion and migration are controlled by integrins delivered to the cell surface which in turn is regulated by the exo- and endocytic trafficking of integrins. The deep integration between trafficking and cell signaling determines the spatial and temporal output from any biochemical cue. Integrin trafficking plays a key role in development and many pathological conditions, especially cancer. Several novel regulators of integrin traffic have been discovered in recent times, including a novel class of integrin carrying vesicles, the intracellular nanovesicles (INVs). The tight regulation of trafficking pathways by cell signaling, where kinases phosphorylate key small GTPases in the trafficking pathway enable coordination of cell response to the extracellular milieu. Integrin heterodimer expression and trafficking differ in different tissues and contexts. In this Chapter, we discuss recent studies on integrin trafficking and its contribution to normal physiological and pathophysiological states.
Collapse
|
17
|
Liu N, Liu K, Yang C. WDR91 specifies the endosomal retrieval subdomain for retromer-dependent recycling. J Cell Biol 2022; 221:213515. [PMID: 36190447 PMCID: PMC9531996 DOI: 10.1083/jcb.202203013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 08/04/2022] [Accepted: 09/19/2022] [Indexed: 12/13/2022] Open
Abstract
Retromer-dependent endosomal recycling of membrane receptors requires Rab7, sorting nexin (SNX)-retromer, and factors that regulate endosomal actin organization. It is not fully understood how these factors cooperate to form endosomal subdomains for cargo retrieval and recycling. Here, we report that WDR91, a Rab7 effector, is the key factor that specifies the endosomal retrieval subdomain. Loss of WDR91 causes defective recycling of both intracellular and cell surface receptors. WDR91 interacts with SNXs through their PX domain, and with VPS35, thus promoting their interaction with Rab7. WDR91 also interacts with the WASH subunit FAM21. In WDR91-deficient cells, Rab7, SNX-retromer, and FAM21 fail to localize to endosomal subdomains, and endosomal actin organization is impaired. Re-expression of WDR91 enables Rab7, SNX-retromer, and FAM21 to concentrate at WDR91-specific endosomal subdomains, where retromer-mediated membrane tubulation and release occur. Thus, WDR91 coordinates Rab7 with SNX-retromer and WASH to establish the endosomal retrieval subdomains required for retromer-mediated endosomal recycling.
Collapse
Affiliation(s)
- Nan Liu
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Kai Liu
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Chonglin Yang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China,Correspondence to Chonglin Yang:
| |
Collapse
|
18
|
Lai M, De Carli A, Filipponi C, Iacono E, La Rocca V, Lottini G, Piazza CR, Quaranta P, Sidoti M, Pistello M, Freer G. Lipid balance remodelling by human positive-strand RNA viruses and the contribution of lysosomes. Antiviral Res 2022; 206:105398. [PMID: 35985406 DOI: 10.1016/j.antiviral.2022.105398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/03/2022] [Accepted: 08/10/2022] [Indexed: 11/27/2022]
Abstract
A marked reorganization of internal membranes occurs in the cytoplasm of cells infected by single stranded positive-sense RNA viruses. Most cell compartments change their asset to provide lipids for membrane rearrangement into replication organelles, where to concentrate viral proteins and enzymes while hiding from pathogen pattern recognition molecules. Because the endoplasmic reticulum is a central hub for lipid metabolism, when viruses hijack the organelle to form their replication organelles, a cascade of events change the intracellular environment. This results in a marked increase in lipid consumption, both by lipolysis and lipophagy of lipid droplets. In addition, lipids are used to produce energy for viral replication. At the same time, inflammation is started by signalling lipids, where lysosomal processing plays a relevant role. This review is aimed at providing an overview on what takes place after human class IV viruses have released their genome into the host cell and the consequences on lipid metabolism, including lysosomes.
Collapse
Affiliation(s)
- Michele Lai
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy.
| | - Alessandro De Carli
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy; Department of Medical Biotechnologies, University of Siena, Italy.
| | - Carolina Filipponi
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy.
| | - Elena Iacono
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy.
| | - Veronica La Rocca
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy; Institute of Life Sciences, Sant'Anna School of Advanced Studies, Pisa, Italy.
| | - Giulia Lottini
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy; Department of Medical Biotechnologies, University of Siena, Italy.
| | - Carmen Rita Piazza
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy; Department of Medical Biotechnologies, University of Siena, Italy.
| | - Paola Quaranta
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy.
| | - Maria Sidoti
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy.
| | - Mauro Pistello
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy.
| | - Giulia Freer
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy.
| |
Collapse
|
19
|
Inhibition of lipid kinase PIKfyve reveals a role for phosphatase Inpp4b in the regulation of PI(3)P-mediated lysosome dynamics through VPS34 activity. J Biol Chem 2022; 298:102187. [PMID: 35760104 PMCID: PMC9304791 DOI: 10.1016/j.jbc.2022.102187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022] Open
Abstract
Lysosome membranes contain diverse phosphoinositide (PtdIns) lipids that coordinate lysosome function and dynamics. The PtdIns repertoire on lysosomes is tightly regulated by the actions of diverse PtdIns kinases and phosphatases; however, specific roles for PtdIns in lysosomal functions and dynamics are currently unclear and require further investigation. It was previously shown that PIKfyve, a lipid kinase that synthesizes PtdIns(3,5)P2 from PtdIns(3)P, controls lysosome "fusion-fission" cycle dynamics, autophagosome turnover, and endocytic cargo delivery. Furthermore, INPP4B, a PtdIns 4-phosphatase that hydrolyzes PtdIns(3,4)P2 to form PtdIns(3)P, is emerging as a cancer-associated protein with roles in lysosomal biogenesis and other lysosomal functions. Here, we investigated the consequences of disrupting PIKfyve function in Inpp4b-deficient mouse embryonic fibroblasts. Through confocal fluorescence imaging, we observed the formation of massively enlarged lysosomes, accompanied by exacerbated reduction of endocytic trafficking, disrupted lysosome fusion-fission dynamics, and inhibition of autophagy. Finally, HPLC scintillation quantification of 3H-myo-inositol labelled phosphoinositides and phosphoinositide immunofluorescence staining, we observed that lysosomal PtdIns(3)P levels were significantly elevated in Inpp4b-deficient cells due to the hyperactivation of phosphatidylinositol 3-kinase catalytic subunit VPS34 enzymatic activity. In conclusion, our study identifies a novel signaling axis that maintains normal lysosomal homeostasis and dynamics, which includes the catalytic functions of Inpp4b, PIKfyve, and VPS34.
Collapse
|
20
|
Larocque G, Royle SJ. Integrating intracellular nanovesicles into integrin trafficking pathways and beyond. Cell Mol Life Sci 2022; 79:335. [PMID: 35657500 PMCID: PMC9166830 DOI: 10.1007/s00018-022-04371-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022]
Abstract
Membrane traffic controls the movement of proteins and lipids from one cellular compartment to another using a system of transport vesicles. Intracellular nanovesicles (INVs) are a newly described class of transport vesicles. These vesicles are small, carry diverse cargo, and are involved in multiple trafficking steps including anterograde traffic and endosomal recycling. An example of a biological process that they control is cell migration and invasion, due to their role in integrin recycling. In this review, we describe what is known so far about these vesicles. We discuss how INVs may integrate into established membrane trafficking pathways using integrin recycling as an example. We speculate where in the cell INVs have the potential to operate and we identify key questions for future investigation.
Collapse
Affiliation(s)
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill Road, Coventry, CV4 7AL, UK.
| |
Collapse
|
21
|
Rivero-Ríos P, Weisman LS. Roles of PIKfyve in multiple cellular pathways. Curr Opin Cell Biol 2022; 76:102086. [PMID: 35584589 PMCID: PMC9108489 DOI: 10.1016/j.ceb.2022.102086] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/27/2022] [Accepted: 04/02/2022] [Indexed: 02/01/2023]
Abstract
Phosphoinositide signaling lipids are crucial for eukaryotes and regulate many aspects of cell function. These signaling molecules are difficult to study because they are extremely low abundance. Here, we focus on two of the lowest abundance phosphoinositides, PI(3,5)P2 and PI(5)P, which play critical roles in cellular homeostasis, membrane trafficking and transcription. Their levels are tightly regulated by a protein complex that includes PIKfyve, Fig4 and Vac14. Importantly, mutations in this complex that decrease PI(3,5)P2 and PI(5)P are linked to human diseases, especially those of the nervous system. Paradoxically, PIKfyve inhibitors which decrease PI(3,5)P2 and PI(5)P, are currently being tested for some neurodegenerative diseases, as well as other diverse diseases including some cancers, and as a treatment for SARS-CoV2 infection. A more comprehensive picture of the pathways that are regulated by PIKfyve will be critical to understand the roles of PI(3,5)P2 and PI(5)P in normal human physiology and in disease.
Collapse
Affiliation(s)
- Pilar Rivero-Ríos
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lois S Weisman
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
22
|
Hasegawa J, Tokuda E, Yao Y, Sasaki T, Inoki K, Weisman LS. PP2A-dependent TFEB activation is blocked by PIKfyve-induced mTORC1 activity. Mol Biol Cell 2022; 33:ar26. [PMID: 35020443 PMCID: PMC9250387 DOI: 10.1091/mbc.e21-06-0309] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transcriptional factor EB (TFEB) is a master regulator of genes required for autophagy and lysosomal function. The nuclear localization of TFEB is blocked by the mechanistic target of rapamycin complex 1 (mTORC1)-dependent phosphorylation of TFEB at multiple sites including Ser-211. Here we show that inhibition of PIKfyve, which produces phosphatidylinositol 3,5-bisphosphate on endosomes and lysosomes, causes a loss of Ser-211 phosphorylation and concomitant nuclear localization of TFEB. We found that while mTORC1 activity toward S6K1, as well as other major mTORC1 substrates, is not impaired, PIKfyve inhibition specifically impedes the interaction of TFEB with mTORC1. This suggests that mTORC1 activity on TFEB is selectively inhibited due to loss of mTORC1 access to TFEB. In addition, we found that TFEB activation during inhibition of PIKfyve relies on the ability of protein phosphatase 2A (PP2A) but not calcineurin/PPP3 to dephosphorylate TFEB Ser-211. Thus when PIKfyve is inhibited, PP2A is dominant over mTORC1 for control of TFEB phosphorylation at Ser-S211. Together these findings suggest that mTORC1 and PP2A have opposing roles on TFEB via phosphorylation and dephosphorylation of Ser-211, respectively, and further that PIKfyve inhibits TFEB activity by facilitating mTORC1-dependent phosphorylation of TFEB.
Collapse
Affiliation(s)
- Junya Hasegawa
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Emi Tokuda
- Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yao Yao
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Takehiko Sasaki
- Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Ken Inoki
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan Medical School, 1137 East Catherine Street, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, University of Michigan Medical School, 1500 East Medical enter Drive, Ann Arbor, MI 48109, USA
| | - Lois S Weisman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109
| |
Collapse
|