Lesson 2 Modeling neurodegeneration in C.elegans

Applied Molecular Cellular Biology

1) What is vimentin? 🔧🧬

  • Class: Type III intermediate filament (IF) protein. Abundant in mesenchymal cells; re-expressed during stress, injury, EMT, and in culture. It stabilizes cell architecture and acts as a mechanosensitive scaffold that organizes signaling, actin, and microtubules.
  • Dynamic, not static: In vivo, vimentin continuously exchanges between polymerized filaments and soluble precursors (ULFs), enabling rapid remodeling during migration and division.
  • Cytoskeletal crosstalk: Binds actin and microtubules, often via plectin, to coordinate cortex organization, adhesion, and mitosis.
  • Knockout phenotype: Vim−/− mice are viable but reveal deficits under challenge, highlighting context-dependent functions.

Quick check: What feature lets vimentin rapidly reorganize during cell migration: stability or subunit exchange?

2) Expression programs and promoter logic 🧠➡️🧪

  • Promoter architecture: Vimentin transcription integrates positive and negative elements (e.g., NF-κB, AP-1, Sp1/Sp3, PEA3, ZBP-89/99, STAT1/3). This combinatorial control shifts with context like growth, differentiation, EMT, cancer, and infection.
  • Epigenetic and RNA-level control:
    • DNA/histone modifications tune promoter accessibility.
    • miRNAs targeting vimentin modulate EMT and invasion (examples: miR-30a in breast cancer, miR-17-5p in colorectal cancer, miR-1275 in gastric cancer).
    • lncRNAs regulate VIM transcription or vimentin turnover (e.g., HBV-related “Dreh” suppresses metastasis by targeting vimentin; VAL diminishes TRIM16-dependent vimentin degradation).

Mnemonic: “PASSS-N” regulators: PEA3, AP-1, Sp1/Sp3, STATs, NF-κB.

3) Assembly, remodeling, and PTMs 🧩⚙️

  • Phosphorylation is the master switch for assembly/disassembly, especially during mitosis and migration. Kinases include PKCε, MAPKAPK-2, Cdk5; sites in N/C-termini control filament segregation and integrin recycling.
  • Proteolysis by caspases, calpains, and even viral proteases disassembles IFs during apoptosis or infection.
  • Other PTMs:
    • S-glutathionylation at Cys328 severs filaments and blocks elongation.
    • O-GlcNAcylation/glycosylation link vimentin to neural differentiation and extracellular interactions.

Quick check: Which PTM both inhibits elongation and induces filament severing at Cys328?

4) From cytoplasm to outdoors: cell-surface and extracellular vimentin 🌐🧲

  • Non-canonical localization: Vimentin can appear on the cell surface or be secreted (often via extracellular vesicles). Levels rise in injuries, infections, cancer, autoimmunity, and aging; serum vimentin has been explored as a colon cancer biomarker and potential vaccine antigen.
  • How does it get out? Injury-triggered membrane repair can externalize vimentin for extended periods; exosomal release from glia can deliver cargo and modulate neuronal responses.
  • Functional consequences: Extracellular vimentin can promote wound closure by binding leader cells and driving myofibroblast transitions.

Open questions the paper flags: Are there distinct extracellular vimentin forms with specific PTM “barcodes”? Which signals recruit tetramers to the surface? How do these differ across pathologies?

5) Vimentin as receptor/ligand: platelets, bacteria, viruses, sugars, RNA 🧷🦠🧪

5.1 Platelets and endothelium

  • Receptor for von Willebrand factor (vWF): Surface vimentin binds the A2 domain of active vWF. Anti-vimentin antibodies or competitive A2 peptides block platelet adhesion under high shear. Vim−/− platelets show reduced adhesion and longer bleeding times.

5.2 Bacterial interactions

  • E. coli K1 meningitis: Surface vimentin is a primary receptor for IbeA; binding triggers CaMKII-Ser82 phosphorylation via α7-nAChR-Ca²⁺, NF-κB and ERK signaling, promoting invasion and PMN transmigration across the BBB. Loss of vimentin protects neonatal mice.
  • Group B Streptococcus: BspC adhesin targets vimentin to drive meningitis.
  • Listeria monocytogenes: InlF binds surface vimentin; colonization of brain is vimentin-dependent and even matrix stiffness increases surface vimentin and adhesion via FAK.
  • Mycobacterium tuberculosis: NK cells use NKp46 which recognizes vimentin on infected monocytes to mediate lysis.

5.3 Viruses

  • Cell-surface or intracellular vimentin can act as receptor/co-receptor aiding viral entry and replication control; the review synthesizes multiple examples and frames vimentin as a potential antiviral target.

5.4 Polysaccharides and RNA

  • O-GlcNAc-bearing ligands: Surface vimentin binds GlcNAc-modified proteins. This has been used to isolate mesenchymal stem cells, deliver drugs to injured vessels via GlcNAc-polymer liposomes, and may facilitate apoptotic cell clearance by inducing vimentin Ser71/Ser38 phosphorylation and filament disassembly to expose tetramers at the surface.
  • P-selectin modulation: Vimentin rod domain binds P-selectin near the PSGL-1 site, blocking neutrophil adhesion and reducing inflammation in models.
  • lncRNA receptor: In nerve injury, surface vimentin binds lncRNA BC088259 to promote Schwann cell migration and regeneration. Mechanism remains to be worked out.

Quick check: Name one bacterial virulence factor that uses vimentin as a host receptor and the downstream signaling it triggers.

6) Vimentin in development, regeneration, EMT, fibrosis, and cancer 🧪🩹🧫

  • Development and regeneration: Vimentin is high in precursor cells, then often replaced by lineage IFs. It resurges in mammary, muscle, liver, nervous regeneration and in culture, coupling EMT, migration, and ECM interaction; supports wound healing and lens repair.
  • EMT and fibrosis: Vimentin is an EMT hallmark and is required for renal fibrosis after ureteral obstruction; it coordinates fibroblast proliferation and keratinocyte differentiation via TGF-β–Slug.
  • Cancer:
    • High vimentin correlates with invasion, motility, and metastasis; AKT1 directly targets vimentin to drive motility; PKCε-dependent phosphorylation regulates integrin recycling.
    • miRNAs/lncRNAs tune EMT via vimentin (miR-30a, miR-17-5p, miR-1275; HBx-Dreh, VAL, FTX), making the VIM network a prognostic and therapeutic axis.
    • Therapeutic angle: Targeting vimentin IFs is proposed in oncology.

Integration point: Vimentin couples mechanics (scaffold, integrins), signals (NF-κB, ERK, AKT), and traffic (vesicles, integrin recycling), letting cells switch between stable and migratory states.

7) Clinical and translational hints 🧪🧭

  • Biomarker potential: Elevated serum vimentin reported in colon cancer; extracellular vimentin appears at injured or inflamed sites, offering targeting handles for drug delivery.
  • Hemostasis: vWF–vimentin interaction contributes to platelet tethering and stroke pathology; blockade reduces adhesion and may modulate bleeding or thrombosis.
  • Host–pathogen axis: Interfering with surface vimentin or its PTM-dependent exposure may curb bacterial/viral entry or enhance immune clearance.

8) Open problems and future work 🔭

  • Form and function outside the cell: Which oligomeric states and PTM patterns of extracellular vimentin map to specific roles? What governs surface recruitment vs exosomal export?
  • Conditional genetics: Tissue-specific VIM knockouts are needed to avoid global adaptation and dissect local roles.

Final synthesis (one-liner)

Vimentin is a dynamic mechano-signaling hub: transcriptionally and epigenetically tuned, post-translationally rewired, and, when externalized, repurposed as a receptor/ligand that shapes hemostasis, inflammation, infection, regeneration, EMT, and cancer.

Quiz

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