USP40

USP40 is a deubiquitinating enzyme that stabilizes diverse substrate proteins by removing degradative ubiquitin marks, thereby controlling endothelial barrier integrity, podocyte survival and adhesion, and cancer cell growth (PMID:38307937, PMID:42068752, PMID:38537774). In the vasculature, USP40 deubiquitinates and inactivates HSP90β, which limits RhoA activation, MLC and cofilin phosphorylation, and NF-κB-driven ICAM1 expression, protecting the endothelial barrier; endothelial-specific USP40 loss worsens experimental lung injury and the metabolite indole-3-acetic acid confers protection through USP40 (PMID:38307937, PMID:38761166). In podocytes, USP40 localizes to the cytoplasm with the intermediate filament nestin and sustains glomerular function: it stabilizes HINT1 to drive p53-mediated responses and removes monoubiquitin from integrin β1 to block its clathrin-mediated endocytosis and retain it at the plasma membrane, with USP40 loss producing severe proteinuria and glomerulosclerosis (PMID:28148530, PMID:35605301, PMID:42068752). In cancer, USP40 removes K48-linked polyubiquitin chains to stabilize substrates including CFLARL (downstream of a GMEB1 bridge), YAP (at K252/K315, in a YAP-driven feedback loop), and Claudin1, promoting proliferation, migration, and stemness (PMID:31046799, PMID:38537774, PMID:38308285).

1. 2017 Medium

   Established the first physiological context for USP40, showing it is a podocyte-cytoplasmic protein bound to nestin and required for normal glomerular structure and permeability.

   Evidence Immunoprecipitation, confocal immunofluorescence, siRNA knockdown, and zebrafish morpholino knockdown with permeability assay

   PMID:28148530

   Open questions at the time

   • Did not establish whether nestin is a deubiquitination substrate
   • Catalytic activity not directly demonstrated in this context
2. 2019 Medium

   Defined USP40 as a catalytic deubiquitinase acting within a complex, removing K48-linked chains from CFLARL with GMEB1 as a bridging adaptor.

   Evidence Reciprocal Co-IP, GST pull-down, ubiquitination assay, and siRNA knockdown rescue in NSCLC and 293FT cells

   PMID:31046799

   Open questions at the time

   • Specific ubiquitination sites on CFLARL not mapped
   • In vivo relevance not tested
3. 2022 Medium

   Linked USP40 to podocyte injury signaling by showing it stabilizes HINT1 to elevate p53, with sequential induction in an FSGS model.

   Evidence USP40 knockout mice, podocyte siRNA knockdown, immunoprecipitation, and mouse FSGS model with sequential expression analysis

   PMID:35605301

   Open questions at the time

   • Ubiquitin chain type on HINT1 not specified
   • Causal ordering of HINT1/USP40/p53/nestin not dissected mechanistically
4. 2024 High

   Established USP40 as an endothelial barrier protector through deubiquitination and inactivation of HSP90β, suppressing RhoA/MLC and NF-κB signaling, and showed it is the required effector of IAA-mediated protection.

   Evidence Ubiquitination assay, EC-specific USP40 knockout mice, lentiviral rescue, TEER, and in vivo LPS lung injury model across two studies

   PMID:38307937 PMID:38761166

   Open questions at the time

   • How USP40 deubiquitination inactivates HSP90β mechanistically not resolved
   • Upstream activation of USP40 by IAA not defined at the molecular level
5. 2024 Medium

   Extended USP40's pro-tumorigenic role by identifying YAP (sites K252/K315) and Claudin1 as K48-linked deubiquitination substrates, with a YAP–USP40 positive feedback loop.

   Evidence Co-IP, site-directed mutagenesis ubiquitination assays, siRNA knockdown, RNA-seq, reporter assays, and xenografts in HCC cells

   PMID:38308285 PMID:38537774

   Open questions at the time

   • Single-lab evidence for each substrate
   • Whether YAP and Claudin1 stabilization are independent or coupled not established
6. 2026 High

   Defined a membrane-trafficking mechanism: USP40 removes monoubiquitin from integrin β1 to block clathrin-mediated endocytosis and retain it at the podocyte plasma membrane, protecting against FSGS.

   Evidence USP40 knockout mice in FSGS model, ubiquitin construct transfection in HEK293, internalization assay, electron microscopy, and podocyte siRNA knockdown

   PMID:42068752

   Open questions at the time

   • Ubiquitin ligase that monoubiquitylates integrin β1 not identified
   • Relationship between integrin β1, HINT1, and nestin pathways in podocytes not integrated

• Whether USP40's many reported substrates reflect distinct tissue-specific functions or a shared recognition mechanism, and the structural basis of its substrate selectivity, remain unresolved.
• No structural model of USP40 substrate engagement
• No unifying recruitment or specificity determinant identified across substrates