CTSL

CTSL encodes a cysteine protease that operates across lysosomal proteostasis, viral entry, and cancer signaling, with both proteolytic and non-proteolytic functions (PMID:35879545, PMID:40961907, PMID:40320169). As a host protease, CTSL is essential for SARS-CoV-2 pathogenesis: it mediates endocytic cleavage and internalization of the viral spike protein, and its knockdown in mouse lungs reduces viral burden, dampens proinflammatory cytokine release, and extends survival (PMID:35879545, PMID:38971996). In the nervous system, CTSL acts together with CTSB to maintain autophagy-lysosomal proteostasis, and their combined loss causes accumulation of ubiquitin-positive structures and selective neuronal death (PMID:40320169). CTSL maturation from its single-chain to active double-chain form requires legumain, and the double-chain enzyme can localize to the nucleus, where—imported via KPNB1 and retained through downregulation of the export factor CRM1/XPO1—it participates in the DNA damage response (PMID:39868276). Beyond catalysis, CTSL functions as a scaffold: it binds PDK1 and blocks its NEDD4L-mediated ubiquitination, stabilizing PDK1 to sustain AKT phosphorylation and PD-L1 expression and thereby promoting tumor immune evasion (PMID:40961907). CTSL protein stability is itself set by competing ubiquitin machinery, with USP20 deubiquitinating and stabilizing it to drive EMT and cancer stem cell renewal while STUB1/CHIP promotes its degradation (PMID:41261048). At the transcriptional level, CTSL expression is controlled through a xenobiotic response element in its promoter that responds to AHR:ARNT signaling (PMID:22871890).

1. 2012 Medium

   Established that CTSL transcription is regulated by an environmental/xenobiotic axis, linking a common promoter variant to a physiological phenotype.

   Evidence Promoter-luciferase reporter with AHR:ARNT co-expression and population genetic association across two cohorts

   PMID:22871890

   Open questions at the time

   • Mechanism linking CTSL level to blood pressure not defined
   • Single-lab cell-based reporter assay
   • No protein-level confirmation of allelic effect
2. 2017 Medium

   Distinguished CTSL from its close relative CTSB by showing they remodel the metastatic proteome through distinct molecular routes.

   Evidence LC-MS/MS quantitative proteomics of lung metastases in tgCTSL vs tgCTSB transgenic breast cancer mice

   PMID:29187882

   Open questions at the time

   • Direct substrates driving the proteome shift not identified
   • Causal contribution to metastasis vs correlation unresolved
3. 2022 High

   Demonstrated in vivo that CTSL is a host protease essential for SARS-CoV-2 pathogenesis, validating it as an antiviral target.

   Evidence Cas13d-mediated Ctsl mRNA knockdown in mouse lungs with viral burden, cytokine, and survival readouts

   PMID:35879545

   Open questions at the time

   • Exact spike cleavage site/step not mapped here
   • Contribution relative to other entry proteases not quantified
4. 2024 Medium

   Connected CTSL function to spike handling at the cellular level, showing it both cleaves/internalizes spike and is transcriptionally induced by spike exposure.

   Evidence Recombinant spike treatment, CTSL knockout, and promoter-reporter assays in HeLa and iPSC-derived alveolarspheres

   PMID:38971996

   Open questions at the time

   • Signaling pathway driving spike-induced CTSL upregulation unknown
   • Single-lab study
5. 2025 Medium

   Revealed that CTSL protein abundance is governed by a ubiquitin tug-of-war, defining USP20 and STUB1 as opposing regulators that control its oncogenic output.

   Evidence Deubiquitinase inhibitor screen, reciprocal Co-IP, ubiquitination assays, and in vivo HNSCC tumor models

   PMID:41261048

   Open questions at the time

   • Ubiquitin linkage type and modified residues not defined
   • Single-lab validation
6. 2025 Medium

   Uncovered a non-proteolytic scaffolding role for CTSL in stabilizing PDK1 to sustain AKT-PD-L1 signaling and tumor immune evasion.

   Evidence Binding/Co-IP and ubiquitination assays with xenograft, immunocompetent mouse, and anti-PD-1 combination models

   PMID:40961907

   Open questions at the time

   • Structural basis of CTSL-PDK1 interaction unresolved
   • Whether catalytic activity is fully dispensable not definitively shown
   • Single-lab study
7. 2025 High

   Defined the cathepsin pair CTSB/CTSL as essential for neuronal autophagy-lysosomal proteostasis and survival of specific neuron populations.

   Evidence Nervous-system-specific conditional CtsB/L double-knockout mice with histology, electron microscopy, and behavioral analysis

   PMID:40320169

   Open questions at the time

   • Substrate(s) whose accumulation kills Purkinje cells not identified
   • Selective vulnerability of Zebrin II-negative cells unexplained
8. 2025 Medium

   Identified legumain as required for CTSL maturation and nuclear pool generation, and CTSL nuclear import (via KPNB1) as essential for the DNA damage response.

   Evidence Activity-based probes, LGMN-/- cells, N-terminomics (NICE), nuclear fractionation, KPNB1/CRM1 manipulation, and PDX models (preprints)

   PMID:39868276

   Open questions at the time

   • Nuclear substrates of CTSL not functionally validated
   • Mechanism coupling nCTSL to DDR machinery unclear
   • Preprint, single lab
9. 2025 Low

   Linked CTSL to autophagy promotion via IL6-JAK-STAT3 signaling in cancer cells.

   Evidence Proliferation, invasion, immunoprecipitation, and immunohistochemistry assays in laryngeal cancer cells

   PMID:39893643

   Open questions at the time

   • Direct molecular link between CTSL and the IL6-JAK-STAT3 axis remains indirect
   • Single-lab study with limited mechanistic follow-up

• How CTSL switches between its proteolytic (lysosomal/viral) and non-proteolytic (PDK1 scaffold, nuclear DDR) functions, and what governs its subcellular partitioning, remains unresolved.
• No unifying model for catalytic vs scaffold activity
• Nuclear substrate spectrum not validated
• Signals determining lysosomal vs nuclear localization unknown