UPS-dependent strategies of protein quality control degradation

UBE4B modulates BET inhibitor sensitivity via KLHL22-JAK2-PIM1 axis in hepatocellular carcinoma

Ubiquitination factor E4B (UBE4B) is crucial to the high mortality rate and poor prognosis associated with hepatocellular carcinoma (HCC). Evidence suggests that aberrant epigenetic modifications significantly contribute to HCC carcinogenesis, making epigenetic mechanisms a promising area for therapeutic intervention. However, the precise role of UBE4B in the epigenetic dysregulation observed in HCC remains elusive. In this study, we silenced UBE4B in HCC cells and exposed them to a panel of epigenetic compounds. Notably, only bromodomain and extraterminal inhibitors (BETis) exhibited resistance to UBE4B silencing, while restoring UBE4B expression partially reversed this resistance. Furthermore, UBE4B deletion led to decreased growth rates and impaired proliferation, resulting in cell cycle arrest and diminished tumorigenicity. However, this deletion did not affect the cell cycle arrest induced by BETi. Interestingly, KLHL22, a ubiquitin substrate of UBE4B, accumulated in UBE4B-deleted cells. Knockdown of KLHL22 restored sensitivity to BETi, accompanied by downregulation of JAK2 and upregulation of its negative regulator, LNK. Additionally, UBE4B deletion resulted in decreased LNK expression, and LNK knockdown increased JAK2 expression and mediated resistance to BETi. Increased JAK2 subsequently targeted PIM1, further reducing the inhibitory effect of BETi. Directly silencing PIM1 in UBE4B-deleted cells restored BETi sensitivity. Overall, our findings provide novel insights into the relationship between UBE4B expression and BETi sensitivity, which is mediated through the KLHL22-JAK2-PIM1 regulatory axis. These findings not only deepen our understanding of the mechanisms underlying HCC progression but also suggest that targeting this axis may present a promising therapeutic strategy for enhancing the treatment outcomes of HCC.

Xerophenone H, a naturally-derived proteasome inhibitor, triggers apoptosis and paraptosis in lung cancer

BACKGROUND

Polycyclic polyprenylated acylphloroglucinols (PPAPs) characterized by unique chemical architectures, exhibit diverse pharmacological activities. Xerophenone H (XeH) is a PPAP extracted from the plant Garcinia multiflora Champ. ex Benth. (Clusiaceae) with a novel and unique chemical structure. Although in vitro screening has revealed the anti-cancer activity of XeH, whose in vivo effectiveness and mechanistic basis required systematic investigation.

METHODS

Cytotoxic effects were evaluated through MTT and colony formation assays. A subcutaneous xenograft model was established to assess in vivo anti-cancer efficacy. To elucidate the underlying mechanism of the anti-cancer effect of XeH, RNA-sequencing and western blotting were performed. A proteasome activity assay was conducted to quantify the effect of XeH. Molecular docking and cellular thermal shift assays were conducted to identify the potential molecular target for XeH.

RESULTS

XeH demonstrated concentration-dependent cytotoxicity in A549 cells (IC₅₀ = 12.16 μM at 48 h). Intratumoral administration (10 mg/kg triweekly) achieved 38.6 % tumor growth inhibition. XeH simultaneously triggered apoptosis and paraptosis in A549 and H460 cells. Mechanistically, XeH promoted the formation of protein aggregates and induced significant endoplasmic reticulum stress in lung cancer cells by directly interacting with PSMB5 and inhibiting proteasome activity.

CONCLUSIONS

XeH, a novel PPAP, was identified as a novel proteasome inhibitor. It effectively downregulated proteasome activity, and induced both apoptosis and paraptosis in lung cancer cells.

Inactivation of SIAH-1 E3 ligase attenuates Aβ toxicity by suppressing ubiquitin-dependent DVE-1 degradation in C. elegans models of Alzheimer's disease

The mitochondrial unfolded protein response (UPRmt), an evolutionarily conserved proteostasis pathway, plays a critical role in the pathogenesis of Alzheimer's disease (AD), characterized by amyloid-β peptide (Aβ) aggregation. Although the transcription factor DVE-1 regulates UPRmt activation in C. elegans and has been implicated in Aβ pathology, its regulatory mechanisms under AD-like conditions remain unclear. Here, using the classical C. elegans muscle-specific AD model (CL2006 strain), we observed UPRmt induction in young adults despite paradoxical depletion of DVE-1 protein concurrent with elevated dve-1 transcript levels. Through integrated genetic and biochemical analyses, we identified SIAH-1, a conserved E3 ubiquitin ligase that partners with the E2 enzyme UBC-25 to interact with DVE-1 and mediate its K48-linked polyubiquitination, as targeting DVE-1 for proteasomal degradation. Disruption of SIAH-1 E3 ubiquitin ligase function or overexpression of DVE-1 significantly reduced Aβ toxicity in both the muscle-expressed Aβ (CL2006) and neuronal Aβ models (gnaIs2). These interventions concurrently suppressed Aβ aggregation in the heat shock-inducible Aβ aggregation model (xchIs15). Mechanistically, this protective effect was associated with restored mitochondrial homeostasis, as evidenced by MitoTracker Red staining and TOMM-20::mCherry fluorescence imaging in muscle-expressed Aβ animals. These assays demonstrated that Aβ accumulation compromises mitochondrial integrity, a phenotype markedly rescued in siah-1 deletion mutants and DVE-1-overexpressing strains. Collectively, these findings establish the SIAH-1/DVE-1 axis as a conserved proteostasis regulator and highlight ubiquitin-dependent mitochondrial quality control as a potential therapeutic target for AD and related proteopathies.

Unclogging of the TOM complex under import stress

Mitochondrial functions and biogenesis depend on the import of more than 1,000 proteins which are synthesized as precursor proteins on cytosolic ribosomes. Mitochondrial protein translocases sort the precursor proteins into the mitochondrial sub-compartments: outer and inner membrane, the intermembrane space and the matrix. The translocase of the outer mitochondrial membrane (TOM complex) constitutes the major import site for most of these precursor proteins. Defective protein translocases, premature folding of the precursor, or depletion of the membrane potential can cause clogging of the TOM channel by a precursor protein. This clogging impairs further protein import and leads to accumulation of precursor proteins in the cell that perturbates protein homeostasis, leading to proteotoxic stress in the cell. Therefore, unclogging of the translocon is critical for maintaining mitochondrial and cellular function. Ubiquitylation and AAA-ATPases play a central role in the extraction of the precursor proteins to deliver them to the proteasome for degradation. Here we summarize our understanding of the molecular mechanisms that remove such translocation-stalled precursor proteins from the translocation channel to regenerate the TOM complex for protein import.

Comprehensive multi-omics analysis elucidates colchicine-induced toxicity mechanisms and unveils the therapeutic potential of MLN4924 and kinase inhibitors

Colchicine is a widely prescribed anti-inflammatory drug for the treatment of gout, familial Mediterranean fever and pericarditis, but its narrow therapeutic window presents a significant risk of severe toxicity. Despite its clinical relevance, the molecular mechanisms underlying colchicine's pharmacological effects and associated toxicity and explored potential therapeutic interventions to mitigate its adverse effects. We showed the colchicine's impact on cellular morphology in human umbilical vein endothelial cells (HUVEC) and HeLa cells including cell rounding and detachment following 24 h of exposure that revealed pronounced cytotoxic effects. We then established a large-scale screening model to identify small molecules capable of reversing colchicine-induced cellular toxicity, and identified MLN4924, an inhibitor of the Cullin-RING E3 ligase (CRL) system, as a promising candidate for mitigating colchicine-induced cellular injury. Through a comprehensive multi-omics approach including transcriptomics, proteomics, phosphoproteomics and ubiquitinomics, we systematically characterized the molecular perturbations caused by colchicine and delineated the protective mechanisms of MLN4924. We found that MLN4924 exerted its protective effects by modulating critical cellular pathways, specifically preventing the dysregulation of cell cycle progression, mitotic disruption and microtubule destabilization triggered by colchicine. Furthermore, proteomic and phosphoproteomic analyses revealed significant alterations in kinase signaling networks, with combined inhibition of CDK1 and PAK1 emerging as an effective strategy to counteract colchicine-induced cellular dysfunction. These results not only provide a detailed molecular characterization of colchicine toxicity but also identify key therapeutic targets, laying the groundwork for the development of targeted interventions to mitigate colchicine-induced adverse effects in clinical practice.

How to exploit the recycling system of a cell

Nature has inspired the design of improved inhibitors for cancer-causing proteins.

Mitochondrial protein import stress

Mitochondria have to import a large number of precursor proteins from the cytosol. Chaperones keep these proteins in a largely unfolded state and guide them to the mitochondrial import sites. Premature folding, mitochondrial stress and import defects can cause clogging of import sites and accumulation of non-imported precursors, representing a critical burden for cellular proteostasis. Here we discuss how cells respond to mitochondrial protein import stress by regenerating clogged import sites and inducing stress responses. The mitochondrial protein import machinery has a dual role by serving as sensor for detecting mitochondrial dysfunction and inducing stress-response pathways. The production of chaperones that fold or sequester precursor proteins in deposits is induced and the proteasomal activity is increased to remove the excess precursor proteins. Together, these pathways reveal how mitochondria are tightly integrated into a cellular proteostasis and stress response network to maintain cell viability.