Commentary: Deubiquitination complex platform: a plausible mechanism for regulating the substrate specificity of deubiquitinating enzymes

Integrating multi-omics and experimental techniques to decode ubiquitinated protein modifications in hepatocellular carcinoma

Background

Ubiquitination, a critical post-translational modification, plays a pivotal role in regulating protein stability and activity, influencing various aspects of cancer development, including metabolic reprogramming, immune evasion, and tumor progression. However, the specific role of ubiquitination in hepatocellular carcinoma (HCC), particularly in relation to the tumor microenvironment (TME), remains poorly understood. This study aims to systematically explore the role of ubiquitination in shaping the TME of HCC, with a focus on its impact on cancer progression and immune modulation.

Methods

We performed bioinformatics analysis by integrating multiple publicly available HCC datasets to assess the ubiquitination status across various cell types in the TME, including plasma cells, fibroblasts, endothelial cells, and epithelial-mesenchymal transition (EMT) cells. Ubiquitination scores were calculated to categorize these cell types, and survival data, along with spatial transcriptomics, were employed to evaluate how different levels of ubiquitination influence HCC progression. In vitro experiments, such as transwell, CCK8, and wound healing assays, were used to further investigate the role of the key ubiquitination gene UBE2C in HCC phenotypes.

Results

Our study revealed that ubiquitination-related genes are significantly upregulated in HCC tissues, with high expression levels correlating with poor prognosis in patients. Pathway analysis showed that these genes are enriched in key processes such as cell cycle regulation, DNA repair, metabolic reprogramming, and p53 signaling. These pathways contribute to the TME by promoting tumor cell proliferation, facilitating matrix remodeling, and enhancing angiogenesis. Notably, UBE2C, a critical ubiquitination enzyme, appears to play a key role in immune evasion, potentially by inhibiting anti-tumor immune responses and reducing the immune system's ability to recognize and eliminate tumor cells. Furthermore, experimental data confirmed that UBE2C overexpression promotes HCC cell proliferation, invasion, and metastasis, further supporting its role in tumor progression and TME remodeling.

Conclusion

This study reveals the multifaceted regulatory roles of ubiquitination in HCC. Ubiquitination not only supports proliferation and anti-apoptotic functions within tumor cells but also promotes tumor progression by modulating the activity of immune and stromal cells. Among all ubiquitination-related genes, UBE2C emerges as a potential prognostic biomarker and therapeutic target in HCC, offering new directions for precision treatment of HCC in the future.

Identification of a deubiquitinating gene-related signature in ovarian cancer using integrated transcriptomic analysis and machine learning framework

BACKGROUND

Ovarian carcinoma represents an aggressive malignancy with poor prognosis and limited therapeutic efficacy. While deubiquitinating (DUB) genes are known to regulate crucial cellular processes and cancer progression, their specific roles in ovarian carcinoma remain poorly understood.

METHODS

We conducted an integrated analysis of single-cell RNA sequencing and bulk transcriptome data from public databases. DUB genes were identified through Genecard database. Using the Seurat package, we performed cell clustering and differential expression analysis. Cell-cell communications were analyzed using CellChat. A DUB-related risk signature (DRS) was developed using machine learning approaches through integration of GEO and TCGA datasets. The prognostic value and immune characteristics of the signature were systematically evaluated.

RESULTS

Our analysis revealed eight distinct cell subtypes in the tumor microenvironment, including epithelial, fibroblast, myeloid, and Treg cells. DUB-high cells were predominantly found in Treg and myeloid populations, exhibiting elevated expression of tumor-related pathways and enhanced cell-cell communication networks, particularly between fibroblasts and myeloid cells. Conversely, DUB-low cells were enriched in epithelial populations with reduced immune activity. The DRS model demonstrated robust prognostic value across multiple independent cohorts. High-risk patients, as classified by the DRS, showed significantly poorer survival outcomes and distinct immune infiltration patterns compared to low-risk patients.

CONCLUSION

This study provides comprehensive insights into DUB gene expression patterns across different cell populations in ovarian carcinoma. The established DRS model offers a promising tool for risk stratification and may guide personalized therapeutic strategies. Our findings highlight the potential role of DUB genes in modulating the tumor immune microenvironment and patient outcomes in ovarian carcinoma.

USP25 stabilizes STAT6 to promote IL-4-induced macrophage M2 polarization and fibrosis

As a leading cause of morbidity and mortality, fibrosis is the common pathway of various chronic inflammatory diseases in organs and causes death in a large number of patients. It can destroy the structure and function of organs and ultimately lead to organ failure, which is a major cause of disability and death in many diseases. However, the regulatory mechanism of organ fibrosis is not well clear and the lack of effective drugs and treatments, which seriously endangers human health and safety. In this study, we found that ubiquitin specific peptidases 25 (USP25) deficiency could protect mice from bleomycin (BLM)-induced pulmonary fibrosis and bile duct ligation (BDL)-induced liver fibrosis. Mechanistically, USP25 deficiency reduced the infiltration of M2 macrophages in the lungs and livers. USP25 inhibits signal transducer and activator of transcription 6 / peroxisome proliferator-activated receptor gamma (STAT6/PPAR-γ) signaling by reducing the K48 specific ubiquitination of STAT6, thereby promoting IL-4-induced M2 macrophages. Overall, our findings support that USP25 promotes the development of fibrosis by facilitating macrophage M2 polarization.

Recent pharmacological insights on abating toxic protein species burden in neurological disorders: Emphasis on 26S proteasome activation

Protein homeostasis (proteostasis) refers to the plethora of mechanisms that safeguard the proper folding of the newly synthesized proteins. It entails various intricately regulated cues that demolish the toxic protein species to prevent their aggregation. The ubiquitin-proteasome system (UPS) is recognized as a salient protein degradation system, with a substantial role in maintaining proteostasis. However, under certain circumstances the protein degradation capacity of the UPS is overwhelmed, leading to the accumulation of misfolded proteins. Several neurodegenerative disorders, such as Alzheimer's disease, Parkinson's disease, Huntington disease, and amyotrophic lateral sclerosis are characterized with the presence of protein aggregates and proteinopathy. Accordingly, enhancing the 26S proteasome degradation activity might delineate a pioneering approach in targeting various proteotoxic disorders. Regrettably, the exact molecular approaches that enhance the proteasomal activity are still not fully understood. Therefore, this review aimed to underscore several signaling cascades that might restore the degradation capacity of this molecular machine. In this review, we discuss the different molecular components of the UPS and how 26S proteasomes are deleteriously affected in many neurodegenerative diseases. Moreover, we summarize different signaling pathways that can be utilized to renovate the 26S proteasome functional capacity, alongside currently known druggable targets in this circuit and various classes of proteasome activators.

Deubiquitinases as novel therapeutic targets for diseases

Deubiquitinating enzymes (DUBs) regulate substrate ubiquitination by removing ubiquitin or cleaving within ubiquitin chains, thereby maintaining cellular homeostasis. Approximately 100 DUBs in humans counteract E3 ubiquitin ligases, finely balancing ubiquitination and deubiquitination processes to maintain cellular proteostasis and respond to various stimuli and stresses. Given their role in modulating ubiquitination levels of various substrates, DUBs are increasingly linked to human health and disease. Here, we review the DUB family, highlighting their distinctive structural characteristics and chain-type specificities. We show that DUB family members regulate key signaling pathways, such as NF-κB, PI3K/Akt/mTOR, and MAPK, and play crucial roles in tumorigenesis and other diseases (neurodegenerative disorders, cardiovascular diseases, inflammatory disorders, and developmental diseases), making them promising therapeutic targets Our review also discusses the challenges in developing DUB inhibitors and underscores the critical role of the DUBs in cellular signaling and cancer. This comprehensive analysis enhances our understanding of the complex biological functions of the DUBs and underscores their therapeutic potential.

Tetrahydrocurcumin targets TRIP13 inhibiting the interaction of TRIP13/USP7/c-FLIP to mediate c-FLIP ubiquitination in triple-negative breast cancer

INTRODUCTION

Triple-negative breast cancer (TNBC) has a high mortality rate and limited treatment options. Tetrahydrocurcumin (THC), a major metabolite of curcumin, has potential antitumor activities. However, the antitumor effects and mechanism of THC in TNBC remain elusive.

OBJECTIVES

To investigate the mechanism of THC in combating TNBC by targeting TRIP13 to disrupt the interaction of the TRIP13/USP7/c-FLIP complex and mediate c-FLIP ubiquitination both in vitro and in vivo.

METHODS

Apoptosis was measured by TUNEL and flow cytometry. Click chemistry-based target fishing, CETSA, DARTS, and SPR were used to identify direct target of THC. Protein interactions was examined using co-immunoprecipitation. The role of USP7 in THC-mediated c-FLIP ubiquitination was evaluated by in vitro deubiquitination assay. Human breast cancer clinical samples were employed to assess the expression of c-FLIP, TRIP13, and USP7. The impact of THC on USP7/TRIP13/c-FLIP was analyzed using co-immunoprecipitation, confocal microscopy, molecular docking and dynamics simulations.

RESULTS

THC effectively inhibits TNBC cell proliferation and tumor growth in vitro and in vivo without significant toxicity. Mechanistically, THC induces extrinsic apoptosis in TNBC primarily by promoting degradation of c-FLIP, a key negative regulator in the apoptotic pathway. Furthermore, utilizing click chemistry-based target fishing, we identified TRIP13, a component of the highly conserved AAA ATPase family, as a direct target of THC in combating TNBC. Interestingly, contrary to previous drug-target studies, the knockdown of TRIP13 further amplified the antitumor effects of THC. After in-depth investigation, it was revealed that TRIP13 forms a trimeric complex with USP7 and c-FLIP in TNBC cells. THC specifically targets TRIP13 to disrupt the interaction of TRIP13/USP7/c-FLIP, leading to the ubiquitination of c-FLIP, ultimately inducing extrinsic apoptosis.

CONCLUSIONS

These findings offer new insights into the novel molecular mechanisms of anti-TNBC effects of THC and present a promising targeted therapeutic strategy for TNBC.

The role and advance of ubiquitination and deubiquitination in depression pathogenesis and treatment

Depression is a common neuropsychiatric disease that is characterized by long-term, repeated low mood, pain and despair, pessimism, and even suicidal tendencies. Increasing evidence has shown that ubiquitination and deubiquitination are closely related to the occurrence of depression, including pathological morphogenesis, neuroplasticity, synaptic transmission, neuroinflammation, and so forth. The development of depression is regulated by intracellular proteins that undergo various posttranslational modifications, including ubiquitination, which falls under the epigenetics category. Although there have been studies and reviews of literature on epigenetics and depression, a systematic review of ubiquitination modification and depression has not been reported. In addition, with the deepening of research on depression and ubiquitination, the development of drugs targeting the ubiquitin system has gradually increased, but it is still not mature, so there is an urgent need to find new antidepressant drug targets. E3 ubiquitin ligases and deubiquitinating enzymes can regulate the occurrence and development of depression in a variety of ways, which may be a direction for the treatment of depression in the future. Therefore, this review describes the latest progress of ubiquitination and deubiquitination in the regulation of depression, summarizes the published signal pathways of ubiquitination and deubiquitination involved in depression, emphasizes the targets and mechanisms of E3 ubiquitin ligases and deubiquitinase in the regulation of depression, and further discusses the therapeutic targets of targeting ubiquitination modification systems to regulate depression.

Chemoproteomic Strategy Identifies PfUCHL3 as the Target of Halofuginone

The human malaria parasite Plasmodium falciparum (P. falciparum) continues to pose a significant public health challenge, leading to millions of fatalities globally. Halofuginone (HF) has shown a significant anti-P. falciparum effect, suggesting its potential as a therapeutic agent for malaria treatment. In this study, we synthesized a photoaffinity labeling probe of HF to identify its direct target in P. falciparum. Our results reveal that ubiquitin carboxyl-terminal hydrolase 3 (PfUCHL3) acts as a crucial target protein of HF, which modulates parasite growth in the intraerythrocytic cycle. In particular, we discovered that HF potentially forms hydrogen bonds with the Leu10, Glu11, and Arg217 sites of PfUCHL3, thereby inducing an allosteric effect by promoting the embedding of the helix 6' region on the protein surface. Furthermore, HF disrupts the expression of multiple functional proteins mediated by PfUCHL3, specifically those that play crucial roles in amino acid biosynthesis and metabolism in P. falciparum. Taken together, this study highlights PfUCHL3 as a previously undisclosed druggable target of HF, which contributes to the development of novel anti-malarial agents in the future.

Ubiquitin-specific protease 1 facilitates hepatocellular carcinoma progression by modulating mitochondrial fission and metabolic reprogramming via cyclin-dependent kinase 5 stabilization

Although deubiquitinases (DUBs) have been well described in liver tumorigenesis, their potential roles and mechanisms have not been fully understood. In this study, we identified ubiquitin-specific protease 1 (USP1) as an oncogene with essential roles during hepatocellular carcinoma (HCC) progression. USP1, with elevated expression levels and clinical significance, was identified as a hub DUB for HCC in multiple bioinformatics datasets. Functionally, USP1 overexpression significantly enhanced the malignant behaviors in HCC cell lines and spheroids in vitro, as well as the zebrafish model and the xenograft model in vivo. In contrast, genetic ablation or pharmacological inhibition of USP1 dramatically impaired the phenotypes of HCC cells. Specifically, ectopic USP1 enhanced aggressive properties and metabolic reprogramming of HCC cells by modulating mitochondrial dynamics. Mechanistically, USP1 induced mitochondrial fission by enhancing phosphorylation of Drp1 at Ser616 via deubiquitination and stabilization of cyclin-dependent kinase 5 (CDK5), which could be degraded by the E3 ligase NEDD4L. The USP1/CDK5 modulatory axis was activated in HCC tissues, which was correlated with poor prognosis of HCC patients. Furthermore, Prasugrel was identified as a candidate USP1 inhibitor for targeting the phenotypes of HCC by an extensive computational study combined with experimental validations. Taken together, USP1 induced malignant phenotypes and metabolic reprogramming by modulating mitochondrial dynamics in a CDK5-mediated Drp1 phosphorylation manner, thereby deteriorating HCC progression.

USP7 promotes cardiometabolic disorders and mitochondrial homeostasis dysfunction in diabetic mice via stabilizing PGC1β

Diabetic cardiomyopathy (DCM) is a major complication of diabetes and is characterized by left ventricular dysfunction. Currently, there is a lack of effective treatments for DCM. Ubiquitin-specific protease 7 (USP7) plays a key role in various diseases. However, whether USP7 is involved in DCM has not been established. In this study, we demonstrated that USP7 was upregulated in diabetic mouse hearts and NMCMs co-treated with HG+PA or H9c2 cells treated with PA. Abnormalities in diabetic heart morphology and function were reversed by USP7 silencing through conditional gene knockout or chemical inhibition. Proteomic analysis coupled with biochemical validation confirmed that PCG1β was one of the direct protein substrates of USP7 and aggravated myocardial damage through coactivation of the PPARα signaling pathway. USP7 silencing restored the expression of fatty acid metabolism-related proteins and restored mitochondrial homeostasis by inhibiting mitochondrial fission and promoting fusion events. Similar effects were also observed in vitro. Our data demonstrated that USP7 promoted cardiometabolic metabolism disorders and mitochondrial homeostasis dysfunction via stabilizing PCG1β and suggested that silencing USP7 may be a therapeutic strategy for DCM.

Friend or foe? Reciprocal regulation between E3 ubiquitin ligases and deubiquitinases

Protein ubiquitination is a post-translational modification that entails the covalent attachment of the small protein ubiquitin (Ub), which acts as a signal to direct protein stability, localization, or interactions. The Ub code is written by a family of enzymes called E3 Ub ligases (∼600 members in humans), which can catalyze the transfer of either a single ubiquitin or the formation of a diverse array of polyubiquitin chains. This code can be edited or erased by a different set of enzymes termed deubiquitinases (DUBs; ∼100 members in humans). While enzymes from these distinct families have seemingly opposing activities, certain E3-DUB pairings can also synergize to regulate vital cellular processes like gene expression, autophagy, innate immunity, and cell proliferation. In this review, we highlight recent studies describing Ub ligase-DUB interactions and focus on their relationships.

MicroRNA-Mediated Regulation of Histone-Modifying Enzymes in Cancer: Mechanisms and Therapeutic Implications

In the past decade, significant advances in molecular research have provided a deeper understanding of the intricate regulatory mechanisms involved in carcinogenesis. MicroRNAs, short non-coding RNA sequences, exert substantial influence on gene expression by repressing translation or inducing mRNA degradation. In the context of cancer, miRNA dysregulation is prevalent and closely associated with various stages of carcinogenesis, including initiation, progression, and metastasis. One crucial aspect of the cancer phenotype is the activity of histone-modifying enzymes that govern chromatin accessibility for transcription factors, thus impacting gene expression. Recent studies have revealed that miRNAs play a significant role in modulating these histone-modifying enzymes, leading to significant implications for genes related to proliferation, differentiation, and apoptosis in cancer cells. This article provides an overview of current research on the mechanisms by which miRNAs regulate the activity of histone-modifying enzymes in the context of cancer. Both direct and indirect mechanisms through which miRNAs influence enzyme expression are discussed. Additionally, potential therapeutic implications arising from miRNA manipulation to selectively impact histone-modifying enzyme activity are presented. The insights from this analysis hold significant therapeutic promise, suggesting the utility of miRNAs as tools for the precise regulation of chromatin-related processes and gene expression. A contemporary focus on molecular regulatory mechanisms opens therapeutic pathways that can effectively influence the control of tumor cell growth and dissemination.