Ubiquitylation at the crossroads of development and disease

Primary disorders of polyubiquitination: Dual roles in autoinflammation and immunodeficiency

The last decades have brought a rapid expansion of the number of primary disorders related to the polyubiquitination pathways in humans. Most of these disorders manifest with two seemingly contradictory clinical phenotypes: autoinflammation, immunodeficiency, or both. We provide an overview of the molecular pathogenesis of these disorders, and their role in inflammation and infection. By focusing on data from human genetic diseases, we explore the complexities of the polyubiquitination pathways and the corresponding clinical phenotypes of their deficiencies. We offer a road map for the discovery of new genetic etiologies. By considering the triggers that induce inflammation, we propose autoinflammation and immunodeficiency as continuous clinical phenotypes.

Discovery of Artesunate (ARS) PROTACs as GPX4 protein degraders for the treatment of bladder cancer

Bladder cancer is the second most prevalent malignancy of the urinary system worldwide, with high incidence and mortality rates. However, existing drugs for bladder cancer treatment often cause numerous adverse reactions. Although artesunate (ARS) exhibits anti-bladder cancer activity, its scope is rather limited and the specific targets remain unclear. Therefore, in this study, the Proteolysis-Targeting Chimera (PROTAC) technology was used to design and synthesize novel ARS derivatives. The antitumor activities of these compounds were evaluated against three human bladder cancer cell lines (T24, RT4, and J82). Of these compounds, A7 exhibited 12-fold stronger antiproliferative activity against bladder cancer cells than ARS. Molecular docking, surface plasmon resonance (SPR), cellular thermal shift assay (CETSA) and western blotting studies demonstrated that A7 directly targeted and degraded glutathione peroxidase 4 (GPX4) protein through the ubiquitin-proteasome system. A7 further induced bladder cancer cell ferroptosis. Furthermore, A7 showed potent tumor suppressive activity in a xenograft T24 nude mouse model. In conclusion, our findings indicate that A7 exerts notable antitumor effects against bladder cancer in vitro and in vivo. This study highlights the tremendous potential of the PROTAC technology in enhancing the efficacy of natural products and identifying therapeutic targets, demonstrating its broad application prospects in the development of natural products-based drugs.

WWP2 deletion aggravates acute kidney injury by targeting CDC20/autophagy axis

INTRODUCTION

Acute kidney injury (AKI) is associated with high morbidity and mortality rates. The molecular mechanisms underlying AKI are currently being extensively investigated. WWP2 is an E3 ligase that regulates cell proliferation and differentiation. Whether WWP2 plays a regulatory role in AKI remains to be elucidated.

OBJECTIVES

We aimed to investigate the implication of WWP2 in AKI and its underlying mechanism in the present study.

METHODS

We utilized renal tissues from patients with AKI and established AKI models in global or tubule-specific knockout (cKO) mice strains to study WWP2's implication in AKI. We also systemically analyzed ubiquitylation omics and proteomics to decipher the underlying mechanism.

RESULTS

In the present study, we found that WWP2 expression significantly increased in the tubules of kidneys with AKI. Global or tubule-specific knockout of WWP2 significantly aggravated renal dysfunction and tubular injury in AKI kidneys, whereas WWP2 overexpression significantly protected tubular epithelial cells against cisplatin. WWP2 deficiency profoundly affected autophagy in AKI kidneys. Further analysis with ubiquitylation omics, quantitative proteomics and experimental validation suggested that WWP2 mediated poly-ubiquitylation of CDC20, a negative regulator of autophagy. CDC20 was significantly decreased in AKI kidneys, and selective inhibiting CDC20 with apcin profoundly alleviated renal dysfunction and tubular injury in the cisplatin model with or without WWP2 cKO, indicating that CDC20 may serve as a downstream target of WWP2 in AKI. Inhibiting autophagy with 3-methyladenine blocked apcin's protection against cisplatin-induced renal tubular cell injury. Activating autophagy by rapamycin significantly protected against cisplatin-induced AKI in WWP2 cKO mice, whereas inhibiting autophagy by 3-methyladenine further aggravated apoptosis in cisplatin-exposed WWP2 KO cells.

CONCLUSION

Taken together, our data indicated that the WWP2/CDC20/autophagy may be an essential intrinsic protective mechanism against AKI. Further activating WWP2 or inhibiting CDC20 may be novel therapeutic strategies for AKI.

Molecular glue-augmented E2-ubiquitin recognition from a computational approach

Ubiquitin (Ub) is a small regulatory protein that tags unwanted or misfolded proteins for degradation by the proteasome. Molecular glues as small molecules stabilizing and augmenting protein-protein interactions have gained increasing attention in ubiquitination. Highly efficient computational approaches for the investigation of thermodynamics of molecular glue (MG)-Ub-protease systems remain absent. In this work, we introduced a cost-effective computational framework for all-atom characterization of the thermodynamics driving force in the cooperativity or molecule glue-induced enhancement of Ub-E2 recognition. Based on the testing bed involving the CDC34A-Ub protein-protein system and 18 unique molecule glues, we illustrate that our method could satisfactorily decoding the interaction thermodynamics inside the multimeric system. Specifically, our method enables both the ranking the protein-ligand MG-(E2-Ub) affinity and qualitatively capture the MG-induced E2-Ub interaction strengthening, which are generally unachievable with standard methods such as MM/GBSA and commonly applied scoring functions (e.g., AutoDock Vina). We additionally explore the general picture of the interfacial interactions in the multimeric complex, identifying important residues in the binding of molecular glue to Ub-E2 complex and also in Ub-E2 binding. Our computational approach could facilitate high-throughput virtual screening of potent molecular glues in assisting protein-protein recognition and ubiquitination.

Neddylation inhibition affects cell proliferation and steroidogenesis in sheep follicular granulosa cells

Neddylation is a biological process that covalently links neuronal precursor cell-expressed developmentally downregulated protein 8 (NEDD8) to its substrate. Its main function is to activate the cullin ubiquitin junction complex, thereby promoting substrate protein degradation. The research of neddylation mainly focus on cell senescence, Alzheimer's disease progression, and tumor treatment. However, the neddylation mechanism underlying follicular granulosa cells (GCs) proliferation and steroidogenesis remains unclear. Therefore, this study aimed to reveal the functions of neddylation in sheep follicular GCs. Here, immunohistochemistry results revealed that NEDD8 was expressed in sheep follicular GCs. The neddylation-specific inhibitor MLN4924 and NEDD8 small interfering (si) RNA (si-NEDD8) were used to inhibit neddylation, significantly attenuating sheep follicular GC proliferation. The RNA sequencing (RNA-Seq) showed that cytochrome P450 11A1 (CYP11A1) and steroidogenic acute regulator (StAR) were significantly downregulated via the inhibition of neddylation. Additionally, qRT-PCR results showed that CYP11A1, StAR and 3β-hydroxysteroid dehydrogenase (3β-HSD) mRNA abundance decreased significantly following the addition of various MLN4924 doses and si-NEDD8, however, CYP19A1 mRNA levels did not significantly differ. Western blotting results showed that inhibition of neddylation also significantly decreased the expression of CYP11A1, 3β-HSD, cytochrome P450 19A1 (CYP19A1), StAR, and androgen receptor (AR). The current study revealed that the inhibition of neddylation affects sheep follicular GC function by inhibiting proliferation and the enzymes involved in synthesis in sheep.

Mechanisms of hematopoietic clonal dominance in VEXAS syndrome

Clonal dominance characterizes hematopoiesis during aging and increases susceptibility to blood cancers and common nonmalignant disorders. VEXAS syndrome is a recently discovered, adult-onset, autoinflammatory disease burdened by a high mortality rate and caused by dominant hematopoietic clones bearing somatic mutations in the UBA1 gene. However, pathogenic mechanisms driving clonal dominance are unknown. Moreover, the lack of disease models hampers the development of disease-modifying therapies. In the present study, we performed immunophenotype characterization of hematopoiesis and single-cell transcriptomics in a cohort of nine male patients with VEXAS syndrome, revealing pervasive inflammation across all lineages. Hematopoietic stem and progenitor cells (HSPCs) in patients are skewed toward myelopoiesis and acquire senescence-like programs. Humanized models of VEXAS syndrome, generated by inserting the causative mutation in healthy HSPCs through base editing, recapitulated proteostatic defects, cytological alterations and senescence signatures of patients' cells, as well as hematological and inflammatory disease hallmarks. Competitive transplantations of human UBA1-mutant and wild-type HSPCs showed that, although mutant cells are more resilient to the inflammatory milieu, probably through the acquisition of the senescence-like state, wild-type ones are progressively exhausted and overwhelmed by VEXAS clones, overall impairing functional hematopoiesis and leading to bone marrow failure. Our study unveils the mechanism of clonal dominance and provides models for preclinical studies and preliminary insights that could inform therapeutic strategies.

CBLB Regulates MAPK-P38 Pathway via MAP3K9 Ubiquitination to Inhibit GBM Cell Invasion and Migration

Glioma cells exhibit high invasiveness and have the ability to evade surgical resection, radiotherapy, and chemotherapy, which are major factors contributing to the challenges in effective treatment and recurrence. The ubiquitin-proteasome system (UPS) plays a crucial role in posttranslational modification, significantly contributing to the aggressive progression of glioblastoma (GBM). This study identified the E3 ubiquitin ligase CBLB as a crucial and abnormally regulated component of the UPS in GBM, noting its significant downregulation compared to normal brain tissue and its negative correlation with malignant phenotypes and poor prognosis. Experimental studies, both in vitro and in vivo, have shown that CBLB can inhibit the migration and invasion of GBM cells. Mechanistically, CBLB directly interacts with MAP3K9 through its RING domain, leading to K48-K63-linked polyubiquitination at the Lys 193 site, thereby promoting MAP3K9 proteasomal-mediated degradation. MAP3K9 downregulation suppresses MAPK-P38 pathway activation. This study identifies CBLB as a tumor suppressor that modulates the MAPK-P38 signaling pathway by promoting the polyubiquitination and degradation of MAP3K9, offering a new therapeutic approach for GBM treatment.

New insights into reductive stress responses and its clinical relation in cancer

Cells are susceptible to both oxidative and reductive stresses, with reductive stress being less studied and potentially therapeutic in cancer. Reductive stress, characterized by an excess of reducing equivalents exceeding the activity of endogenous oxidoreductases, can lead to an imbalance in homeostasis, causing an increase in reactive oxygen species induction, affecting cellular antioxidant load and flux. Unlike oxidative stress, reductive stress has been understudied and poorly understood, and there is still much to learn about its mechanisms in cancer, its therapeutic potential, and how cancer cells react to it. Changes in redox balance and interference with redox signaling are linked to cancer cell growth, metastasis, and resistance to chemotherapy and radiation. Overconsumption of reducing equivalents can reduce metabolism, alter protein disulfide bond formation, disrupt mitochondrial homeostasis, and disrupt cancer cell signaling pathways. Novel approaches to delivering or using cancer medicines and techniques to influence redox biology have been discovered. Under reductive stress, cancer cells may coordinate separate pools of redox pairs, potentially impacting biology.

APC/C-mediated ubiquitylation of extranucleosomal histone complexes lacking canonical degrons

Non-degradative histone ubiquitylation plays a myriad of well-defined roles in the regulation of gene expression and choreographing DNA damage repair pathways. In contrast, the contributions of degradative histone ubiquitylation on genomic processes has remained elusive. Recently, the APC/C has been shown to ubiquitylate histones to regulate gene expression in pluripotent cells, but the molecular mechanism is unclear. Here we show that despite directly binding to the nucleosome through subunit APC3, the APC/C is unable to ubiquitylate nucleosomal histones. In contrast, extranucleosomal H2A/H2B and H3/H4 complexes are broadly ubiquitylated by the APC/C in an unexpected manner. Using a combination of cryo-electron microscopy (cryo-EM) and biophysical and enzymatic assays, we demonstrate that APC8 and histone tails direct APC/C-mediated polyubiquitylation of core histones in the absence of traditional APC/C substrate degron sequences. Taken together, our work implicates APC/C-nucleosome tethering in the degradation of diverse chromatin-associated proteins and extranucleosomal histones for the regulation of transcription and the cell cycle and for preventing toxicity due to excess histone levels.

USP37 as a novel regulator of NRF2 protein stability and chemoresistance in HCC

Chemoresistance is a prevalent issue in cancer, resulting in a poor prognosis. The transcription factor nuclear factor (erythroid-derived 2)-like 2 (NRF2), a key regulator in cellular antioxidant responses, is implicated in cell survival, proliferation, and chemoresistance. It represents a promising target for treating Hepatocellular carcinoma (HCC). The NRF2 activity has been recently revealed to be controlled by the ubiquitination process mediated by the KEAP1-CUL3 E3 ligase, highlighting the importance of deubiquitination regulation. However, the specific deubiquitinase (DUB) responsible for NRF2 in liver cancer remains unclear. In this study, we demonstrate that Ubiquitin-Specific Protease 37 (USP37) acts as a novel regulator of NRF2 protein. Mechanistically, USP37 modulates the stability of NRF2 through enzymatic activity-dependent deubiquitination. Additionally, USP37 interacts with NRF2 and facilitates its deubiquitination. Elevated USP37 levels were associated with higher levels of NRF2 protein in samples from human patients. Importantly, the knockdown of USP37 results in increased NRF2 degradation and enhances cellular sensitivity to chemotherapy. Overall, our findings manifested the significant involvement of the USP37-NRF2 axis in regulating therapeutic interventions for HCC.

Advancing the Metabolic Dysfunction-Associated Steatotic Liver Disease Proteome: A Post-Translational Outlook

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a prevalent liver disorder with limited treatment options. This review explores the role of post-translational modifications (PTMs) in MASLD pathogenesis, highlighting their potential as therapeutic targets. We discuss the impact of PTMs, including their phosphorylation, ubiquitylation, acetylation, and glycosylation, on key proteins involved in MASLD, drawing on studies that use both human subjects and animal models. These modifications influence various cellular processes, such as lipid metabolism, inflammation, and fibrosis, contributing to disease progression. Understanding the intricate PTM network in MASLD offers the potential for developing novel therapeutic strategies that target specific PTMs to modulate protein function and alleviate disease pathology. Further research is needed to fully elucidate the complexity of PTMs in MASLD and translate these findings into effective clinical applications.

Research progress on AMPK in the pathogenesis and treatment of MASLD

Metabolic dysfunction-associated steatotic liver disease (MASLD; formerly known as non-alcoholic fatty liver disease, NAFLD) has become one of the most prevalent chronic liver diseases worldwide, with its incidence continuously rising alongside the epidemic of metabolic disorders. AMP-activated protein kinase (AMPK), as a key regulator of cellular energy metabolism, influences multiple pathological processes associated with MASLD. This review systematically summarizes the regulatory roles of AMPK in lipid metabolism, inflammatory response, cell apoptosis, and fibrosis. Additionally, it discusses the latest developments of AMPK activators from preclinical to clinical studies, while analyzing the major challenges currently faced and potential strategies for resolution. A deeper understanding of AMPK regulatory mechanisms will contribute to the development of more effective therapeutic approaches for MASLD.

MMFuncPhos: A Multi-Modal Learning Framework for Identifying Functional Phosphorylation Sites and Their Regulatory Types

Protein phosphorylation plays a crucial role in regulating a wide range of biological processes, and its dysregulation is strongly linked to various diseases. While many phosphorylation sites have been identified so far, their functionality and regulatory effects are largely unknown. Here, a deep learning model MMFuncPhos, based on a multi-modal deep learning framework, is developed to predict functional phosphorylation sites. MMFuncPhos outperforms existing functional phosphorylation site prediction approaches. EFuncType is further developed based on transfer learning to predict whether phosphorylation of a residue upregulates or downregulates enzyme activity for the first time. The functional phosphorylation sites predicted by MMFuncPhos and the regulatory types predicted by EFuncType align with experimental findings from several newly reported protein phosphorylation studies. The study contributes to the understanding of the functional regulatory mechanism of phosphorylation and provides valuable tools for precision medicine, enzyme engineering, and drug discovery. For user convenience, these two prediction models are integrated into a web server which can be accessed at http://pkumdl.cn:8000/mmfuncphos.

UFMylation Modulates OFIP Stability and Centrosomal Localization

BACKGROUND

OFIP, also known as KIAA0753, is a centrosomal and pericentriolar satellite protein implicated in ciliogenesis, centriolar duplication, and microtubule stability. In humans, genetic mutations affecting OFIP have been implicated in the pathogenesis of Oral-Facial-Digital (OFD) Syndrome and Joubert Syndrome. Ubiquitin-fold Modifier 1 (UFM1), the most recently identified ubiquitin-like protein, is covalently transferred to its substrates, in a process known as UFMylation. This modification has recently emerged as a key regulator of various biological processes by altering their stability, activity, or localization.

METHODS

The interaction between UFL1 and OFIP, as well as the UFMylation of OFIP, were assessed through immunoprecipitation and immunoblotting analyses. The mRNA levels of OFIP were examined using reverse transcription quantitative PCR (RT-qPCR). Immunofluorescence microscopy was employed to examine the localization and distribution patterns of OFIP.

RESULTS

Our findings demonstrate that UFL1 interacts with OFIP both in vivo and in vitro. We also found that OFIP undergoes UFMylation, and UFL1 promotes the OFIP UFMylation. Mechanistic studies demonstrate that OFIP UFMylation inhibits its protein stability and maintains its proper centrosomal localization. However, the efficacy of these regulatory mechanisms varies significantly between different cell types, being notably pronounced in HeLa cells but markedly reduced in RPE1 cells.

CONCLUSIONS

OFIP is identified as a novel substrate for UFMylation. UFL1-mediated OFIP UFMylation is essential for its stability and centrosomal localization in HeLa cells. However, these effects are not observed in RPE1 cells, highlighting cell type-specific heterogeneity in the role of OFIP UFMylation.

The Deubiquitinating Enzyme USP4 Promotes Trophoblast Dysfunction by Stabilizing RYBP

Previous studies have suggested that impaired spiral artery remodeling, placental dysfunction, and insufficient trophoblast infiltration are the etiology and pathogenesis of Preeclampsia (PE). Ring 1 and YY1 binding protein (RYBP) has been reported to be associated with trophoblast dysfunction. However, the molecular mechanism of RYBP involved in trophoblasts in the pathogenesis of PE is poorly defined. RYBP and Ubiquitin-specific peptidase 4 (USP4) mRNA levels were determined using real-time quantitative polymerase chain reaction (RT-qPCR). RYBP, USP4, p-PI3K, PI3K, p-AKT, and AKT protein levels were measured using western blot assay. Cell viability, proliferation, apoptosis, invasion, and migration were assessed using 3-(4, 5-dimethyl-2-thiazolyl)-2, 5-diphenyl-2-H-tetrazolium bromide (MTT), 5-ethynyl-2'-deoxyuridine (EdU), flow cytometry, transwell, and wound healing assays. After ubibrowser database analysis, the interaction between USP4 and RYBP was verified using Co-immunoprecipitation (CoIP) assay. RYBP and USP4 expression were upregulated in placental tissues from PE patients. By using JEG-3 and HTR-8/SVneo trophoblast cells, RYBP overexpression or USP4 upregulation could hinder cell viability, proliferation, invasion, migration, and promote apoptosis. Mechanistically, USP4 could trigger the deubiquitination of RYBP and prevent its degradation. In addition, USP4 repressed the PI3K/AKT signaling pathway by regulating RYBP. In total, Decreased USP4-mediated ubiquitination results in an adverse impact on trophoblast function by enhancing RYBP expression, providing a novel therapeutic target for PE.

Characteristics of viral ovarian tumor domain protease from two emerging orthonairoviruses and identification of Yezo virus human infections in northeastern China as early as 2012

Emerging tick-borne orthonairovirus infections pose a growing global concern, with limited understanding of the viral ovarian tumor-like cysteine proteases (vOTUs) encoded by novel orthonairoviruses. These vOTUs, a group of deubiquinylases (DUBs), disrupt the innate immune response. Yezo virus (YEZV), a recently discovered pathogenic orthonairovirus, was first reported in Japan in 2021. In this study, we successfully isolated and identified YEZV and a new orthonairovirus, Jiànchuān tick virus (JCTV), from Ixodes persulcatus and Haemaphysalis montgomeryi ticks, respectively, in China. We found that the vOTU domains encoded by YEZV and JCTV exhibited both DUB and deISGylase activities, though with potentially less broad deISGylation compared to that of Crimean-Congo hemorrhagic fever virus (CCHFV) during natural infection. Phylogenetic analysis of global vOTUs, including 83 new sequences, revealed a high diversity of this domain. Interestingly, retrospective screening of tick-bite patients from 2012 to 2016 in northeastern China traced YEZV infections as far back as 2012, identifying four cases. Additionally, YEZV primarily infected I. persulcatus (31.4%) and Dermacentor nuttalli (10.5%) in northern China, while JCTV exhibited high infection rates in H. montgomeryi (81.3%) in southern China. In summary, our work emphasizes the active surveillance of orthonairovirus infections and the imperative need for the development of vOTU domain-targeted anti-virals, offering potential therapeutic solutions for a broad spectrum of orthonairoviruses.IMPORTANCEThe vOTUs, a group of DUBs, mimic the functions of host DUBs to enhance viral infectivity and may serve as potential drug targets. vOTUs from different orthonairoviruses exhibit distinct preferences toward ubiquitin (Ub) and ubiquitin-like protein interferon stimulated gene 15 (ISG15). In this study, we investigated the deubiquitinase and deISGylase functions of various orthonairoviral vOTUs using both an overexpression system and natural viral infections in vitro. Our findings illustrate that the vOTUs from YEZV and JCTV can cleave both Ub and ISG15 in an overexpression system, but these viruses exhibit potentially narrower deISGylation capacity than CCHFV during natural infection. This suggests that the diversity of vOTUs may have a potential relationship with the pathogenesis.

Loss-of-function mutations in the dystonia gene THAP1 impair proteasome function by inhibiting PSMB5 expression

The 26S proteasome is a multi-catalytic protease that serves as the endpoint for protein degradation via the ubiquitin-proteasome system. Proteasome function requires the concerted activity of 33 distinct gene products, but how the expression of proteasome subunits is regulated in mammalian cells remains poorly understood. Leveraging coessentiality data from the DepMap project, here we characterize an essential role for the dystonia gene THAP1 in maintaining the basal expression of PSMB5. PSMB5 insufficiency resulting from loss of THAP1 leads to defects in proteasome assembly, impaired proteostasis and cell death. Exploiting the fact that the toxicity associated with loss of THAP1 can be rescued upon exogenous expression of PSMB5, we define the transcriptional targets of THAP1 through RNA-seq analysis and perform a deep mutational scan to systematically assess the function of thousands of single amino acid THAP1 variants. Altogether, these data identify THAP1 as a critical regulator of proteasome function and suggest that aberrant proteostasis may contribute to the pathogenesis of THAP1 dystonia.

UBE2T/CDC42/CD276 signaling axis mediates brain metastasis of triple-negative breast cancer via lysosomal autophagy

BACKGROUND

Advanced triple-negative breast cancer (TNBC) is prone to brain metastasis (BrM). The precise molecular mechanism responsible for this phenomenon has not yet been completely established, so it is vital to comprehend the molecular mechanism behind it.

METHODS

The protein chip analysis was conducted to identify any abnormal UBE2T protein expression in TNBC, especially BrM. Here, we used public databases and bioinformatics analysis as well as clinical samples from different cohorts to investigate the interrelationship between UBE2T/CDC42/CD276. This predicted relationship was then repeatedly validated using different in vivo and in vitro experimental methods. Additionally, multiple experimental approaches were implemented, encompassing western blotting, Co-IP, GST pull-down, flow cytometry, mass spectrometry, immunofluorescence, immunohistochemistry, and qRT-PCR to reveal the molecular mechanism of UBE2T-mediated immune escape and BrM.

RESULTS

Our results indicate that expressed at elevated levels in breast cancer, UBE2T is negatively linked to patient prognosis, especially in BrM of TNBC. Data from clinical samples from our different cohorts and TCGA indicate a significant correlation between UBE2T and immunosuppression. Mechanistically, UBE2T directly interacts with CDC42, promoting its K48-linked polyubiquitination and proteasomal degradation, thereby inhibiting CDC42 from degrading CD276 via the autophagy-lysosomal pathway, indirectly upregulating CD276 and thereby impairing the CD8+ T cells function, ultimately mediating tumor immune escape and BrM. Finally, animal experimental results also showed that inhibition of UBE2T elevated the TNBC sensitivity to immune checkpoint CD276 blockade and inhibited BrM of TNBC.

CONCLUSIONS

In conclusion, our results indicate a new mechanism whereby UBE2T-mediated ubiquitination positively controls the UBE2T/CDC42/CD276 axis to upregulate tumor cell expression of CD276 and thereby impair CD8+ T cells function, ultimately leading to tumor cell immune escape and BrM.

The E3 ubiquitin ligase Nedd4 fosters developmental myelination in the mouse central and peripheral nervous system

Ubiquitination is a major post-translational regulatory mechanism that tunes numerous aspects of ubiquitinated target proteins, including localization, stability, and function. During differentiation and myelination, Oligodendrocytes (OLs) in the central nervous system and Schwann cells (SCs) in the peripheral nervous system undergo major cellular changes, including the tightly controlled production of large and accurate amounts of proteins and lipids. Such processes have been implied to depend on regulatory aspects of ubiquitination, with E3 ubiquitin ligases being generally involved in the selection of specific ubiquitination substrates by ligating ubiquitin to targets and granting target selectivity. In this study, we have used multiple transgenic mouse lines to investigate the functional impact of the E3 ubiquitin ligase Nedd4 in the OL- and SC-lineages. Our findings in the developing spinal cord indicate that Nedd4 is required for the correct accumulation of differentiated OLs and ensures proper myelination, supporting and further expanding previously suggested conceptual models. In sciatic nerves, we found that Nedd4 is required for timely radial sorting of axons by SCs as a pre-requirement for correct onset of myelination. Moreover, Nedd4 ensures correct myelin thickness in both SCs and spinal cord OLs.

Improving regulatory T cell-based therapy: insights into post-translational modification regulation

Regulatory T (Treg) cells are pivotal for maintaining immune homeostasis and play essential roles in various diseases, such as autoimmune diseases, graft-versus-host disease (GVHD), tumors, and infectious diseases. Treg cells exert suppressive function via distinct mechanisms, including inhibitory cytokines, granzyme or perforin-mediated cytolysis, metabolic disruption, and suppression of dendritic cells. Forkhead Box P3 (FOXP3), the characteristic transcription factor, is essential for Treg cell function and plasticity. Cumulative evidence has demonstrated that FOXP3 activity and Treg cell function are modulated by a variety of post-translational modifications (PTMs), including ubiquitination, acetylation, phosphorylation, methylation, glycosylation, poly(ADP-ribosyl)ation, and uncharacterized modifications. This review describes Treg cell suppressive mechanisms and summarizes the current evidence on PTM regulation of FOXP3 and Treg cell function. Understanding the regulatory role of PTMs in Treg cell plasticity and function will be helpful in designing therapeutic strategies for autoimmune diseases, GVHD, tumors, and infectious diseases.

Prenylation-dependent membrane localization of a deubiquitinating enzyme and its role in regulating G protein-mediated signaling in yeast

Miy1 is a highly conserved deubiquitinating enzyme in yeast with MINDY1 as its human homolog. Miy1 is known to act on K48-linked polyubiquitin chain, but its biological function is unknown. Miy1 has a putative prenylation site, suggesting it as a membrane-associated protein that may contribute to the regulation of cell signaling. Here, we demonstrate that Miy1 is localized in the plasma membrane and nuclear periphery. Mutating the putative prenylation site in Miy1 or disrupting the farnesyltransferase activity impairs its localization. Consistent with a role of Miy1 in regulating the ubiquitination status of membrane proteins, the miy1Δ mutants exhibit a higher level of ubiquitinated conjugates at the plasma membrane. To examine a role of Miy1 in regulating cell signaling across plasma membrane, we focused on the pheromone response, as both Ste2, the receptor for mating pheromone, and Gpa1, the cognate Gα protein of Ste2, are well known to be regulated by ubiquitination. We find that Miy1 interacts with Gpa1, regulates its level of ubiquitination and abundance. Pheromone-induced MAP kinase Fus3 activation is also altered in the MIY1-disrupted mutants. The findings demonstrate that Miy1 is a membrane-associated deubiquitinating enzyme and a regulator of G protein-mediated signaling.

Streptococcus mutans regulates ubiquitin modification of Candida albicans in the bacterial-fungal interaction

The ecological interplay between Streptococcus mutans and Candida albicans within dental plaque biofilms is an important factor driving pathogenesis of dental caries. This study aimed to investigate S. mutans regulation of C. albicans growth and virulence through extracellular membrane vesicles (EMVs) and modulation of ubiquitination, a key protein post-translational modification. We established a transwell co-culture model to enable "contact-independent" interactions between S. mutans and C. albicans. S. mutans EMVs were found to directly associate with C. albicans cells and promote biofilm formation and growth. Quantitative ubiquitination profiling revealed S. mutans dramatically alters the ubiquitination landscape in C. albicans. We identified 10,661 ubiquitination sites across the C. albicans proteome and their enrichment in pathways related to translation, metabolism, and stress adaptation. Co-culture with S. mutans led to upregulation of ubiquitination on 398 proteins involved in sugar catabolism and generation of reducing power. S. mutans upregulated ubiquitination of superoxide dismutase-3 of C. albicans, inducing its degradation and heightened reactive oxygen species levels, and concomitantly stimulated C. albicans growth. Our findings elucidate EMVs and ubiquitination modulation as key mechanisms governing the S. mutans-C. albicans interplay and provide new insights into the promotion of a cariogenic oral biofilm environment. This study significantly advances understanding of the complex molecular interactions underlying dental plaque dysbiosis and caries pathogenesis.

Identification of WDR74 and TNFRSF12A as biomarkers for early osteoarthritis using machine learning and immunohistochemistry

Background

Osteoarthritis (OA) is a chronic joint condition that causes pain, limited mobility, and reduced quality of life, posing a threat to healthy aging. Early detection is crucial for improving prognosis. Recent research has focused on the role of ubiquitination-related genes (URGs) in early OA prediction. This study aims to integrate URG expression data with machine learning (ML) to identify biomarkers that improve diagnosis and prognosis in the early stages of OA.

Methods

OA single-cell RNA sequencing datasets were collected from the GEO database. Single-cell analysis was performed to investigate the composition and relationships of chondrocytes in OA. The potential intercellular communication mechanisms were explored using the CellChat R package. URGs were retrieved from GeneCards, and ubiquitination scores were calculated using the AUCell package. Gene module analysis based on co-expression network analysis was conducted to identify core genes. Additionally, ML analysis was performed to identify core URGs and construct a diagnostic model. We employed XGBoost, a gradient-boosting ML algorithm, to identify core URGs and construct a diagnostic model. The model's performance was evaluated using the area under the curve (AUC) of the receiver operating characteristic (ROC) curve. In addition, we explored the relationship between core URGs and immune processes. The ChEA3 database was utilized to predict the transcription factors regulated by core ubiquitination-related genes. The expression of select URGs was validated using qRT-PCR and immunohistochemistry (IHC).

Results

We identified WDR74 and TNFRSF12A as pivotal ubiquitination-related genes associated with OA, exhibiting considerable differential expression. The diagnostic model constructed with URGs exhibited remarkable accuracy, with area under the curve (AUC) values consistently exceeding 0.9. The expression levels of WDR74 and TNFRSF12A were significantly higher in the IL-1β-induced group in an in vitro qPCR experiment. The IHC validation on human knee joint specimens confirmed the upregulation of WDR74 and TNFRSF12A in OA tissues, corroborating their potential as diagnostic biomarkers.

Conclusions

WDR74 and TNFRSF12A as principal biomarkers highlighted their attractiveness as therapeutic targets. The identification of core biomarkers might facilitate early intervention options, potentially modifying the illness trajectory and enhancing patient outcomes.

Involvement of USP7 in aggravating Kawasaki disease by promoting TGFβ2 signaling mediated endothelial-mesenchymal transition and coronary artery remodeling

Kawasaki disease (KD), characterized by systematic vasculitis, is a leading cause of pediatric heart disease. Although recent studies have highlighted the critical role of deubiquitinases in vascular pathophysiology, their specific contribution to KD remains largely unknown. Herein, we investigated the function of the deubiquitinase USP7 in both KD patients and a CAWS-induced KD murine model. USP7 expression level is increased both in HCAECs induced by KD sera and cardiac CD31+ endothelial cells of KD mice. Whereas knockout of USP7 increases the cellular proportion of endothelial cells and potentially attenuates the elevated EndoMT, fibrosis, and inflammation in cardiac tissue of KD mice, consistently with the in vitro experiment observed in HCAECs induced by TGF-β2. Mechanistically, USP7 interacts with SMAD2/3, enhancing their protein stability by removing the K48 ubiquitin chain from both proteins and preventing their proteasome degradation, thus increasing the p-SMAD2 levels and nuclear entry. Importantly, intraperitoneal injection of USP7 inhibitor, P22077 elicited a robust anti-EndoMT and anti-vascular inflammation effect in KD model mice. Therefore, our study uncovered a previously unrecognized function of increased USP7 in KD by augmenting TGFβ2/SMAD2/SMAD3 signaling, thus facilitating the transcription of genes implicated in the EndoMT, cardiac fibrosis, and vascular remodeling. Our finding suggests that USP7 could serve as a potential therapeutic target for the prevention and treatment of coronary artery lesions in KD and related vascular diseases.

USP39 promotes retinal pathological angiogenesis in retinopathy of prematurity by stabilizing SIRT2 expression through deubiquitination

BACKGROUND

Retinopathy of prematurity (ROP) is a major cause of childhood blindness worldwide, highlighted by retinal neovascularization. Ubiquitin is present throughout the retina. The deubiquitinating enzyme ubiquitin-specific protease 39 (USP39) has been reported to be involved in angiogenesis. Here, this study aimed to investigate the effects of USP39 on ROP and its associated mechanism.

METHODS

Hypoxia-induced human retinal microvascular endothelial cells (hRMECs) were adopted for functional analyses. Detection of mRNA and protein was conducted using quantitative real-time PCR and western blotting. Cell migration, invasion and angiogenesis were evaluated using transwell and tube formation assays. Protein interaction was determined by immunoprecipitation assay. Oxygen-induced retinopathy (OIR) mouse models were used for in vivo analysis.

RESULTS

USP39 level was higher in hypoxia-induced hRMECs, functionally, USP39 silencing reversed hypoxia-induced migration, invasion and angiogenesis in hRMECs. In further mechanism analysis, we found that USP39 stabilized SIRT2 protein expression in hRMECs by inducing SIRT2 deubiquitination. Moreover, SIRT2 up-regulation abated hypoxia-evoked migration, invasion and angiogenesis in hRMECs. Besides that, the inhibitory effects of USP39 silencing on hypoxia-induced metastatic and angiogenic behaviors were abolished after SIRT2 overexpression. In addition, USP39 silencing blocked the activation of phosphoinositide 3-kinase (PI3K)/protein kinase B pathway (AKT) by regulating SIRT2. In vivo assay showed that levels of USP39, SIRT2, matrix metalloproteinase (MMP)-2 (MMP-2), MMP-9 and Vascular endothelial growth factor A (VEGFA) were increased in the retinas of OIR mice, while intravitreal injection of USP39 short hairpin RNA (shRNA) could reduce their expression.

CONCLUSION

USP39 stabilized SIRT2 expression by deubiquitination and promoted hypoxia-induced metastatic and angiogenic behaviors of RMECs in vitro, as well as retinal angiogenesis in vivo.

Beyond destruction: emerging roles of the E3 ubiquitin ligase Hakai

Hakai protein (CBLL1 gene) was identified as an E3 ubiquitin ligase of E-cadherin complex, inducing its ubiquitination and degradation, thus inducing epithelial-to-mesenchymal transition. Most of the knowledge about the protein was associated to its E3 ubiquitin ligase canonical role. However, important recent published research has highlighted the noncanonical role of Hakai, independent of its E3 ubiquitin ligase activity, underscoring its involvement in the N6-methyladenosine (m6A) writer complex and its impact on the methylation of RNA. The involvement of Hakai in this mRNA modification process has renewed the relevance of this protein as an important contributor in cancer. Moreover, Hakai potential as a cancer biomarker and its prognostic value in malignant disease also emphasize its untapped potential in precision medicine, which would also be discussed in detail in our review. The development of the first small-molecule inhibitor that targets its atypical substrate binding domain is a promising step that could eventually lead to patient benefit, and we would cover its discovery and ongoing efforts toward its use in clinic.

RLIM-specific activity reporters define variant pathogenicity in Tonne-Kalscheuer syndrome

Tonne-Kalscheuer syndrome (TOKAS; MIM: 300978) is an X-linked recessive disorder with devastating consequences for patients, such as intellectual disability, developmental delay, and multiple congenital abnormalities. TOKAS is associated with hemizygous variants in the RLIM gene, which encodes a RING-type E3 ubiquitin ligase. The current sustained increase in reported RLIM variants of uncertain significance creates an urgent need to develop assays that can screen these variants and experimentally determine their pathogenicity and disease association. Here, we engineered flow cytometry-based RLIM-specific reporters to measure RLIM activity in TOKAS. This paper describes the design and use of RLIM-specific reporters to determine the pathogenicity of a TOKAS RLIM gene variant. Our data demonstrate that RLIM-specific flow cytometry reporters based on either the full length or a degron region of the substrate REX1 measure RLIM activity in cells. Further, we describe the TOKAS variant RLIM p.Asn581Lys and, using reporter assays, determine that it disrupts RLIM catalytic activity. These data reveal how the p.Asn581Lys variant impairs RLIM function and suggests pathogenic mechanisms. The use of RLIM-specific reporters will greatly accelerate the resolution of variants of uncertain significance and disease association in TOKAS.

Heterozygous UBR5 variants result in a neurodevelopmental syndrome with developmental delay, autism, and intellectual disability

E3 ubiquitin ligases have been linked to developmental diseases including autism, Angelman syndrome (UBE3A), and Johanson-Blizzard syndrome (JBS) (UBR1). Here, we report variants in the E3 ligase UBR5 in 29 individuals presenting with a neurodevelopmental syndrome that includes developmental delay, autism, intellectual disability, epilepsy, movement disorders, and/or genital anomalies. Their phenotype is distinct from JBS due to the absence of exocrine pancreatic insufficiency and the presence of autism, epilepsy, and, in some probands, a movement disorder. E3 ubiquitin ligases are responsible for transferring ubiquitin to substrate proteins to regulate a variety of cellular functions, including protein degradation, protein-protein interactions, and protein localization. Knocking out ubr-5 in C. elegans resulted in a lower movement score compared to the wild type, supporting a role for UBR5 in neurodevelopment. Using an in vitro autoubiquitination assay and confocal microscopy for the human protein, we found decreased ubiquitination activity and altered cellular localization in several variants found in our cohort compared to the wild type. In conclusion, we found that variants in UBR5 cause a neurodevelopmental syndrome that can be associated with a movement disorder, reinforcing the role of the UBR protein family in a neurodevelopmental disease that differs from previously described ubiquitin-ligase-related syndromes. We also provide evidence for the pathogenic potential loss of UBR5 function with functional experiments in C. elegans and in vitro ubiquitination assays.

Interplay between β-propeller subunits WDR26 and muskelin regulates the CTLH E3 ligase supramolecular complex

The Pro/N-degron recognizing C-terminal to LisH (CTLH) complex is an E3 ligase of emerging interest in the developmental biology field and for targeted protein degradation (TPD) modalities. The human CTLH complex forms distinct supramolecular ring-shaped structures dependent on the multimerization of WDR26 or muskelin β-propeller proteins. Here, we find that, in HeLa cells, CTLH complex E3 ligase activity is dictated by an interplay between WDR26 and muskelin in tandem with muskelin autoregulation. Proteomic experiments revealed that complex-associated muskelin protein turnover is a major ubiquitin-mediated degradation event dependent on the CTLH complex in unstimulated HeLa cells. We observed that muskelin and WDR26 binding to the scaffold of the complex is interchangeable, indicative of the formation of separate WDR26 and muskelin complexes, which correlated with distinct proteomes in WDR26 and muskelin knockout cells. We found that mTOR inhibition-induced degradation of Pro/N-degron containing protein HMGCS1 is distinctly regulated by a muskelin-specific CTLH complex. Finally, we found that mTOR inhibition also activated muskelin degradation, likely as an autoregulatory feedback mechanism to regulate CTLH complex activity. Thus, rather than swapping substrate receptors, the CTLH E3 ligase complex controls substrate selectivity through the differential association of its β-propeller oligomeric subunits WDR26 and muskelin.

Targeted protein degradation: expanding the technology to facilitate the clearance of neurotoxic proteins in neurodegenerative diseases

In neurodegenerative diseases (NDDs), disruptions in protein homeostasis hinder the clearance of misfolded proteins, causing the formation of misfolded protein oligomers and multimers. The accumulation of these abnormal proteins results in the onset and progression of NDDs. Removal of non-native protein is essential for cell to maintain proteostasis. In recent years, targeted protein degradation (TPD) technologies have become a novel means of treating NDDs by removing misfolded proteins through the intracellular protein quality control system. The TPD strategy includes the participation of two primary pathways, namely the ubiquitin-proteasome pathway (for instance, PROTAC, molecular glue and hydrophobic tag), and the autophagy-lysosome pathway (such as LYTAC, AUTAC and ATTEC). In this review, we systematically present the mechanisms of various TPD strategies employed for neurotoxic protein degradation in NDDs. The article provides an overview of the design, in vitro and in vivo anti-NDD activities and pharmacokinetic properties of these small-molecular degraders. Finally, the advantages, challenges and perspectives of these TPD technologies in NDDs therapy are discussed, providing ideas for further development of small molecule degraders in the realm of NDDs.

Perspectives on Synthetic Protein Circuits in Mammalian Cells

Mammalian synthetic biology aims to engineer cellular behaviors for therapeutic applications, such as enhancing immune cell efficacy against cancers or improving cell transplantation outcomes. Programming complex biological functions necessitates an understanding of molecular mechanisms governing cellular responses to stimuli. Traditionally, synthetic biology has focused on transcriptional circuits, but recent advances have led to the development of synthetic protein circuits, leveraging programmable binding, proteolysis, or phosphorylation to modulate protein interactions and cellular functions. These circuits offer advantages including robust performance, rapid functionality, and compact design, making them suitable for cellular engineering or gene therapies. This review outlines the post-translational toolkit, emphasizing synthetic protein components utilizing proteolysis or phosphorylation to program mammalian cell behaviors. Finally, we focus on key differences between rewiring native signaling pathways and creating orthogonal behaviors, alongside a proposed framework for translating synthetic protein circuits from tool development to pre-clinical applications in biomedicine.

Ubiquitination in pyroptosis pathway: A potential therapeutic target for sepsis

Sepsis remains a significant clinical challenge, causing numerous deaths annually and representing a major global health burden. Pyroptosis, a unique form of programmed cell death characterized by cell lysis and the release of inflammatory mediators, is a crucial factor in the pathogenesis and progression of sepsis, septic shock, and organ dysfunction. Ubiquitination, a key post-translational modification influencing protein fate, has emerged as a promising target for managing various inflammatory conditions, including sepsis. This review integrates the current knowledge on sepsis, pyroptosis, and the ubiquitin system, focusing on the molecular mechanisms of ubiquitination within pyroptotic pathways activated during sepsis. By exploring how modulating ubiquitination can regulate pyroptosis and its associated inflammatory signaling pathways, this review provides insights into potential therapeutic strategies for sepsis, highlighting the need for further research into these complex molecular networks.

Structure of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquitin ligase complex

Cullin-RING E3 ubiquitin ligases (CRLs) constitute the largest family of ubiquitin ligase and play important roles in regulation of proteostasis. Here we presented the cryo-EM structure of CRL1FBXO4, a member of Cullin-1 E3 ligase. CRL1FBXO4 adopts a homodimer architecture. Structural analysis revealed that in the CRL1FBXO4 protomer, the substrate recognition subunit FBXO4 interacts both the adaptor protein SKP1, and the scaffold protein CUL1 via hydrophobic and electrostatic interactions. Two FBXO4 forms a domain-swapped dimer in the CRL1FBXO4 structure, which constitutes the basis for the dimerization of CRL1FBXO4. Inspired by the cryo-EM density, we modeled the architecture of whole CRL1FBXO4 as a symmetrical dimer, which provides insights into CRL1FBXO4-medaited turnover of oncogene proteins.

Proteome Profiling of S. cerevisiae Strains Lacking the Ubiquitin-Conjugating Enzymes Ubc4 and Ubc5 During Exponential Growth and After Heat Shock Treatment

The Ubiquitin-Proteasome System (UPS) governs numerous cellular processes by modulating protein stability and activity via the conjugation of the small protein ubiquitin, either as a single molecule or as linkages with distinct functions. Dysregulation of the UPS has been associated with many diseases, including neurodegenerative and neurodevelopmental diseases, as well as cancer. Ubiquitin-conjugating enzymes (E2s) are important players of the UPS that work together with ubiquitin ligases (E3s) to promote substrate ubiquitylation. In this study, we conduct a comparative proteome-wide abundance profiling of S. cerevisiae cells during the exponential growth phase with and without heat shock treatment. We focus on cells with deletions of the two highly homologous E2s, UBC4 or UBC5, and use isobaric tag-based quantitative mass spectrometry to elucidate differences and similarities in their proteomic profiles. Our analysis revealed that the deletion of Ubc4 has a stronger effect on the proteome compared to the deletion of Ubc5, particularly in exponentially growing cells. In contrast, the effect on the proteome of deleting Ubc5 becomes evident only after heat shock, and even then, it remains minor compared to Ubc4. Furthermore, we identified proteins increasing in the absence of each enzyme, which may represent candidate substrates, potentially contributing to a better understanding of their cellular role.

YOD1 sustains NOD2-mediated protective signaling in colitis by stabilizing RIPK2

Inflammatory bowel disease (IBD) is a disorder causing chronic inflammation in the gastrointestinal tract, and its pathophysiological mechanisms are still under investigation. Here, we find that mice deficient of YOD1, a deubiquitinating enzyme, are highly susceptible to dextran sulfate sodium (DSS)-induced colitis. The bone marrow transplantation experiment reveals that YOD1 derived from hematopoietic cells inhibits DSS colitis. Moreover, YOD1 exerts its protective role by promoting nucleotide-binding oligomerization domain 2 (NOD2)-mediated physiological inflammation in macrophages. Mechanistically, YOD1 inhibits the proteasomal degradation of receptor-interacting serine/threonine kinase 2 (RIPK2) by reducing its K48 polyubiquitination, thereby increasing RIPK2 abundance to enhance NOD2 signaling. Consistently, the protective function of muramyldipeptide, a NOD2 ligand, in experimental colitis is abolished in mice deficient of YOD1. Importantly, YOD1 is upregulated in colon-infiltrating macrophages in patients with colitis. Collectively, this study identifies YOD1 as a novel regulator of colitis.

USP36 promotes colorectal cancer progression through inhibition of p53 signaling pathway via stabilizing RBM28

Colorectal cancer (CRC) stands as the second most common cause of cancer-related mortality globally and p53, a widely recognized tumor suppressor, contributes to the development of CRC. Ubiquitin-specific protease 36 (USP36), belonging to the deubiquitinating enzyme family, is involved in tumor progression across multiple cancers. However, the underlying molecular mechanism in which USP36 regulates p53 signaling pathway in CRC is unclear. Here, our study revealed that USP36 was increased in CRC tissues and associated with unfavorable prognosis. Functionally, elevated USP36 could promote proliferation, migration, and invasion of CRC cells in vitro and in vivo. Mechanistically, USP36 could interact with and stabilize RBM28 via deubiquitination at K162 residue. Further, upregulated RBM28 could bind with p53 to suppress its transcriptional activity and therefore inactivate p53 signaling pathway. Collectively, our investigation identified the novel USP36/RBM28/p53 axis and its involvement in promoting cell proliferation and metastasis in CRC, which presents a promising therapeutic strategy for CRC treatment.

Clr4SUV39H1 ubiquitination and non-coding RNA mediate transcriptional silencing of heterochromatin via Swi6 phase separation

Transcriptional silencing by RNAi paradoxically relies on transcription, but how the transition from transcription to silencing is achieved has remained unclear. The Cryptic Loci Regulator complex (CLRC) in Schizosaccharomyces pombe is a cullin-ring E3 ligase required for silencing that is recruited by RNAi. We found that the E2 ubiquitin conjugating enzyme Ubc4 interacts with CLRC and mono-ubiquitinates the histone H3K9 methyltransferase Clr4SUV39H1, promoting the transition from co-transcriptional gene silencing (H3K9me2) to transcriptional gene silencing (H3K9me3). Ubiquitination of Clr4 occurs in an intrinsically disordered region (Clr4IDR), which undergoes liquid droplet formation in vitro, along with Swi6HP1 the effector of transcriptional gene silencing. Our data suggests that phase separation is exquisitely sensitive to non-coding RNA (ncRNA) which promotes self-association of Clr4, chromatin association, and di-, but not tri- methylation instead. Ubc4-CLRC also targets the transcriptional co-activator Bdf2BRD4, down-regulating centromeric transcription and small RNA (sRNA) production. The deubiquitinase Ubp3 counteracts both activities.

Genetic Code Expansion Approaches to Decipher the Ubiquitin Code

The covalent attachment of Ub (ubiquitin) to target proteins (ubiquitylation) represents one of the most versatile PTMs (post-translational modifications) in eukaryotic cells. Substrate modifications range from a single Ub moiety being attached to a target protein to complex Ub chains that can also contain Ubls (Ub-like proteins). Ubiquitylation plays pivotal roles in most aspects of eukaryotic biology, and cells dedicate an orchestrated arsenal of enzymes to install, translate, and reverse these modifications. The entirety of this complex system is coined the Ub code. Deciphering the Ub code is challenging due to the difficulty in reconstituting enzymatic machineries and generating defined Ub/Ubl-protein conjugates. This Review provides a comprehensive overview of recent advances in using GCE (genetic code expansion) techniques to study the Ub code. We highlight strategies to site-specifically ubiquitylate target proteins and discuss their advantages and disadvantages, as well as their various applications. Additionally, we review the potential of small chemical PTMs targeting Ub/Ubls and present GCE-based approaches to study this additional layer of complexity. Furthermore, we explore methods that rely on GCE to develop tools to probe interactors of the Ub system and offer insights into how future GCE-based tools could help unravel the complexity of the Ub code.

TRIM55 restricts the progression of hepatocellular carcinoma through ubiquitin-proteasome-mediated degradation of NF90

Hepatocellular carcinoma (HCC) is a prevalent malignant tumor worldwide. Tripartite motif containing 55 (TRIM55), also known as muscle-specific ring finger 2 (Murf2), belongs to the TRIM protein family and serves as an E3 ligase. Recently, the function and mechanism of TRIM55 in the advancement of solid tumors have been elucidated. However, the role of TRIM55 and its corresponding protein substrates in HCC remains incompletely explored. In this study, we observed a significant reduction in TRIM55 expression in HCC tissues. The downregulation of TRIM55 expression correlated with larger tumor size and elevated serum alpha-fetoprotein (AFP), and predicted unfavorable overall and tumor-free survival. Functional experiments demonstrated that TRIM55 suppressed the proliferation, migration, and invasion of HCC cells in vitro, as well as hindered HCC growth and metastasis in vivo. Additionally, TRIM55 exhibited a suppressive effect on HCC angiogenesis. Mechanistically, TRIM55 interacted with nuclear factor 90 (NF90), a double-stranded RNA-binding protein responsible for regulating mRNA stability and gene transcription, thereby facilitating its degradation via the ubiquitin-proteasome pathway. Furthermore, TRIM55 attenuated the association between NF90 and the mRNA of HIF1α and TGF-β2, consequently reducing their stability and inactivating the HIF1α/VEGF and TGFβ/Smad signaling pathways. In conclusion, our findings unveil the important roles of TRIM55 in suppressing the progression of HCC partly by promoting the degradation of NF90 and subsequently modulating its downstream pathways, including HIF1α/VEGF and TGFβ/Smad signaling.

Multi-omics reveals lactylation-driven regulatory mechanisms promoting tumor progression in oral squamous cell carcinoma

BACKGROUND

Lactylation, a post-translational modification, is increasingly recognized for its role in cancer progression. This study investigates its prevalence and impact in oral squamous cell carcinoma (OSCC).

RESULTS

Immunohistochemical staining of 81 OSCC cases shows lactylation levels correlate with malignancy grading. Proteomic analyses of six OSCC tissue pairs reveal 2765 lactylation sites on 1033 proteins, highlighting its extensive presence. These modifications influence metabolic processes, molecular synthesis, and transport. CAL27 cells are subjected to cleavage under targets and tagmentation assay for accessible-chromatin with high-throughput sequencing, and transcriptomic sequencing pre- and post-lactate treatment, with 217 genes upregulated due to lactylation. Chromatin immunoprecipitation-quantitative PCR and real-time fluorescence quantitative PCR confirm the regulatory role of lactylation at the K146 site of dexh-box helicase 9 (DHX9), a key factor in OSCC progression. CCK8, colony formation, scratch healing, and Transwell assays demonstrate that lactylation mitigates the inhibitory effect of DHX9 on OSCC, thereby promoting its occurrence and development.

CONCLUSIONS

Lactylation actively modulates gene expression in OSCC, with significant effects on chromatin structure and cellular processes. This study provides a foundation for developing targeted therapies against OSCC, leveraging the role of lactylation in disease pathogenesis.

Super Enhanced Purification of Denatured-Refolded Ubiquitinated Proteins by ThUBD Revealed Ubiquitinome Dysfunction in Liver Fibrosis

Ubiquitination is crucial for maintaining protein homeostasis and plays a vital role in diverse biological processes. Ubiquitinome profiling and quantification are of great scientific significance. Artificial ubiquitin-binding domains (UBDs) have been widely employed to capture ubiquitinated proteins. The success of this enrichment relies on recognizing native spatial structures of ubiquitin and ubiquitin chains by UBDs under native conditions. However, the use of native lysis conditions presents significant challenges, including insufficient protein extraction, heightened activity of deubiquitinating enzymes and proteasomes in removing the ubiquitin signal, and purification of a substantial number of contaminant proteins, all of which undermine the robustness and reproducibility of ubiquitinomics. In this study, we introduced a novel approach that combines denatured-refolded ubiquitinated sample preparation (DRUSP) with a tandem hybrid UBD for ubiquitinomic analysis. The samples were effectively extracted using strongly denatured buffers and subsequently refolded using filters. DRUSP yielded a significantly stronger ubiquitin signal, nearly three times greater than that of the Control method. Then, eight types of ubiquitin chains were quickly and accurately restored; therefore, they were recognized and enriched by tandem hybrid UBD with high efficiency and no biases. Compared with the Control method, DRUSP showed extremely high efficiency in enriching ubiquitinated proteins, improving overall ubiquitin signal enrichment by approximately 10-fold. Moreover, when combined with ubiquitin chain-specific UBDs, DRUSP had also been proven to be a versatile approach. This new method significantly enhanced the stability and reproducibility of ubiquitinomics research. Finally, DRUSP was successfully applied to deep ubiquitinome profiling of early mouse liver fibrosis with increased accuracy, revealing novel insights for liver fibrosis research.

The ubiquitin-specific protease 21 is critical for cancer cell mitochondrial function and regulates proliferation and migration

Ubiquitin-specific proteases (USPs) are the main members of deubiquitinases (DUBs) that catalyze removing ubiquitin chains from target proteins, thereby modulating their half-life and function. Enzymatic activity of USP21 regulates protein degradation which is critical for maintaining cell homeostasis. USP21 determines the stability of oncogenic proteins and therefore is implicated in carcinogenesis. In this study, we investigated the effect of USP21 deletion on cancer cell metabolism. Transcriptomic and proteomic analysis of USP21 KO HAP-1 cells revealed that endogenous USP21 is critical for the expression of genes and proteins involved in mitochondrial function. Additionally, we have found that the deletion of USP21 reduced STAT3 activation and STAT3-dependent gene and protein expression in cancer cells. Genetic deletion of USP21 impaired mitochondrial respiration and disturbed ATP production. This resulted in cellular consequences such as inhibition of cell proliferation and migration. Presented results provide new insights into the biology of USP21, suggesting novel mechanisms for controlling STAT3 activity and mitochondrial function in tumor cells. Taken together, our findings indicate that targeting USP21 dysregulates the energy status of cancer cells offering new perspectives for anticancer therapy.

The role of ubiquitination in health and disease

Ubiquitination is an enzymatic process characterized by the covalent attachment of ubiquitin to target proteins, thereby modulating their degradation, transportation, and signal transduction. By precisely regulating protein quality and quantity, ubiquitination is essential for maintaining protein homeostasis, DNA repair, cell cycle regulation, and immune responses. Nevertheless, the diversity of ubiquitin enzymes and their extensive involvement in numerous biological processes contribute to the complexity and variety of diseases resulting from their dysregulation. The ubiquitination process relies on a sophisticated enzymatic system, ubiquitin domains, and ubiquitin receptors, which collectively impart versatility to the ubiquitination pathway. The widespread presence of ubiquitin highlights its potential to induce pathological conditions. Ubiquitinated proteins are predominantly degraded through the proteasomal system, which also plays a key role in regulating protein localization and transport, as well as involvement in inflammatory pathways. This review systematically delineates the roles of ubiquitination in maintaining protein homeostasis, DNA repair, genomic stability, cell cycle regulation, cellular proliferation, and immune and inflammatory responses. Furthermore, the mechanisms by which ubiquitination is implicated in various pathologies, alongside current modulators of ubiquitination are discussed. Enhancing our comprehension of ubiquitination aims to provide novel insights into diseases involving ubiquitination and to propose innovative therapeutic strategies for clinical conditions.

Inhibition of neddylation disturbs zygotic genome activation through histone modification change and leads to early development arrest in mouse embryos

Post-translational modification and fine-tuned protein turnover are of great importance in mammalian early embryo development. Apart from the classic protein degradation promoting ubiquitination, new forms of ubiquitination-like modification are yet to be fully understood. Here, we demonstrate the function and potential mechanisms of one ubiquitination-like modification, neddylation, in mouse preimplantation embryo development. Treated with specific inhibitors, zygotes showed a dramatically decreased cleavage rate and almost all failed to enter the 4-cell stage. Transcriptional profiling showed genes were differentially expressed in pathways involving cell fate determination and cell differentiation, including several down-regulated zygotic genome activation (ZGA) marker genes. A decreased level of phosphorylated RNA polymerase II was detected, indicating impaired gene transcription inside the embryo cell nucleus. Proteomic data showed that differentially expressed proteins were enriched in histone modifications. We confirmed the lowered in methyltransferase (KMT2D) expression and a decrease in histone H3K4me3. At the same time, acetyltransferase (CBP/p300) reduced, while deacetylase (HDAC6) increased, resulting in an attenuation in histone H3K27ac. Additionally, we observed the up-regulation in YAP1 and RPL13 activities, indicating potential abnormalities in the downstream response of Hippo signaling pathway. In summary, we found that inhibition of neddylation induced epigenetic changes in early embryos and led to abnormalities in related downstream signaling pathways. This study sheds light upon new forms of ubiquitination regulating mammalian embryonic development and may contribute to further investigation of female infertility pathology.

NUP37 accumulation mediated by TRIM28 enhances lipid synthesis to accelerate HCC progression

Elevated intracellular lipid synthesis is important for hepatocellular carcinoma (HCC) progression. Our study aimed to identify the role of nucleoporin 37 (NUP37) in lipid synthesis and HCC progression. The expression of NUP37 was significantly upregulated in HCC and associated with a poor prognosis. NUP37 silencing suppressed lipid synthesis, proliferation, migration, and invasion of HCC cells in vitro, and restrained tumor growth in xenograft mouse models in vivo. Next, we found the high expression of NUP37 in HCC was related to post-translational modifications. Tripartite motif-containing 28 (TRIM28) was identified as an interacting protein of NUP37 and upregulated its protein level. The subsequent analysis revealed that TRIM28-mediated SUMOylation of NUP37 at Lys114/118/246 inhibited K27-linked polyubiquitination of NUP37, which is one reason for its high expression level in HCC. In conclusion, TRIM28 SUMOylates NUP37 to prevent its ubiquitination and proteasomal degradation, increasing the stability of the NUP37 protein, thereby promoting lipid synthesis and the progression of HCC.

Amelioration of nonalcoholic fatty liver disease by inhibiting the deubiquitylating enzyme RPN11

Nonalcoholic fatty liver disease (NAFLD), including its more severe manifestation nonalcoholic steatohepatitis (NASH), is a global public health challenge. Here, we explore the role of deubiquitinating enzyme RPN11 in NAFLD and NASH. Hepatocyte-specific RPN11 knockout mice are protected from diet-induced liver steatosis, insulin resistance, and steatohepatitis. Mechanistically, RPN11 deubiquitinates and stabilizes METTL3 to enhance the m6A modification and expression of acyl-coenzyme A (CoA) synthetase short-chain family member 3 (ACSS3), which generates propionyl-CoA to upregulate lipid metabolism genes via histone propionylation. The RPN11-METTL3-ACSS3-histone propionylation pathway is activated in the livers of patients with NAFLD. Pharmacological inhibition of RPN11 by Capzimin ameliorated NAFLD, NASH, and related metabolic disorders in mice and reduced lipid contents in human hepatocytes cultured in 2D and 3D. These results demonstrate that RPN11 is a novel regulator of NAFLD/NASH and that suppressing RPN11 has therapeutic potential for the treatment.

The activation of the Notch signaling pathway by UBE2C promotes the proliferation and metastasis of hepatocellular carcinoma

UBE2C, a ubiquitin-conjugating enzyme, functions as an oncogene in different types of human cancers. Nonetheless, the exact influence of UBE2C on the development of HCC via regulation of ubiquitination remains uncertain. Here, we found that UBE2C displayed elevated levels of expression in HCC and was associated with an unfavorable prognosis, as evidenced by the analysis of the TCGA database and the examination of clinical specimens. The role of UBE2C in HCC revealed its ability to promote the growth and metastasis of HCC. Mechanistically, UBE2C activated Notch signaling, as evidenced by the upregulation of N1ICD and Hes1, crucial components of the Notch pathway, and activation of the RBP-JK luciferase reporter by UBE2C. Finally, rescue experiments demonstrated that the oncogenic role of UBE2C was eliminated through treatment with the Notch inhibitor DAPT, while overexpression of N1ICD alleviated the anticarcinogenic impact of knockdown of UBE2C. Altogether, the results of our study indicate that UBE2C plays a role in the activation of Notch signaling and could potentially serve as a viable target for therapeutic interventions in HCC.

Mitochondrial DNA Programs Lactylation of cGAS to Induce IFN Responses in Patients with Systemic Lupus Erythematosus

Mitochondrial DNA (mtDNA) is frequently released from mitochondria, activating cGAS-STING signaling and inducing type I IFNs (IFN-Is) in systemic lupus erythematosus (SLE). Meanwhile, whether and how the glycolytic pathway was involved in such IFN-I responses in human SLE remain unclear. In this study, we found that monocytes from SLE patients exerted robust IFN-I generation and elevated level of cytosolic mtDNA. Transfection of mtDNA into THP-1 macrophages was efficient in inducing IFN-I responses, together with the strong glycolytic pathway that promoted lactate production, mimicking the SLE phenotype. Blockade of lactate generation abrogated such IFN-I responses and, vice versa, exogenous lactate enhanced the IFN-I generation. Mechanistically, lactate promoted the lactylation of cGAS, which inhibited its binding to E3 ubiquitination ligase MARCHF5, blocking cGAS degradation and leading to strong IFN-I responses. In accordance, targeting lactate generation alleviated disease development in humanized SLE chimeras. Collectively, cytosolic mtDNA drives metabolic adaption toward the glycolytic pathway, promoting lactylation of cGAS for licensing IFN-I responses in human SLE and thereby assigning the glycolytic pathway as a promising therapeutic target for SLE.