Ubiquitination in the regulation of inflammatory cell death and cancer

Hypoxia-mediated high expression of TRIM15 promotes malignant progression of high-grade serous ovarian cancer through activation of AKT signaling pathway by K63 ubiquitination

The tripartite motif (TRIM) family member TRIM15 is an E3 ubiquitin ligase that is abnormally expressed in a variety of tumors, but its role and mechanism in high-grade serous ovarian cancer (HGSOC) are unclear. Here, we found for the first time that TRIM15 was upregulated in HGSOC and was associated with poor overall survival. Functional experiments showed that TRIM15 drove the proliferation of HGSOC cells and inhibited the apoptosis of tumor cells in vivo and in vitro. In terms of mechanism, we found that TRIM15 contributed to the malignant proliferation of HGSOC cells by promoting the activation of AKT and that there was a direct binding between them. TRIM15 induced lysine-63 (K63) ubiquitination of AKT through its Ring domain, which in turn activated the AKT signaling pathway. In addition, TRIM15-mediated K63 ubiquitination occurs mainly in the pleckstrin homology (PH) domain of AKT. We further identified other proteins and their functions regulated by TRIM15 in HGSOC cells by ubiquitin proteomic analysis. Furthermore, hypoxia-inducible factor-1α promoted TRIM15 transcriptional activation by binding to the hypoxia response elements of the TRIM15 promoter. Our study suggests that TRIM15 induces K63 ubiquitination of the AKT PH domain through its Ring domain and activates the AKT signaling pathway, thereby promoting HGSOC progression. In addition, the abnormally high expression of TRIM15 was associated with the hypoxic microenvironment of HGSOC tissues.

Ubiquitin-conjugating enzyme E2S (UBE2S) as a prognostic biomarker and regulator of tumorigenesis in osteosarcoma

Ubiquitin-conjugating enzyme E2S (UBE2S) is a member of ubiquitin conjugating enzymes with unclear association with osteosarcoma (OS). This study aimed to assess UBE2S's predictive value in OS using data from TCGA and GEO databases. Kaplan-Meier survival analysis and ROC curves were used for prognostic evaluation, and a nomogram was developed for prognostic prediction. Potential biological functions, pathways, and correlations with tumor immune microenvironment, immunotherapy response, and drug sensitivity were analyzed. UBE2S overexpression was linked to poor prognosis, and the nomogram effectively predicted OS survival outcomes. UBE2S was found to impact tumorigenesis pathways, immune landscape, and treatment sensitivity in OS. Transcriptome sequencing, RT-qPCR, Western Blotting, and immunohistochemistry confirmed that UBE2S is abnormally overexpressed in OS. Additionally, a series of in vitro experiments showed that UBE2S knockdown reduced OS cell proliferation and migration while promoting apoptosis. In vivo experiments also confirmed that UBE2S knockdown could inhibit OS cell growth. In summary, our research demonstrates that UBE2S is a reliable prognostic factor for OS. Its abnormal overexpression enhances OS proliferation and migration, indicating its significance for future personalized treatment strategies in OS.

Mechanisms and therapeutic strategies for NLRP3 degradation via post-translational modifications in ubiquitin-proteasome and autophagy lysosomal pathway

The NLRP3 inflammasome is crucial for immune responses. However, its overactivation can lead to severe inflammatory diseases, underscoring its importance as a target for therapeutic intervention. Although numerous inhibitors targeting NLRP3 exist, regulating its degradation offers an alternative and promising strategy to suppress its activation. The degradation of NLRP3 is primarily mediated by the proteasomal and autophagic pathways. The review not only elaborates on the traditional concepts of ubiquitination and NLRP3 degradation but also investigates the important roles of indirect regulatory modifications, such as phosphorylation, acetylation, ubiquitin-like modifications, and palmitoylation-key post-translational modifications (PTMs) that influence NLRP3 degradation. Additionally, we also discuss the potential targets that may affect NLRP3 degradation during the proteasomal and autophagic pathways. By unraveling these complex regulatory mechanisms, the review aims to enhance the understanding of NLRP3 regulation and its implications for developing therapeutic strategies to combat inflammatory diseases.

RIPK3 in necroptosis and cancer

Receptor-interacting protein kinase-3 is essential for the cell death pathway called necroptosis. Necroptosis is activated by the death receptor ligands and pattern recognition receptors of the innate immune system, leading to significant consequences in inflammation and in diseases, particularly cancer. Necroptosis is highly proinflammatory compared with other modes of cell death because cell membrane integrity is lost, resulting in releases of cytokines and damage-associated molecular patterns that potentiate inflammation and activate the immune system. We discuss various ways that necroptosis is triggered along with its potential role in cancer and therapy.

The E3 Ligase NEDD4L Prevents Colorectal Cancer Liver Metastasis via Degradation of PRMT5 to Inhibit the AKT/mTOR Signaling Pathway

Colorectal cancer is the second most common cause of cancer mortality worldwide, and liver metastasis is the major cause of death of patients with colorectal cancer. Dysfunctional E3 ligase activity has recently been shown to be associated with colorectal cancer. However, the key E3 ligases affecting colorectal cancer liver metastasis remain unknown. Therefore, an shRNA library targeting 156 E3 ubiquitin ligases has been used to perform an in vivo loss-of-function screen of a human colorectal cancer cell line in a mouse model of liver metastasis. The screen reveals that neural precursor cell expressed developmentally down-regulated gene 4-like (NEDD4L) knockdown promotes colorectal cancer liver metastasis. Mechanistic studies reveal that NEDD4L binds to the PPNAY motif in protein arginine methyltransferase 5 (PRMT5) and ubiquitinates PRMT5 to promote its degradation. PRMT5 degradation attenuates the arginine methylation of AKT1 to inhibit the AKT/mTOR signaling pathway. The effect of NEDD4L decreases colorectal cancer cell proliferation to suppress colonization. This study is the first to show that PRMT5 is a substrate of NEDD4L and reveals not only the metastasis-inhibiting function of NEDD4L but also a novel mechanism by which NEDD4L prevents colorectal cancer liver metastasis. These findings may provide a new preventive strategy for liver metastasis.

Targeted plasma proteomics reveals organ damage signatures of AIDS- and noncommunicable disease-related deaths in people with HIV

Antiretroviral therapy (ART) is shifting the primary driver of mortality for people with HIV (PWH) from opportunistic infections to noncommunicable diseases (NCDs). Protein biomarkers differentiating both AIDS-related and NCDs-related deaths from PWH may help early and precise risk prediction and intervention. We conduct a nested case-control study where 126 HIV deaths, 162 age-sex-matched HIV survivors and 152 HIV-negative controls are analyzed with 92 protein biomarkers of the Olink Organ Damage panel by proximity extension assays (PEA). Using LASSO regression, logistic regression, and ROC analysis, twelve proteins are significantly associated with HIV death, of which six (SIRT5, PPM1B, PSMA1, GALNT10, VEGFC, PTN) are specifically associated with NCDs-related death, two (RCOR1, SERPINA9) are specifically associated with AIDS-related death, and four (CA12, CA14, RARRES1, EDIL3) are associated with both. Three of these proteins are replicable in the external validation sample. The adjusted protein panels consisting of significantly associated proteins selected through both LASSO and logistic regression model well predicted NCDs-related death (AUC = 0.970) and AIDS-related death (AUC = 0.960) in PWH. The selected proteins also displayed a significant correlation with traditional biomarkers of NCDs among PWH (P < 0.05). The potential clinical utility of these biomarkers could shed light on pathogenesis of end-stage organ dysfunction in PWH.

RNF128 promotes gastric cancer progression by inhibiting autophagy-dependent ferroptosis through Beclin1 ubiquitination

As an important protein post-translational modification process, ubiquitination plays an indispensable role in the regulation of gastric cancer (GC) occurrence and development. And recent studies have demonstrated that this modification is closely related to regulated cell death. This suggests that our therapeutic approach to inhibit the malignant progression of GC by regulating the intracellular death mode through ubiquitination modification becomes possible. Although ubiquitination modification has been well described in some tumorigenesis, its potential role and specific mechanisms are still unknown. In the present study, we identified RNF128, an E3 ubiquitin ligase with a RING structural domain, whose expression was significantly increased in GC. In-depth studies showed that knockdown of RNF128 significantly inhibited GC cell proliferation and increased intracellular autophagic flux and lipid peroxidation production, and we hypothesized that autophagy-dependent ferroptosis might be the main mode of death mediated by RNF128. Mechanistically, RNF128 directly binds and ubiquitinates degradation of Beclin1 through its PA structural domain and significantly inhibits the Beclin1/solute transport family 7 member 11(SLC7A11)/glutathione peroxidase 4(GPX4) axis. Taken together, our study reports for the first time that RNF128 acts as a tumor promoter to inhibit autophagy-dependent ferroptosis in GCs by targeting Beclin1. These data provide new insights into the activation of intracellular ferroptosis to inhibit malignant tumor progression and are expected to provide a new strategy for molecular therapy in clinical GC patients.

ENC1 Promotes the Malignant Progression and Metastasis by Suppressing TRIM21 Mediated Vimentin Degradation in Wilms Tumor

Ectodermal neural cortex 1 (ENC1) is significantly upregulated in various cancers and shows a positive correlation with poor prognosis and advanced clinical stages, such as colorectal cancer, endometrial cancer and breast cancer. However, the role of ENC1 in Wilms tumor (WT) has not been previously reported. In this study, we conducted several in vitro functional experiments and established xenograft models to confirm the oncogenic potential of ENC1. The binding proteins of ENC1 were identified through co-immunoprecipitation and mass spectrometry to screen the mechanism of malignant progression. Further analysis elucidated the mechanism by which ENC1 promotes tumorigenesis. The results demonstrated that ENC1 was significantly overexpressed in tumor and recurrence samples, with elevated ENC1 expression showing a significant negative correlation with both overall survival and recurrence-free survival of patients. Functionally, the role of ENC1 in tumor oncogenicity was elucidated through the assessment of tumor cell proliferation, migration, and invasion capabilities. Mechanistically, through immunoprecipitation and mass spectrometry, we identified Vimentin as an interacting protein of ENC1. ENC1 competed with the E3 ubiquitin ligase TRIM21 for Vimentin binding, thereby reducing the ubiquitination level of Vimentin and enhancing its protein stability. In conclusion, this study demonstrates that ENC1 functions as a novel oncogenic target for Wilms tumor by disrupting TRIM21-mediated ubiquitination of Vimentin, which presents novel insights for the treatment of Wilms tumor and the development of prognostic markers.

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.

MYCBP2-mediated HNF4α ubiquitination reprogrammed lipid metabolism in MASH-associated hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a major global health burden, with metabolic dysfunction-associated steatohepatitis (MASH) emerging as a significant risk factor. The scarcity of effective pharmacological treatments for MASH and its progression to HCC underscores the need for deeper molecular insights. Our study identifies Myc-binding protein 2 (MYCBP2), an E3 ubiquitin ligase, as a potential tumor suppressor in MASH-related HCC. Through transcriptomic and proteomic analyses, we observed significant downregulation of MYCBP2 in HCC tissues. In vitro and in vivo experiments demonstrate that MYCBP2 inhibits HCC cell proliferation, migration, and invasion by modulating lipid metabolism pathways. Mechanistically, MYCBP2 promotes the ubiquitination and degradation of Hepatocyte Nuclear Factor 4 Alpha (HNF4α). This ubiquitination occurs via K33- and K48-linked polyubiquitin chains at lysines 300 and 307 of HNF4α. The results showed that MYCBP2 influences the expression of lipid metabolism-related genes and attenuates HNF4α's regulatory role in lipid metabolism through the mediated ubiquitination and degradation of HNF4α. Our findings elucidate the MYCBP2-HNF4α axis as a novel regulatory pathway in MASH-related HCC and highlight the broader implications of ubiquitination in cancer metabolism, offering a promising metabolic target for therapeutic intervention.

Hexosamine biosynthesis dysfunction-induced LIFR N-glycosylation deficiency exacerbates steatotic liver ischemia/reperfusion injury

BACKGROUND

More and more steatotic livers undergo resection or transplantation but they exhibit higher susceptibility to ischemia-reperfusion injury (IRI), which results in increased perioperative complication morbidity and mortality. IRI is driven by various cytokines and receptors, both of which are extensively modified by N-glycosylation. We aim to elucidate susceptibility of steatotic livers to IRI from the perspective of N-glycosylation.

METHODS

Differentially expressed genes and glycoproteins were identified with RNA-seq and N-glycoproteomics. Myeloid LIF or hepatocyte LIFR knockout mice were developed to examine the function of LIF and LIFR. Modalities including phosphoproteomics, ChIP-seq, single cell RNA-seq, metabolomics and immunoblotting were utilized to investigate underlying mechanisms.

RESULTS

LIF transcription in myeloid cells and LIFR N-glycosylation in hepatocytes were substantially induced by IRI of normal livers. LIF and LIFR protected normal livers from IRI through activating STAT3 and promoting downstream TNFAIP3 expression, which was facilitated by LIFR N-glycosylation. Mechanistically, N-glycosylation at N238 stabilized LIFR protein by disrupting TRIM28-mediated K48 ubiquitination at LIFR K254. Furthermore, N-glycosylation at N358/N658/N675 of LIFR facilitated LIF/LIFR/gp130 complex formation and subsequent signal transduction. However, in steatotic livers, myeloid cell LIF transcription was partially inhibited due to hepatic microenvironment L-arginine insufficiency, while hepatocyte LIFR N-glycosylation was defective due to intracellular UDP-GlcNAc exhaustion. Importantly, combined L-arginine and GlcNAc treatment reversed LIF expression and LIFR N-glycosylation insufficiency, which represents potential therapeutic strategy to protect steatotic livers.

CONCLUSIONS

LIF expression and LIFR N-glycosylation insufficiency aggravates steatotic liver IRI, which can be reversed by combined L-arginine and GlcNAc treatment.

TRIM36 Inhibits the Development of AOM/DSS-Induced Colitis-Associated Colorectal Cancer by Promoting the Ubiquitination and Degradation of GRB7

Colorectal cancer (CRC) is among the most common cancer types for both sexes. Tripartite motif 36 (TRIM36) has been reported to be aberrantly expressed in several cancer types, suggesting its involvement in cancer progression. However, the role of TRIM36 in the colorectal carcinogenesis remain unknown. In our in vivo experiments, we investigated the role of TRIM36 in AOM/DSS-induced colitis-associated carcinogenesis using TRIM36-knockout (TRIM36 KO) mice. Subsequently, we overexpressed and knocked down TRIM36 expression in two CRC cell lines to further confirm the role of TRIM36 in vitro. The UALCAN database revealed a significant decrease in TRIM36 levels in CRC tissues, including colon adenocarcinoma and rectum adenocarcinoma. A significant correlation was observed between TRIM36 levels and the histological subtype, individual cancer stage, and nodal metastasis status. The downregulation of TRIM36 in CRC tissues was further confirmed using our own collected clinical specimens. Low expression of TRIM36 was found to be associated with unfavorable overall survival and recurrence-free survival in CRC. TRIM36 KO promoted inflammation, inhibited autophagy, and facilitated the development of AOM/DSS-induced CRC. TRIM36 overexpression inhibited proliferation, migration, and invasion, while activated autophagy in CRC cells. TRIM36 directly bound to and regulated the ubiquitination of GRB7 protein. The tumor-suppressive role of TRIM36 in CRC cells was mediated by GRB7. The TRIM36/GRB7 axis may represent a promising therapeutic target for the treatment of CRC.

TRIM38 Suppresses the Progression of Colorectal Cancer via Enhancing CCT6A Ubiquitination to Inhibit the MYC Pathway

Emerging evidence reveals the pivotal function of tripartite motif protein (TRIM) in colorectal cancer (CRC). However, the precise function of TRIM38 and its underlying mechanism in CRC remains to be elucidated, especially regarding its putative ubiquitination function. Here, it is identified that TRIM38 is downregulated in CRC tissues by DNA hypermethylation of its promoter. Further analysis demonstrates that decreased TRIM38 is correlated with unfavorable clinical features and poor prognosis. Moreover, TRIM38 functions as a tumor suppressor by inhibiting cell proliferation, metastasis, and AOM/DSS-induced tumorigenesis in CRC cells. Mechanistically, TRIM38 binds to the substrate protein CCT6A, leading to the degradation and K48-linked ubiquitination of CCT6A at the K127/K138 residues. The elevation of CCT6A protein level caused by TRIM38 downregulation diminishes the degradation of c-Myc protein, thereby activating the MYC pathway. The study elucidates a novel mechanism of TRIM38/CCT6A/c-Myc axis regulating CRC, potentially offering a new therapeutic target for its treatment.

N6-methyladenosine-mediated EIF3H promotes anaplastic thyroid cancer progression and ferroptosis resistance by stabilizing β-catenin

Anaplastic thyroid cancer (ATC) patients suffer from a poor prognosis with very limited treatment options. The accumulation of β-catenin and the activation of downstream signaling is one of the main events in ATC, while the role of JAMM family in ATC remains unknown. In this study, we aimed to identify a new deubiquitinating enzyme regulating β-catenin in ATC. We found that EIF3H was positively correlated with β-catenin, and the knockdown of EIF3H deactivated the Wnt/β-catenin signaling pathway in ATC. Further exploration revealed that EIF3H interacted with, deubiquitylated, and stabilized β-catenin by acting as a deubiquitinating enzyme. Mechanistically, EIF3H removed the K48-linked ubiquitin chain on β-catenin by binding the N tails of β-catenin. The knockdown of EIF3H could inhibit ATC cell proliferation, invasion, and ferroptosis resistance by regulating β-catenin. In addition, the dysregulation of EIF3H was associated with m6A modification in the 3'UTR and a m6A reader, IGF2BP2. In summary, the EIF3H/β-catenin axis promotes ATC progression and ferroptosis resistance by activating the Wnt/β-catenin signaling pathway. The EIF3H/β-catenin axis may serve as a potential diagnostic marker and a therapeutic target in ATC.

USP13: A therapeutic target for combating tumorigenesis and antitumor therapy resistance

Ubiquitin-specific peptidase 13 (USP13) has emerged as a key regulator of proteins critical to the hallmarks of cancer, playing an essential role in cellular regulation. This deubiquitinating enzyme, often overexpressed in malignancies, wields its molecular scissors precisely, snipping ubiquitin tags to rescue oncoproteins from degradation. Our review highlights the dual role of USP13 in cancer biology: while it predominantly fuels tumor growth and metastasis, USP13 occasionally functions as a tumor suppressor. USP13 is as a formidable factor in cancer therapy, fortifying tumors against an arsenal of treatments. It bolsters DNA repair mechanisms, ignites prosurvival autophagy, and even reprograms cell lineages to evade targeted therapies. However, USP13 is also a promising target in the treatment of cancer. We highlight burgeoning strategies to neutralize USP13, from small molecule inhibitors to innovative protein degraders, which may disarm cancer resistance mechanisms. We also offer suggestions for future USP13 research, emphasizing the need for structural insights and more potent inhibitors. This review highlights the critical role of USP13 in cancer and underscores its potential as a therapeutic target for advancing cancer treatment.

UFMylation of NLRP3 Prevents Its Autophagic Degradation and Facilitates Inflammasome Activation

NLRP3 (NOD, LRR and pyrin domain-containing protein 3) inflammasome is important for host defense against infections and maintaining homeostasis. Aberrant activation of NLRP3 inflammasome is closely related to various inflammatory diseases. Post-translational modifications are critical for NLRP3 inflammasome regulation. However, the mechanism of NLRP3 inflammasome activation remains incompletely understood. Here, it is demonstrated that the Ufm1 E3 ligase Ufl1 mediated UFMylation is essential for NLRP3 inflammasome activation. Mechanistically, Ufl1 binds and UFMylates NLRP3 in the priming stage of NLRP3 activation, thereby sustaining the stability of NLRP3 by preventing NLRP3 K63-linked ubiquitination and the subsequent autophagic degradation. It is further demonstrated that myeloid cell-specific Ufl1 or Ufm1 deficiency in mice significantly alleviated inflammatory responses and tissue damage following lipopolysaccharide (LPS)-induced endotoxemia and alum-induced peritonitis. Thus, the findings offer new insights into potential therapeutic targets for NLRP3 inflammasome-related diseases by targeting the UFMylation system.

The Role and Mechanisms of Ubiquitin-Proteasome System-Mediated Ferroptosis in Neurological Disorders

Ferroptosis is a form of cell death elicited by an imbalance in intracellular iron concentrations, leading to enhanced lipid peroxidation. In neurological disorders, both oxidative stress and mitochondrial damage can contribute to ferroptosis, resulting in nerve cell dysfunction and death. The ubiquitin-proteasome system (UPS) refers to a cellular pathway in which specific proteins are tagged with ubiquitin for recognition and degradation by the proteasome. In neurological conditions, the UPS plays a significant role in regulating ferroptosis. In this review, we outline how the UPS regulates iron metabolism, ferroptosis, and their interplay in neurological diseases. In addition, we discuss the future application of small-molecule inhibitors and identify potential drug targets. Further investigation into the mechanisms of UPS-mediated ferroptosis will provide novel insights and strategies for therapeutic interventions and clinical applications in neurological diseases.

CircSATB1 Promotes Colorectal Cancer Liver Metastasis through Facilitating FKBP8 Degradation via RNF25-Mediated Ubiquitination

Colorectal cancer (CRC) is one of the most common cancers worldwide and liver metastasis is the leading reason for its mortality. Circular RNAs (circRNAs) are conclusively associated with the progression of various cancers, rendering the exploration of its specific mechanisms in colorectal cancer liver metastasis(CRLM) highly valuable. Combined with GEO (Gene Expression Omnibus) databases and clinical data in our center, we found that high expression of circSATB1 is closely related to the progression of CRLM. Functionally, circSATB1 could significantly promote the metastatic ability of CRC cells in vitro and in vivo. Mechanistically, circSATB1 facilitated the RNF25-mediated ubiquitylation and degradation of FKBP8, releasing its inhibitory effects on mTOR signaling. In this process, circSATB1 acted as a scaffold for RNF25-FKBP8 complexes. Additionally, circSATB1 could be packaged in exosomes and secreted from the CRC primary tumors into plasma. In conclusion, this study uncovered a new circSATB1 that acts as a potent promoter of CRLM and offers novel insights into the precision therapeutic strategies for CRLM.

The role of ACSL4 in stroke: mechanisms and potential therapeutic target

Stroke, as a neurological disorder with a poor overall prognosis, has long plagued the patients. Current stroke therapy lacks effective treatments. Ferroptosis has emerged as a prominent subject of discourse across various maladies in recent years. As an emerging therapeutic target, notwithstanding its initial identification in tumor cells associated with brain diseases, it has lately been recognized as a pivotal factor in the pathological progression of stroke. Acyl-CoA synthetase long-chain family member 4 (ACSL4) is a potential target and biomarker of catalytic unsaturated fatty acids mediating ferroptosis in stroke. Specifically, the upregulation of ACSL4 leads to heightened accumulation of lipid peroxidation products and reactive oxygen species (ROS), thereby exacerbating the progression of ferroptosis in neuronal cells. ACSL4 is present in various tissues and involved in multiple pathways of ferroptosis. At present, the pharmacological mechanisms of targeting ACSL4 to inhibit ferroptosis have been found in many drugs, but the molecular mechanisms of targeting ACSL4 are still in the exploratory stage. This paper introduces the physiopathological mechanism of ACSL4 and the current status of the research involved in ferroptosis crosstalk and epigenetics, and summarizes the application status of ACSL4 in modern pharmacology research, and discusses the potential application value of ACSL4 in the field of stroke.

Functions and mechanisms of non-histone post-translational modifications in cancer progression

Protein post-translational modifications (PTMs) refer to covalent and enzymatic alterations to folded or nascent proteins during or after protein biosynthesis to alter the properties and functions of proteins. PTMs are modified in a variety of types and affect almost all aspects of cell biology. PTMs have been reported to be involved in cancer progression by influencing multiple signaling pathways. The mechanism of action of histone PTMs in cancer has been extensively studied. Notably, evidence is mounting that PTMs of non-histone proteins also play a vital role in cancer progression. In this review, we provide a systematic description of main non-histone PTMs associated with cancer progression, including acetylation, lactylation, methylation, ubiquitination, phosphorylation, and SUMOylation, based on recent studies.

Deubiquitinase OTUD7B stabilizes HNF4α to alleviate pressure overload-induced cardiac hypertrophy by regulating fatty acid oxidation and inhibiting ferroptosis

BACKGROUND

Cardiac hypertrophy, a leading cause of heart failure, threatens global public health. Deubiquitinating enzymes (DUBs) are critical in cardiac pathophysiology by regulating protein stability, function, and degradation. Here, we investigated the role and regulating mechanism of ovarian tumor domain-containing 7B (OTUD7B) in cardiac hypertrophy by modulating fatty acid metabolism.

METHODS

Mice subjected to transverse aortic constriction (TAC) and cardiomyocytes treated with phenylephrine (PE) were used to explore the role of OTUD7B in myocardial hypertrophy. The potential molecular mechanisms underlying OTUD7B's regulation of cardiac hypertrophy were explored through transcriptome analysis and further validated in cardiomyocytes.

RESULTS

Reduced OTUD7B expression was observed in hypertrophic hearts following TAC surgery. Cardiac-specific OTUD7B deficiency exacerbated, while OTUD7B overexpression mitigated, pressure overload-induced hypertrophy and cardiac dysfunction both in vivo and in vitro. OTUD7B knockdown resulted in ferroptosis, as evidenced by decreased mitochondrial cristae, increased Fe2+ ion content, lipid peroxide accumulation, while OTUD7B overexpression inhibited ferroptosis. Mechanistically, transcriptomic analysis identified OTUD7B plays a role in the regulation of fatty acid metabolism and pathological cardiac hypertrophy. OTUD7B was found to directly bind to HNF4α, a transcription factor regulating fatty acid oxidation-related genes. Further, OTUD7B exerted deubiquitination activity to stabilize the HNF4α protein by removing K48-linked ubiquitin chains, thereby preventing its degradation via the proteasomal pathway and linking the HNF4α degradation and ferroptosis. Finally, ferroptosis inhibitors, ferrostatin-1, alleviated OTUD7B inhibition-induced ferroptosis, fatty acid metabolism suppression, and myocardial hypertrophy.

CONCLUSIONS

We confirmed that OTUD7B is involved in the regulation of ferroptosis in pressure overload-induced cardiac hypertrophy and highlighted that OTUD7B alleviates cardiac hypertrophy by regulating ferroptosis and fatty acid oxidation through deubiquitination and stabilization of HNF4α.

The USP43/RNF2 axis negatively regulates antiviral innate immunity by promoting TBK1 ubiquitination and degradation

The E3 ubiquitin ligase usually regulates the substrate proteins ubiquitination and degradation, but the study of itself post-translational modification and stability is still elusive. Here, we reveal that E3 ubiquitin ligase ring finger protein 2 (RNF2) is deubiquitinated and stabilized by ubiquitin specific peptidase 43 (USP43) through interactome and quantitative ubiquitinome mass spectrometry analysis. This study demonstrated that USP43, as a deubiquitinating enzyme, negatively regulates the expression of type I interferon (IFN) and the Usp43 deficient enhances antiviral innate immune response against VSV infection both in vitro and in vivo. Mechanistically, USP43 negatively regulates antiviral immunity by promoting RNF2-mediated TBK1 ubiquitination and degradation. USP43 stabilizes RNF2 by removing K48-linked ubiquitination of RNF2 at Lys239 and Lys249, while RNF2 promotes TBK1 degradation by increasing K48-linked ubiquitination of TBK1 at Lys670. These findings uncover the E3 ubiquitin ligase RNF2 post-translational ubiquitination modification and stability regulation, and reveals a novel mechanism that the USP43/RNF2 axis in regulating antiviral innate immunity.

Immune cell metabolic dysfunction in Parkinson's disease

Parkinson's disease (PD) is a multi-system disorder characterized histopathologically by degeneration of dopaminergic neurons in the substantia nigra pars compacta. While the etiology of PD remains multifactorial and complex, growing evidence suggests that cellular metabolic dysfunction is a critical driver of neuronal death. Defects in cellular metabolism related to energy production, oxidative stress, metabolic organelle health, and protein homeostasis have been reported in both neurons and immune cells in PD. We propose that these factors act synergistically in immune cells to drive aberrant inflammation in both the CNS and the periphery in PD, contributing to a hostile inflammatory environment which renders certain subsets of neurons vulnerable to degeneration. This review highlights the overlap between established neuronal metabolic deficits in PD with emerging findings in central and peripheral immune cells. By discussing the rapidly expanding literature on immunometabolic dysfunction in PD, we aim to draw attention to potential biomarkers and facilitate future development of immunomodulatory strategies to prevent or delay the progression of PD.

Role of long non-coding RNAs in the regulation of ferroptosis in tumors

Normal cells begin to grow indefinitely and immortalize to form tumor cells after an external stimulus resulting in a genetic mutation. Effective killing of tumor cells is the basis of various cancer therapies. Ferroptosis is a class of cell death types dependent on iron and cellular lipid peroxidation. Tumors themselves are iron-dependent, and conventional radiotherapy also sensitizes cancer cells to ferroptosis. Increasing the sensitivity of tumor cells to ferroptosis may be a potential therapeutic strategy to overcome the resistance mechanisms of conventional cancer therapy. Long noncoding RNAs (LncRNAs) are a class of transcripts more than 200 nucleotides in length that regulate gene expression at multiple levels and are involved in biological processes such as cell differentiation, cell cycle arrest, and maintenance of tumor stemness. Recent studies have found that lncRNAs regulate ferroptosis of tumor cells through multiple mechanisms and may influence or ameliorate tumor resistance to chemotherapeutic agents. With the continuous maturation of nanomaterials technology, it may provide new means for cancer treatment by regulating the levels of ferroptosis-related lncRNAs inside tumors as well as increasing the levels of Fe2+ and ROS inside tumors. In this paper, we systematically introduce the regulatory mechanism of lncRNAs in ferroptosis, the role of ferroptosis in tumor immunotherapy and the application of lncRNAs combined with ferroptosis in nanomaterials, which provides new perspectives for tumor therapy.

Leveraging AI to Explore Structural Contexts of Post-Translational Modifications in Drug Binding

Post-translational modifications (PTMs) play a crucial role in allowing cells to expand the functionality of their proteins and adaptively regulate their signaling pathways. Defects in PTMs have been linked to numerous developmental disorders and human diseases, including cancer, diabetes, heart, neurodegenerative and metabolic diseases. PTMs are important targets in drug discovery, as they can significantly influence various aspects of drug interactions including binding affinity. The structural consequences of PTMs, such as phosphorylation-induced conformational changes or their effects on ligand binding affinity, have historically been challenging to study on a large scale, primarily due to reliance on experimental methods. Recent advancements in computational power and artificial intelligence, particularly in deep learning algorithms and protein structure prediction tools like AlphaFold3, have opened new possibilities for exploring the structural context of interactions between PTMs and drugs. These AI-driven methods enable accurate modeling of protein structures including prediction of PTM-modified regions and simulation of ligand-binding dynamics on a large scale. In this work, we identified small molecule binding-associated PTMs that can influence drug binding across all human proteins listed as small molecule targets in the DrugDomain database, which we developed recently. 6,131 identified PTMs were mapped to structural domains from Evolutionary Classification of Protein Domains (ECOD) database. Scientific contribution. Using recent AI-based approaches for protein structure prediction (AlphaFold3, RoseTTAFold All-Atom, Chai-1), we generated 14,178 models of PTM-modified human proteins with docked ligands. Our results demonstrate that these methods can predict PTM effects on small molecule binding, but precise evaluation of their accuracy requires a much larger benchmarking set. We also found that phosphorylation of NADPH-Cytochrome P450 Reductase, observed in cervical and lung cancer, causes significant structural disruption in the binding pocket, potentially impairing protein function. All data and generated models are available from DrugDomain database v1.1 (http://prodata.swmed.edu/DrugDomain/) and GitHub (https://github.com/kirmedvedev/DrugDomain). This resource is the first to our knowledge in offering structural context for small molecule binding-associated PTMs on a large scale.

A panel of six immune-related mRNAs as biomarkers for tuberculosis diagnosis

Objective

This study aims to screen common immunological markers of lung tissues and blood for diagnosis of tuberculosis (TB).

Methods

Differentially expressed miRNAs (DEmRs) and mRNAs (DEGs) were obtained by whole-transcriptome sequencing profiles on 18F-FDG PET/CT high and low metabolic active regions in lung tissues of nine TB patients. Common miRNAs were screened by intersecting with DEmRs, four miRNA GEO datasets, and their target mRNAs were predicted through the miRTarbase and Tarbase databases. Then these mRNAs were intersected with DEGs, mRNAs from blood samples and immune-related genes, to construct a miRNA-mRNA interaction network, and the hub genes were identified by Cytoscape. The relationship between immune infiltration and hub genes were evaluated using Cibersort. Finally, a diagnostic model based on Lasso regression analysis was established and validated by qRT-PCR.

Results

Five common miRNAs were obtained in both blood and tissues. Six immune-related mRNAs (NEDD4, PLTP, RNASEL, SEMA7A, TAPBP, and THBS1) were screened out. A diagnostic model was established and validated in the blood samples of 30 pairs (TB/health volunteers). The AUC for the 6-mRNA combination was 0.79.

Conclusion

We screened six mRNAs as a combination for diagnosing tuberculosis.

Peli1, regulated by m6A modification, suppresses NLRP3 inflammasome activation in atherosclerosis by inhibiting YB-1

The activation of pyrin domain-containing-3 (NLRP3) inflammasome in macrophages is a risk factor accelerating the progression of atherosclerosis (AS). Here, the function of pellino 1 (Peli1) in regulating the activation of NLRP3 inflammasome during the development of AS was investigated. Our results showed that Y-box binding protein 1 (YB-1) knockdown could inhibit the progression of AS in vivo, and YB-1 silencing repressed oxidized low-density lipoprotein (ox-LDL)-mediated lipid accumulation and inflammation in macrophages by inactivating NLRP3 inflammasome. E3 ubiquitination ligase Peli1 mediated ubiquitination-dependent degradation of YB-1 during AS progression. Moreover, it was found that YTH domain-containing 2 (YTHDC2) recognized methyltransferase-like 3 (METTL3)-mediated Peli1 N6-methyladenosine (m6A) modification and mediated Peli1 mRNA degradation. Rescue studies revealed that YB-1 upregulation abrogated the repressive effect of Peli1 upregulation on AS progression both in vitro and in vivo. Taken together, Peli1, regulated by m6A modification, inhibited YB-1-mediated activation of NLRP3 inflammasome in macrophages by promoting YB-1 ubiquitination to suppress the progression of AS.

Ubiquitin Ligases in Control: Regulating NLRP3 Inflammasome Activation

Ubiquitin ligases play pivotal roles in the regulation of NLR family pyrin domain containing 3 (NLRP3) inflammasome activation, a critical process in innate immunity and inflammatory responses. This review explores the intricate mechanisms by which various E3 ubiquitin ligases exert both positive and negative influences on NLRP3 inflammasome activity through diverse post-translational modifications. Negative regulation of NLRP3 inflammasome assembly is mediated by several E3 ligases, including F-box and leucine-rich repeat protein 2 (FBXL2), tripartite motif-containing protein 31 (TRIM31), and Casitas B-lineage lymphoma b (Cbl-b), which induce K48-linked ubiquitination of NLRP3, targeting it for proteasomal degradation. Membrane-associated RING-CH 7 (MARCH7) similarly promotes K48-linked ubiquitination leading to autophagic degradation, while RING finger protein (RNF125) induces K63-linked ubiquitination to modulate NLRP3 function. Ariadne homolog 2 (ARIH2) targets the nucleotide-binding domain (NBD) domain of NLRP3, inhibiting its activation, and tripartite motif-containing protein (TRIM65) employs dual K48 and K63-linked ubiquitination to suppress inflammasome assembly. Conversely, Pellino2 exemplifies a positive regulator, promoting NLRP3 inflammasome activation through K63-linked ubiquitination. Additionally, ubiquitin ligases influence other components critical for inflammasome function. TNF receptor-associated factor 3 (TRAF3) mediates K63 polyubiquitination of apoptosis-associated speck-like protein containing a CARD (ASC), facilitating its degradation, while E3 ligases regulate caspase-1 activation and DEAH-box helicase 33 (DHX33)-NLRP3 complex formation through specific ubiquitination events. Beyond direct inflammasome regulation, ubiquitin ligases impact broader innate immune signaling pathways, modulating pattern-recognition receptor responses and dendritic cell maturation. Furthermore, they intricately control NOD1/NOD2 signaling through K63-linked polyubiquitination of receptor-interacting protein 2 (RIP2), crucial for nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and mitogen-activated protein kinase (MAPK) activation. Furthermore, we explore how various pathogens, including bacteria, viruses, and parasites, have evolved sophisticated strategies to hijack the host ubiquitination machinery, manipulating NLRP3 inflammasome activation to evade immune responses. This comprehensive analysis provides insights into the molecular mechanisms underlying inflammasome regulation and their implications for inflammatory diseases, offering potential avenues for therapeutic interventions targeting the NLRP3 inflammasome. In conclusion, ubiquitin ligases emerge as key regulators of NLRP3 inflammasome activation, exhibiting a complex array of functions that finely tune immune responses. Understanding these regulatory mechanisms not only sheds light on fundamental aspects of inflammation but also offers potential therapeutic avenues for inflammatory disorders and infectious diseases.

Ubiquitination of gasdermin D N-terminal domain directs its membrane translocation and pore formation during pyroptosis

Gasdermin D (GSDMD) is a critical pyroptosis mediator, consisting of one N-terminal pore-forming domain and one C-terminal auto-inhibitory domain. The free N-terminal domain (GD-NT), which is released through caspase-1/11 cleavage, exhibits distinct features from the full-length GSDMD (GD-FL), including oligomerization, membrane translocation, and pore-formation. However, the underlying mechanisms are not well elucidated. Here, we found that GD-NT, but not GD-FL, was massively ubiquitinated in cells. The K63-linked polyubiquitination of GD-NT at Lys236/237 (human/mouse), catalyzed by TRAF1, directly prompted its membrane translocation and pore-formation during pyroptosis. Inhibition of GD-NT ubiquitination via site-directed mutations or the UBA1 inhibitor PYR-41 suppressed cell death in several pyroptosis cell models. Additionally, applying PYR-41 in septic mice efficiently suppressed the release of IL-18 and TNFα. Thus, GD-NT ubiquitination is a key regulatory mechanism controlling its membrane localization and activation, which may provide a novel target for modulating immune activity in pyroptosis-related diseases.

USP39/SMC4 promotes hepatoma cell proliferation and 5-FU resistance

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality, characterized by a high rate of postoperative recurrence and poor long-term survival outcomes. Structural maintenance of chromosome 4 (SMC4) is frequently overexpressed in various types of cancer and plays a pivotal role in tumor cell growth, migration, and invasion. Bioinformatics analysis has revealed a significant correlation between the tumor-node metastasis (TNM) stage (P < 0.01) and SMC4 expression (P < 0.05), and SMC4 was associated with poor prognosis in HCC. Furthermore, SMC4 was identified as an independent prognostic factor for HCC. Ubiquitin-specific peptidase 39 (USP39) was found whether the regulation was observed to affect protein synthesis or stability through bioinformatics analysis and immunoprecipitation. The expression levels and cellular localization of SMC4 and USP39 in hepatoma cells were evaluated using quantitative real-time PCR (qPCR), western blotting, and immunohistochemistry (IHC), all of which indicated significantly elevated expression of USP39 and SMC4 in HCC. The roles of the SMC4/USP39 were further investigated through several assays, including the 3-(4,5-Dimethylthiazol-2-yl) -2,5- diphenyltetrazolium bromide (MTT) assay, 5-ethynyl-2'-deoxyuridine (EdU) incorporation assay, and wound healing assay. The results demonstrated that USP39/SMC4 plays a crucial role in enhancing the viability and proliferation of HepG2 cells. Additionally, bioinformatics analysis identified ZNF207 and TIAL1 as potential target proteins of SMC4. Drug-resistant hepatoma cell lines were established, and both MTT and EdU assays were performed to assess cell viability and proliferation. The results demonstrated that HepG2/5-FU cells regained their sensitivity to 5-FU following the knockdown of SMC4. Additionally, the knockdown of either TIAL1 or ZNF207 also restored 5-FU sensitivity in HepG2/5-FU cells, effectively inhibiting cell viability and proliferation. Our study underscores the significant role of the USP39/SMC4 in HCC development and suggests that SMC4 may contribute to the regulation of drug resistance in hepatoma cell lines, potentially through interactions with TIAL1 and ZNF207.

TRIM21-mediated ubiquitination and phosphorylation of ERK1/2 promotes cell proliferation and drug resistance in pituitary adenomas

BACKGROUND

Pituitary adenomas (PAs) are common intracranial tumors and the TRIM family plays a crucial role in cell proliferation and therapeutic resistance of tumors. However, the role of the TRIM family in PAs is not well recognized.

METHODS

CRISPR screening explored the role of the TRIM family in cell proliferation and drug resistance in PAs. In vitro and in vivo experiments were performed to evaluate the effects of Tripartite Motif Containing 21 (TRIM21). RNA-sequencing, mass spectrometry, immunoprecipitation, and ubiquitination experiments were performed to explore the molecular mechanism. NanoBiT assays were used to screen the drugs reducing TRIM21 expression.

RESULTS

CRISPR-Cas9 screens identified that TRIM21 facilitated cell proliferation and drug resistance in PAs. Mechanistically, TRIM21 interacted with ERK1/2 through PRY-SPRY domain, leading to ERK1/2 K27-linked ubiquitination. The ERK1/2 ubiquitination promotes the interaction between ERK1/2 and MEK1/2, thereby facilitating the phosphorylation of ERK1/2. However, an excess presence of TRIM21 suppressed the phosphorylation of ERK1/2 and cell proliferation via activating ERK1/2 negative feedback pathways. Importantly, TRIM21 was upregulated in dopamine-resistant prolactinomas and cabergoline-resistant MMQ cells. Furthermore, drug screening identified that Fimepinostat and Quisinostat, can reduce the protein levels of TRIM21, inhibit tumor progression, and increase drug sensitivity.

CONCLUSIONS

TRIM21 may represent a therapeutic target for tumors, and inhibiting TRIM21 could be a potential strategy for tumor treatment.

[64Cu]Cu(DDC)2 NPs: A Novel PET Probe for Noninvasive Visualization of NPL4 Expression in Tumors In Vivo

Nuclear protein localization 4 (NPL4) plays a key role in the ubiquitination pathway and has emerged as a promising target for cancer therapy. The ditiocarb-copper complex, Cu(DDC)2, an anticancer metabolite derived from the antialcoholism drug disulfiram (DSF), exhibits a high affinity for NPL4. Thus, quantifying NPL4 expression in tumors is crucial for ubiquitination research and for developing NPL4-targeted diagnostic and therapeutic strategies. In this study, we replaced the cold copper ion in Cu(DDC)2 with the positron-emitting isotope copper-64 and developed three methods for visualizing NPL4 in tumors in vivo using positron emission tomography/computed tomography (PET/CT): (1) an in vivo "synthesis-free" method for preparing [64Cu]Cu(DDC)2, (2) an in vitro synthesis method, and (3) a stabilization method using PEG5000-PLA5000 (PP) to enhance [64Cu]Cu(DDC)2's hydrophilicity by preparing [64Cu]Cu(DDC)2 NPs. Micro-PET/CT imaging showed minimal uptake of [64Cu]Cu(DDC)2 in NPL4-positive tumors with the in vivo "synthesis-free" method, resulting in poor lesion visualization. However, in vitro synthesized [64Cu]Cu(DDC)2 and [64Cu]Cu(DDC)2 NPs successfully visualized NPL4-positive U87MG tumors. Compared to [64Cu]Cu(DDC)2, [64Cu]Cu(DDC)2NPs demonstrated significantly higher tumor uptake (7.2 ± 0.7% ID/g vs 3.8 ± 0.6% ID/g at 12 h postinjection, P = 0.001) and tumor-to-muscle (T/M) ratio (7.8 ± 1.2 vs. 3.2 ± 0.7, P = 0.001). Tumor uptake of [64Cu] Cu (DDC)2NPs was consistent with NPL4 expression levels and was inhibited by an excess of Cu(DDC)2. The optimal PP stabilizer concentration was determined to be 0.0005%. This study successfully developed a PET probe, [64Cu]Cu(DDC)2NPs, and established a novel imaging modality for in vivo visualization of NPL4 expression, potentially guiding future NPL4-targeted therapies.

SOX11 exacerbates ferroptosis to reduce lenvatinib resistance in liver cancer cells by promoting ubiquitination degradation of SREBF1 through upregulating UBE3A

Lenvatinib is one of the most commonly used first-line drugs for liver cancer. However, lenvatinib resistance occurs in a large proportion of patients, posing a significant challenge. Ferroptosis, an iron-dependent form of cell death, plays a pivotal role in overcoming drug resistance. This study investigates the role of SRY-related HMG-box transcription factor 11 (SOX11) in regulating lenvatinib resistance in liver cancer through its impact on ferroptosis. qRT-PCR, western blot, and immunohistochemistry were performed to examine the expression of key molecules in patient samples and cell lines. Functional studies, including cell viability and proliferation assays, colony formation assays, flow cytometry, and measurements of iron metabolism markers, were conducted to explore the biological effects of these molecules. Additionally, Co-IP, ChIP, dual-luciferase reporter assays, and in vivo tumorigenesis experiments were performed to uncover the underlying regulatory mechanisms. Our results showed that UBE3A was markedly downregulated in lenvatinib-resistant liver cancer tissues and cells, and its overexpression markedly reduced lenvatinib resistance in liver cancer cells by promoting ferroptosis. Mechanically, UBE3A reduced lenvatinib resistance in lenvatinib-resistant liver cancer cells by mediating ubiquitination-independent degradation of SREBF1. In addition, SOX11 upregulation reduced lenvatinib resistance in liver cancer cells by promoting ferroptosis through transcriptionally activated UBE3A expression. In summary, SOX11 upregulation promoted ferroptosis in liver cancer cells by promoting SREBF1 ubiquitination degradation through transcriptionally elevating UBE3A expression, thereby sensitizing lenvatinib-resistant liver cancer cells to lenvatinib.

Neolignan Kadsurenin F Modulates Proteostatic Pathways and Possesses Potent Anti-Inflammatory Properties

Kadsurenin F, a natural neolignan-type compound, has been described as a constituent of various members of the Lauraceae family such as Aniba spp. or Nectandra spp., but can also be found in various Piper species such as Piper kadsura Ohwi (Piperaceae). This species is traditionally used to treat asthma, rheumatic pain, arthritis, and digestive problems. Recently, several studies have highlighted the significant anti-inflammatory potential of P. kadsura extracts and secondary metabolites. Here, we report the isolation of kadsurenin F as an active component of P. kadsura. We found that kadsurenin F increases oxidative load and suppresses proteasome functionality in normal diploid human fibroblasts, and after administration in Drosophila flies. Moreover, kadsurenin F likely possesses anti-inflammatory properties, as apart from suppressing proteasome activity, it reversed inflammatory phenotypes and inhibited NO production in RAW 264.7 macrophage cells when administered in parallel with LPS. Our findings suggest that the kadsurenin F scaffold can be used for the development of novel highly bioactive proteasome inhibitors and/or anti-inflammatory compounds.

SPC25 upregulates CCND1 to promote the progression of esophageal squamous cell carcinoma by inhibiting MDM2-mediated E2F1 ubiquitination

Esophageal squamous cell carcinoma (ESCC) is highly malignant worldwide. Despite significant advances in the treatment of ESCC, the prognosis remains unfavourable, necessitating research into its mechanisms and treatments. Spindle component 25 (SPC25) can ensure the fidelity of mitotic progression and the accurate segregation of chromosomes, thus plays an important role in the development of malignant tumors, but its role in ESCC is yet to be determined. In this study, the expression of SPC25 was assessed by IHC in 88 primary ESCC samples, with its expression being correlated with advanced clinical features. The function of SPC25 in the proliferation, migration and tumorigenicity of ESCC cells was verified in vitro and in vivo. Mechanistically, SPC25 facilitated tumorigenesis through promoting CCND1 expression. As the transcription factor for CCND1, E2F1 is stabilized by SPC25 through binding the ubiquitin ligase MDM2, resulting in enhanced E2F1 expression, which in turn promotes the expression of CCND1. In addition, overexpression of CCND1 counteracted the effects of SPC25 silencing. Collectively, we demonstrated that the aberrant expression of SPC25 inhibited E2F1 ubiquitination and promoted CCND1 expression, thus accelerating the progression of ESCC. These findings propose novel insights into the role of SPC25 in ESCC and provide potential therapeutic strategies for targeting SPC25 in ESCC patients.

A novel mechanism in regulating drug sensitivity, growth, and apoptosis of bortezomib-resistant multiple myeloma cells: the USP4/KLF2/HMGA2 cascade

BACKGROUND

Multiple myeloma (MM) is a malignant disorder originating from plasma cells. Bortezomib (BTZ) resistance has become a huge obstacle to MM treatment. Herein, we elucidated the action of Kruppel-like factor 2 (KLF2), a crucial transcription factor (TF), on BTZ resistance of MM.

METHODS

Two BTZ-resistant cell lines (MM1.S/BTZ and NCI-H929/BTZ) were generated and used. KLF2 mRNA was quantified by quantitative PCR, and protein expression was analyzed by immunoblotting. MTT cell cytotoxicity assay was used to test BTZ sensitivity. Cell growth was detected by MTT and EdU assays. Flow cytometry was used for apoptosis and cycle distribution analyses. The USP4/KLF2 relationship was examined by Co-IP and protein stability assays. The KLF2/HMGA2 interplay was confirmed by luciferase and ChIP assays.

RESULTS

Upregulation of KLF2 was observed in MM serum and BTZ-resistant MM cells. Depletion of KLF2 suppressed cell growth and enhanced apoptosis and BTZ sensitivity in MM1.S/BTZ and NCI-H929/BTZ cells. Moreover, USP4 increased the stability of KLF2 protein by deubiquitination and affected cell growth, apoptosis and BTZ sensitivity via KLF2. KLF2 functioned as a regulator of HMGA2 transcription and modulated cell growth, apoptosis and BTZ sensitivity through HMGA2. Additionally, USP4 modulated HMGA2 expression via KLF2 in the two BTZ-resistant cell lines.

CONCLUSION

Our study demonstrates the crucial role of the USP4/KLF2/HMGA2 cascade in regulating cell growth, apoptosis and BTZ sensitivity in BTZ-resistant MM cells, providing novel targets for improving anti-MM efficacy of BTZ.

Ubiquitin-Proteasome System in Periodontitis: Mechanisms and Clinical Implications

The progression of periodontitis, a bacteria-driven inflammatory and bone-destructive disease, involves myriad cellular and molecular mechanisms. Protein regulation significantly influences the pathogenesis and management of periodontitis. However, research regarding its regulatory role in periodontitis remains relatively limited. The ubiquitin-proteasome system (UPS), which mainly involves ubiquitination by E3 ubiquitin ligases (E3s) and deubiquitination by deubiquitinating enzymes (DUBs), is the primary intracellular and non-lysosomal mechanism of protein degradation. Recent studies have provided compelling evidence to support the involvement of UPS in periodontitis progression. Increasing evidence indicated that E3s, such as CUL3, Nedd4-2, Synoviolin, FBXL19, PDLIM2, TRIMs and TRAFs, modulate inflammatory responses and bone resorption in periodontitis through multiple classical signalling pathways, including NLRP3, GSDMD, NF-κB, Wnt/β-catenin and Nrf2. Meanwhile, DUBs, including OTUD1, A20, CYLD, UCH-L1 and USPs, also broadly modulate periodontitis progression by regulating signalling pathways such as NF-κB, Wnt/β-catenin, NLRP3, and BMP2. Therefore, the modulation of E3s and DUBs has proven to be an effective therapy against periodontitis. This review provides a comprehensive overview of the regulatory role of ubiquitinating and deubiquitinating enzymes in periodontitis progression and the underlying mechanisms. Finally, we summarise several chemical and genetic methods that regulate UPS enzymes and pave the way for the development of targeted therapies for periodontitis.

USP1 promotes pancreatic cancer progression and autophagy by deubiquitinating ATG14

Pancreatic ductal adenocarcinoma (PDAC) is characterized by extremely poor prognosis, high mortality, and limited therapeutic strategy. Autophagy is hyperactivated in PDAC, and targeting autophagy is emerging as a promising therapeutic strategy. The dysfunction of deubiquitinase ubiquitin-specific peptidase 1 (USP1) results in tumorigenesis and chemotherapy resistance. However, little is known about how USP1 regulates autophagy and its mechanism in tumor progression and drug sensitivity in PDAC. In this study, we found USP1 elevated in pancreatic cancer and USP1 expression inversely correlated with overall survival. USP1 depletion inhibited cell proliferation, epithelial-mesenchymal transition, and migration in PDAC cells. Interestingly, USP1 knockdown or inhibition reduced autophagy initiation and autophagy flux. By screening of interacting protein using coimmunoprecipitation, we identified that USP1 interacted with ATG14 (autophagy-related gene 14) protein, acting as a core component in autophagy initiation. Furthermore, USP1 overexpression deubiquitinated and enhanced ATG14 protein stability by reduced binding ubiquitin levels, whereas USP1 inhibition promoted its proteasome-dependent degradation. Notably, USP1 depletion or a novel USP1 inhibitor I-138 dramatically delayed tumor growth in xenograft model. USP1 inhibitor synergistically enhanced the anticancer efficiency of cisplatin in PDAC cells. Collectively, our study identifies USP1 as the first deubiquitinase in the modulation of ATG14 deubiquitination and unveils a regulatory role for USP1 in autophagy and PDAC progression. Targeting USP1 using a selective inhibitor I-138 may provide an effective strategy for chemotherapy treatment and combating drug resistance in autophagy-activated pancreatic cancer.

Comprehensive analysis reveals the prognostic and immunological role of PSMD13 in hepatocellular carcinoma

Immune cell infiltration in liver hepatocellular carcinoma (LIHC) is promising for immunotherapy. However, effective predictive markers to accurately predict a tumour's immune status are lacking. PSMD13, a native component of the 26 S proteasome subunit involved in intracellular metabolism, has an unclear association with cancer and immunity. Using bioinformatics analysis of data from the TCGA, we investigated the expression patterns, prognostic values, gene functions, and tumour immune relationships of PSMD13 in LIHC. We developed a prognostic model that incorporates PSMD13 for LIHC and validated the biological functions of PSMD13 in LIHC cells. Furthermore, we analysed the associations between PSMD13 expression and the tumour immune markers CD206 and CD8 in 101 paired liver tissues using immunohistochemistry. PSMD13 was upregulated in LIHC and served as a prognostic biomarker of LIHC. The knockdown of PMSD13 significantly affected the proliferation, migration, and colony formation of LIHC cells. PSMD13 was closely associated with the infiltration of M2 macrophages and the expression of various tumour immune checkpoints. Our study revealed that PSMD13 is a crucial component contributing to the malignant behaviour of LIHC, indicating its essential role in both the prognosis and potential immune microenvironment profile of LIHC.

Advancements in omics technologies: Molecular mechanisms of acute lung injury and acute respiratory distress syndrome (Review)

Acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) is an inflammatory response arising from lung and systemic injury with diverse causes and associated with high rates of morbidity and mortality. To date, no fully effective pharmacological therapies have been established and the relevant underlying mechanisms warrant elucidation, which may be facilitated by multi‑omics technology. The present review summarizes the application of multi‑omics technology in identifying novel diagnostic markers and therapeutic strategies of ALI/ARDS as well as its pathogenesis.

LINC01004/hsa-mir-125b-2-3p axis restrains ferroptosis in hepatocellular carcinoma by targeting HSPA4 via ceRNA mechanism

BackgroundHepatocellular carcinoma (HCC) is a primary cancer, accounting for 90% of primary liver cancer, mainly occurring in patients with cirrhosis and chronic liver disease.ObjectiveTo investigate the latent mechanisms of hepatocellular carcinoma (HCC) and find therapeutic targets.MethodsDifferentially expressed and overall survival related genes of HCC, and cell death related genes were intersected to obtain latent target genes. These genes were analyzed using ROC curve for diagnosing HCC. RT-qPCR and Western blot were performed to detect the expression level of genes. Wound healing tests were performed with or without si-HSPA4. Potential ceRNA axis was forecasted using TargetScan and miRanda and the dual luciferase reporter gene assay was used to verify the results. Finally, the images of H&E dye liquor-stained HCC tissue section, the CT images for patients in different tumor stage.ResultsLINC01004/hsa-miR-125b-2-3p/HSPA4 axis was forecasted and then was verified using dual-luciferase reporter assay. HSPA4 knockdown caused significant reduction of cell proliferation and ferroptosis. Si-HSPA4 related ferroptosis was generated through impairing iron transport via targeting restrain GPX4. For human subjects, the RT-qPCR analysis revealed the that the larger the tumor diameter, the higher the LINC01004, HSPA4, and GPX4 expression, and the lower the hsa-miR-125b-2-3p expression.ConclusionLINC01004/hsa-miR-125b-2-3p/HSPA4 regulatory axis involved in the ferroptosis of the progression of HCC via GPX4 dependent method, providing new therapeutic targets for HCC patients.

Ubiquitin-specific protease 7 exacerbates acute pancreatitis progression by enhancing ATF4-mediated autophagy

Acute pancreatitis (AP) is a serious inflammatory disease with high incidence rate and mortality. It was confirmed that overactivation of autophagy in acinar cells can increase the risk of AP. Nevertheless, the regulatory mechanism of autophagy in AP is unclear. The role of ubiquitin-specific peptidase 7 (USP7) in controlling autophagy during AP development was examined in this study. AR42J cells were subjected to caerulein to establish a cell model of AP. ELISA utilized to assess IL-6, IL-1β, and TNF-α secretion levels. Cell viability and death were detected using CCK8 assay and flow cytometry, respectively. The interaction between USP7 and ATF4 was analyzed by Co-IP assay. USP7 and ATF4 were abnormally overexpressed in AP patients and cellular models. Loss of function of USP7 increased cell viability, but alleviated cell death and secretions of inflammatory cytokines including IL-6, IL-1β, and TNF-α in AP cellular models. Importantly, autophagy level was activated in AP cells, and could be repressed after USP7 knockdown, and rapamycin treatment greatly diminished the beneficial functions mediated by USP7 downregulation in AP cells. Mechanically, ATF4, an activator of stress autophagy in AP, was proved to be a deubiquitination modification target downstream of USP7, and its protein stability was weakened after USP7 reduction. ATF4 upregulation abolished the protective effect of USP7 silencing on caerulein-induced autophagy, inflammation, and cell injury in AR42J cells. USP7 knockdown reduced inflammation and cell injury during AP progression by inhibiting ATF4-mediated autophagy activation.

Narrative review of 3D bioprinting for the construction of in vitro tumor models: present and prospects

Background and Objective

The conventional in vitro research on tumor mechanisms is typically based on two-dimensional (2D) culture of tumor cells, which has many limitations in replicating in vivo tumorigenesis processes. In contrast, the three-dimensional (3D) bioprinting has paved the way for the construction of more biomimetic in vitro tumor models. This article comprehensively elucidates the features of 3D bioprinting and meticulously summarizes its applications in several selected tumors, aiming to offer valuable insights for future relevant studies.

Methods

A literature search was conducted in the databases of PubMed and Web of Science for articles on 3D bioprinting for in vitro tumor model construction.

Key Content and Findings

This article introduces various 3D bioprinting technologies for in vitro tumor model construction, focusing on their pros and cons, principles, and protocols. Several in vitro tumor models are presented, detailing their utility in tumorigenesis research and their constraints. To date, 3D bioprinting has been widely applied in oncology, addressing the limitation of traditional 2D tumor cell culture in replicating tumor microenvironment (TME).

Conclusions

Advanced 3D bioprinting technology accurately replicates the complex TME and the heterogeneity of intratumor structures, enabling further in vitro tumor studies. It significantly fuels our understanding of tumor pathophysiology and offers new hope for cancer patients.

Lactylation-driven transcriptional activation of FBXO33 promotes gallbladder cancer metastasis by regulating p53 polyubiquitination

Gallbladder cancer (GBC) is the most common malignant tumor of the biliary tract and is often prone to early distant metastasis. However, the mechanisms underlying GBC's invasive metastasis remain unclear. This study identified that F-box only protein 33 (FBXO33) expression is significantly elevated in GBC and is negatively associated with patient prognosis. In vivo and in vitro experiments demonstrated that knockdown of FBXO33 inhibits epithelial-mesenchymal transition (EMT) progression in GBC, while overexpression of FBXO33 promotes EMT progression. Mechanistically, FBXO33 regulates EMT progression by modulating the polyubiquitination of p53 at K291 and K292. Moreover, the upregulation of FBXO33 in GBC is driven by transcriptional regulation mediated by Yin Yang-1 (YY1). The lactylation modification of YY1 at K183 was found to be essential for the transcriptional activation of FBXO33. These findings underscore the role of the lactylation-driven FBXO33-p53 axis in promoting the invasive metastasis of GBC.

TRIM44 facilitates aggressive behaviors in multiple myeloma through promoting ZEB1 deubiquitination

BACKGROUND

Tripartite motif-containing 44 (TRIM44) involves in various tumor development. This study investigated role of TRIM44 in multiple myeloma (MM).

MATERIALS AND METHODS

TRIM44 levels in bone marrow tissues and MM cell lines was detected by quantitative reverse transcription PCR (RT-qPCR). Cell viability, migration, and invasion of MM cells were evaluated under the interference of TRIM44 expression. The role of TRIM44 on regulating tumor growth in vivo was also investigated in subcutaneous tumor xenograft models. The protein interact between TRIM44 and Zinc Finger E-Box Binding Homeobox 1 (ZEB1) was also studied according IP followed by western blotting assay.

RESULTS

TRIM44 was all highly expressed in collected bone marrow tissues and MM cell lines. Cell viability, migration, and invasion of MM cells with low expression of TRIM44 was significantly inhibited. Over-expression of TRIM44 can down-regulate the ZEB1 ubiquitination to enhance the protein stability.

CONCLUSIONS

TRIM44 exerts as an oncogenic factor to induce the oncogenesis of MM by stabilizing ZEB1.

E2F1 activates USP19 to affect the stability of c-Myc to facilitate the progression of hepatocellular carcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) is the most common malignant tumor worldwide with a high mortality rate. Herein, this study aims to explore the molecular mechanisms of E2F transcription factor 1 (E2F1), ubiquitin specific peptidase 19 (USP19) and c-Myc in regulating HCC progression.

METHODS

RT-qPCR and western blotting were utilized to assess mRNA and protein expression, respectively. The behavior of cells was examined through Methylthiazolyldiphenyl-tetrazolium bromide (MTT), flow cytometry, transwell, and cell sphere formation assays. Glycolysis-related indicators were detected by kits. The interaction between USP19 and c-Myc was measured by co-immunoprecipitation (Co-IP). Dual-luciferase reporter assay and Chromatin Immunoprecipitation (ChIP) assays were used to assess the binding of E2F1 and USP19 promoter. A mouse xenograft model was established for the purpose of analysis in vivo.

RESULTS

High level of c-Myc was observed in HCC tissues and cells. Silencing c-Myc results in the suppression of cell migration, invasion, proliferation, and glycolysis or promotion of apoptosis. USP19 directly bound to c-Myc, and maintained its stability by removing ubiquitination on c-Myc. Overexpression of c-Myc in HCC cells rescued the anti-tumor effect of USP19 deletion. E2F1 promoted USP19 transcription, and increased USP19 expression counteracts the effects of E2F1 depletion on cell behaviors. In vivo, USP19 knockdown controlled HCC growth by modulating c-Myc.

CONCLUSION

E2F1 activated USP19 transcription, thereby stabilizing c-Myc via deubiquitination and accelerating HCC progression.

Ubiquitin-proteasome system: a potential participant and therapeutic target in antiphospholipid syndrome

APS (antiphospholipid syndrome) is an autoimmune disease characterized by thrombosis, pregnancy complications and persistent elevation of aPLs (antiphospholipid antibodies). Dysfunction of innate immune cells, ECs (endothelial cells), platelets and trophoblast cells are central to the development of APS. The UPS (ubiquitin-proteasome system) is a highly conserved post-translational modification in eukaryotes. Imbalance of the UPS potentially disrupts the protein homeostasis network and provokes prothrombotic and proinflammatory signaling during APS progression. In vivo, low-dose proteasome inhibitors are believed to effectively inhibit the production of proinflammatory factors and the clinical manifestations of APS. In this review, we would like to summarize the likely contribution of dysregulated UPS to the pathogenesis of APS. Given the significant progress made in understanding the molecular mechanisms of the UPS and how alterations in the UPS lead to the development of autoimmune diseases, targeting the UPS may represent a novel therapeutic strategy.

Implication of protein post translational modifications in gastric cancer

Gastric cancer (GC) is one of the most common and highly lethal malignant tumors worldwide, and its occurrence and development are regulated by multiple molecular mechanisms. Post-translational modifications (PTM) common forms include ubiquitylation, phosphorylation, acetylation and methylation. Emerging research has highlighted lactylation and glycosylation. The diverse realm of PTM and PTM crosstalk is linked to many critical signaling events involved in neoplastic transformation, carcinogenesis and metastasis. This review provides a comprehensive overview of the impact of PTM on the occurrence and progression of GC. Specifically, aberrant PTM have been shown to alter the proliferation, migration, and invasion capabilities of GC cells. Moreover, PTM are closely associated with resistance to chemotherapeutic agents in GC. Notably, this review also discusses the phenomenon of PTM crosstalk, highlighting the interactions among PTM and their roles in regulating signaling pathways and protein functions. Therefore, in-depth investigation into the mechanisms of PTM and the development of targeted therapeutic strategies hold promise for advancing early diagnosis, treatment, and prognostic evaluation of GC, offering novel insights and future research directions.

OTUB1 mediates PARP1 deubiquitination to alleviate NAFLD by regulating HMGB1

Nonalcoholic fatty liver disease (NAFLD) is a common chronic disease characterized by hepatocyte steatosis, which excludes alcohol, drugs and other definite liver damage-related factors. It has been reported that OTUB1 serves a significant role in the regulation of glucose and lipid metabolism. The present study aimed to investigate the molecular mechanism underlying the effect of OTUB1 on regulating NAFLD. The NAFLD mouse model was induced via high-fat-diet, and glucose and insulin tolerance tests were then performed. In addition, the serum levels of total cholesterol (TC) and triglycerides (TG) were detected. The serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST) and alkaline phosphatase (ALP) were assessed using the corresponding biochemical assays. Hematoxylin and eosin, and periodic acid-Schiff staining was carried out to evaluate the liver pathology in mice. The expression levels of the NAFLD-related genes and inflammatory genes were determined by reverse transcription-quantitative PCR, Western blot analysis and immunofluorescence staining. Furthermore, the regulatory association between OTUB1 and poly (adenosine diphosphate-ribose) polymerase (PARP)-1 was assessed by co-immunoprecipitation assay. The results showed that OTUB1 was significantly upregulated in both in vitro and in vivo NAFLD models. Knockout of OTUB1 significantly improved affected glucose tolerance and insulin sensitivity, decreased TG and TC content, and decreased ALT, AST and ALP levels. In addition, the results show that OTUB1 can regulate the expression of PARP1 by inhibiting the ubiquitination of PARP1, while PARP1 knockout can inhibit liver inflammation by regulating HMGB1, thereby improving NAFLD. Targeting OTUB1 could be a potential therapeutic strategy for the NAFLD.

USP9X PROMOTES LPS-INDUCED FIBROBLAST CELL APOPTOSIS, INFLAMMATION, AND OXIDATIVE STRESS BY REGULATION OF TBL1XR1 DEUBIQUITINATION

ABSTRACT

Background: Ubiquitination and deubiquitination are involved in the progression of human diseases, including acute pneumonia. In this study, we aimed to explore the functions of ubiquitin-specific peptidase 9X-linked (USP9X) in lipopolysaccharide (LPS)-treated WI-38 cells. Methods: WI-38 cells were treated with LPS to induce the cellular damage and inflammation. 3-(4, 5-Dimethyl-2-thiazolyl)-2, 5-diphenyl-2-H-tetrazolium bromide (MTT) assay, and 5-ethynyl-2'-deoxyuridine (EdU) assay were performed to examine the proliferation of LPS-treated WI-38 cells. Flow cytometry analysis was conducted to detect LPS-treated WI-38 cell apoptosis. ELISA kits were utilized to determine the concentrations of inflammatory factors (IL-1β and TNF-α). Superoxide dismutase activity and reactive oxygen species level were examined with related kits. Ubibrowser (http://ubibrowser.bio-it.cn/ubibrowser/), ubiquitination assay, and co-immunoprecipitation assay demonstrated the interaction between USP9X and transducin β-like 1X related protein 1 (TBL1XR1). qRT-PCR assay and western blot assay were manipulated to determine the expression of USP9X and TBL1XR1. TBL1XR1 and USP9X knockdown experiments were conducted to explore their functions on LPS-induced WI-38 cell injury and inflammation. Results: TBL1XR1 expression was upregulated in LPS-treated WI-38 cells. TBL1XR1 knockdown promoted cell proliferation and repressed apoptosis, inflammation, and oxidative stress in LPS-treated WI-38 cells. Moreover, USP9X deubiquitinated TBL1XR1 to regulate TBL1XR1 expression. USP9X knockdown restored the effects of LPS on WI-38 cell proliferation, apoptosis, inflammation, and oxidative stress, but these effects of USP9X knockdown were further abolished by TBL1XR1 overexpression. In addition, USP9X promoted the NF-κB signaling pathway by the deubiquitination of TBL1XR1. Conclusion: USP9X promoted the apoptosis, inflammation, and oxidative stress of LPS-stimulated WI-38 cells through the deubiquitination of TBL1XR1.