USP1-regulated reciprocal differentiation of Th17 cells and Treg cells by deubiquitinating and stabilizing TAZ

Targeting USP1 Potentiates Radiation-Induced Type I IFN-Dependent Antitumor Immunity by Enhancing Oligo-Ubiquitinated SAR1A-Mediated STING Trafficking and Activation

The magnitude of Type I interferon (IFN) mediated innate immune response within the tumor microenvironment (TME) critically influences the effectiveness of radiotherapy. Unfortunately, due to a myriad of resistance mechanisms, the double-stranded DNA (dsDNA) signals produced by tumor cells postradiotherapy often induce a diminished response from immune cells. Through chemical screening targeting deubiquitinating enzymes, we identified USP1 (Ubiquitin Specific Peptidase 1) inhibitor as an enhancer of post-radiotherapy dsDNA responses. Mechanistically, within the context of immune-stimulatory cells in TME, USP1 serves as a suppressor in the stress-mediated stages of the cGAS (Cyclic GMP-AMP synthase) -STING (Stimulator of interferon genes protein) signaling pathway, specifically affecting the trafficking of STING from endoplasmic reticulum to Golgi apparatus. It is elucidated that SAR1A (Secretion associated Ras related GTPase 1A) requires K27-linked oligo-ubiquitination to assemble the STING-COP-II (Coat protein II) transport complex for STING trafficking. USP1 counteracts this activation by removing SAR1A ubiquitination, thereby blocking STING trafficking and activation. Consequently, pharmacological USP1 inhibition using ML323 sustains SAR1A ubiquitination and COP-II complex formation, significantly enhancing STING trafficking and subsequent Type I IFN production. This intervention substantially amplifies radiotherapy-induced immune activation in the TME, providing a strategic approach to overcome therapeutic resistance and synergize radiotherapy with immunotherapies.

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.

USP25 Promotes the Antimycobacterial Response of Macrophages Through Stabilizing B-Raf and C-Raf

Ubiquitin-specific peptidase 25 (USP25) is one of the best-characterized deubiquitinating enzymes and plays a vital regulatory role in various biological processes, especially in cancer development and immune regulation. However, the exact role of USP25 and its underlying mechanisms in macrophage activation and immunogenicity during Mycobacterium tuberculosis infection remain unclear. In this study, we found that M tuberculosis infection induced USP25 expression in human and mouse macrophages. In particular, USP25 expression is elevated in multiple cell types, especially monocytes, in patients with tuberculosis. Additionally, USP25 deficiency in macrophages and mice resulted in compromised immunity against M tuberculosis infection, accompanied by reduced expressions of various proinflammatory cytokines and chemokines. Mechanistically, USP25 in macrophages promoted the activation of the ERK signaling pathway through deubiquitination and stabilization of B-Raf and C-Raf. These findings collectively suggest the critical roles of USP25 in M tuberculosis infection and its potential as a therapeutic target.

Unravelling the role of ubiquitin-specific proteases in breast carcinoma: insights into tumour progression and immune microenvironment modulation

Breast cancer is a prevalent malignancy worldwide, and its treatment has increasingly shifted towards precision medicine, with immunotherapy emerging as a key therapeutic strategy. Deubiquitination, an essential epigenetic modification, is regulated by deubiquitinating enzymes (DUBs) and plays a critical role in immune function and tumor progression. Ubiquitin-specific proteases (USPs), a prominent subgroup of DUBs, are involved in regulating immune cell functions, antigen processing, and T cell development in the context of breast cancer. Certain USPs also modulate the differentiation of immune cells, such as myeloid-derived suppressor cells (MDSCs) and regulatory T cells (Tregs), within the breast cancer immune microenvironment. Furthermore, several USPs influence the expression of PD-L1, thus affecting the efficacy of immune checkpoint inhibitors. The overexpression of USPs may promote immune evasion, contributing to the development of treatment resistance. This review elucidates the role of USPs in modulating the immune microenvironment and immune responses in breast cancer. Additionally, it discusses effective strategies for combining USP inhibitors with other therapeutic agents to enhance treatment outcomes. Therefore, targeting USPs presents the potential to enhance the efficacy of immunotherapy and overcome drug resistance, offering a more effective treatment strategy for breast cancer patients.

Ubiquitin-Specific Protease Inhibitors for Cancer Therapy: Recent Advances and Future Prospects

Cancer management has traditionally depended on chemotherapy as the mainstay of treatment; however, recent advancements in targeted therapies and immunotherapies have offered new options. Ubiquitin-specific proteases (USPs) have emerged as promising therapeutic targets in cancer treatment due to their crucial roles in regulating protein homeostasis and various essential cellular processes. This review covers the following: (1) the structural and functional characteristics of USPs, highlighting their involvement in key cancer-related pathways, and (2) the discovery, chemical structures, mechanisms of action, and potential clinical implications of USP inhibitors in cancer therapy. Particular attention is given to the role of USP inhibitors in enhancing cancer immunotherapy, e.g., modulation of the tumor microenvironment, effect on regulatory T cell function, and influence on immune checkpoint pathways. Furthermore, this review summarizes the current progress and challenges of clinical trials involving USP inhibitors as cancer therapy. We also discuss the complexities of achieving target selectivity, the ongoing efforts to develop more specific and potent USP inhibitors, and the potential of USP inhibitors to overcome drug resistance and synergize with existing cancer treatments. We finally provide a perspective on future directions in targeting USPs, including the potential for personalized medicine based on specific gene mutations, underscoring their significant potential for enhancing cancer treatment. By elucidating their mechanisms of action, clinical progress, and potential future applications, we hope that this review could serve as a useful resource for both basic scientists and clinicians in the field of cancer therapeutics.

The other side of the coin: protein deubiquitination by Ubiquitin-Specific Protease 1 in cancer progression and therapy

Reversible protein ubiquitination is a crucial factor in cellular homeostasis, with Ubiquitin-Specific Protease 1 (USP1) serving as a key deubiquitinase involved in DNA damage response (DDR) and repair mechanisms in cancer. While ubiquitin ligases have been extensively studied, research on the reverse process of ubiquitination, particularly the mechanisms involving USP1, remains relatively limited. USP1 is overexpressed in various cancers, influencing tumor initiation and progression by regulating multiple associated proteins. Inhibiting USP1 effectively suppresses tumor proliferation and migration and may help overcome resistance to cisplatin and PARP inhibitors. As a potential synthetic lethal target, USP1 demonstrates significant research potential. This review highlights the biological mechanisms of USP1 in cancer progression, the signaling pathways it regulates, and the latest advancements in USP1 inhibitors, while also analyzing the opportunities and challenges of targeting USP1. By adopting the perspective of "the other side of the coin," this review aims to underscore the crucial yet often overlooked role of the deubiquitinase USP1, contrasting it with the extensively studied ubiquitin ligases, and emphasizing its therapeutic potential in cancer treatment.

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.

Multiomic analysis of lactylation and mitochondria-related genes in hepatocellular carcinoma identified MRPL3 as a new prognostic biomarker

Background

Recent research has highlighted lactate's crucial role in epigenetic regulation, particularly by influencing histone modifications that drive the initiation and progression of hepatocellular carcinoma (HCC). While mitochondria are known to regulate tumor behavior, the interaction between lactate metabolism and mitochondrial function in cancer tissues remains underexplored. Understanding this relationship may provide deeper insights into tumor metabolic reprogramming and reveal novel therapeutic targets for HCC and other malignancies.

Methods

We conducted a comprehensive screening of lactylation- and mitochondria-associated genes (LMRGs) in HCC patients, followed by clustering based on these genes. Prognostic outcomes and pathway enrichment were analyzed across the identified clusters. Additionally, we developed a prognostic model based on LMRGs, examining its implications for survival, immune response, and drug sensitivity. In vitro experiments were performed to validate the expression patterns and functional role of MRPL3 in HCC.

Results

We developed a prognostic model, named the LMRG model, incorporating three key genes: ACACA, MRPL3, and MRPS23. This model revealed significant differences in survival outcomes, immune responses, and drug sensitivity between patients with high and low LMRG scores. MRPL3 was found to be overexpressed in HCC, playing a critical role in tumor growth and metastasis. These results were further validated through in vitro experiments, confirming MRPL3's role in HCC cell proliferation and invasion.

Conclusion

We created a predictive model, LMRG, and identified MRPL3 as a key biomarker. Our findings suggest that MRPL3 has significant potential as a reliable predictive biomarker for clinical applications in HCC diagnosis and treatment.

Butyrate Metabolism-Related Gene Signature in Tumor Immune Microenvironment in Lung Adenocarcinoma: A Comprehensive Bioinformatics Study

BACKGROUND

Experimental results have verified the suppressive impact of butyrate on tumor formation. Nevertheless, there is a limited understanding of the hidden function of butyrate metabolism within the tumor immune microenvironment (TIME) of lung adenocarcinoma (LUAD). This research aimed at digging the association between genes related to butyrate metabolism (butyrate metabolism-related genes [BMRGs) and immune infiltrates in LUAD patients.

METHODS

Through analyzing The Cancer Genome Atlas dataset (TCGA), the identification of 38 differentially expressed BMRGs was made between LUAD and normal samples. Later, a prognostic signature made up of nine BMRGs was made to evaluate the risk score of LUAD subjects. Notably, high-risk scores emerged as negative prognostic indicators for overall survival in LUAD subjects. Additionally, BMRGs displayed associations with immunocyte infiltration levels, immune pathway activities, and pivotal prognostic hub BMRGs.

RESULTS

One key prognostic BMRG, PTGDS, exhibited a robust correlation with T cells, the chemokine-related pathway, and the TCR signaling pathway. This study suggests that investigating the interplay between butyrate metabolism and T cells could present a promising novel approach to cancer treatment. OncoPredict analysis further unveiled distinct sensitivities of nine medicine in high- and low-risk groups, facilitating the selection of optimal treatment strategies for individual LUAD patients.

CONCLUSIONS

The study establishes that the BMRG signature serves as a sensitive predictive biomarker, providing profound insights into the crucial effect of butyrate metabolism in the context of LUAD TIME.

RNF213 promotes Treg cell differentiation by facilitating K63-linked ubiquitination and nuclear translocation of FOXO1

Autoreactive CD4+ T helper cells are critical players that orchestrate the immune response both in multiple sclerosis (MS) and in other neuroinflammatory autoimmune diseases. Ubiquitination is a posttranslational protein modification involved in regulating a variety of cellular processes, including CD4+ T cell differentiation and function. However, only a limited number of E3 ubiquitin ligases have been characterized in terms of their biological functions, particularly in CD4+ T cell differentiation and function. In this study, we found that the RING finger protein 213 (RNF213) specifically promoted regulatory T (Treg) cell differentiation in CD4+ T cells and attenuated autoimmune disease development in an FOXO1-dependent manner. Mechanistically, RNF213 interacts with Forkhead Box Protein O1 (FOXO1) and promotes nuclear translocation of FOXO1 by K63-linked ubiquitination. Notably, RNF213 expression in CD4+ T cells was induced by IFN-β and exerts a crucial role in the therapeutic efficacy of IFN-β for MS. Together, our study findings collectively emphasize the pivotal role of RNF213 in modulating adaptive immune responses. RNF213 holds potential as a promising therapeutic target for addressing disorders associated with Treg cells.

Stability and plasticity of regulatory T cells in health and disease

The mechanisms that negatively regulate inflammation upon a pathogenic stimulus are crucial for the maintenance of tissue integrity and organ function. T regulatory cells are one of the main drivers in controlling inflammation. The ability of T regulatory cells to adapt to different inflammatory cues and suppress inflammation is one of the relevant features of T regulatory cells. During this process, T regulatory cells express different transcription factors associated with their counterparts, Th helper cells, including Tbx21, GATA-3, Bcl6, and Rorc. The acquisition of this transcription factor helps the T regulatory cells to suppress and migrate to the different inflamed tissues. Additionally, the T regulatory cells have different mechanisms that preserve stability while acquiring a particular T regulatory cell subtype. This review focuses on describing T regulatory cell subtypes and the mechanisms that maintain their identity in health and diseases.

Exploring the immune-modulating properties of boswellic acid in experimental autoimmune encephalomyelitis

Multiple sclerosis (MS) is a condition where the central nervous system loses its myelin coating due to autoimmune inflammation. The experimental autoimmune encephalomyelitis (EAE) simulates some aspects of human MS. Boswellic acids are natural compounds derived from frankincense extract, known for their anti-inflammatory properties. The purpose of this research was to investigate therapeutic potential of boswellic acids. Mice were divided into three groups: low-dose (LD), high-dose (HD), and control groups (CTRL). Following EAE induction, the mice received daily doses of boswellic acid for 25 days. Brain tissue damage, clinical symptoms, and levels of TGF-β, IFN-γ, and IL-17 cytokines in cell cultured supernatant of lymphocytes were assessed. Gene expression of transcription factors in brain was measured using real-time PCR. The levels of brain demyelination were significantly lower in the treatment groups compared to the CTRL group. Boswellic acid reduced the severity and duration of EAE symptoms. Furthermore, boswellic acid decreased the amounts of IFN-γ and IL-17, also the expression of T-bet and ROR-γt in brain. On the contrary, it increased the levels of TGF-β and the expression FoxP3 and GATA3. Our findings suggest that boswellic acids possess therapeutic potential for EAE by modulating the immune response and reducing inflammation.

Deubiquitinating enzymes: potential regulators of the tumor microenvironment and implications for immune evasion

Ubiquitination and deubiquitination are important forms of posttranslational modification that govern protein homeostasis. Deubiquitinating enzymes (DUBs), a protein superfamily consisting of more than 100 members, deconjugate ubiquitin chains from client proteins to regulate cellular homeostasis. However, the dysregulation of DUBs is reportedly associated with several diseases, including cancer. The tumor microenvironment (TME) is a highly complex entity comprising diverse noncancerous cells (e.g., immune cells and stromal cells) and the extracellular matrix (ECM). Since TME heterogeneity is closely related to tumorigenesis and immune evasion, targeting TME components has recently been considered an attractive therapeutic strategy for restoring antitumor immunity. Emerging studies have revealed the involvement of DUBs in immune modulation within the TME, including the regulation of immune checkpoints and immunocyte infiltration and function, which renders DUBs promising for potent cancer immunotherapy. Nevertheless, the roles of DUBs in the crosstalk between tumors and their surrounding components have not been comprehensively reviewed. In this review, we discuss the involvement of DUBs in the dynamic interplay between tumors, immune cells, and stromal cells and illustrate how dysregulated DUBs facilitate immune evasion and promote tumor progression. We also summarize potential small molecules that target DUBs to alleviate immunosuppression and suppress tumorigenesis. Finally, we discuss the prospects and challenges regarding the targeting of DUBs in cancer immunotherapeutics and several urgent problems that warrant further investigation.

USP47 inhibits m6A-dependent c-Myc translation to maintain regulatory T cell metabolic and functional homeostasis

The functional integrity of Tregs is interwoven with cellular metabolism; however, the mechanisms governing Treg metabolic programs remain elusive. Here, we identified that the deubiquitinase USP47 inhibited c-Myc translation mediated by the RNA N6-methyladenosine (m6A) reader YTHDF1 to maintain Treg metabolic and functional homeostasis. USP47 positively correlated with the tumor-infiltrating Treg signature in samples from patients with colorectal cancer and gastric cancer. USP47 ablation compromised Treg homeostasis and function in vivo, resulting in the development of inflammatory disorders, and boosted antitumor immune responses. USP47 deficiency in Tregs triggered the accumulation of the c-Myc protein and in turn exacerbated hyperglycolysis. Mechanistically, USP47 prevented YTHDF1 ubiquitination to attenuate the association of YTHDF1 with translation initiation machinery, thereby decreasing m6A-based c-Myc translation efficiency. Our findings reveal that USP47 directs m6A-dependent metabolic programs to orchestrate Treg homeostasis and suggest novel approaches for selective immune modulation in cancer and autoimmune diseases by targeting of USP47.

Ubiquitin-specific peptidase 1: assessing its role in cancer therapy

Reversible protein ubiquitination represents an essential determinator of cellular homeostasis, and the ubiquitin-specific enzymes, particularly deubiquitinases (DUBs), are emerging as promising targets for drug development. DUBs are composed of seven different subfamilies, out of which ubiquitin-specific proteases (USPs) are the largest family with 56 members. One of the well-characterized USPs is USP1, which contributes to several cellular biological processes including DNA damage response, immune regulation, cell proliferation, apoptosis, and migration. USP1 levels and activity are regulated by multiple mechanisms, including transcription regulation, phosphorylation, autocleavage, and proteasomal degradation, ensuring that the cellular function of USP1 is performed in a suitably modulated spatio-temporal manner. Moreover, USP1 with deregulated expression and activity are found in several human cancers, indicating that targeting USP1 is a feasible therapeutic approach in anti-cancer treatment. In this review, we highlight the essential role of USP1 in cancer development and the regulatory landscape of USP1 activity, which might provide novel insights into cancer treatment.

TRIM11 attenuates Treg cell differentiation by p62-selective autophagic degradation of AIM2

Ubiquitination is an important protein modification that regulates diverse biological processes, including CD4+ T cell differentiation and functions. However, the function of most E3 ubiquitin ligases in CD4+ T cell differentiation and CD4+ T cell-mediated pathological diseases remains unclear. In this study, we find that tripartite motif-containing motif 11 (TRIM11) specifically negatively regulates regulatory T (Treg) cell differentiation in CD4+ T cells and promotes autoimmune disease development in an AIM2-dependent manner. Mechanistically, TRIM11 interacts with absent in melanoma 2 (AIM2) and promotes the selective autophagic degradation of AIM2 by inducing AIM2 ubiquitination and binding to p62 in CD4+ T cells. AIM2 attenuates AKT and FOXO1 phosphorylation, MYC signaling, and glycolysis, thereby promoting the stability of Treg cells during experimental autoimmune encephalomyelitis (EAE). Our findings suggest that TRIM11 serves as a potential target for immunotherapeutic intervention for dysregulated immune responses that lead to autoimmunity and cancers.

Spotlights on ubiquitin-specific protease 12 (USP12) in diseases: from multifaceted roles to pathophysiological mechanisms

Ubiquitination is one of the most significant post-translational modifications that regulate almost all physiological processes like cell proliferation, autophagy, apoptosis, and cell cycle progression. Contrary to ubiquitination, deubiquitination removes ubiquitin from targeted protein to maintain its stability and thus regulate cellular homeostasis. Ubiquitin-Specific Protease 12 (USP12) belongs to the biggest family of deubiquitinases named ubiquitin-specific proteases and has been reported to be correlated with various pathophysiological processes. In this review, we initially introduce the structure and biological functions of USP12 briefly and summarize multiple substrates of USP12 as well as the underlying mechanisms. Moreover, we discuss the influence of USP12 on tumorigenesis, tumor immune microenvironment (TME), disease, and related signaling pathways. This study also provides updated information on the roles and functions of USP12 in different types of cancers and other diseases, including prostate cancer, breast cancer, lung cancer, liver cancer, cardiac hypertrophy, multiple myeloma, and Huntington's disease. Generally, this review sums up the research advances of USP12 and discusses its potential clinical application value which deserves more exploration in the future.

USP12 promotes antiviral responses by deubiquitinating and stabilizing IFI16

Deubiquitinating enzymes (DUBs) regulate antiviral immune response through targeting DNA sensor signaling pathway members. As one of the DNA sensors, interferon (IFN)-γ inducible protein 16 (IFI16) play a major role in response to virus infections through activating the canonical STING/TBK-1/IRF3 signaling pathway. Only a few studies discuss the function of DUBs in IFI16-mediated antiviral response. Ubiquitin-specific protease 12 (USP12), which is one of the major members of the USP family, participates in various biological functions. However, whether USP12 regulates the nucleic acid sensor to modulate antiviral immune responses has not yet been elucidated. In this study, we found that knockout or knockdown of USP12 impaired the HSV-1-induced expressions of IFN-β, CCL-5, IL-6, and downstream interferon-stimulated genes (ISGs). Moreover, USP12 deficiency increased HSV-1 replication and host susceptibility to HSV-1 infection. Mechanistically, USP12 inhibited the proteasome-dependent degradation of IFI16 through its deubiquitinase activity, thereby maintaining IFI16 stability and promoting IFI16-STING-IRF3- and p65-mediated antiviral signaling. Overall, our findings demonstrate an essential role of USP12 in DNA-sensing signaling and contribute to the understanding of deubiquitination-mediated regulation of innate antiviral responses.

RNF157 attenuates CD4+ T cell-mediated autoimmune response by promoting HDAC1 ubiquitination and degradation

Background: CD4⁺ T cells play an important role in body development and homeostasis. Quantitative and functional changes in CD4⁺ T cells result in abnormal immune responses, which lead to inflammation, cancer, or autoimmune diseases, such as multiple sclerosis (MS). Ubiquitination plays an essential role in the differentiation and functioning of CD4⁺ T cells. However, the function of several E3 ubiquitin ligases in CD4⁺ T cell differentiation and T cell-mediated pathological diseases remains unclear. Methods: RNA sequencing data were analyzed to identify the E3 ubiquitin ligases that participate in the pathogenesis of MS. Furthermore, conditional knockout mice were generated. Specifically, flow cytometry, qPCR, western blot, CO-IP and cell transfer adoptive experiments were performed. Results: In this study, we identified The RING finger 157 (RNF157) as a vital regulator of CD4⁺ T cell differentiation; it promoted Th1 differentiation but attenuated Th17 differentiation and CCR4 and CXCR3 expressions in CD4⁺ T cells, thereby limiting experimental autoimmune encephalomyelitis development. Mechanistically, RNF157 in CD4⁺ T cells targeted HDAC1 for K48-linked ubiquitination and degradation. Notably, RNF157 expression was significantly decreased and showed a significant negative correlation with RORγt expression in patients with MS. Conclusions: Our study highlights the critical role of RNF157 in regulating CD4⁺ T cell functions in autoimmune diseases and suggests RNF157 as a potential target in adaptive immune responses against MS and other autoimmune disorders.