Decoding Deubiquitinases: Roles, Mechanisms, and Therapeutic Implications

Ubiquitination is crucial for regulating diverse cellular functions, including protein degradation, cell cycle progression, signal transduction and gene expression. This intricate process is mediated by the ubiquitin proteasome system. Within this system, ubiquitin-specific protease 10 (USP10) is a key member that, through its deubiquitinase activity, orchestrates multiple cellular processes, such as DNA damage repair, immune and inflammatory responses, environmental adaptation and autophagy. The biological activity and protein stability of USP10 are extensively regulated by post-translational modifications, including PARylation, histone methylation and ubiquitination. Functionally, USP10 has a dual role in tumorigenesis: It can either promote or suppress cancer progression and metastasis by influencing oncogenic signaling pathways. Beyond cancer, USP10 has been implicated in the pathogenesis of cardiovascular and neurodegenerative diseases, as well as organ fibrosis, underscoring its broad physiological relevance. Decades of research have spurred the development of a range of USP10 inhibitors, such as Spautin-1, P22077, HBX19818, Wu-5 and D1. The present review provides a comprehensive overview of recent advances in understanding the role of USP10 in maintaining homeostasis and dissects the pathological mechanisms in human diseases. The review further highlights the potential of precise USP10-targeted interventions as promising therapeutic strategies for disease prevention and treatment.

Exosomes are nanovesicles originating from multivesicular bodies and are released by all cell types. They contain proteins, lipids, microRNAs, mRNAs and DNA fragments, which act as mediators of intercellular communications by inducing phenotypic changes in recipient cells. Tumor-derived exosomes have been shown to play critical roles in different stages of tumor development and metastasis of almost all types of cancer. One of the ways by which exosomes affect tumorigenesis is to manipulate the tumor microenvironments to create tumor permissive “niches”. Whether breast cancer cell secreted exosomes manipulate epithelial cells of the mammary duct to facilitate tumor development is not known. To address whether and how breast cancer cell secreted exosomes manipulate ductal epithelial cells we studied the interactions between exosomes isolated from conditioned media of 3 different breast cancer cell lines (MDA-MB-231, T47DA18 and MCF7), representing three different types of breast carcinomas, and normal human primary mammary epithelial cells (HMECs). Our studies show that exosomes released by breast cancer cell lines are taken up by HMECs, resulting in the induction of reactive oxygen species (ROS) and autophagy. Inhibition of ROS by N-acetyl-L-cysteine (NAC) led to abrogation of autophagy. HMEC-exosome interactions also induced the phosphorylation of ATM, H2AX and Chk1 indicating the induction of DNA damage repair (DDR) responses. Under these conditions, phosphorylation of p53 at serine 15 was also observed. Both DDR responses and phosphorylation of p53 induced by HMEC-exosome interactions were also inhibited by NAC. Furthermore, exosome induced autophagic HMECs were found to release breast cancer cell growth promoting factors. Taken together, our results suggest novel mechanisms by which breast cancer cell secreted exosomes manipulate HMECs to create a tumor permissive microenvironment.

Interactions of high mobility group box protein 1 (HMGB1) with nucleic acids: Implications in DNA repair and immune responses

ADP-ribosylation is an essential post-translational modification that contributes to key cellular processes, such as DNA damage repair, cell-cycle progression, chromatin remodeling, mitochondrial function, and immune responses in mammalian cells. This modification derives from NAD+ and is regulated by dedicated writer, eraser, and reader proteins that govern its installation, removal, and recognition. Traditionally viewed as a protein-centered modification, ADP-ribosylation has recently been extended to nucleic acids, with ADP-ribosylated DNA and RNA now identified in both mammalian and bacterial systems. These discoveries reveal previously underappreciated layers of nucleic acid-based regulation and suggest that NAD+-dependent chemistry integrates genome maintenance, RNA metabolism, and cellular stress responses. In this review, we first outline the major mammalian ADP-ribosylation machineries, including the families of writer, eraser, and reader proteins, and discuss how their activities are coordinated. We then examine emerging roles of ADP-ribosylation in mitochondria, with a focus on mitochondrial DNA repair and metabolic control. Finally, we highlight recent advances in understanding NAD+-dependent modifications of DNA and RNA in mammalian and bacterial cells, including terminal and nucleobase-linked ADP-ribosylation and NAD capping, and discuss outstanding questions regarding their physiological functions and interplay with protein post-translational modification and other nucleic acid modifications.

Nano-sized ambient black carbon (BC) is hypothesized to pose a serious threat to human health. After emission into the air, the atmospheric oxidation process can modify its physiochemical properties and change its biological responses. In this study, we aimed to compare different DNA damage and repair responses promoted by fresh BC (FBC) and ozone oxidized-BC (OBC). The cell apoptosis, cell arrest, DNA damage and repair were investigated in A549 cells after treatment with FBC and OBC. Associated gene expressions were measured with the reverse transcription quantitative polymerase chain reaction (RT-qPCR) method. Both FBC and OBC could induce cell apoptosis in A549 cells with up-regulated gene of promyelocytic leukemia protein (pml) and down-regulated gene of anti-apoptotic B-cell lymphoma-2 (bcl-2). FBC caused cell cycle arrest at S and G2/M phases, which was associated with up-regulated ataxia telangiectasia mutated (atm), checkpoint kinase 2 (chk2), structural maintenance of chromosomes 1 (smc1) and cell division cycle 25 homolog A (cdc25a) genes. OBC promoted cell cycle arrest at the S phase with up-regulated genes of atm, chk2 and smc1. Both FBC and OBC induced oxidative DNA damage and time-dependent DNA repair responses with increased gene expressions of breast cancer susceptibility protein 1 (brca1), recombination protein A paralog B (rad51b), methyl methanesulfonate-sensitivity protein 22-like and tonsoku-like (mms22l). Compared to FBC, OBC could cause more sufficient DNA damage repair responses through cell cycle arrest at the S phase, resulting in relatively weaker DNA damages.

Targeting ADP-ribosylation as an antimicrobial strategy

Afamelanotide, a potent analogue of α-melanocyte-stimulating hormone, is known to stimulate melanogenesis by binding to the melanocortin 1 receptor. Additionally, in experimental models it has anti-inflammatory and antioxidative effects. Consequently, afamelanotide is employed and under development as a therapeutic agent for patients with photodermatoses, who can experience debilitating effects from exposure to sunlight’s ultraviolet radiation (UVR) and visible light. However, limited knowledge exists regarding the scope of the effects of afamelanotide in humans in vivo. This study evaluated the short-term impact of afamelanotide on UVR-induced acute inflammatory and DNA damage repair skin responses in healthy volunteers. Skin biopsies from seven healthy volunteers (skin type II–III, age range 27–43 years) were taken firstly prior to afamelanotide treatment, and procedures were then repeated 6 days following administration of a single 16-mg subcutaneous implant of afamelanotide. Volunteers received 2 × minimal erythema doses of UVR (broadband UVB, Philips TL12 lamp; Philips, Amsterdam, the Netherlands) to buttock skin. Biopsies were collected 24 h post-UVR exposure and from unirradiated skin, before and after afamelanotide administration. Samples underwent gene expression analysis using bulk RNA-Seq and Ingenuity Pathway Analysis. Transcriptomic analysis demonstrated that without afamelanotide, UVR irradiation resulted in 625 significantly differentially expressed genes (DEGs) compared with nonirradiated skin (> 1 log2 fold change, q < 0.05). In contrast, with afamelanotide, the DEGs between irradiated and nonirradiated skin reduced to 183, a factor of 3.4 less DEGs. These included genes associated with inflammatory and immune responses, including tumour necrosis factor (TNF) receptors and interleukins, and with DNA repair. Top predicted upstream regulators (with the highest z-score) in UVR-irradiated vs. nonirradiated skin were the same regardless of afamelanotide treatment. These included proinflammatory mediators such as TNF, interleukin-1 signalling, interferon-γ, and Toll-like receptor 3. However, the number of DEGs associated in the predicted activation of such upstream regulators and overall z-scores were reduced in skin following afamelanotide administration. Additionally, in untreated skin, UVR-induced proinflammatory pathways were enriched, but conversely this was not observed in skin following afamelanotide intervention. Oxidative stress and DNA damage repair pathways also appeared reduced after afamelanotide intervention, including oxidative-stress-induced senescence, DNA methylation and the DNA double strand break response. Transcriptomic analysis also demonstrated that, through comparison of skin under the same irradiation conditions, intervention with afamelanotide significantly upregulated premelanosome protein (PMEL gene), which plays a role in the synthesis of melanosomes. In conclusion, in addition to promoting melanogenesis, in this study afamelanotide reduced the magnitude of UVR-induced proinflammatory and DNA damage repair and oxidative stress responses in human skin, indicating its potential broad, innovative scope in treatment of UVR-induced skin disorders. This research was sponsored by CLINUVEL (UK) Ltd.

Proteomic Analyses Reveal Divergent Ubiquitylation Site Patterns in Murine Tissues

Genomic instability is a hallmark of neoplastic transformation that leads to the accumulation of mutations, and generates a state of replicative stress in neoplastic cells associated with dysregulated DNA damage repair (DDR) responses. The importance of increasing mutations in driving cancer progression is well established, whereas relatively little attention has been devoted to the DNA displaced to the cytosol of cancer cells, a byproduct of genomic instability and of the ensuing DDR response. The presence of DNA in the cytosol promotes the activation of viral defense pathways in all cells, leading to activation of innate and adaptive immune responses. In fact, the improper accumulation of cytosolic DNA in normal cells is known to drive severe autoimmune pathology. Thus, cancer cells must evade cytoplasmic DNA detection pathways to avoid immune-mediated destruction. The main sensor for cytoplasmic DNA is the cyclic GMP-AMP synthase, cGAS. Upon activation by cytosolic DNA, cGAS catalyzes the formation of the second messenger cGAMP, which activates STING (stimulator of IFN genes), leading to the production of type I interferon (IFN-I). IFN-I is a critical effector of cell-mediated antiviral and antitumor immunity, and its production by cancer cells can be subverted by several mechanisms. However, the key upstream regulator of cytosolic DNA-mediated immune stimulation is the DNA exonuclease 3'-repair exonuclease 1 (TREX1). Here, we will discuss evidence in support of a role of TREX1 as an immune checkpoint that, when up-regulated, hinders the development of antitumor immune responses.

Mono-ADP-ribosylation (MARylation) is a post-translational modification that regulates a variety of biological processes, including DNA damage repair, cell proliferation, metabolism, and stress and immune responses. In mammals, MARylation is mainly catalyzed by ADP-ribosyltransferases (ARTs), which consist of two groups: ART cholera toxin-like (ARTCs) and ART diphtheria toxin-like (ARTDs, also known as PARPs). The human ARTC (hARTC) family is composed of four members: two active mono-ADP-ARTs (hARTC1 and hARTC5) and two enzymatically inactive enzymes (hARTC3 and hARTC4). In this study, we systematically examined the homology, expression, and localization pattern of the hARTC family, with a particular focus on hARTC1. Our results showed that hARTC3 interacted with hARTC1 and promoted the enzymatic activity of hARTC1 by stabilizing hARTC1. We also identified vesicle-associated membrane protein-associated protein B (VAPB) as a new target of hARTC1 and pinpointed Arg50 of VAPB as the ADP-ribosylation site. Furthermore, we demonstrated that knockdown of hARTC1 impaired intracellular calcium homeostasis, highlighting the functional importance of hARTC1-mediated VAPB Arg50 ADP-ribosylation in regulating calcium homeostasis. In summary, our study identified a new target of hARTC1 in the endoplasmic reticulum and suggested that ARTC1 plays a role in regulating calcium signaling.

Ion channels play key regulatory roles in cancer pathophysiology. They are also considered promising therapeutic targets. The transient receptor potential melastatin 4 (TRPM4) is a nonselective monovalent cation channel, recently identified as critical in necrosis by sodium overload. Multiple studies have demonstrated that this gene is a potential player in cancer biology; however, its comprehensive role in various cancer types remains largely unexplored. In this study, we conducted a comprehensive bioinformatics analysis of TRPM4 across multiple cancer types, examining its expression patterns, prognostic significance, and clinical relevance. We investigated epigenetic modifications, the DNA damage repair response, as well as alternative splicing and intronic polyadenylation associated with TRPM4. In addition, we analyzed signaling pathways related to tumorigenesis and immune responses, alongside assessing immune cell infiltration in tumor microenvironments. We systematically delineate the expression heterogeneity of TRPM4 across pan-cancer and its clinical implications: it acts as a risk factor indicating poor prognosis in ACC, LGG, PAAD, MESO, and UVM, whereas it exhibits a protective role in KIRP and UCEC. Mechanistically, TRPM4 is involved not only in epigenetic regulation and DNA damage repair responses but also modulates post-transcriptional processes such as alternative splicing and intronic polyadenylation. Furthermore, TRPM4 expression is significantly associated with multiple tumor-related signaling pathways and immunomodulatory molecules. More importantly, through tumor microenvironment infiltration analysis, we observed spatial co-localization of TRPM4 with CD68⁺ tumor-associated macrophages, suggesting that TRPM4 may exert a potential immunomodulatory function by shaping the tumor immune microenvironment through influencing immune cell infiltration. Our research highlights TRPM4 as a promising biomarker and a therapeutic target for cancer treatment. Future investigations should focus on elucidating the mechanistic role of TRPM4 in modulating immune response and tumor progression, potentially paving the way for innovative therapeutic strategies in oncology.

Ubiquitin-proteasome system (UPS) mediates 80% to 85% of the protein degradation in eukaryotic cells. The characteristics of UPS pathway are dependent on ATP, efficient and highly selective. Ubiquitination not only participates in protein degradation, but also directly affects protein activity and localization. Ubiquitination can regulate multiple cellular processes including cell cycle progression, apoptosis, transcriptional regulation, DNA damage repair and immune response. More and more datasets about UPS are published, and it is necessary to organize and analyze these data efficiently. We re-view the related bioinformatics studies in UPS datasets, such as collection of UPS related proteins, construction and analysis of ubiquitination networks, prediction of ubiquitination sites and motifs. Some potential perspectives are also discussed.

Cellular functions are regulated through the gene expression program by the transcription of new messenger RNAs (mRNAs), alternative RNA splicing, and protein synthesis. To this end, the post-translational modifications (PTMs) of proteins add another layer of complexity, creating a continuously fine-tuned regulatory network. ADP-ribosylation (ADPr) is an ancient reversible modification of cellular macromolecules, regulating a multitude of key functional processes as diverse as DNA damage repair (DDR), transcriptional regulation, intracellular transport, immune and stress responses, and cell survival. Additionally, due to the emerging role of ADP-ribosylation in pathological processes, ADP-ribosyltransferases (ARTs), the enzymes involved in ADPr, are attracting growing interest as new drug targets. In this review, an overview of human ARTs and their related biological functions is provided, mainly focusing on the regulation of ADP-ribosyltransferase Diphtheria toxin-like enzymes (ARTD)-dependent RNA functions. Finally, in order to unravel novel gene functional relationships, we propose the analysis of an inventory of human gene clusters, including ARTDs, which share conserved sequences at 3′ untranslated regions (UTRs).

Most proteins undergo ubiquitination, a process by which ubiquitin proteins bind to their substrate proteins; by contrast, deubiquitination is a process that reverses ubiquitination. Deubiquitinating enzymes (DUBs) function to remove ubiquitin proteins from the protein targets and serve an essential role in regulating DNA repair, protein degradation, apoptosis and immune responses. Abnormal regulation of DUBs may affect a number of cellular processes and may lead to a variety of human diseases, including cancer. Therefore, it is important to identify abnormally expressed DUBs to identify DUB-related diseases and biological mechanisms. The present study aimed to develop a multiplex polymerase chain reaction screening platform comprising primers for various DUB genes. This assay was used to identify p53-related DUBs in HCT116 p53+/+ and p53-/- cells. The results demonstrated that ubiquitin-specific peptidase5 (USP5) and ovarian tumor deubiquitinase6A (OTUD6A) were differentially expressed in p53+/+ and p53-/- HCT116 cells. Based on the data obtained through DUB screening, the protein expression levels of USP5 and OTUD6A were examined by western blotting, which confirmed that both of these DUBs were also expressed differentially in p53+/+ and p53-/- HCT116 cells. In conclusion, results from the DUB screening performed by the present study revealed that the expression of USP5 and OTUD6A may be affected by p53, and this method may be useful for the rapid and cost-effective identification of possible biomarkers.

The SMAD-specific E3 ubiquitin protein ligase 2 (SMURF2) has emerged as a critical regulator in cancer biology, modulating the stability of Hypoxia-Inducible Factor 1-alpha (HIF1α) and influencing a network of hypoxia-driven pathways within the tumor microenvironment (TME). SMURF2 targets HIF1α for ubiquitination and subsequent proteasomal degradation, disrupting hypoxic responses that promote cancer cell survival, metabolic reprogramming, angiogenesis, and resistance to therapy. Beyond its role in HIF1α regulation, SMURF2 exerts extensive control over cellular processes central to tumor progression, including chromatin remodeling, DNA damage repair, ferroptosis, and cellular stress responses. Notably, SMURF2's ability to promote ferroptotic cell death through GSTP1 degradation offers an alternative pathway to overcome apoptosis resistance, expanding therapeutic options for refractory cancers. This review delves into the multifaceted interactions between SMURF2 and HIF1α, emphasizing how their interplay impacts metabolic adaptations like the Warburg effect, immune evasion, and therapeutic resistance. We discuss SMURF2's dual functionality as both a tumor suppressor and, in certain contexts, an oncogenic factor, underscoring its potential as a highly versatile therapeutic target. Furthermore, modulating the SMURF2-HIF1α axis presents an innovative approach to destabilize hypoxia-dependent pathways, sensitizing tumors to chemotherapy, radiotherapy, and immune-based treatments. However, the complexity of SMURF2's interactions necessitate a thorough assessment of potential off-target effects and challenges in specificity, which must be addressed to optimize its clinical application. This review concludes by proposing future directions for research into the SMURF2-HIF1α pathway, aiming to refine targeted strategies that exploit this axis and address the adaptive mechanisms of aggressive tumors, ultimately advancing the landscape of precision oncology.