Insights into the ISG15 transfer cascade by the UBE1L activating enzyme

Interferon-induced protein ISG15 in the central nervous system, quo vadis?

The ubiquitin-like interferon (IFN)-stimulated gene 15 (ISG15) is a unique molecular effector that functions both intra- and extracellularly. Central to its pleiotropic nature is the ability to coordinate cellular responses following its conjugation to target proteins via ISGylation or in its free form. The activity of ISG15 is highly context-dependent: in the case of viral infections, ISG15 can serve as a pro- or antiviral factor. While ISG15 has been studied extensively, several gaps persist in our understanding of its role in dysregulated immune homeostasis. In particular, the role of ISG15 in the central nervous system (CNS), which has traditionally been considered an immune-privileged site, remains ill-defined. Interestingly, elevated ISG15 expression is observed in the CNS following instances of brain injury, autoimmunity, neurodegeneration, and viral infection. In this review, we seek to provide a comprehensive analysis of these studies as they pertain to ISG15 and its potential roles in the CNS. Furthermore, we discuss questions and challenges in the field while highlighting ISG15 as a potential diagnostic biomarker or therapeutic target. Impact statement While ISG15 has been studied extensively, several gaps remain in our understanding of its role in dysregulated immune homeostasis and its impact within the central nervous system (CNS). In this review, we provide a comprehensive analysis of the emerging roles of ISG15 in brain injury, autoimmunity, neurodegeneration, and viral infection within the CNS.

ISG15-Dependent Stabilisation of USP18 Is Necessary but Not Sufficient to Regulate Type I Interferon Signalling in Humans

Type I interferon (IFN) signalling induces the expression of several hundred IFN-stimulated genes (ISGs) that provide an unfavourable environment for viral replication. To prevent an overexuberant response and autoinflammatory disease, IFN signalling requires tight control. One critical regulator is the ubiquitin-like protein IFN-stimulated gene 15 (ISG15), evidenced by autoinflammatory disease in patients with inherited ISG15 deficiencies. Current models suggest that ISG15 stabilises ubiquitin-specific peptidase 18 (USP18), a well-established negative regulator of IFN signalling. USP18 also functions as an ISG15-specific peptidase that cleaves ISG15 from ISGylated proteins; however, USP18's catalytic activity is dispensable for controlling IFN signalling. Here, we show that the ISG15-dependent stabilisation of USP18 involves hydrophobic interactions reliant on tryptophan 123 (W123) in ISG15. Nonetheless, while USP18 stabilisation is necessary, it is not sufficient for the regulation of IFN signalling; ISG15 C-terminal mutants with significantly reduced affinity still stabilised USP18, yet the magnitude of signalling resembled ISG15-deficient cells. Hence, USP18 requires non-covalent interactions with the ISG15 C-terminal diGlycine motif to promote its regulatory function. It shows ISG15 is a repressor of type I IFN signalling beyond its role as a USP18 stabiliser.

Chemical Tools for Probing the Ub/Ubl Conjugation Cascades

Conjugation of ubiquitin (Ub) and structurally related ubiquitin-like proteins (Ubls), essential for many cellular processes, employs multi-step reactions orchestrated by specific E1, E2 and E3 enzymes. The E1 enzyme activates the Ub/Ubl C-terminus in an ATP-dependent process that results in the formation of a thioester linkage with the E1 active site cysteine. The thioester-activated Ub/Ubl is transferred to the active site of an E2 enzyme which then interacts with an E3 enzyme to promote conjugation to the target substrate. The E1-E2-E3 enzymatic cascades utilize labile intermediates, extensive conformational changes, and vast combinatorial diversity of short-lived protein-protein complexes to conjugate Ub/Ubl to various substrates in a regulated manner. In this review, we discuss various chemical tools and methods used to study the consecutive steps of Ub/Ubl activation and conjugation, which are often too elusive for direct studies. We focus on methods developed to probe enzymatic activities and capture and characterize stable mimics of the transient intermediates and transition states, thereby providing insights into fundamental mechanisms in the Ub/Ubl conjugation pathways.

Identification of significant hub genes and pathways associated with metastatic breast cancer and tolerogenic dendritic cell via bioinformatics analysis

Metastatic breast cancer (MBC) is an advanced-stage breast cancer associated with more than 90 % of cancer-related deaths. Immunosuppressive properties of tolerogenic dendritic cells (tolDCs) in tumour immune microenvironment (TIME) may be a risk factor for the rapid progression to MBC. However, the exact connections between the two are unknown. The aim of the current study is to uncover gene signatures and key pathways associated with MBC and tolDCs via an integrated bioinformatics approach. Gene expression profiles of MBC and tolDCs were retrieved from Gene Expression Omnibus (GEO) to identify common differentially expressed genes (DEGs). From DGE analysis, 529 upregulated common DEGs and 367 downregulated common DEGs had been identified. In enrichment analysis, common DEGs enriched in GO terms of defense response to virus and KEGG pathway of transcriptional misregulation in cancer were reported to be significantly associated with MBC and tolDCs. From the constructed PPI networks, 23 hub genes were identified, although only 5 genes were significant; 3 upregulated (ISG15, OAS2 and RSAD2) and 2 downregulated (eEF2 and PPARG) as they were found to be significantly correlated and had the same expression trend as predicted in validation analysis of overall survival (OS) analysis, expression levels, immune infiltration analysis and immunohistochemistry (IHC) analysis. These 5 hub genes can now be exploited in developing novel therapeutic interventions and as diagnostic biomarkers for enhancing the clinical outcomes of MBC patients.

ISG15 accelerates acute kidney injury and the subsequent AKI-to-CKD transition by promoting TGFβR1 ISGylation

Rationale: Acute kidney injury (AKI) has substantial rates of mortality and morbidity, coupled with an absence of efficacious treatment options. AKI commonly transits into chronic kidney disease (CKD) and ultimately culminates in end-stage renal failure. The interferon-stimulated gene 15 (ISG15) level was upregulated in the kidneys of mice injured by ischemia-reperfusion injury (IRI), cisplatin, or unilateral ureteral obstruction (UUO), however, its role in AKI development and subsequent AKI-to-CKD transition remains unknown. Methods: Isg15 knockout (Isg15 KO) mice challenged with bilateral or unilateral IRI, cisplatin, or UUO were used to investigate its role in AKI. We established cellular models with overexpression or knockout of ISG15 and subjected them to hypoxia-reoxygenation, cisplatin, or transforming growth factor- β1 (TGF-β1) stimulation. Renal RNA-seq data obtained from AKI models sourced from public databases and our studies, were utilized to examine the expression profiles of ISG15 and its associated genes. Additionally, published single cell RNA-seq data from human kidney allograft biopsies and mouse IRI model were analyzed to investigate the expression patterns of ISG15 and the type I TGF-β receptor (TGFβR1). Western blotting, qPCR, co-immunoprecipitation, and immunohistochemical staining assays were performed to validate our findings. Results: Alleviated pathological injury and renal function were observed in Isg15 KO mice with IRI-, cisplatin-, or UUO-induced AKI and the following AKI-to-CKD transition. In hypoxia-reoxygenation, cisplatin or TGF-β1 treated HK-2 cells, knockout ISG15 reduced stimulus-induced cell fibrosis, while overexpression of ISG15 with modification capacity exacerbated cell fibrosis. Immunoprecipitation assays demonstrated that ISG15 promoted ISGylation of TGFβR1, and inhibited its ubiquitination. Moreover, knockout of TGFβR1 blocked ISG15's fibrosis-exacerbating effect in HK-2 cells, while overexpression of TGFβR1 abolished the renal protective effect of ISG15 knockout during IRI-induced kidney injury. Conclusions: ISG15 plays an important role in the development of AKI and subsequent AKI-to-CKD transition by promoting TGFβR1 ISGylation.

Mechanisms of USP18 deISGylation revealed by comparative analysis with its human paralog USP41

The ubiquitin-like protein ISG15 (interferon-stimulated gene 15) regulates the host response to bacterial and viral infections through its conjugation to proteins (ISGylation) following interferon production. ISGylation is antagonized by the highly specific cysteine protease USP18, which is the major deISGylating enzyme. However, mechanisms underlying USP18's extraordinary specificity towards ISG15 remains elusive. Here, we show that USP18 interacts with its paralog USP41, whose catalytic domain shares 97% identity with USP18. However, USP41 does not act as a deISGylase, which led us to perform a comparative analysis to decipher the basis for this difference, revealing molecular determinants of USP18's specificity towards ISG15. We found that USP18 C-terminus, as well as a conserved Leucine at position 198, are essential for its enzymatic activity and likely act as functional surfaces based on AlphaFold predictions. Finally, we propose that USP41 antagonizes conjugation of the understudied ubiquitin-like protein FAT10 (HLA-F adjacent transcript 10) from substrates in a catalytic-independent manner. Altogether, our results offer new insights into USP18's specificity towards ISG15, while identifying USP41 as a negative regulator of FAT10 conjugation.