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Summary: Precise regulation of Type I interferon signaling is crucial for combating infection and cancer while avoiding autoimmunity. Type I interferon signaling is negatively regulated by USP18. USP18 cleaves ISG15, an interferon-induced ubiquitin-like modification, via its canonical catalytic function, and inhibits Type I interferon receptor activity through its scaffold role. USP18 loss-of-function dramatically impacts immune regulation, pathogen susceptibility, and tumor growth. However, prior studies have reached conflicting conclusions regarding the relative importance of catalytic versus scaffold function. Here, we develop biochemical and cellular methods to systematically define the physiological role of USP18. By comparing a patient-derived mutation impairing scaffold function (I60N) to a mutation disrupting catalytic activity (C64S), we demonstrate that scaffold function is critical for cancer cell vulnerability to Type I interferon. Surprisingly, we discovered that human USP18 exhibits minimal catalytic activity, in stark contrast to mouse USP18. These findings resolve human USP18's mechanism-of-action and enable USP18-targeted therapeutics.

Highlights USP18 knockdown results in transcriptome-wide changes that cause a switch from proliferation to muscle cell differentiation. Fully differentiated muscles cells (or simply 'myotubes') formed in absence of USP18 lack sarcomeric integrity (in both cell culture and engineered muscle models). An increase in USP18 expression during muscle cell differentiation is independent of its role in the interferon type 1 stimulated response. During normal muscle cell differentiation, USP18 accumulates in the cell nucleus regulating multiple cellular processes, including proliferation, differentiation initiation and muscle cell maturation. In the absence of USP18, muscle cells stop proliferating and undergo accelerated fusion as part of the differentiation process by altering the expression levels of myogenic regulatory (co-)transcription factors, whereas maturation is impaired due to reduced expression of calcium-flux genes and sarcomeric genes.

Nowadays, robotic technology for gait training is becoming a common tool in rehabilitation hospitals. However, its effectiveness is still controversial. Traditional control strategies do not adequately integrate human intention and interaction and little is known regarding the impact of exoskeleton control strategies on muscle coordination, physical effort, and user acceptance. In this article, we benchmarked three types of exoskeleton control strategies in a sample of seven healthy volunteers: trajectory assistance (TC), compliant assistance (AC), and compliant assistance with EMG-Onset stepping control (OC), which allows the user to decide when to take a step during the walking cycle. This exploratory study was conducted within the EUROBENCH project facility. Experimental procedures and data analysis were conducted following EUROBENCH’s protocols. Specifically, exoskeleton kinematics, muscle activation, heart and breathing rates, skin conductance, as well as user-perceived effort were analyzed. Our results show that the OC controller showed robust performance in detecting stepping intention even using a corrupt EMG acquisition channel. The AC and OC controllers resulted in similar kinematic alterations compared to the TC controller. Muscle synergies remained similar to the synergies found in the literature, although some changes in muscle contribution were found, as well as an overall increase in agonist-antagonist co-contraction. The OC condition led to the decreased mean duration of activation of synergies. These differences were not reflected in the overall physiological impact of walking or subjective perception. We conclude that, although the AC and OC walking conditions allowed the users to modulate their walking pattern, the application of these two controllers did not translate into significant changes in the overall physiological cost of walking nor the perceived experience of use. Nonetheless, results suggest that both AC and OC controllers are potentially interesting approaches that can be explored as gait rehabilitation tools. Furthermore, the INTENTION project is, to our knowledge, the first study to benchmark the effects on human–exoskeleton interaction of three different exoskeleton controllers, including a new EMG-based controller designed by us and never tested in previous studies, which has made it possible to provide valuable third-party feedback on the use of the EUROBENCH facility and testbed, enriching the apprenticeship of the project consortium and contributing to the scientific community.

The potency and selectivity of a small molecule inhibitor are key parameters to assess during the early stages of drug discovery. In particular, it is very informative for characterizing compounds in a relevant cellular context in order to reveal potential off-target effects and drug efficacy. Activity-based probes are valuable tools for that purpose, however, obtaining cellular target engagement data in a high-throughput format has been particularly challenging. Here, we describe a new methodology named ABPP-HT (high-throughput-compatible activity-based protein profiling), implementing a semi-automated proteomic sample preparation workflow that increases the throughput capabilities of the classical ABPP workflow approximately ten times while preserving its enzyme profiling characteristics. Using a panel of deubiquitylating enzyme (DUB) inhibitors, we demonstrate the feasibility of ABPP-HT to provide compound selectivity profiles of endogenous DUBs in a cellular context at a fraction of time as compared to previous methodologies.

Ubiquitylation and ISGylation are protein post-translational modifications (PTMs) and two of the main events involved in the activation of pattern recognition receptor (PRRs) signals allowing the host defense response to viruses. As with similar viruses, SARS-CoV-2, the virus causing COVID-19, hijacks these pathways by removing ubiquitin and/or ISG15 from proteins using a protease called PLpro, but also by interacting with enzymes involved in ubiquitin/ISG15 machinery. These enable viral replication and avoidance of the host immune system. In this review, we highlight potential points of therapeutic intervention in ubiquitin/ISG15 pathways involved in key host–pathogen interactions, such as PLpro, USP18, TRIM25, CYLD, A20, and others that could be targeted for the treatment of COVID-19, and which may prove effective in combatting current and future vaccine-resistant variants of the disease.

Enzymes that bind and process ubiquitin, a small 76-amino-acid protein, have been recognized as pharmacological targets in oncology, immunological disorders, and neurodegeneration. Mass spectrometry technology has now reached the capacity to cover the proteome with enough depth to interrogate entire biochemical pathways including those that contain DUBs and E3 ligase substrates. We have recently characterized the breast cancer cell (MCF7) deep proteome by detecting and quantifying ~10,000 proteins, and within this data set, we can detect endogenous expression of 65 deubiquitylating enzymes (DUBs), whereas matching transcriptomics detected 78 DUB mRNAs. Since enzyme activity provides another meaningful layer of information in addition to the expression levels, we have combined advanced mass spectrometry technology, pre-fractionation, and more potent/selective ubiquitin active-site probes with propargylic-based electrophiles to profile 74 DUBs including distinguishable isoforms for 5 DUBs in MCF7 crude extract material. Competition experiments with cysteine alkylating agents and pan-DUB inhibitors combined with probe labeling revealed the proportion of active cellular DUBs directly engaged with probes by label-free quantitative (LFQ) mass spectrometry. This demonstrated that USP13, 39, and 40 are non-reactive to probe, indicating restricted enzymatic activity under these cellular conditions. Our extended chemoproteomics workflow increases depth of covering the active DUBome, including isoform-specific resolution, and provides the framework for more comprehensive cell-based small-molecule DUB selectivity profiling.

Resumen: La alergia a las proteínas de leche de vaca no mediada por IgE es una patología frecuente, en cuyo manejo están implicados profesionales de diferentes áreas existiendo a día de hoy una gran variabilidad en la forma de abordar su diagnóstico, tratamiento, seguimiento y prevención. Con el objetivo de unificar pautas de actuación se ha elaborado un documento de consenso entre cuatro de las sociedades científicas implicadas en el abordaje de niños con dicha patología. Abstract: Non-IgE-mediated cow's milk allergy is a frequent disorder in paediatrics. As patients might be seen by professionals from different specialties and levels of expertise, a great variability in diagnostic procedures and disease monitoring is commonly observed. Therefore, four scientific societies involved in its management have developed a consensus document providing specific recommendations related to its prevention, diagnosis, treatment and follow up.

Non-IgE-mediated cow's milk allergy is a frequent disorder in paediatrics. As patients might be seen by professionals from different specialties and levels of expertise, a great variability in diagnostic procedures and disease monitoring is commonly observed. Therefore, four scientific societies involved in its management have developed a consensus document providing specific recommendations related to its prevention, diagnosis, treatment and follow up. Resumen: La alergia a las proteínas de leche de vaca no mediada por IgE es una patología frecuente, en cuyo manejo están implicados profesionales de diferentes áreas existiendo a día de hoy una gran variabilidad en la forma de abordar su diagnóstico, tratamiento, seguimiento y prevención. Con el objetivo de unificar pautas de actuación se ha elaborado un documento de consenso entre cuatro de las sociedades científicas implicadas en el abordaje de niños con dicha patología.

Interferon-induced ubiquitin (Ub)-like modifier ISG15 covalently modifies host and viral proteins to restrict viral infections. Its function is counteracted by the canonical deISGylase USP18 or Ub-specific protease 18. Notwithstanding indications for the existence of other ISG15 cross-reactive proteases, these remain to be identified. Here, we identify deubiquitinase USP16 as an ISG15 cross-reactive protease by means of ISG15 activity-based profiling. Recombinant USP16 cleaved pro-ISG15 and ISG15 isopeptide-linked model substrates in vitro, as well as ISGylated substrates from cell lysates. Moreover, interferon-induced stimulation of ISGylation was increased by depletion of USP16. The USP16-dependent ISG15 interactome indicated that the deISGylating function of USP16 may regulate metabolic pathways. Targeted enzymes include malate dehydrogenase, cytoplasmic superoxide dismutase 1, fructose-bisphosphate aldolase A, and cytoplasmic glutamic-oxaloacetic transaminase 1. USP16 may thus contribute to the regulation of a subset of metabolism-related proteins during type-I interferon responses. [ABSTRACT FROM AUTHOR]