UbiProt: a database of ubiquitylated proteins

BACKGROUND: Post-translational protein modification with ubiquitin, or ubiquitylation, is one of the hottest topics in a modern biology due to a dramatic impact on diverse metabolic pathways and involvement in pathogenesis of severe human diseases. A great number of eukaryotic proteins was found to be ubiquitylated. However, data about particular ubiquitylated proteins are rather disembodied. DESCRIPTION: To fill a general need for collecting and systematizing experimental data concerning ubiquitylation we have developed a new resource, UbiProt Database, a knowledgebase of ubiquitylated proteins. The database contains retrievable information about overall characteristics of a particular protein, ubiquitylation features, related ubiquitylation and de-ubiquitylation machinery and literature references reflecting experimental evidence of ubiquitylation. UbiProt is available at for free. CONCLUSION: UbiProt Database is a public resource offering comprehensive information on ubiquitylated proteins. The resource can serve as a general reference source both for researchers in ubiquitin field and those who deal with particular ubiquitylated proteins which are of their interest. Further development of the UbiProt Database is expected to be of common interest for research groups involved in studies of the ubiquitin system

People who use drugs show no increase in pre-existing T-cell cross-reactivity toward SARS-CoV-2 but develop a normal polyfunctional T-cell response after standard mRNA vaccination

People who use drugs (PWUD) are at a high risk of contracting and developing severe coronavirus disease 2019 (COVID-19) and other infectious diseases due to their lifestyle, comorbidities, and the detrimental effects of opioids on cellular immunity. However, there is limited research on vaccine responses in PWUD, particularly regarding the role that T cells play in the immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we show that before vaccination, PWUD did not exhibit an increased frequency of preexisting cross-reactive T cells to SARS-CoV-2 and that, despite the inhibitory effects that opioids have on T-cell immunity, standard vaccination can elicit robust polyfunctional CD4+ and CD8+ T-cell responses that were similar to those found in controls. Our findings indicate that vaccination stimulates an effective immune response in PWUD and highlight targeted vaccination as an essential public health instrument for the control of COVID-19 and other infectious diseases in this group of high-risk patients

Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence

During the COVID-19 pandemic we utilized an AI-driven T cell epitope prediction tool, the NEC Immune Profiler (NIP) to scrutinize and predict regions of T cell immunogenicity (hotspots) from the entire SARS-CoV-2 viral proteome. These immunogenic regions offer potential for the development of universally protective T cell vaccine candidates. Here, we validated and characterized T cell responses to a set of minimal epitopes from these AI-identified universal hotspots. Utilizing a flow cytometry-based T cell activation-induced marker (AIM) assay, we identified 59 validated screening hits, of which 56% (33 peptides) have not been previously reported. Notably, we found that most of these novel epitopes were derived from the non-spike regions of SARS-CoV-2 (Orf1ab, Orf3a, and E). In addition, ex vivo stimulation with NIP-predicted peptides from the spike protein elicited CD8+ T cell response in PBMC isolated from most vaccinated donors. Our data confirm the predictive accuracy of AI platforms modelling bona fide immunogenicity and provide a novel framework for the evaluation of vaccine-induced T cell responses

Multiomic analyses implicate a neurodevelopmental program in the pathogenesis of cerebral arachnoid cysts

Cerebral arachnoid cysts (ACs) are one of the most common and poorly understood types of developmental brain lesion. To begin to elucidate AC pathogenesis, we performed an integrated analysis of 617 patient-parent (trio) exomes, 152,898 human brain and mouse meningeal single-cell RNA sequencing transcriptomes and natural language processing data of patient medical records. We found that damaging de novo variants (DNVs) were highly enriched in patients with ACs compared with healthy individuals (P = 1.57 × 10-33). Seven genes harbored an exome-wide significant DNV burden. AC-associated genes were enriched for chromatin modifiers and converged in midgestational transcription networks essential for neural and meningeal development. Unsupervised clustering of patient phenotypes identified four AC subtypes and clinical severity correlated with the presence of a damaging DNV. These data provide insights into the coordinated regulation of brain and meningeal development and implicate epigenomic dysregulation due to DNVs in AC pathogenesis. Our results provide a preliminary indication that, in the appropriate clinical context, ACs may be considered radiographic harbingers of neurodevelopmental pathology warranting genetic testing and neurobehavioral follow-up. These data highlight the utility of a systems-level, multiomics approach to elucidate sporadic structural brain disease

Enzymatic Digestion of Hyaluronan-Based Brain Extracellular Matrix in vivo Can Induce Seizures in Neonatal Mice

It is well-known that hyaluronic acid (HA) as a component of brain extracellular matrix (ECM) plays a pivotal role in the nervous system and is involved in synaptic plasticity changes in vascular cognitive impairment and dementia. HA breakdown is a feature of the acute stage of stroke injury and may be detrimental through enhancement of the inflammatory response. Recent studies have shown that knockout mice lacking hyaluronic acid synthetase demonstrates epileptic phenotype in vivo and removal of HA leads to delayed development of epileptiform activity in cultured hippocampal neurons in vitro. Here, we studied whether digestion of hyaluronic acid in the hippocampus in early postnatal period can trigger seizures. Hyaluronidase (Hyal) (5 U/μl) was bilaterally injected into C57BL/6j mice (P17) CA1 field of hippocampus using the stereotaxic method to remove hyaluronan-based ECM. Transcriptome analysis of hippocampal tissue 2 h after enzymatic digestion of hyaluronan-based brain ECM revealed increased gene expression of proteins involved in inflammation reactions (TLR2, CCL2,3,5), neuroinflammation, axonal guidance and ephrin receptor signaling, versus the vehicle group. Mice injected with hyaluronidase exhibited delayed audiogenic seizures and improvement in working memory 72 h after injection, while there were no changes in locomotor activity, anxious level and exploratory behavior due to the open field test. The obtained results point to a link between the activation of neuroinflammation by enzymatic digestion of hyaluronan-based brain ECM during the neonatal period and their subsequent reactivity to seizures, which may play an important role in the functional features of the developing brain, including its seizure propensity

A new cofilin-dependent mechanism for the regulation of brain mitochondria biogenesis and degradation

The aim was to study the role of post-translational modifications of cofilin in the regulation of respiration and autophagy in murine brain mitochondria. Materials and Methods. The experiments were performed with C57BL/6 mice. To obtain cytoplasmic and mitochondrial fractions of the brain tissue, differential centrifugation was used. Expressions of cofilin, phospho-cofilin, K48- and K63-associated chains of ubiquitin, and the autophagy marker LC3B were determined using electrophoresis, immunoprecipitation and Western blot methods. To study the processes of ubiquitination, we used PR619 — the inhibitor of deubiquitinating enzymes. Respiratory activity of brain mitochondria was evaluated using high-resolution fluorespirometry. Results. Modification of cofilin by non-canonical K63 multiubiquitin chains in the cytoplasm and mitochondria from murine brain was demonstrated. Different levels of phospho-cofilin, cofilin, and its ubiquitinated proteoforms were found. PR619, the inhibitor of deubiquitinating enzymes, affects the expression of phosphorylated and ubiquitinated forms of cofilin in the mitochondria and cytoplasm, at the same time it changes the activity of tissue respiration and mitophagy. Conclusion. The sensitivity of cofilin to the inhibitor of deubiquitinating enzymes indicates the existence of a new non-catabolic mechanism of cofilin modification, which may be involved in the regulation of mitochondrial functions, specifically, the mitochondrial respiration and autophagy. The data help understand the molecular mechanisms of mitochondrial function in normal and pathological conditions, which may be useful in developing novel methods for the treatment of diseases of the nervous system

Multiomic analyses implicate a neurodevelopmental program in the pathogenesis of cerebral arachnoid cysts

Cerebral arachnoid cysts (ACs) are one of the most common and poorly understood types of developmental brain lesion. To begin to elucidate AC pathogenesis, we performed an integrated analysis of 617 patient–parent (trio) exomes, 152,898 human brain and mouse meningeal single-cell RNA sequencing transcriptomes and natural language processing data of patient medical records. We found that damaging de novo variants (DNVs) were highly enriched in patients with ACs compared with healthy individuals (P = 1.57 × 10−33). Seven genes harbored an exome-wide significant DNV burden. AC-associated genes were enriched for chromatin modifiers and converged in midgestational transcription networks essential for neural and meningeal development. Unsupervised clustering of patient phenotypes identified four AC subtypes and clinical severity correlated with the presence of a damaging DNV. These data provide insights into the coordinated regulation of brain and meningeal development and implicate epigenomic dysregulation due to DNVs in AC pathogenesis. Our results provide a preliminary indication that, in the appropriate clinical context, ACs may be considered radiographic harbingers of neurodevelopmental pathology warranting genetic testing and neurobehavioral follow-up. These data highlight the utility of a systems-level, multiomics approach to elucidate sporadic structural brain disease.<br/