Bridging therapy-induced phenotypes and genetic immune dysregulation to study interleukin-2-induced immunotoxicology.

Interleukin-2 (IL-2) holds promise for the treatment of cancer and autoimmune diseases, but its high-dose usage is associated with systemic immunotoxicity. Differential IL-2 receptor (IL-2R) regulation might impact function of cells upon IL-2 stimulation, possibly inducing cellular changes similar to patients with hypomorphic IL2RB mutations, presenting with multiorgan autoimmunity. Here, we show that sustained high-dose IL-2 stimulation of human lymphocytes drastically reduces IL-2Rß surface expression especially on T cells, resulting in impaired IL-2R signaling which correlates with high IL-2Rα baseline expression. IL-2R signaling in NK cells is maintained. CD4+ T cells, especially regulatory T cells are more broadly affected than CD8+ T cells, consistent with lineage-specific differences in IL-2 responsiveness. Given the resemblance of cellular characteristics of high-dose IL-2-stimulated cells and cells from patients with IL-2Rß defects, impact of continuous IL-2 stimulation on IL-2R signaling should be considered in the onset of clinical adverse events during IL-2 therapy.

Creation of a pandemic memory by tracing COVID-19 infections and immunity in Luxembourg (CON-VINCE).

BACKGROUND: During the COVID-19 pandemic swift implementation of research cohorts was key. While many studies focused exclusively on infected individuals, population based cohorts are essential for the follow-up of SARS-CoV-2 impact on public health. Here we present the CON-VINCE cohort, estimate the point and period prevalence of the SARS-CoV-2 infection, reflect on the spread within the Luxembourgish population, examine immune responses to SARS-CoV-2 infection and vaccination, and ascertain the impact of the pandemic on population psychological wellbeing at a nationwide level. METHODS: A representative sample of the adult Luxembourgish population was enrolled. The cohort was followed-up for twelve months. SARS-CoV-2 RT-qPCR and serology were conducted at each sampling visit. The surveys included detailed epidemiological, clinical, socio-economic, and psychological data. RESULTS: One thousand eight hundred sixty-five individuals were followed over seven visits (April 2020-June 2021) with the final weighted period prevalence of SARS-CoV-2 infection of 15%. The participants had similar risks of being infected regardless of their gender, age, employment status and education level. Vaccination increased the chances of IgG-S positivity in infected individuals. Depression, anxiety, loneliness and stress levels increased at a point of study when there were strict containment measures, returning to baseline afterwards. CONCLUSION: The data collected in CON-VINCE study allowed obtaining insights into the infection spread in Luxembourg, immunity build-up and the impact of the pandemic on psychological wellbeing of the population. Moreover, the study holds great translational potential, as samples stored at the biobank, together with self-reported questionnaire information, can be exploited in further research. TRIAL REGISTRATION: Trial registration number: NCT04379297, 10 April 2020.

COBREXA.jl: constraint-based reconstruction and exascale analysis.

SUMMARY: COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose is to facilitate the integration of modern high performance computing environments with the processing and analysis of large-scale metabolic models of challenging complexity. We report the architecture of the package, and demonstrate how the design promotes analysis scalability on several use-cases with multi-organism community models. AVAILABILITY AND IMPLEMENTATION: https://doi.org/10.17881/ZKCR-BT30. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PredictProtein - Predicting Protein Structure and Function for 29 Years.

Since 1992 PredictProtein (https://predictprotein.org) is a one-stop online resource for protein sequence analysis with its main site hosted at the Luxembourg Centre for Systems Biomedicine (LCSB) and queried monthly by over 3,000 users in 2020. PredictProtein was the first Internet server for protein predictions. It pioneered combining evolutionary information and machine learning. Given a protein sequence as input, the server outputs multiple sequence alignments, predictions of protein structure in 1D and 2D (secondary structure, solvent accessibility, transmembrane segments, disordered regions, protein flexibility, and disulfide bridges) and predictions of protein function (functional effects of sequence variation or point mutations, Gene Ontology (GO) terms, subcellular localization, and protein-, RNA-, and DNA binding). PredictProtein's infrastructure has moved to the LCSB increasing throughput; the use of MMseqs2 sequence search reduced runtime five-fold (apparently without lowering performance of prediction methods); user interface elements improved usability, and new prediction methods were added. PredictProtein recently included predictions from deep learning embeddings (GO and secondary structure) and a method for the prediction of proteins and residues binding DNA, RNA, or other proteins. PredictProtein.org aspires to provide reliable predictions to computational and experimental biologists alike. All scripts and methods are freely available for offline execution in high-throughput settings.

Analysis: Flawed Datasets of Monkeypox Skin Images.

The self-proclaimed first publicly available dataset of Monkeypox skin images consists of medically irrelevant images extracted from Google and photography repositories through a process denominated web-scrapping. Yet, this did not stop other researchers from employing it to build Machine Learning (ML) solutions aimed at computer-aided diagnosis of Monkeypox and other viral infections presenting skin lesions. Neither did it stop the reviewers or editors from publishing these subsequent works in peer-reviewed journals. Several of these works claimed extraordinary performance in the classification of Monkeypox, Chickenpox and Measles, employing ML and the aforementioned dataset. In this work, we analyse the initiator work that has catalysed the development of several ML solutions, and whose popularity is continuing to grow. Further, we provide a rebuttal experiment that showcases the risks of such methodologies, proving that the ML solutions do not necessarily obtain their performance from the features relevant to the diseases at issue.

Presenting and sharing clinical data using the eTRIKS Standards Master Tree for tranSMART.

MOTIVATION: Standardization and semantic alignment have been considered one of the major challenges for data integration in clinical research. The inclusion of the CDISC SDTM clinical data standard into the tranSMART i2b2 via a guiding master ontology tree positively impacts and supports the efficacy of data sharing, visualization and exploration across datasets. RESULTS: We present here a schema for the organization of SDTM variables into the tranSMART i2b2 tree along with a script and test dataset to exemplify the mapping strategy. The eTRIKS master tree concept is demonstrated by making use of fictitious data generated for four patients, including 16 SDTM clinical domains. We describe how the usage of correct visit names and data labels can help to integrate multiple readouts per patient and avoid ETL crashes when running a tranSMART loading routine. AVAILABILITY AND IMPLEMENTATION: The eTRIKS Master Tree package and test datasets are publicly available at https://doi.org/10.5281/zenodo.1009098 and a functional demo installation at https://public.etriks.org/transmart/datasetExplorer/ under eTRIKS-Master Tree branch, where the discussed examples can be visualized.

Data and knowledge management in translational research: implementation of the eTRIKS platform for the IMI OncoTrack consortium.

BACKGROUND: For large international research consortia, such as those funded by the European Union's Horizon 2020 programme or the Innovative Medicines Initiative, good data coordination practices and tools are essential for the successful collection, organization and analysis of the resulting data. Research consortia are attempting ever more ambitious science to better understand disease, by leveraging technologies such as whole genome sequencing, proteomics, patient-derived biological models and computer-based systems biology simulations. RESULTS: The IMI eTRIKS consortium is charged with the task of developing an integrated knowledge management platform capable of supporting the complexity of the data generated by such research programmes. In this paper, using the example of the OncoTrack consortium, we describe a typical use case in translational medicine. The tranSMART knowledge management platform was implemented to support data from observational clinical cohorts, drug response data from cell culture models and drug response data from mouse xenograft tumour models. The high dimensional (omics) data from the molecular analyses of the corresponding biological materials were linked to these collections, so that users could browse and analyse these to derive candidate biomarkers. CONCLUSIONS: In all these steps, data mapping, linking and preparation are handled automatically by the tranSMART integration platform. Therefore, researchers without specialist data handling skills can focus directly on the scientific questions, without spending undue effort on processing the data and data integration, which are otherwise a burden and the most time-consuming part of translational research data analysis.

The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide.

Education and training are two essential ingredients for a successful career. On one hand, universities provide students a curriculum for specializing in one's field of study, and on the other, internships complement coursework and provide invaluable training experience for a fruitful career. Consequently, undergraduates and graduates are encouraged to undertake an internship during the course of their degree. The opportunity to explore one's research interests in the early stages of their education is important for students because it improves their skill set and gives their career a boost. In the long term, this helps to close the gap between skills and employability among students across the globe and balance the research capacity in the field of computational biology. However, training opportunities are often scarce for computational biology students, particularly for those who reside in less-privileged regions. Aimed at helping students develop research and academic skills in computational biology and alleviating the divide across countries, the Student Council of the International Society for Computational Biology introduced its Internship Program in 2009. The Internship Program is committed to providing access to computational biology training, especially for students from developing regions, and improving competencies in the field. Here, we present how the Internship Program works and the impact of the internship opportunities so far, along with the challenges associated with this program.

Confronting the catalytic dark matter encoded by sequenced genomes.

The post-genomic era has provided researchers with a deluge of protein sequences. However, a significant fraction of the proteins encoded by sequenced genomes remains without an identified function. Here, we aim at determining how many enzymes of uncertain or unknown function are still present in the Saccharomyces cerevisiae and human proteomes. Using information available in the Swiss-Prot, BRENDA and KEGG databases in combination with a Hidden Markov Model-based method, we estimate that >600 yeast and 2000 human proteins (>30% of their proteins of unknown function) are enzymes whose precise function(s) remain(s) to be determined. This illustrates the impressive scale of the 'unknown enzyme problem'. We extensively review classical biochemical as well as more recent systematic experimental and computational approaches that can be used to support enzyme function discovery research. Finally, we discuss the possible roles of the elusive catalysts in light of recent developments in the fields of enzymology and metabolism as well as the significance of the unknown enzyme problem in the context of metabolic modeling, metabolic engineering and rare disease research.

SmartR: an open-source platform for interactive visual analytics for translational research data.

SUMMARY: In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre-clinical or OMICS data combined with strong visual analytical capabilities will significantly accelerate the scientific progress by making data more accessible and hypothesis generation easier. The open data warehouse tranSMART is capable of storing a variety of data types and has a growing user community including both academic institutions and pharmaceutical companies. tranSMART, however, currently lacks interactive and dynamic visual analytics and does not permit any post-processing interaction or exploration. For this reason, we developed SmartR , a plugin for tranSMART, that equips the platform not only with several dynamic visual analytical workflows, but also provides its own framework for the addition of new custom workflows. Modern web technologies such as D3.js or AngularJS were used to build a set of standard visualizations that were heavily improved with dynamic elements. AVAILABILITY AND IMPLEMENTATION: The source code is licensed under the Apache 2.0 License and is freely available on GitHub: https://github.com/transmart/SmartR . CONTACT: reinhard.schneider@uni.lu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

nala: text mining natural language mutation mentions.

MOTIVATION: The extraction of sequence variants from the literature remains an important task. Existing methods primarily target standard (ST) mutation mentions (e.g. 'E6V'), leaving relevant mentions natural language (NL) largely untapped (e.g. 'glutamic acid was substituted by valine at residue 6'). RESULTS: We introduced three new corpora suggesting named-entity recognition (NER) to be more challenging than anticipated: 28-77% of all articles contained mentions only available in NL. Our new method nala captured NL and ST by combining conditional random fields with word embedding features learned unsupervised from the entire PubMed. In our hands, nala substantially outperformed the state-of-the-art. For instance, we compared all unique mentions in new discoveries correctly detected by any of three methods (SETH, tmVar, or nala ). Neither SETH nor tmVar discovered anything missed by nala , while nala uniquely tagged 33% mentions. For NL mentions the corresponding value shot up to 100% nala -only. AVAILABILITY AND IMPLEMENTATION: Source code, API and corpora freely available at: http://tagtog.net/-corpora/IDP4+ . CONTACT: nala@rostlab.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

siRNA screen identifies QPCT as a druggable target for Huntington's disease.

Huntington's disease (HD) is a currently incurable neurodegenerative condition caused by an abnormally expanded polyglutamine tract in huntingtin (HTT). We identified new modifiers of mutant HTT toxicity by performing a large-scale 'druggable genome' siRNA screen in human cultured cells, followed by hit validation in Drosophila. We focused on glutaminyl cyclase (QPCT), which had one of the strongest effects on mutant HTT-induced toxicity and aggregation in the cell-based siRNA screen and also rescued these phenotypes in Drosophila. We found that QPCT inhibition induced the levels of the molecular chaperone αB-crystallin and reduced the aggregation of diverse proteins. We generated new QPCT inhibitors using in silico methods followed by in vitro screening, which rescued the HD-related phenotypes in cell, Drosophila and zebrafish HD models. Our data reveal a new HD druggable target affecting mutant HTT aggregation and provide proof of principle for a discovery pipeline from druggable genome screen to drug development.

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes.

Despite our rapidly growing knowledge about the human genome, we do not know all of the genes required for some of the most basic functions of life. To start to fill this gap we developed a high-throughput phenotypic screening platform combining potent gene silencing by RNA interference, time-lapse microscopy and computational image processing. We carried out a genome-wide phenotypic profiling of each of the approximately 21,000 human protein-coding genes by two-day live imaging of fluorescently labelled chromosomes. Phenotypes were scored quantitatively by computational image processing, which allowed us to identify hundreds of human genes involved in diverse biological functions including cell division, migration and survival. As part of the Mitocheck consortium, this study provides an in-depth analysis of cell division phenotypes and makes the entire high-content data set available as a resource to the community.

BioTextQuest(+): a knowledge integration platform for literature mining and concept discovery.

SUMMARY: The iterative process of finding relevant information in biomedical literature and performing bioinformatics analyses might result in an endless loop for an inexperienced user, considering the exponential growth of scientific corpora and the plethora of tools designed to mine PubMed(®) and related biological databases. Herein, we describe BioTextQuest(+), a web-based interactive knowledge exploration platform with significant advances to its predecessor (BioTextQuest), aiming to bridge processes such as bioentity recognition, functional annotation, document clustering and data integration towards literature mining and concept discovery. BioTextQuest(+) enables PubMed and OMIM querying, retrieval of abstracts related to a targeted request and optimal detection of genes, proteins, molecular functions, pathways and biological processes within the retrieved documents. The front-end interface facilitates the browsing of document clustering per subject, the analysis of term co-occurrence, the generation of tag clouds containing highly represented terms per cluster and at-a-glance popup windows with information about relevant genes and proteins. Moreover, to support experimental research, BioTextQuest(+) addresses integration of its primary functionality with biological repositories and software tools able to deliver further bioinformatics services. The Google-like interface extends beyond simple use by offering a range of advanced parameterization for expert users. We demonstrate the functionality of BioTextQuest(+) through several exemplary research scenarios including author disambiguation, functional term enrichment, knowledge acquisition and concept discovery linking major human diseases, such as obesity and ageing. AVAILABILITY: The service is accessible at http://bioinformatics.med.uoc.gr/biotextquest. CONTACT: g.pavlopoulos@gmail.com or georgios.pavlopoulos@esat.kuleuven.be SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Constitutive activation of oncogenic PDGFRα-mutant proteins occurring in GIST patients induces receptor mislocalisation and alters PDGFRα signalling characteristics.

BACKGROUND: Gastrointestinal stromal tumours (GIST) are mainly characterised by the presence of activating mutations in either of the two receptor tyrosine kinases c-KIT or platelet-derived growth factor receptor-α (PDGFRα). Most mechanistic studies dealing with GIST mutations have focused on c-KIT and far less is known about the signalling characteristics of the mutated PDGFRα proteins. Here, we study the signalling capacities and corresponding transcriptional responses of the different PDGFRα proteins under comparable genomic conditions. RESULTS: We demonstrate that the constitutive signalling via the oncogenic PDGFRα mutants favours a mislocalisation of the receptors and that this modifies the signalling characteristics of the mutated receptors. We show that signalling via the oncogenic PDGFRα mutants is not solely characterised by a constitutive activation of the conventional PDGFRα signalling pathways. In contrast to wild-type PDGFRα signal transduction, the activation of STAT factors (STAT1, STAT3 and STAT5) is an integral part of signalling mediated via mutated PDGF-receptors. Furthermore, this unconventional STAT activation by mutated PDGFRα is already initiated in the endoplasmic reticulum whereas the conventional signalling pathways rather require cell surface expression of the receptor. Finally, we demonstrate that the activation of STAT factors also translates into a biologic response as highlighted by the induction of STAT target genes. CONCLUSION: We show that the overall oncogenic response is the result of different signatures emanating from different cellular compartments. Furthermore, STAT mediated responses are an integral part of mutated PDGFRα signalling.

The HIV mutation browser: a resource for human immunodeficiency virus mutagenesis and polymorphism data.

Huge research effort has been invested over many years to determine the phenotypes of natural or artificial mutations in HIV proteins--interpretation of mutation phenotypes is an invaluable source of new knowledge. The results of this research effort are recorded in the scientific literature, but it is difficult for virologists to rapidly find it. Manually locating data on phenotypic variation within the approximately 270,000 available HIV-related research articles, or the further 1,500 articles that are published each month is a daunting task. Accordingly, the HIV research community would benefit from a resource cataloguing the available HIV mutation literature. We have applied computational text-mining techniques to parse and map mutagenesis and polymorphism information from the HIV literature, have enriched the data with ancillary information and have developed a public, web-based interface through which it can be intuitively explored: the HIV mutation browser. The current release of the HIV mutation browser describes the phenotypes of 7,608 unique mutations at 2,520 sites in the HIV proteome, resulting from the analysis of 120,899 papers. The mutation information for each protein is organised in a residue-centric manner and each residue is linked to the relevant experimental literature. The importance of HIV as a global health burden advocates extensive effort to maximise the efficiency of HIV research. The HIV mutation browser provides a valuable new resource for the research community. The HIV mutation browser is available at: http://hivmut.org.

Cohort-specific boolean models highlight different regulatory modules during Parkinson's disease progression.

Parkinson's disease (PD) involves complex molecular interactions and diverse comorbidities. To better understand its molecular mechanisms, we employed systems medicine approaches using the PD map, a detailed repository of PD-related interactions and applied Probabilistic Boolean Networks (PBNs) to capture the stochastic nature of molecular dynamics. By integrating cohort-level and real-world patient data, we modeled PD's subtype-specific pathway deregulations, providing a refined representation of its molecular landscape. Our study identifies key regulatory biomolecules and pathways that vary across PD subtypes, offering insights into the disease's progression and patient stratification. These findings have significant implications for the development of targeted therapeutic interventions.

BioKC: a collaborative platform for curation and annotation of molecular interactions.

Curation of biomedical knowledge into systems biology diagrammatic or computational models is essential for studying complex biological processes. However, systems-level curation is a laborious manual process, especially when facing ever-increasing growth of domain literature. New findings demonstrating elaborate relationships between multiple molecules, pathways and cells have to be represented in a format suitable for systems biology applications. Importantly, curation should capture the complexity of molecular interactions in such a format together with annotations of the involved elements and support stable identifiers and versioning. This challenge calls for novel collaborative tools and platforms allowing to improve the quality and the output of the curation process. In particular, community-based curation, an important source of curated knowledge, requires support in role management, reviewing features and versioning. Here, we present Biological Knowledge Curation (BioKC), a web-based collaborative platform for the curation and annotation of biomedical knowledge following the standard data model from Systems Biology Markup Language (SBML). BioKC offers a graphical user interface for curation of complex molecular interactions and their annotation with stable identifiers and supporting sentences. With the support of collaborative curation and review, it allows to construct building blocks for systems biology diagrams and computational models. These building blocks can be published under stable identifiers and versioned and used as annotations, supporting knowledge building for modelling activities.

Genetically stratified Parkinson's disease with freezing of gait is related to specific pattern of cognitive impairment and non-motor dominant endophenotype.

Background: Freezing of gait (FOG) is an important milestone in the individual disease trajectory of people with Parkinson's disease (PD). Based on the cognitive model of FOG etiology, the mechanism behind FOG implies higher executive dysfunction in PDFOG+. To test this model, we investigated the FOG-related phenotype and cognitive subdomains in idiopathic PD (iPD) patients without genetic variants linked to PD from the Luxembourg Parkinson's study. Methods: A cross-sectional analysis comparing iPDFOG+ (n = 118) and iPDFOG- (n = 378) individuals was performed, followed by the application of logistic regression models. Consequently, regression models were fitted for a subset of iPDFOG+ (n = 35) vs. iPDFOG- (n = 126), utilizing a detailed neuropsychological battery to assess the association between FOG and cognitive subdomains. Both regression models were adjusted for sociodemographic confounders and disease severity. Results: iPDFOG+ individuals presented with more motor complications (MDS-UPDRS IV) compared to iPDFOG- individuals. Moreover, iPDFOG+ individuals exhibited a higher non-motor burden, including a higher frequency of hallucinations, higher MDS-UPDRS I scores, and more pronounced autonomic dysfunction as measured by the SCOPA-AUT. In addition, iPDFOG+ individuals showed lower sleep quality along with lower quality of life (measured by PDSS and PDQ-39, respectively). The cognitive subdomain analysis in iPDFOG+ vs. iPDFOG- indicated lower scores in Benton's Judgment of Line Orientation test and CERAD word recognition, reflecting higher impairment in visuospatial, executive function, and memory encoding. Conclusion: We determined a significant association between FOG and a clinical endophenotype of PD with higher non-motor burden. While our results supported the cognitive model of FOG, our findings point to a more widespread cortical impairment across cognitive subdomains beyond the executive domain in PDFOG+ with additional higher impairment in visuospatial function and memory encoding.

DS-PACK: Tool assembly for the end-to-end support of controlled access human data sharing.

The EU General Data Protection Regulation (GDPR) requirements have prompted a shift from centralised controlled access genome-phenome archives to federated models for sharing sensitive human data. In a data-sharing federation, a central node facilitates data discovery; meanwhile, distributed nodes are responsible for handling data access requests, concluding agreements with data users and providing secure access to the data. Research institutions that want to become part of such federations often lack the resources to set up the required controlled access processes. The DS-PACK tool assembly is a reusable, open-source middleware solution that semi-automates controlled access processes end-to-end, from data submission to access. Data protection principles are engraved into all components of the DS-PACK assembly. DS-PACK centralises access control management and distributes access control enforcement with support for data access via cloud-based applications. DS-PACK is in production use at the ELIXIR Luxembourg data hosting platform, combined with an operational model including legal facilitation and data stewardship.