Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps

Cytoscape Web: bringing network biology to the browser

Since its introduction in 2003, Cytoscape has been a de facto standard for visualizing and analyzing biological networks. We now introduce Cytoscape Web (https://web.cytoscape.org), an online implementation that captures the interface and key visualization functionality of the desktop while providing integration with web tools and databases. Cytoscape Web enhances accessibility, simplifying collaboration through online data sharing. It integrates with Cytoscape desktop via the CX2 network exchange format and with the Network Data Exchange for storing and sharing networks. The platform supports extensibility through an App framework for UI components and Service Apps for algorithm integration, fostering community-driven development of new analysis tools. Overall, Cytoscape Web enhances network biology by providing a versatile, accessible, and collaborative online platform that adapts to evolving computational challenges, laying a foundation for future incorporation of advanced network analysis capabilities by the community.

Single-sample, multi-omic mass spectrometry for investigating mechanisms of drug toxicity

Poor therapeutic index is a principal cause of drug attrition during development. A case in point is L-asparaginase (ASNase), an enzyme-drug approved for treatment of pediatric acute lymphoblastic leukemia (ALL) but too toxic for adults. To elucidate potentially targetable mechanisms for mitigation of ASNase toxicity, we performed multi-omic profiling of the response to sub-toxic and toxic doses of ASNase in mice. We collected whole blood samples longitudinally, processed them to plasma, and extracted metabolites, lipids, and proteins from a single 20-µL plasma sample. We analyzed the extracts using multiple reaction monitoring (MRM) of 500+ water soluble metabolites, 750+ lipids, and 375 peptides on a triple quadrupole LC-MS/MS platform. Metabolites, lipids, and peptides that were modulated in a dose-dependent manner appeared to converge on antioxidation, inflammation, autophagy, and cell death pathways, prompting the hypothesis that inhibiting those pathways might decrease ASNase toxicity while preserving anticancer activity. Overall, we provide here a streamlined, three-in-one LC-MS/MS workflow for targeted metabolomics, lipidomics, and proteomics and demonstrate its ability to generate new insights into mechanisms of drug toxicity.

Ion suppression correction and normalization for non-targeted metabolomics

Ion suppression is a major problem in mass spectrometry (MS)-based metabolomics; it can dramatically decrease measurement accuracy, precision, and sensitivity. Here we report a method, the IROA TruQuant Workflow, that uses a stable isotope-labeled internal standard (IROA-IS) library plus companion algorithms to: 1) measure and correct for ion suppression, and 2) perform Dual MSTUS normalization of MS metabolomic data. We evaluate the method across ion chromatography (IC), hydrophilic interaction liquid chromatography (HILIC), and reversed-phase liquid chromatography (RPLC)-MS systems in both positive and negative ionization modes, with clean and unclean ion sources, and across different biological matrices. Across the broad range of conditions tested, all detected metabolites exhibit ion suppression ranging from 1% to >90% and coefficients of variation ranging from 1% to 20%, but the Workflow and companion algorithms are highly effective at nulling out that suppression and error. To demonstrate a routine application of the Workflow, we employ the Workflow to study ovarian cancer cell response to the enzyme-drug L-asparaginase (ASNase). The IROA-normalized data reveal significant alterations in peptide metabolism, which have not been reported previously. Overall, the Workflow corrects ion suppression across diverse analytical conditions and produces robust normalization of non-targeted metabolomic data.

The variegated canalized-1 tomato mutant is linked to photosystem assembly

The recently described canal-1 tomato mutant, which has a variegated leaf phenotype, has been shown to affect canalization of yield. The corresponding protein is orthologous to AtSCO2 -SNOWY COTYLEDON 2, which has suggested roles in thylakoid biogenesis. Here we characterize the canal-1 mutant through a multi-omics approach, by comparing mutant to wild-type tissues. While white canal-1 leaves are devoid of chlorophyll, green leaves of the mutant appear wild-type-like, despite an impaired protein function. Transcriptomic data suggest that green mutant leaves compensate for this impaired protein function by upregulation of transcription of photosystem assembly and photosystem component genes, thereby allowing adequate photosystem establishment, which is reflected in their wild-type-like proteome. White canal-1 leaves, however, likely fail to reach a certain threshold enabling this overcompensation, and plastids get trapped in an undeveloped state, while additionally suffering from high light stress, indicated by the overexpression of ELIP homolog genes. The metabolic profile of white and to a lesser degree also green tissues revealed upregulation of amino acid levels, that was at least partially mediated by transcriptional and proteomic upregulation. These combined changes are indicative of a stress response and suggest that white tissues behave as carbon sinks. In summary, our work demonstrates the relevance of the SCO2 protein in both photosystem assembly and as a consequence in the canalization of yield.

Prognostic genome and transcriptome signatures in colorectal cancers

Colorectal cancer is caused by a sequence of somatic genomic alterations affecting driver genes in core cancer pathways1. Here, to understand the functional and prognostic impact of cancer-causing somatic mutations, we analysed the whole genomes and transcriptomes of 1,063 primary colorectal cancers in a population-based cohort with long-term follow-up. From the 96 mutated driver genes, 9 were not previously implicated in colorectal cancer and 24 had not been linked to any cancer. Two distinct patterns of pathway co-mutations were observed, timing analyses identified nine early and three late driver gene mutations, and several signatures of colorectal-cancer-specific mutational processes were identified. Mutations in WNT, EGFR and TGFβ pathway genes, the mitochondrial CYB gene and 3 regulatory elements along with 21 copy-number variations and the COSMIC SBS44 signature correlated with survival. Gene expression classification yielded five prognostic subtypes with distinct molecular features, in part explained by underlying genomic alterations. Microsatellite-instable tumours divided into two classes with different levels of hypoxia and infiltration of immune and stromal cells. To our knowledge, this study constitutes the largest integrated genome and transcriptome analysis of colorectal cancer, and interlinks mutations, gene expression and patient outcomes. The identification of prognostic mutations and expression subtypes can guide future efforts to individualize colorectal cancer therapy.

Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses

Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.

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.

Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum

Introduction: Genome-scale metabolic models (GEMs) are organism-specific knowledge bases which can be used to unravel pathogenicity or improve production of specific metabolites in biotechnology applications. However, the validity of predictions for bacterial proliferation in in vitro settings is hardly investigated. Methods: The present work combines in silico and in vitro approaches to create and curate strain-specific genome-scale metabolic models of Corynebacterium striatum. Results: We introduce five newly created strain-specific genome-scale metabolic models (GEMs) of high quality, satisfying all contemporary standards and requirements. All these models have been benchmarked using the community standard test suite Metabolic Model Testing (MEMOTE) and were validated by laboratory experiments. For the curation of those models, the software infrastructure refineGEMs was developed to work on these models in parallel and to comply with the quality standards for GEMs. The model predictions were confirmed by experimental data and a new comparison metric based on the doubling time was developed to quantify bacterial growth. Discussion: Future modeling projects can rely on the proposed software, which is independent of specific environmental conditions. The validation approach based on the growth rate calculation is now accessible and closely aligned with biological questions. The curated models are freely available via BioModels and a GitHub repository and can be used. The open-source software refineGEMs is available from https://github.com/draeger-lab/refinegems.

Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation

Post-translational modifications (PTMs) play key roles in regulating cell signaling and physiology in both normal and cancer cells. Advances in mass spectrometry enable high-throughput, accurate, and sensitive measurement of PTM levels to better understand their role, prevalence, and crosstalk. Here, we analyze the largest collection of proteogenomics data from 1,110 patients with PTM profiles across 11 cancer types (10 from the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium [CPTAC]). Our study reveals pan-cancer patterns of changes in protein acetylation and phosphorylation involved in hallmark cancer processes. These patterns revealed subsets of tumors, from different cancer types, including those with dysregulated DNA repair driven by phosphorylation, altered metabolic regulation associated with immune response driven by acetylation, affected kinase specificity by crosstalk between acetylation and phosphorylation, and modified histone regulation. Overall, this resource highlights the rich biology governed by PTMs and exposes potential new therapeutic avenues.

Visualization of automatically combined disease maps and pathway diagrams for rare diseases

Introduction: Investigation of molecular mechanisms of human disorders, especially rare diseases, require exploration of various knowledge repositories for building precise hypotheses and complex data interpretation. Recently, increasingly more resources offer diagrammatic representation of such mechanisms, including disease-dedicated schematics in pathway databases and disease maps. However, collection of knowledge across them is challenging, especially for research projects with limited manpower. Methods: In this article we present an automated workflow for construction of maps of molecular mechanisms for rare diseases. The workflow requires a standardized definition of a disease using Orphanet or HPO identifiers to collect relevant genes and variants, and to assemble a functional, visual repository of related mechanisms, including data overlays. The diagrams composing the final map are unified to a common systems biology format from CellDesigner SBML, GPML and SBML+layout+render. The constructed resource contains disease-relevant genes and variants as data overlays for immediate visual exploration, including embedded genetic variant browser and protein structure viewer. Results: We demonstrate the functionality of our workflow on two examples of rare diseases: Kawasaki disease and retinitis pigmentosa. Two maps are constructed based on their corresponding identifiers. Moreover, for the retinitis pigmentosa use-case, we include a list of differentially expressed genes to demonstrate how to tailor the workflow using omics datasets. Discussion: In summary, our work allows for an ad-hoc construction of molecular diagrams combined from different sources, preserving their layout and graphical style, but integrating them into a single resource. This allows to reduce time consuming tasks of prototyping of a molecular disease map, enabling visual exploration, hypothesis building, data visualization and further refinement. The code of the workflow is open and accessible at https://gitlab.lcsb.uni.lu/minerva/automap/.

A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance

As a conceptual model of disease mechanisms, a disease map integrates available knowledge and is applied for data interpretation, predictions and hypothesis generation. It is possible to model disease mechanisms on different levels of granularity and adjust the approach to the goals of a particular project. This rich environment together with requirements for high-quality network reconstruction makes it challenging for new curators and groups to be quickly introduced to the development methods. In this review, we offer a step-by-step guide for developing a disease map within its mainstream pipeline that involves using the CellDesigner tool for creating and editing diagrams and the MINERVA Platform for online visualisation and exploration. We also describe how the Neo4j graph database environment can be used for managing and querying efficiently such a resource. For assessing the interoperability and reproducibility we apply FAIR principles.

New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells

COVID-19 is one of the deadliest respiratory diseases, and its emergence caught the pharmaceutical industry off guard. While vaccines have been rapidly developed, treatment options for infected people remain scarce, and COVID-19 poses a substantial global threat. This study presents a novel workflow to predict robust druggable targets against emerging RNA viruses using metabolic networks and information of the viral structure and its genome sequence. For this purpose, we implemented pymCADRE and PREDICATE to create tissue-specific metabolic models, construct viral biomass functions and predict host-based antiviral targets from more than one genome. We observed that pymCADRE reduces the computational time of flux variability analysis for internal optimizations. We applied these tools to create a new metabolic network of primary bronchial epithelial cells infected with SARS-CoV-2 and identified enzymatic reactions with inhibitory effects. The most promising reported targets were from the purine metabolism, while targeting the pyrimidine and carbohydrate metabolisms seemed to be promising approaches to enhance viral inhibition. Finally, we computationally tested the robustness of our targets in all known variants of concern, verifying our targets' inhibitory effects. Since laboratory tests are time-consuming and involve complex readouts to track processes, our workflow focuses on metabolic fluxes within infected cells and is applicable for rapid hypothesis-driven identification of potentially exploitable antivirals concerning various viruses and host cell types.

Asxl1 deletion disrupts MYC and RNA polymerase II function in granulocyte progenitors

Mutations in the gene Additional Sex-Combs Like 1 (ASXL1) are recurrent in myeloid malignancies as well as the pre-malignant condition clonal hematopoiesis, where they are universally associated with poor prognosis. However, the role of ASXL1 in myeloid lineage maturation is incompletely described. To define the role of ASXL1 in myelopoiesis, we employed single cell RNA sequencing and a murine model of hematopoietic-specific Asxl1 deletion. In granulocyte progenitors, Asxl1 deletion leads to hyperactivation of MYC and a quantitative decrease in neutrophil production. This loss of granulocyte production was not accompanied by significant changes in the landscape of covalent histone modifications. However, Asxl1 deletion results in a decrease in RNAPII promoter-proximal pausing in granulocyte progenitors, indicative of a global increase in productive transcription. These results suggest that ASXL1 inhibits productive transcription in granulocyte progenitors, identifying a new role for this epigenetic regulator in myeloid development.

Translating desktop success to the web in the cytoscape project

Cytoscape is an open-source bioinformatics environment for the analysis, integration, visualization, and query of biological networks. In this perspective piece, we describe our project to bring the Cytoscape desktop application to the web while explaining our strategy in ways relevant to others in the bioinformatics community. We examine opportunities and challenges in developing bioinformatics software that spans both the desktop and web, and we describe our ongoing efforts to build a Cytoscape web application, highlighting the principles that guide our development.

Cytoscape.js 2023 update: a graph theory library for visualization and analysis

SUMMARY

Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. This update describes new features and enhancements introduced over many new versions from 2015 to 2022.

AVAILABILITY AND IMPLEMENTATION

Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality

Biomolecular networks, including genome-scale metabolic models (GSMMs), assemble the knowledge regarding the biological processes that happen inside specific organisms in a way that allows for analysis, simulation, and exploration. With the increasing availability of genome annotations and the development of powerful reconstruction tools, biomolecular networks continue to grow ever larger. While visual exploration can facilitate the understanding of such networks, the network sizes represent a major challenge for current visualisation systems. Building on promising results from the area of immersive analytics, which among others deals with the potential of immersive visualisation for data analysis, we present a concept for a hybrid user interface that combines a classical desktop environment with a virtual reality environment for the visual exploration of large biomolecular networks and corresponding data. We present system requirements and design considerations, describe a resulting concept, an envisioned technical realisation, and a systems biology usage scenario. Finally, we discuss remaining challenges.

SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more

Visualization is a key recurring requirement for effective analysis of relational data. Biology is no exception. It is imperative to annotate and render biological models in standard, widely accepted formats. Finding graph-theoretical properties of pathways as well as identifying certain paths or subgraphs of interest in a pathway are also essential for effective analysis of pathway data. Given the size of available biological pathway data nowadays, automatic layout is crucial in understanding the graphical representations of such data. Even though there are many available software tools that support graphical display of biological pathways in various formats, there is none available as a service for on-demand or batch processing of biological pathways for automatic layout, customized rendering and mining paths or subgraphs of interest. In addition, there are many tools with fine rendering capabilities lacking decent automatic layout support.

To fill this void, we developed a web service named SyBLaRS (Systems Biology Layout and Rendering Service) for automatic layout of biological data in various standard formats as well as construction of customized images in both raster image and scalable vector formats of these maps. Some of the supported standards are more generic such as GraphML and JSON, whereas others are specialized to biology such as SBGNML (The Systems Biology Graphical Notation Markup Language) and SBML (The Systems Biology Markup Language). In addition, SyBLaRS supports calculation and highlighting of a number of well-known graph-theoretical properties as well as some novel graph algorithms turning a specified set of objects of interest to a minimal pathway of interest.

We demonstrate that SyBLaRS can be used both as an offline layout and rendering service to construct customized and annotated pictures of pathway models and as an online service to provide layout and rendering capabilities for systems biology software tools.

SyBLaRS is open source and publicly available on GitHub and freely distributed under the MIT license. In addition, a sample deployment is available here for public consumption.

Stochastic dynamics of Type-I interferon responses

Interferon (IFN) activates the transcription of several hundred of IFN stimulated genes (ISGs) that constitute a highly effective antiviral defense program. Cell-to-cell variability in the induction of ISGs is well documented, but its source and effects are not completely understood. The molecular mechanisms behind this heterogeneity have been related to randomness in molecular events taking place during the JAK-STAT signaling pathway. Here, we study the sources of variability in the induction of the IFN-alpha response by using MxA and IFIT1 activation as read-out. To this end, we integrate time-resolved flow cytometry data and stochastic modeling of the JAK-STAT signaling pathway. The complexity of the IFN response was matched by fitting probability distributions to time-course flow cytometry snapshots. Both, experimental data and simulations confirmed that the MxA and IFIT1 induction circuits generate graded responses rather than all-or-none responses. Subsequently, we quantify the size of the intrinsic variability at different steps in the pathway. We found that stochastic effects are transiently strong during the ligand-receptor activation steps and the formation of the ISGF3 complex, but negligible for the final induction of the studied ISGs. We conclude that the JAK-STAT signaling pathway is a robust biological circuit that efficiently transmits information under stochastic environments.

We investigate the impact of intrinsic and extrinsic noise on the reliability of interferon signaling. Information must be transduced robustly despite existing biochemical variability and at the same time the system has to allow for cellular variability to tune it against changing environments. Getting insights into stochasticity in signaling networks is crucial to understand cellular dynamics and decision-making processes. To this end, we developed a detailed stochastic computational model based on single cell data. We are able to show that reliability is achieved despite high noise at the receptor level.

Design considerations for representing systems biology information with the Systems Biology Graphical Notation

Visual representations are commonly used to explore, analyse, and communicate information and knowledge in systems biology and beyond. Such visualisations not only need to be accurate but should also be aesthetically pleasing and informative. Using the example of the Systems Biology Graphical Notation (SBGN) we will investigate design considerations for graphically presenting information from systems biology, in particular regarding the use of glyphs for types of information, the style of graph layout for network representation, and the concept of bricks for visual network creation.

Analyzing causal relationships in proteomic profiles using CausalPath

CausalPath (causalpath.org) evaluates proteomic measurements against prior knowledge of biological pathways and infers causality between changes in measured features, such as global protein and phospho-protein levels. It uses pathway resources to determine potential causality between observable omic features, which are called prior relations. The subset of the prior relations that are supported by the proteomic profiles are reported and evaluated for statistical significance. The end result is a network model of signaling that explains the patterns observed in the experimental dataset. For complete details on the use and execution of this protocol, please refer to Babur et al. (2021).

WikiPathways: connecting communities

WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of the scientific community developing and curating biological knowledge in pathway models, WikiPathways lowers all barriers for accessing and using its content. Increasingly more content creators, initiatives, projects and tools have started using WikiPathways. Central in this growth and increased use of WikiPathways are the various communities that focus on particular subsets of molecular pathways such as for rare diseases and lipid metabolism. Knowledge from published pathway figures helps prioritize pathway development, using optical character and named entity recognition. We show the growth of WikiPathways over the last three years, highlight the new communities and collaborations of pathway authors and curators, and describe various technologies to connect to external resources and initiatives. The road toward a sustainable, community-driven pathway database goes through integration with other resources such as Wikidata and allowing more use, curation and redistribution of WikiPathways content.