Unraveling the glycosphingolipid metabolism by leveraging transcriptome-weighted network analysis on neuroblastic tumors.

Background: Glycosphingolipids (GSLs) are membrane lipids composed of a ceramide backbone linked to a glycan moiety. Ganglioside biosynthesis is a part of the GSL metabolism, which involves sequential reactions catalyzed by specific enzymes that in part have a poor substrate specificity. GSLs are deregulated in cancer, thus playing a role as potential biomarkers for personalized therapy or subtype classification.

Identifications of Similarity Metrics for Patients With Cancer: Protocol for a Scoping Review.

Background: Understanding the similarities of patients with cancer is essential to advancing personalized medicine, improving patient outcomes, and developing more effective and individualized treatments. It enables researchers to discover important patterns, biomarkers, and treatment strategies that can have a significant impact on cancer research and oncology. In addition, the identification of previously successfully treated patients supports oncologists in making treatment decisions for a new patient who is clinically or molecularly similar to the previous patient.

Extending cBioPortal for Therapy Recommendation Documentation in Molecular Tumor Boards: Development and Usability Study.

Background: In molecular tumor boards (MTBs), patients with rare or advanced cancers are discussed by a multidisciplinary team of health care professionals. Software support for MTBs is lacking; in particular, tools for preparing and documenting MTB therapy recommendations need to be developed.

Objective: We aimed to implement an extension to cBioPortal to provide a tool for the documentation of therapy recommendations from MTB sessions in a secure and standardized manner.

Glucosylceramide Synthase Inhibitors Induce Ceramide Accumulation and Sensitize H3K27 Mutant Diffuse Midline Glioma to Irradiation.

H3K27M mutant (mut) diffuse midline glioma (DMG) is a lethal cancer with no effective cure. The glycosphingolipids (GSL) metabolism is altered in these tumors and could be exploited to develop new therapies. We tested the effect of the glucosylceramide synthase inhibitors (GSI) miglustat and eliglustat on cell proliferation, alone or in combination with temozolomide or ionizing radiation.

Creation of a structured molecular genomics report for Germany as a local adaption of HL7's Genomic Reporting Implementation Guide.

Objective: The objective was to develop a dataset definition, information model, and FHIR® specification for key data elements contained in a German molecular genomics (MolGen) report to facilitate genomic and phenotype integration in electronic health records.

Materials And Methods: A dedicated expert group participating in the German Medical Informatics Initiative reviewed information contained in MolGen reports, determined the key elements, and formulated a dataset definition. HL7's Genomics Reporting Implementation Guide (IG) was adopted as a basis for the FHIR® specification which was subjected to a public ballot.

Analysis of RBP expression and binding sites identifies PTBP1 as a regulator of CD19 expression in B-ALL.

Despite massive improvements in the treatment of B-ALL through CART-19 immunotherapy, a large number of patients suffer a relapse due to loss of the targeted epitope. Mutations in the locus and aberrant splicing events are known to account for the absence of surface antigen. However, early molecular determinants suggesting therapy resistance as well as the time point when first signs of epitope loss appear to be detectable are not enlightened so far.

Interaction between Bacteria and the Immune System for Cancer Immunotherapy: The α-GalCer Alliance.

Non-conventional T cells, such as γδ T and invariant natural killer T (iNKT) cells, are emerging players in fighting cancer. Alpha-galactosylceramide (α-GalCer) is used as an exogenous ligand to activate iNKT cells. Human cells don't have a direct pathway producing α-GalCer, which, however, can be produced by bacteria.

Interactive and Reproducible Workflows for Exploring and Modeling RNA-seq Data with pcaExplorer, Ideal, and GeneTonic.

The generation and interpretation of results from transcriptome profiling experiments via RNA sequencing (RNA-seq) can be a complex task. While raw data quality control, alignment, and quantification can be streamlined via efficient algorithms that can deliver the preprocessed expression matrix, a common bottleneck in the analysis of such large datasets is the subsequent in-depth, iterative processes of data exploration, statistical testing, visualization, and interpretation. Specific tools for these workflow steps are available but require a level of technical expertise which might be prohibitive for life and clinical scientists, who are left with essential pieces of information distributed among different tabular and list formats.

cbpManager: a web application to streamline the integration of clinical and genomic data in cBioPortal to support the Molecular Tumor Board.

Background: Extensive sequencing of tumor tissues has greatly improved our understanding of cancer biology over the past years. The integration of genomic and clinical data is increasingly used to select personalized therapies in dedicated tumor boards (Molecular Tumor Boards) or to identify patients for basket studies. Genomic alterations and clinical information can be stored, integrated and visualized in the open-access resource cBioPortal for Cancer Genomics.

Challenges and Experiences Extending the cBioPortal for Cancer Genomics to a Molecular Tumor Board Platform.

In Molecular Tumor Boards (MTBs), therapy recommendations for cancer patients are discussed. To aid decision-making based on the patient's molecular profile, the research platform cBioPortal was extended based on users' requirements. Additionally, a comprehensive dockerized workflow was developed to support the deployment of cBioPortal and connected services.

i2dash: Creation of Flexible, Interactive, and Web-based Dashboards for Visualization of Omics Data.

Data visualization and interactive data exploration are important aspects of illustrating complex concepts and results from analyses of omics data. A suitable visualization has to be intuitive and accessible. Web-based dashboards have become popular tools for the arrangement, consolidation, and display of such visualizations.