Workshops and courses

ELIXIR node event Data-driven modelling of intercellular interactions in the tumour microenvironment

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Date: 25 January 2023

Monocyte-derived macrophages help maintain tissue homeostasis and defend the organism against pathogens. In tumours, recent studies have uncovered complex macrophage populations, including tumour-associated macrophages, which support tumorigenesis through cancer hallmarks such as immunosuppression, angiogenesis or matrix remodelling. In the case of chronic lymphocytic leukaemia, these macrophages are known as nurse-like cells and they protect leukemic cells from spontaneous apoptosis contributing to their chemoresistance. We propose an agent-based model of monocyte differentiation into nurse-like cells upon contact with leukemic B cells in vitro. We performed patient-specific model calibrations using cultures of peripheral blood mononuclear cells from patients. Using our model, we were able to reproduce temporal survival dynamics of cancer cells in a patient-specific manner and to identify patient groups related to distinct macrophage phenotypes. Our results show a potentially important role of phagocytosis in the polarization process of nurse-like cells and in promoting cancer cells' enhanced survival

About the speaker

Dr Vera Pancaldi was trained as a physicist and soon found her way in systems and computational biology. Since 2018 she leads a computational biology team at the Cancer Research Center of Toulouse(CRCT) working on modelling cancer and its interactions with the immune system.       

Her main current focus is understanding the relationship between genome architecture and heterogeneity at various levels and relating heterogeneity in the phenotype of tumour infiltrating immune cells to patient's response to immunotherapy.

Contact: Daniel Thomas Lopez - dthlopez@ebi.ac.uk

Keywords: UniProt: The Universal Protein Resource, Proteins (proteins), Fermentation, Microbial ecosystems webinar, Antimicrobial resistance, Ensembl, DNA & RNA (dna-rna), BLAST, Open Targets Platform, Cross domain (cross-domain), Chemical biology (chemical-biology), Drug discovery, Drug target identification, UniRule, ARBA, Automated annotation, MetaboLights: Metabolomics repository and reference database, Chemical Entities of Biological Interest, ChEBI, Metabolites, Molecular building blocks of life, Human Cell Atlas Data Coordination Platform, Single-cell transcriptomics, HCA data portal, Programmatic access, API, Python, Complex Portal, macromolecular assembly, InterPro, Boolean modelling, Europe PubMed Central, Literature (literature), Open access, Protein Data Bank in Europe - Knowledge Base, 3D structure, AlphaFold Database, DeepMind, Artificial intelligence, AI, Structure prediction, cancer, Boolean, Ensembl Genomes, European Nucleotide Archive, Data archive, Raw sequencing data, RNAcentral, Non-coding RNA, ncRNA, GPU, Data protection, Job dispatcher, Bioimage analysis resource, Accessibility, Missense variation, Biostatistics, Rfam, non-coding RNA, Infernal software, Sequence annotation, Root microbiome, Abiotic stress, land management, Plant genotype, Plant webinar series, HPC, database development, cross-linked databases, Plant database, data infrastructure, Plant breeding, Data standards, data managemnet, data sharing, Hyb-Seq method, Flowering plants, Crop improvement, Pangenomics, Pangenomes, Virtual humans, Drug-target identification, plant-microbe interactions, Spatial transcriptomics, Plant research, Drug targets, Machine learning, Mathematical modelling, plant science, Data integration, plant-environment interaction, Phenotyping, field phenotyping, Deep phenotyping, EOSC-Life, NHGRI-EBI GWAS Catalog, clinical data, genome-wide association, plants, European Variation Archive, EVA, Variant clusters, Variant data annotation, Constraint-based metabolic modelling, UniProt knowledgebase, protein variant impact, disease-associated protein variants, Bioethics, FAIR principles, ELSI, cohort data, translational research, BioModels database, Mathematical modeling, Reproducibity, Systems biology models, workflows, federated analysis, polygenic risk scores, IntAct Molecular Interaction Database, PSICQUIC, IMEx, Complex portal, Agent-based modelling, Macrophages, Tumorigenesis

Organizer: European Bioinformatics Institute (EBI)

Host institutions: EMBL-EBI

Capacity: 500

Event types:

  • Workshops and courses

Scientific topics: Computational biology, Personalised medicine, Oncology

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