3D microenvironment drives glioma matrisome remodeling and invasive phenotypes - replication data

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The dataset was generated to comprehensively characterize the phenotypic, morphological, mechanical, functional, and molecular properties of human glioblastoma (GBM) cells in two-dimensional (2D) and three-dimensional (3D) culture models. The study focuses on two human GBM cell lines, LN229 and U87, and integrates quantitative imaging, morphometric and biomechanical analyses with functional assays and molecular profiling to investigate cellular plasticity and the functional properties of GBM cells in different culture configurations. The dataset includes: (A) quantitative morphological and morphometric characterization of LN229 and U87 cells and 3D spheroids, including measurements of cell and spheroid size, area, perimeter, shape, and circularity, together with image-based planimetric analysis; (B) atomic force microscopy (AFM)-based characterization of cellular and spheroid mechanical properties, including quantitative assessment of Young’s modulus and cell/spheroid stiffness; (C) functional analysis of cellular behavior, including wound-healing/scratch assays, tubule formation, and 3D spheroid invasion assays; (D) gene expression analysis by quantitative PCR, focusing on genes involved in cell adhesion and cell–matrix interactions; (E) proteomic profiling of LN229 and U87 cells cultured in 2D and 3D conditions, followed by functional annotation and enrichment analysis of differentially abundant proteins, including Gene Ontology-based analysis of biological processes and molecular functions. The proteomic dataset includes analyses of proteins showing increased or decreased abundance and highlights processes related to cell adhesion, extracellular matrix interactions, integrin binding, collagen binding, cell migration, and cell–matrix adhesion. The dataset provides an integrated multi-level view of GBM cellular plasticity, linking changes in cell and spheroid morphology with biomechanical properties, migratory and invasive behavior, extracellular matrix interactions, gene expression, and proteomic alterations. By combining quantitative image analysis with functional, mechanical, and molecular datasets, it enables investigation of the relationships between cellular architecture, mechanical phenotype, adhesion, migration, invasion, and molecular adaptation in 2D versus 3D GBM models. The dataset may serve as a resource for studying glioblastoma cellular heterogeneity, adaptation to different culture configurations, mechanobiology, and the cellular mechanisms underlying plasticity, adhesion, migration, and invasive behavior.

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