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Transcriptomic Profiling of adherent (2D) and spheroid (3D) cultures of SW480 colorectal cancer cells

ABSTRACT: Cellular behavior and phenotype are profoundly influenced by the culture microenvironment. Traditional two-dimensional (2D) adherent culture systems, while widely used, fail to recapitulate the complex architecture, cell-cell interactions, and cell-matrix contacts that characterize the native tissue environment. In contrast, three-dimensional (3D) culture systems more faithfully mimic in vivo conditions, better reflecting the spatial organization, nutrient and oxygen gradients, and signaling dynamics found within tumors. Notably, 3D spheroid culture has emerged as a valuable approach for enriching stem-like cell populations, which are thought to drive tumor initiation, progression, therapeutic resistance, and recurrence. Understanding the transcriptomic differences between cells cultured under 2D and 3D conditions is therefore critical for interpreting in vitro findings and identifying the molecular programs associated with the stem-like state. In this study, we cultured SW480 colorectal cancer cells under two distinct conditions: conventional 2D adherent culture and 3D matrigel-based spheroid culture. To systematically characterize the transcriptomic differences between these two culture systems, we performed RNA sequencing (RNA-seq) analysis on cells derived from both conditions. This comparative approach enabled us to identify differentially expressed genes and associated biological pathways, providing insight into how the 3D spheroid microenvironment reprograms the transcriptome and potentially enriches for stem-like cellular characteristics in SW480 cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE345612 | GEO | 2026/09/24

REPOSITORIES: GEO

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