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A new 3D culture system to identify disease-relevant genes in colorectal cancer

ABSTRACT: A new 3D culture system to identify disease-relevant genes in colorectal cancer

PROVIDER: PRJNA307082 | ENA |

REPOSITORIES: ENA

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A new 3D culture system to identify disease-relevant genes in colorectal cancer [Exome-Seq]

Project description:It is increasingly appreciated that properties of cultured epithelial cells differ dramatically in 2D compared to 3D, and the latter more faithfully recapitulates in vivo behavior. By studying a battery of human colorectal cancer (CRC) cell lines in type-1 collagen, we have found that HCA-7 cells form colonies with two distinctive and persistent morphological and functional properties. We observed predominantly single-layered polarized cysts (cystic colonies, CC) and a smaller fraction displaying disorganized solid masses (spiky colonies, SC) that were highly invasive in vivo. Despite overall genomic similarity, CC and SC exhibited distinct and dynamic patterns of gene expression in 3D.

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A new 3D culture system to identify disease-relevant genes in colorectal cancer

Project description:This SuperSeries is composed of the SubSeries listed below.

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Establishment and characterization of a 3D model culture system of primary human ovarian cells: Silk-Ovarioids

Project description:In vitro models that mimic ovaries are instrumental in unraveling physio-pathological mechanisms underlining follicle activation and growth. Three-dimensional (3D) systems that replicate the heterogeneity and cell-cell communication among different ovarian cell types are biologically most relevant. However, such models using human primary ovarian cells have not yet been established and standardized. Here, we developed and characterized long-term cultured 3D models of primary ovarian somatic cells, isolated from normal adult tissues, using Biosilk as a scaffold. We successfully created both cortex- and medulla-derived 3D systems (Silk-Ovarioids). Through transcriptomics, proteomics, and immunostaining, we identified the presence of key ovarian somatic cell types (granulosa, stroma, endothelial and perivascular cells). Notably, the Silk-Ovarioids exhibit the formation of a proangiogenic hypoxic core, as evidenced by the formation of vessel-like structures after 6 weeks of culture. The Silk-Ovarioids have low inter/intra-batch variability and long-term culture stability, highlighting their potential as a robust step towards a bioengineered patient-specific artificial ovary.

2025-08-25 | PXD048710 | Pride

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Project description: Not available

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Project description:Our study developed a novel 3D co-culture system to mimic the in vivo ECM dynamics. Using this system, we examined the interaction between primary dermal papilla cells isolated from patients with neonatal keratinocytes.

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Integrated Genomics Approach to Identify Biologically Relevant Alterations in Fewer Samples.

Project description:Integrated Genomics Approach to Identify Biologically Relevant Alterations in Fewer Samples.

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Integrated Genomics Approach to Identify Biologically Relevant Alterations in Fewer Samples.

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