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Updated: Jul 12, 2025
Molecular Profiling of the Invasive Tumor Microenvironment in a 3-Dimensional Model of Colorectal Cancer Cells and Ex vivo Fibroblasts
Published on: April 29, 2014
Comparative analysis between 2D and 3D colorectal cancer culture models for insights into cellular morphological and
Zaid Nsaif Abbas1, Ali Z Al-Saffar2, Saba Mahdi Jasim3
1Department of Molecular and Medical Biotechnology, College of Biotechnology, Al-Nahrain University, Jadriya, Baghdad, Iraq.
Abstract:
Drug development is a time-consuming and expensive process, given the low success rate of clinical trials. Now, anticancer drug developments have shifted to three-dimensional (3D) models which are more likely to mimic tumor behavior compared to traditional two-dimensional (2D) cultures. A comparative study among different aspects was conducted between 2D and 3D cultures using colorectal cancer (CRC) cell lines, in addition, Formalin-Fixed Paraffin-Embedded (FFPE) block samples of patients with CRC were used for evaluation. Compared to the 2D culture, cells grown in 3D displayed significant (p < 0.01) differences in the pattern of cell proliferation over time, cell death phase profile, expression of tumorgenicity-related genes, and responsiveness to 5-fluorouracil, cisplatin, and doxorubicin. Epigenetically, 3D cultures and FFPE shared the same methylation pattern and microRNA expression, while 2D cells showed elevation in methylation rate and altered microRNA expression. Lastly, transcriptomic study depending on RNA sequencing and thorough bioinformatic analyses showed significant (p-adj < 0.05) dissimilarity in gene expression profile between 2D and 3D cultures involving thousands of genes (up/down-regulated) of multiple pathways for each cell line. Taken together, the study provides insights into variations in cellular morphologies between cells cultured in 2D and 3D models.
Insights
Three-dimensional (3D) cell cultures and patient samples show similar epigenetic patterns, unlike traditional 2D cultures. This highlights 3D models
Area of Science:
- Oncology
- Cell Biology
- Epigenetics
Background:
- Drug development faces challenges with low clinical trial success rates.
- Three-dimensional (3D) cell culture models offer improved tumor mimicry over traditional two-dimensional (2D) cultures.
- Colorectal cancer (CRC) research increasingly utilizes advanced 3D models.
Purpose of the Study:
- To comparatively analyze 2D and 3D colorectal cancer (CRC) cell cultures and Formalin-Fixed Paraffin-Embedded (FFPE) patient samples.
- To investigate differences in cellular behavior, gene expression, and drug response between 2D and 3D models.
- To evaluate epigenetic variations, including methylation and microRNA expression, across different culture models.
Main Methods:
- Comparative analysis of 2D and 3D CRC cell cultures.
- Evaluation of Formalin-Fixed Paraffin-Embedded (FFPE) patient samples.
- Cell proliferation, cell death, gene expression (RNA sequencing), methylation patterns, and microRNA profiling were assessed.
- Bioinformatic analyses were employed for transcriptomic data interpretation.
Main Results:
- 3D cultures exhibited significant differences (p < 0.01) in proliferation, cell death, tumorgenicity gene expression, and drug responsiveness compared to 2D cultures.
- 3D cultures and FFPE samples shared similar methylation patterns and microRNA expression, contrasting with 2D cultures.
- Transcriptomic analysis revealed significant gene expression profile dissimilarities (p-adj < 0.05) between 2D and 3D cultures, impacting multiple pathways.
Conclusions:
- 3D cell culture models more accurately reflect in vivo tumor characteristics than 2D cultures.
- Epigenetic profiles (methylation, microRNA) of 3D cultures align with patient FFPE samples, underscoring their translational relevance.
- Significant transcriptomic variations highlight the importance of choosing appropriate cell culture models for anticancer drug development and research.
