Comparative analysis between 2D and 3D colorectal cancer culture models for insights into cellular morphological and transcriptomic variations
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 c...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-10-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-45144-w |
| _version_ | 1797647371454119936 |
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| author | Zaid Nsaif Abbas Ali Z. Al-Saffar Saba Mahdi Jasim Ghassan M. Sulaiman |
| author_facet | Zaid Nsaif Abbas Ali Z. Al-Saffar Saba Mahdi Jasim Ghassan M. Sulaiman |
| author_sort | Zaid Nsaif Abbas |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-11T15:15:16Z |
| format | Article |
| id | doaj.art-f21165992a1b4954ad29b562162b3c88 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-11T15:15:16Z |
| publishDate | 2023-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-f21165992a1b4954ad29b562162b3c882023-10-29T12:23:30ZengNature PortfolioScientific Reports2045-23222023-10-0113111610.1038/s41598-023-45144-wComparative analysis between 2D and 3D colorectal cancer culture models for insights into cellular morphological and transcriptomic variationsZaid Nsaif Abbas0Ali Z. Al-Saffar1Saba Mahdi Jasim2Ghassan M. Sulaiman3Department of Molecular and Medical Biotechnology, College of Biotechnology, Al-Nahrain UniversityDepartment of Molecular and Medical Biotechnology, College of Biotechnology, Al-Nahrain UniversityOncology Teaching Hospital, Medical City, Ministry of HealthDivision of Biotechnology, Department of Applied Sciences, University of TechnologyAbstract 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.https://doi.org/10.1038/s41598-023-45144-w |
| spellingShingle | Zaid Nsaif Abbas Ali Z. Al-Saffar Saba Mahdi Jasim Ghassan M. Sulaiman Comparative analysis between 2D and 3D colorectal cancer culture models for insights into cellular morphological and transcriptomic variations Scientific Reports |
| title | Comparative analysis between 2D and 3D colorectal cancer culture models for insights into cellular morphological and transcriptomic variations |
| title_full | Comparative analysis between 2D and 3D colorectal cancer culture models for insights into cellular morphological and transcriptomic variations |
| title_fullStr | Comparative analysis between 2D and 3D colorectal cancer culture models for insights into cellular morphological and transcriptomic variations |
| title_full_unstemmed | Comparative analysis between 2D and 3D colorectal cancer culture models for insights into cellular morphological and transcriptomic variations |
| title_short | Comparative analysis between 2D and 3D colorectal cancer culture models for insights into cellular morphological and transcriptomic variations |
| title_sort | comparative analysis between 2d and 3d colorectal cancer culture models for insights into cellular morphological and transcriptomic variations |
| url | https://doi.org/10.1038/s41598-023-45144-w |
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