Transcriptomic Profiling of 3D Glioblastoma Tumoroids for the Identification of Mechanisms Involved in Anticancer Drug Resistance

Abstract

Background/Aim: Among various types of brain tumors, glioblastoma is the most malignant and highly aggressive brain tumor that possesses a high resistance against anticancer drugs. To understand the underlined mechanisms of tumor drug resistance, a new and more effective research approach is required. The three dimensional (3D) in vitro cell culture models could be a potential approach to study cancer features and biology, as well as screen for anticancer agents due to the close mimicry of the 3D tumor microenvironments. Materials and Methods: With our developed 3D alginate scaffolds, Ilumina RNA-sequencing was used to transcriptomically analyze and compare the gene expression profiles between glioblastoma cells in traditional 2-dimensional (2D) monolayer and in 3D Ca-alginate scaffolds at day 14. To verify the reliability and accuracy of Illumina RNA-Sequencing data, ATP-binding cassette transporter genes were chosen for quantitative real-time polymerase chain reaction) verification. Results: The results showed that 7,411 and 3,915 genes of the 3D glioblastoma were up-regulated and down-regulated, respectively, compared with the 2D-cultured glioblastoma. Furthermore, the Kyoto Encyclopaedia of Genes and Genomes pathway analysis revealed that genes related to the cell cycle and DNA replication were enriched in the group of down-regulated gene. On the other hand, the genes involved in mitogen-activated protein kinase signaling, autophagy, drug metabolism through cytochrome P450, and ATP-binding cassette transporter were found in the up-regulated gene collection. Conclusion: 3D glioblastoma tumoroids might potentially serve as a powerful platform for exploring glioblastoma biology. They can also be valuable in anti-glioblastoma drug screening, as well as the identification of novel molecular targets in clinical treatment of human glioblastoma.

The Normal and Brain Tumor Vasculature: Morphological and Functional Characteristics and Therapeutic Targeting

“…More recently, striking differences in gene expression between 2D and 3D culture of GBM have been reported (Ma et al, 2018) which mirrored the phenotypic differences. This is in agreement with another study (Chaicharoenaudomrung et al, 2020) where GBM cells were cultured in Ca-alginate 3D scaffolds before next-generation sequencing (Illumina), and this uncovered cellular pathways (Map kinase, autophagy, and cell metabolism) for 3D different to 2D cultures. Musah-Eroje and Watson (2019) developed a new 3D model of GBM which seems to more accurately reflect the complexity of the GBM micro-environment.…”

Jejunal Transcriptomic Profiling for Differences in Feed Conversion Ratio in Slow-Growing Chickens

“…RNA-seq library preparation, sequencing, and analysis were carried out by Vishuo Biomedical Ltd. (Bangkok, Thailand), following the procedure of [ 28 ]. For RNA-seq preparation, poly (A) mRNA isolation was performed using the NEBNext ® Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA, USA).…”

Dynamic Interactions between Tumor Cells and Brain Microvascular Endothelial Cells in Glioblastoma

“…Along with the benefits of their low cost and high reproducibility, they overcome several limitations of both the classical 2D cell cultures and in vivo models. In particular, their complex organization makes them more informative than the 2D models, as they recapitulate the GBM milieu without its intrinsic limitations, such as the differences in protein and gene expressions observed in 2D models [133][134][135]. On the other hand, unlike the in vivo models, they are less expensive, less variable and, more importantly, they do not raise ethical problems.…”