Changes in Global Gene Expression Associated with 3D Structure of Tumors: An Ex Vivo Matrix-Free Mesothelioma Spheroid Model
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Tumor microenvironments present significant barriers to anti-tumor agents. Molecules involved in multicellular tumor microenvironments, however, are difficult to study ex vivo. Here, we generated a matrix-free tumor spheroid model using the NCI-H226 mesothelioma cell line and compared the gene expression profiles of spheroids and monolayers using microarray analysis. Microarray analysis revealed that 142 probe sets were differentially expressed between tumor spheroids and monolayers. Gene ontology analysis revealed that upregulated genes were primarily related to immune response, wound response, lymphocyte stimulation and response to cytokine stimulation, whereas downregulated genes were primarily associated with apoptosis. Among the 142 genes, 27 are located in the membrane and related to biologic processes of cellular movement, cell-to-cell signaling, cellular growth and proliferation and morphology. Western blot analysis validated elevation of MMP2, BAFF/BLyS/TNFSF13B, RANTES/CCL5 and TNFAIP6/TSG-6 protein expression in spheroids as compared to monolayers. Thus, we have reported the first large scale comparison of the transcriptional profiles using an ex vivo matrix-free spheroid model to identify genes specific to the three-dimensional biological structure of tumors. The method described here can be used for gene expression profiling of tumors other than mesothelioma.
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In hepatocellular carcinoma models, monolayers showed enrichment in structural gene expression, whereas spheroids upregulated genes related to metabolism and biosynthesis.
“A similar trend was observed in hepatocellular carcinoma models, where monolayers showed enrichment in structural gene expression, whereas spheroids upregulated genes related to metabolism and biosynthesis [196,197,198].”
From Modeling Tumor Microenvironment Complexity In Vitro: Spheroids as Physiologically Relevant Tumor Models and Strategies for Their Analysis (2025) · cites this paper as [198]
The Results sections on global gene-expression profiling and functional analysis compare mesothelioma spheroids with monolayers, not hepatocellular carcinoma models. Searches for hepatocellular carcinoma and for structural, metabolism, and biosynthesis gene categories found no passage in our copy reporting the claimed pattern in hepatocellular carcinoma. (LLM, conf=0.76)
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- Authors
- Kim, H., Phung, Y., & Ho, M.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Ho, Mitchell
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-06-21
- Volume
- 7
- Issue
- 6
- Pages
- e39556
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3380922
- OpenAlex
- W2051738870
- Cited by
- 68
- References
- 25
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 2 · 2023: 8 · 2022: 3 · 2021: 9 · 2020: 8 · 2019: 4 · 2018: 4 · 2017: 3 · 2016: 9 · 2015: 6 · 2014: 3 · 2013: 1 · 2012: 2
- FWCI
- 1.90
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS ONE (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Mesothelioma Applied Research Foundation
- National Institutes of Health
- National Cancer Institute
- Topics
- Health Sciences › Medicine › Oncology › Cancer Cells and Metastasis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Occupational and environmental lung diseases
- Keywords
- mesothelioma, tumor spheroids, tumor microenvironment, gene expression profiling, MMP-2, CCL5/RANTES, immune response genes, apoptosis, ex vivo tumor model
- MeSH terms
- Humans, Lymphocytes, Mesothelioma, Neoplasms, Wound Healing, Blotting, Western, Signal Transduction, Gene Expression, Spheroids, Cellular, Cell Culture Techniques, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Cell Line, Tumor
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