Three-dimensional (3D) cancer models are revolutionising research, allowing for the recapitulation of an in vivo-like response through the use of an in vitro system, which is more complex and physiologically relevant than traditional monolayer cultures. Cancers such as ovarian (OvCa) are prone to developing resistance, are often lethal, and stand to benefit greatly from the enhanced modelling emulated by 3D cultures. However, the current models often fall short of the predicted response, where reproducibility is limited owing to the lack of standardised methodology and established protocols. This meta-analysis aims to assess the current scope of 3D OvCa models and the differences in the genetic profiles presented by a vast array of 3D cultures. An analysis of the literature (Pubmed.gov) spanning 2012-2022 was used to identify studies with paired data of 3D and 2D monolayer counterparts in addition to RNA sequencing and microarray data. From the data, 19 cell lines were found to show differential regulation in their gene expression profiles depending on the bio-scaffold (i.e., agarose, collagen, or Matrigel) compared to 2D cell cultures. The top genes differentially expressed in 2D vs. 3D included C3, CXCL1, 2, and 8, IL1B, SLP1, FN1, IL6, DDIT4, PI3, LAMC2, CCL20, MMP1, IFI27, CFB, and ANGPTL4. The top enriched gene sets for 2D vs. 3D included IFN-α and IFN-γ response, TNF-α signalling, IL-6-JAK-STAT3 signalling, angiogenesis, hedgehog signalling, apoptosis, epithelial-mesenchymal transition, hypoxia, and inflammatory response. Our transversal comparison of numerous scaffolds allowed us to highlight the variability that can be induced by these scaffolds in the transcriptional landscape and identify key genes and biological processes that are hallmarks of cancer cells grown in 3D cultures. Future studies are needed to identify which is the most appropriate in vitro/preclinical model to study tumour microenvironments.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10340606PMC
http://dx.doi.org/10.3390/cancers15133350DOI Listing

Publication Analysis

Top Keywords

transcriptional landscape
8
cultures
5
landscape ovarian
4
ovarian cancer
4
cancer cell
4
models
4
cell models
4
models three-dimensional
4
three-dimensional cancer
4
cancer models
4

Similar Publications

Deciphering heat wave effects on wheat grain: focusing on the starch fraction.

Front Plant Sci

December 2024

LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, Portugal.

Wheat is an essential staple food, and its production and grain quality are affected by extreme temperature events. These effects are even more relevant considering the increasing food demand for a growing world population and the predicted augmented frequency of heat waves. This study investigated the impact of simulated heat wave (HW) conditions imposed during grain filling on starch granule characteristics, endosperm ultrastructure, and transcriptomic modulation of genes involved in starch synthesis and degradation.

View Article and Find Full Text PDF

Medulloblastoma (MB) is the most prevalent malignant brain tumor in children, exhibiting clinical and genomic heterogeneity. Of the four major subgroups, Group 3 tumors (MYC-MB), display high levels of MYC and metastasis rates. Despite treatment with surgery, radiation, and chemotherapy, patients with Group 3 MB are more likely to develop aggressive recurrent tumors with poor survival.

View Article and Find Full Text PDF

Quantitative redox proteomics links thioredoxin to heavy ion resistance in Deinococcus radiodurans.

Free Radic Biol Med

December 2024

State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; School of Basic Medicine, Anhui Medical University, Hefei 230032, China; Department of Biomedicine, Medical College, Guizhou University, Guiyang, 550025, China; Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang 110122, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Second Clinical Medicine Collage, Guangzhou Higher Education Mega Center, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China; Hengyang Medical School, University of South China, Hengyang 421001, China. Electronic address:

Heavy ion radiotherapy is an effective treatment for tumors, but its therapeutic efficacy is limited in cancer cells with radiation resistance. Deinococcus radiodurans, well known for its extremely resisting various stresses, was used to explore radioresistant mechanism. We used quantitative redox proteomics to track the dynamic changes in the global redox state after C irradiation.

View Article and Find Full Text PDF

Single-cell analysis of cerebrospinal fluid reveals common features of neuroinflammation.

Cell Rep Med

December 2024

Department of Neurology, Technical University of Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany. Electronic address:

Neuroinflammation is often characterized by immune cell infiltrates in the cerebrospinal fluid (CSF). Here, we apply single-cell RNA sequencing to explore the functional characteristics of these cells in patients with various inflammatory, infectious, and non-inflammatory neurological disorders. We show that CSF is distinct from the peripheral blood in terms of both cellular composition and gene expression.

View Article and Find Full Text PDF

Sucrose is an essential energy substance for tree peony (Paeonia Suffruticosa) floral organ development. However, little is known about the sucrose regulatory network in tree peony. In this study, the promoter sequence of the tree peony sucrose transporter gene PsSUT2 was cloned.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!