Cell Culture Model Systems
The Cell Culture Models Team of VTT explores the broad spectrum of mammalian cell culture technologies, with the aim to provide better and more representative models for cancer drug & drug target discovery, or target validation. Since cancer is a complex disease with an immense intrinsic heterogeneity, we strife for better in vitro models that mimic cell biology and cell-cell interactions in tumor tissues more comprehensively than traditional, reductionist monolayer cell cultures.
2D and 3D Models
The focus of the team is primarily centering on prostate, breast, and head & neck cancers. These solid, epithelial cancers form complex multicellular structures in vivo, and interact with non-tumor cell types such as stromal cells or components of the immune system. Organotypic, three-dimensional (3D) culture of such tumor cells in vitro mimics many of the in vivo properties of solid tumors, such as glandular epithelial differentiation, resulting in the formation of spheroids (prostaspheres and mammaspheres), and acinar structures. More reductionist 2D monolayer cell culture systems do not address many of the complex multicellular processes that shape tumor tissues. Furthermore, we have developed cell culture systems that display pronounced invasive properties, also in an inducible fashion. These will provide unique models to investigate tumor cell invasiveness and cancer metastasis in real time. Furthermore, co-culture models with stromal or other, non-epithelial cell types are currently under development.
The profound understanding of cell biology and the dynamics of key gene networks involved is most critical for how informative cell culture model systems really are. This also defines how well such models truly reflect the properties of solid tumors in vivo, and their value for target validation. A critical component of our activities is therefore the comprehensive characterization of models, e.g. by genome-wide expression analyses, proteomic and phospho-proteomics studies, and the “deep” genetic characterization. We also investigate the role of fundamental components of human cell culture, such as serum and growth factors, on cell biology and phenotype. We characterize the effects of changing cell culture conditions on morphology, epithelial differentiation, gene & protein expression, or cell migration/invasiveness. Based on genome-wide expression studies combined with proteomics, we generate informative gene signatures that reflect critical aspects of tumor biology in vivo, and may have prognostic value for predicting patient e.g. outcome and therapy resistance. Furthermore, we develop and characterize isogenic models for hormone-refractory prostate cancer.
Assays Development & Systems Biology
The purpose of generating better models is closely linked to developing more informative assays that are closer to tumor biology. Truly informative assays will take the effects of tumor cell heterogeneity, cell differentiation, cell-cell contacts, and tumor/host interactions into account, and go beyond simple measurements of cell proliferation and growth. Apart from biomarker expression analyses and cell-biology based assays that measure e.g. apoptosis, we rely mainly on microscopic systems as the primary readout for biologically relevant phenotypic changes. Live cell, real-time imaging using confocal microscopy is combined with automated computational image analysis. The aim here is to quantitatively measure dynamic process such as invasion in 3D cell cultures in collaboration with the Signal and Image Processing Team of VTT. These assays are generally suitable for compound screening and particularly for testing individual or combinatorial effects of bioactive natural compounds (see Plant Biotechnology).
Standardization & Miniaturization
To facilitate the generation of large scale, meaningful and informative data, our cell culture model systems have been miniaturized and standardized. Much effort has been spent to assure reproducibility and robustness of our assays. We have explored dozens of morphological parameters for automated image analysis, followed by stringent statistical evaluation, and developed tools to plot and interpret the data in a meaningful fashion Cost reduction and speeding up the overall throughput of such assays are also important aspects.
Genetics & Epigenetics
Our team is also actively investigating the role of genetic and epigenetic alterations and their role in tumor progression, therapy resistance, and invasiveness. We have developed an siRNA library for functional screening pruposes that covers all known genes with a known epigenetic function or containing a protein domain with certified eigenetic activity. Furthermore, we develop isogenic models to experimentally address aspects such as hormone-refractory prostate cancer, which are characterized on the level of DNA copy-number changes (CGH arrays), gene expression (Illumina bead arrays), and alternative splicing (Affymetrix Exon arrays, Nimblegen arrays; paired end RNA sequencing).