PREDECT Protocols for Complex 2D/3D Cultures

PREDECT, a European IMI consortium, has assumed the task to generate robust 2D and 3D culture platforms. Protocols established for 2D and 3D monoculture and stromal coculture models of increasing complexity (spheroid, stirred-tank bioreactor, Matrigel- and collagen-embedded cultures) have been established between six laboratories within academia, biotech, and pharma. These models were tested using three tumor cell lines (MCF7, LNCaP, and NCI-H1437), covering three pathologies (breast, prostate, and lung), but should be readily transferable to other model systems. Fluorescent protein tagged cell lines were used for all platforms, allowing for online measurement of growth curves and drug responses to treatments. All methods, from culture setup to phenotypic characterization and gene expression profiling are described in this chapter.The adaptable methodologies and detailed protocols described here should help to include these models more readily to the drug discovery pipeline.

Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids

In oncology, two-dimensional in-vitro culture models are the standard test beds for the discovery and development of cancer treatments, but in the last decades, evidence emerged that such models have low predictive value for clinical efficacy. Therefore they are increasingly complemented by more physiologically relevant 3D models, such as spheroid micro-tumor cultures. If suitable fluorescent labels are applied, confocal 3D image stacks can characterize the structure of such volumetric cultures and, for example, cell proliferation. However, several issues hamper accurate analysis. In particular, signal attenuation within the tissue of the spheroids prevents the acquisition of a complete image for spheroids over 100 micrometers in diameter. And quantitative analysis of large 3D image data sets is challenging, creating a need for methods which can be applied to large-scale experiments and account for impeding factors. We present a robust, computationally inexpensive 2.5D method for the segmentation of spheroid cultures and for counting proliferating cells within them. The spheroids are assumed to be approximately ellipsoid in shape. They are identified from information present in the Maximum Intensity Projection (MIP) and the corresponding height view, also known as Z-buffer. It alerts the user when potential bias-introducing factors cannot be compensated for and includes a compensation for signal attenuation.

Abstract 1698: Systems pathology for characterization of cancer model systems in a multicenter IMI-PREDECT project

Despite of our increased understanding of cancer biology, the majority of anti-cancer therapies fail at late-stage clinical trials. Thus, there is an urgent need to develop and validate novel preclinical models that could predict drug efficacy in humans. For this purpose, as a part of IMI-PREDECT public-private research consortium, this study describes methodology and infrastructure for characterization and comparison of preclinical models for drug target validation applying a systems pathology approach. Formalin-fixed paraffin-embedded (FFPE) samples from 1050 different in vitro and in vivo models of breast, prostate and lung cancers, as well as 364 clinical tumors from the same origin, were collected from 26 PREDECT collaborators across the EU. We established standard operating procedures for central processing of FFPE samples, including tissue microarray (TMA) construction and immunohistochemistry (IHC) with 15 different antibodies (CK8, Ki67, p-histone H3, ER, AR, p-AKT, p-ERK, p-p38, γH2AX, cleaved caspase 3, p-MET, HIF1α, p63, vimentin, E-cadherin). We constructed 50 TMA blocks, from which sections were cut and stained as well as digitized using whole slide imaging. Images were hosted on a WebMicroscope digital pathology platform and sample metadata on a PREDECT Metadata database (MBase). We developed image analysis methods for the detection and quantification of IHC biomarkers in the 48,800 stained TMA spots. As a proof-of-concept, we compared MCF-7 on several preclinical platforms including cell cultures, xenografts and xenograft tissue slices. Our results of the integrated biomarker phenotype suggest that of the various MCF-7 in vivo and ex vivo complex cell culture models, the xenograft tissue slice model was the most similar model platform to human clinical samples. In summary, we established a systems pathology approach to analyse and compare novel preclinical cancer models with IHC and digital imaging. The intention is that this large database will be made publicly available on the web as images and summary data that could be broadly useful to the community of cancer researchers and drug developers in comparing cancer model systems. The established infrastructure and workflow integrating molecular and digital pathology in a large-scale consortium setting could be applied to quantitative characterisation of consortium data in collaborations similar to PREDECT.

Citation Format: Sami Blom, Yinhai Wang, Tauno Metsalu, Tiina Vesterinen, Teijo Pellinen, Anne Grote, Nina Linder, Jenni Säilä, Katja Välimäki, Ruusu-Maria Kovanen, Outi Monni, Panu Kovanen, Emma Davies, Kristin Stock, Marta Estrada, Georgios Sflomos, Sylvia Grünewald, Catarina Brito, Julia Schüler, Ronald de Hoogt, Cathrin Brisken, Heiko van der Kuip, Wytske van Weerden, Simon Barry, Wolgang Sommergruber, Elizabeth Anderson, Matthias Nees, Juha Klefström, Jaak Vilo, Emmy Verschuren, Ralph Graeser, John Hickman, Johan Lundin, Olli Kallioniemi. Systems pathology for characterization of cancer model systems in a multicenter IMI-PREDECT project. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1698. doi:10.1158/1538-7445.AM2015-1698

Three-dimensional models of cancer for pharmacology and cancer cell biology: capturing tumor complexity in vitro/ex vivo

Cancers are complex and heterogeneous pathological "organs" in a dynamic interplay with their host. Models of human cancer in vitro, used in cancer biology and drug discovery, are generally highly reductionist. These cancer models do not incorporate complexity or heterogeneity. This raises the question as to whether the cancer models' biochemical circuitry (not their genome) represents, with sufficient fidelity, a tumor in situ. Around 95% of new anticancer drugs eventually fail in clinical trial, despite robust indications of activity in existing in vitro pre-clinical models. Innovative models are required that better capture tumor biology. An important feature of all tissues, and tumors, is that cells grow in three dimensions. Advances in generating and characterizing simple and complex (with added stromal components) three-dimensional in vitro models (3D models) are reviewed in this article. The application of stirred bioreactors to permit both scale-up/scale-down of these cancer models and, importantly, methods to permit controlled changes in environment (pH, nutrients, and oxygen) are also described. The challenges of generating thin tumor slices, their utility, and potential advantages and disadvantages are discussed. These in vitro/ex vivo models represent a distinct move to capture the realities of tumor biology in situ, but significant characterization work still remains to be done in order to show that their biochemical circuitry accurately reflects that of a tumor.

Abstract 2023: Complex in vitro and in vivo prostate cancer models for the PREDECT consortium

The failure of many drugs in the clinic - drugs proven to be active in pre-clinical assays - has raised question marks on the predictive power of these models, often based on cell line data. The divergence of these cell lines from the original tumors, and their rapid growth as simple monocultures on 2D plastic were highlighted as potentially causing these issues. Implantation of the cell lines into mice adds complexity to these models, but the crosstalk with mouse stroma also leads to confounding results (eg, HGF, IL-6).

PREDECT, a European consortium funded by the Innovative Medicines Initiative (IMI), has the goal to build and characterise more predictive Oncology model platforms for three pathologies (lung, breast and prostate). Signalling pathways and heterogeneity of these model platforms are compared to each other as well as to primary human tissue using a central TMA-based platform.

For prostate cancer, a 3D tumor growth assay system was established recently using RFP/FLuc-labelled LNCaP, PC346C, or VCaP human prostate cancer cells grown in a matrix of Matrigel, collagen, or a mix of the two, in the presence or absence of GFP/RLuc labelled human stromal cells (WPMY, or an immortalised cancer-associated fibroblast cell line, CAF). Cell densities, ratios, and matrix concentrations/volumes were optimised for cells cultured for 3 weeks. In an approach to improve tumor-stroma crosstalk in vivo, LNCaP cells pre-grown in 3D cultures with or without human stromal cells were implanted orthotopically into SCID mice. Growth of the tumor and stromal cells was monitored by in vivo bioluminescence, and the effect of the co-implantation on the primary tumor and metastasis was analysed via ex-vivo luciferase assays and IHC.

Whereas LNCaP and PC346C cells readily formed spheroids in 3D culture, VCaPs remained as single cells. Growth of VCaPs was facilitated by pre-forming spheroids in vitro, followed by matrix embedding. Addition of stromal cells stimulated growth of not only the tumor, but also the stromal cells in some conditions, as monitored using RFP and GFP live cell imaging. 3D, as well as stromal cell-mediated treatment resistance was observed. Using the fluorescent dyes Hoechst, EdU, and NucView, the proliferative status of individual cells within spheroids could be analysed in situ. Finally, paraffin-embedding of the 3D cultures allowed for TMA analysis and comparison to other models and patient samples.Results will also be shown on the orthotopic growth of LNCaP tumors and the effect of stromal cell co-implantation.

Introducing complexity to cell culture may help to generate more realistic, and thus also more predictive models - in a first step using even standard cell lines.

Citation Format: Suzana Vidic, Norbert Esser, Ronald de Hoogt, Ingrid Verberne, Ira Kogan-Sakin, Yan Stein, Varda Rotter, Michael Barbier, Yolanda Chong, Sabine De Breucker, Karine Smans, Malin Akerfelt, Matthias Nees, Peter King, Ian Hickson, Wytske van Weerden, Ralph Graeser. Complex in vitro and in vivo prostate cancer models for the PREDECT consortium. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2023. doi:10.1158/1538-7445.AM2014-2023

Dlx1 and Rgs5 in the ductus arteriosus: vessel-specific genes identified by transcriptional profiling of laser-capture microdissected endothelial and smooth muscle cells

Closure of the ductus arteriosus (DA) is a crucial step in the transition from fetal to postnatal life. Patent DA is one of the most common cardiovascular anomalies in children with significant clinical consequences especially in premature infants. We aimed to identify genes that specify the DA in the fetus and differentiate it from the aorta. Comparative microarray analysis of laser-captured microdissected endothelial (ECs) and vascular smooth muscle cells (SMCs) from the DA and aorta of fetal rats (embryonic day 18 and 21) identified vessel-specific transcriptional profiles. We found a strong age-dependency of gene expression. Among the genes that were upregulated in the DA the regulator of the G-protein coupled receptor 5 (Rgs5) and the transcription factor distal-less homeobox 1 (Dlx1) exhibited the highest and most significant level of differential expression. The aorta showed a significant preferential expression of the Purkinje cell protein 4 (Pcp4) gene. The results of the microarray analysis were validated by real-time quantitative PCR and immunohistochemistry. Our study confirms vessel-specific transcriptional profiles in ECs and SMCs of rat DA and aorta. Rgs5 and Dlx1 represent novel molecular targets for the regulation of DA maturation and closure.

Translation of a tumor microenvironment mimicking 3D tumor growth co-culture assay platform to high-content screening

For drug discovery, cell-based assays are becoming increasingly complex to mimic more realistically the nature of biological processes and their diversifications in diseases. Multicellular co-cultures embedded in a three-dimensional (3D) matrix have been explored in oncology to more closely approximate the physiology of the human tumor microenvironment. High-content analysis is the ideal technology to characterize these complex biological systems, although running such complex assays at higher throughput is a major endeavor. Here, we report on adapting a 3D tumor co-culture growth assay to automated microscopy, and we compare various imaging platforms (confocal vs. nonconfocal) with correlating automated image analysis solutions to identify optimal conditions and settings for future larger scaled screening campaigns. The optimized protocol has been validated in repeated runs where established anticancer drugs have been evaluated for performance in this innovative assay.

Impaired appetitively as well as aversively motivated behaviors and learning in PDE10A-deficient mice suggest a role for striatal signaling in evaluative salience attribution

Phosphodiesterase 10A (PDE10A) hydrolyzes both cAMP and cGMP, and is a key element in the regulation of medium spiny neuron (MSN) activity in the striatum. In the present report, we investigated the effects of targeted disruption of PDE10A on spatial learning and memory as well as aversive and appetitive conditioning in C57BL/6J mice. Because of its putative role in motivational processes and reward learning, we also determined the expression of the immediate early gene zif268 in striatum and anterior cingulate cortex. Animals showed decreased response rates in scheduled appetitive operant conditioning, as well as impaired aversive conditioning in a passive avoidance task. Morris water maze performance revealed not-motor related spatial learning and memory deficits. Anxiety and social explorative behavior was not affected in PDE10A-deficient mice. Expression of zif268 was increased in striatum and anterior cingulate cortex, which suggests alterations in the neural connections between striatum and anterior cingulate cortex in PDE10A-deficient mice. The changes in behavior and plasticity in these PDE10A-deficient mice were in accordance with the proposed role of striatal MSNs and corticostriatal connections in evaluative salience attribution.

The Hepatocarcinoma Cell Line HepG2 Does Not Express a GHS-R1a-Type Ghrelin Receptor

The interaction of ghrelin, a 28-residue acylated peptide, with the growth hormone secretagogue receptor 1a (GHS-R1a) has been studied mostly in cells expressing a recombinant GHS-R1a. As awareness is growing on the importance to study G protein-coupled receptors in a natural environment, we studied the effect of ghrelin in the human hepatocellular HepG2 cell line because it has been described in literature to respond to ghrelin. Despite extensive efforts, we were not able to confirm mRNA expression of GHS-R1a by reverse transcription PCR, radioligand binding, or ghrelin-induced GHS-R1a receptor activation; therefore, we conclude that HepG2 cells do not express GHS-R1a. On the other hand, we confirmed a modest effect of ghrelin on the up-regulation of IRS-1 phosphorylation, which might suggest the existence of an alternative ghrelin receptor in HepG2 cells.

Alterations in the brain-gut axis underlying visceral chemosensitivity in Nippostrongylus brasiliensis-infected mice

BACKGROUND & AIMS

Visceral hypersensitivity, a hallmark of irritable bowel syndrome, is generally considered to be mechanosensitive in nature and mediated via spinal afferents. Both stress and inflammation are implicated in visceral hypersensitivity, but the underlying molecular mechanisms of visceral hypersensitivity are unknown.

METHODS

Mice were infected with Nippostrongylus brasiliensis (Nb) larvae, exposed to environmental stress and the following separate studies performed 3-4 weeks later. Mesenteric afferent nerve activity was recorded in response to either ramp balloon distention (60 mm Hg), or to an intraluminal perfusion of hydrochloric acid (50 mmol/L), or to octreotide administration (2 micromol/L). Intraperitoneal injection of cholera toxin B-488 identified neurons projecting to the abdominal viscera. Fluorescent neurons in dorsal root and nodose ganglia were isolated using laser-capture microdissection. RNA was hybridized to Affymetrix Mouse whole genome arrays for analysis to evaluate the effects of stress and infection.

RESULTS

In mice previously infected with Nb, there was no change in intestinal afferent mechanosensitivity, but there was an increase in chemosensitive responses to intraluminal hydrochloric acid when compared with control animals. Gene expression profiles in vagal but not spinal visceral sensory neurons were significantly altered in stressed Nb-infected mice. Decreased afferent responses to somatostatin receptor 2 stimulation correlated with lower expression of vagal somatostatin receptor 2 in stressed Nb-infected mice, confirming a link between molecular data and functional sequelae.

CONCLUSIONS

Alterations in the intestinal brain-gut axis, in chemosensitivity but not mechanosensitivity, and through vagal rather than spinal pathways, are implicated in stress-induced postinflammatory visceral hypersensitivity.

Molecular profiling of murine sensory neurons in the nodose and dorsal root ganglia labeled from the peritoneal cavity

Vagal afferent neurons are thought to convey primarily physiological information, whereas spinal afferents transmit noxious signals from the viscera to the central nervous system. To elucidate molecular identities for these different properties, we compared gene expression profiles of neurons located in nodose ganglia (NG) and dorsal root ganglia (DRG) in mice. Intraperitoneal administration of Alexa Fluor-488-conjugated cholera toxin B allowed enrichment for neurons projecting to the viscera. Fluorescent neurons in DRG (from T10 to T13) and NG were isolated using laser-capture microdissection. Gene expression profiles of these afferent neurons, obtained by microarray hybridization, were analyzed using multivariate spectral map analysis, significance analysis of microarrays (SAM) algorithm, and fold-difference filtering. A total of 1,996 genes were differentially expressed in DRG vs. NG, including 41 G protein-coupled receptors and 60 ion channels. Expression profiles obtained on laser-captured neurons were contrasted to those obtained on whole ganglia, demonstrating striking differences and the need for microdissection when studying visceral sensory neurons because of dilution of the signal by somatic sensory neurons. Furthermore, we provide a detailed catalog of all adrenergic and cholinergic, GABA, glutamate, serotonin, and dopamine receptors; voltage-gated potassium, sodium, and calcium channels; and transient receptor potential cation channels present in afferents projecting to the peritoneal cavity. Our genome-wide expression profiling data provide novel insight into molecular signatures that underlie both functional differences and similarities between NG and DRG sensory neurons. Moreover, these findings will offer novel insight into mode of action of pharmacological agents modulating visceral sensation.