This has resulted in attempts to bridge the gap between over-simplified cell culture approaches and the more meaningful, but inefficient, in vivo models with reproducible ex vivo techniques. invasion was imaged by confocal or epi-fluorescence microscopy and quantified by determining the average cumulative sprout length Baricitinib (LY3009104) per spheroid. The tumor microenvironment was manipulated by treatment of the slice with small molecule inhibitors or using different genetically designed mouse models as donors. Results Both epi-fluorescence Baricitinib (LY3009104) and confocal microscopy were applied to precisely quantify cell invasion in this ex lover vivo approach. Usage of a red-emitting membrane dye in addition to tissue clearing drastically improved epi-fluorescence imaging. Preparation of brain slices from of a genetically designed mouse with a loss of a specific cell surface protein resulted in significantly impaired tumor cell invasion. Furthermore, jasplakinolide treatment of either tumor cells or brain slice significantly reduced tumor cell invasion. Conclusion We present an optimized invasion assay that closely displays in vivo invasion by the implantation of glioma cells into organotypic adult brain slice cultures with a preserved cytoarchitecture. The diversity of applications including manipulation of the tumor cells as well as the microenvironment, permits the investigation of rate limiting factors of cell migration in a reliable context. This model will be a useful Baricitinib (LY3009104) tool for the discovery of the molecular mechanisms underlying glioma cell invasion and, ultimately, the development of novel therapeutic Baricitinib (LY3009104) strategies. Keywords: migration, organotypic brain slices, tumor microenvironment, glioblastoma, three-dimensional invasion assay Background Glioblastoma is the most frequent and malignant main brain tumor, with a median survival of 12C15?months after diagnosis. Despite extensive surgical resection, chemo-, and radiotherapy, glioblastoma is still considered incurable [1C3]. The diffuse infiltration of tumor cells into adjacent healthy brain tissue is a major cause of treatment failure, and so the characterization of signaling pathways and effector molecules that drive glioblastoma invasion is usually a major aim in glioblastoma research (for reviews observe [4, 5]). Most studies of tumor cell migration involve simple and inexpensive two-dimensional methods like the in vitro scratch and Boyden chamber/transwell assays. However, recent studies have shown striking differences in protein functions in two- and three-dimensional contexts [6C8]. Furthermore, in vivo tumor cells are embedded in a three-dimensional matrix consisting of the extracellular matrix (ECM) and multiple cell types, which can all interact with tumor cells. Emerging evidence highlights the substantial impact of these reciprocal interactions within the tumor microenvironment on tumor cell invasion [9], and therefore the requirement for an invasion assay that closely mimics the environmental milieu that glioma cells encounter in vivo. Invading glioblastoma cells follow unique anatomical features called Scherers structures. These include meninges and the subjacent subarachnoid space, blood vessels, myelinated nerve fibers and the extracellular space between neuronal or glial processes in the brain parenchyma [10]. Taking into account that glioblastoma cells migrate along these pre-existing multicellular structures – that cannot just be mimicked by co-cultivation of the relevant cell types – we used organotypic murine brain slice cultures as a three-dimensional invasion matrix. Preserving essential features of the host tissue such as neuronal connectivity, glial-neuronal interactions and an authentic ECM, organotypic brain slice cultures have mainly been used to study developmental, structural and electrophysiological aspects of neuronal circuits (for reviews observe [11, JTK4 12]). Previously, these organotypic cultures have also been presented as a novel tool to examine the migratory behavior of ex lover vivo implanted tumor cells [13C16]. However, the reported methods were based on human brain slices, or the extent of invasion observed was rather low and did not reflect the high infiltration capacity of glioblastoma cells in vivo. Here, we present an optimized and reproducible protocol to assess highly infiltrating glioma cells in an adult murine brain slice. In particular, we show that the usage of a membrane dye with red-shifted fluorescence spectra and tissue clearing results in greatly increased image quality. Finally, we present a selection of application examples, including the treatment of tumor cells or the manipulation of the tumor cell environment by pharmacological inhibitors and the use of genetically altered mice as brain slice donors. Knowledge gained from in vitro and high-throughput methods can be functionally validated by this method, accentuating its value as link between in vitro and animal studies. Methods Preparation of brain slices 6C8?week aged C57Bl/6 wild-type or knockout mice were euthanized, the brain was isolated and the cerebellum removed with a scalpel. Using insect forceps the brain was transferred to the vibratome (Leica VT1200 S) platform and immediately fixed to this device by applying a drop of superglue. The lateral short side of the brain was placed facing the knife, in Baricitinib (LY3009104) order to reduce mechanical stress. 350?m solid.