Methods in molecular biology最新文献

Therapeutic development and research in the neurodegenerative disease field encounters many challenges such as availability of reproducible and scalable cellular model systems that are biologically, physiologically, and pharmacologically relevant. These cellular models must be informative of cellular mechanisms of diseases and predictive for therapeutics efficacy and toxicity testing during drug discovery and development. Neural spheroids fill the gap of cellular models of the brain that are functional, versatile in neural cell type composition, robust, and scalable for high-throughput screening (HTS). We have previously developed a protocol to aggregate pre-determined ratios of differentiated human-induced pluripotent stem cell (hiPSC)-derived neurons and astrocytes in a scaffold-free environment to form 3D brain-region specific spheroids. By mixing different neuronal types, neural spheroids can be used to simulate the neuronal-type heterogeneity of distinct brain regions in vivo, including the prefrontal cortex (PFC) and ventral tegmental area (VTA). Here, we present a detailed description of a method for generating functional brain region-specific spheroids with HTS-compatible assay readout that monitors changes in neural network activity by measuring calcium oscillations. The versatility of the platform is such that these neural spheroids cellular assays are applicable for a wide range of disease modeling, compound validation, and screening and are limited only by the availability of input cells, including neural subtype, disease cells, and immune cells such as microglia.

Stroke is the second leading cause of mortality worldwide, with retinal ischemia as its prominent complication. However, the pathology of retinal ischemia has not been fully elucidated, resulting in a lack of effective treatment. Stem cell therapy has been suggested to be therapeutic in retinal ischemia, with mitochondrial transfer potentially one of the underlying mechanisms. To investigate the mitochondrial function in retinal ischemia and the potential of mitochondrial transfer from mesenchymal stem cells (MSCs), in vivo middle cerebral artery occlusion (MCAO) model and in vitro oxygen-glucose deprivation (OGD) model were utilized in combination. In vivo, rats subjected to MCAO were randomly administered intravenous MSCs or vehicles. Laser doppler was used to measure the blood flow in the brain and the eye, along with immunohistochemical staining for assessing cellular degeneration. In vitro, retinal pigment epithelium (RPE) cells exposed to OGD were cocultured with or without MSCs. Mitochondrial function was measured by mitochondrial respiration, mitochondrial network analysis, mitochondria live cell imaging, and immunocytochemistry. The results demonstrated improved cell survival and restored mitochondrial function following MSC therapy. This chapter details the protocols necessary to produce the in vivo and in vitro models of ischemic stroke along with an assessment of mitochondrial function. Elucidating the mechanisms of mitochondrial transfer will further the knowledge in regenerative medicine and may enable new targets of therapeutics for stroke, especially for retinal ischemia.

Retinal organoids (ROs) derived from human-induced pluripotent stem cells (hiPSCs) serve as relevant models for studying retinal disease pathogenesis, as well as furthering gene therapy efforts. These complex, three-dimensional (3D), multicellular structures recapitulate the development and functionality of the maturing human retina. Here, we describe an in-depth method for the generation of ROs from hiPSCs and evaluate the morphology of these multilayered structures.

In vitro skin aging models represent a valuable tool for the study of age-related pathologies and potential treatments. However, the currently available models do not adequately represent the complex microenvironment of the dermis since they generally focus on cutaneous cellular senescence, rather than the full range of factors that contribute to the aging process, such as structural and compositional alteration of the dermal extracellular matrix. The following protocol describes the extraction and characterization of human adult extracellular matrix scaffolds for use in in vitro aging models.

Aging adversely affects the self-renewal and differentiation capabilities of stem cells, which impairs tissue regeneration as well as the homeostasis. Epigenetic mechanisms, specifically DNA methylation, play a key role in the maintenance of pluripotency in stem cells and regulation of pluripotency-related gene expression. Age-related modifications in methylation patterns could influence the expression of genes critical for stem cell potency maintenance, including transcription factors Nanog and Sox2. The following chapter describes a step-by-step bisulfite sequencing protocol for detection of methylation changes in the aging stem cells and provides valuable insights into the stem cells epigenetic profile. Further, the methodology describes the steps of genomic DNA extraction, bisulfite conversion, real-time PCR amplification, and sequencing for an in-depth view of the epigenetic profile derived from aging stem cells.

Human brain organoids (HBOs) derived from pluripotent stem cells hold great potential for disease modeling and high-throughput compound screening, given their structural and functional resemblance to fetal brain tissues. These organoids can mimic early stages of brain development, offering a valuable in vitro model to study both normal and disordered neurodevelopment. However, current methods of generating HBOs are often low throughput and variable in organoid differentiation and involve lengthy, labor-intensive processes, limiting their broader application in both academic and industrial research. Key challenges include high costs of growth factors, variability in organoid size and function, suboptimal maturation, and manual handling that reduces throughput. Here, we present a standard operating procedure (SOP) for the scalable production of HBOs using a novel pillar plate system that simplifies the spheroid transfer process and allows miniature organoid culture. This method enables the reproducible generation of HBOs without the need for extensive manual intervention, providing a streamlined solution for high-throughput screening (HTS). The resulting assay-ready pillar plate with HBOs is optimized for compound testing, in situ staining, and analysis, offering an efficient platform to advance neurodevelopmental research and therapeutic screening.

Stem cell nanotechnology (SCN) is an important scientific field to guide stem cell-based research of nanoparticles. Currently, nanoparticles (NPs) have a rich spectrum regarding the sources from which they are obtained (metallic, polymeric, etc.), the methods of obtaining them (physical, chemical, biological), and their shape, size, electrical charge, etc. properties. It is also essential to expand green synthesis applications for the use of NPs in the field of biomedical sciences. For this purpose, there is a need to produce NPs using biological sources (plant, microorganism, algae, yeast etc.…), characterization and investigation of their effects on biological activities of stem cells. This process involves long and laborious procedures, and there may be differences in methods between individual laboratories.In this protocol, biofabrication and characterization of ZnO NPs using dried leaves of Camellia sinensis is described. This experimental setup includes conventional and novel methods that can be applied to biofabricate and characterize the NPs and to examine the viability, apoptotic, and necrotic effects on human adipose tissue-derived mesenchymal stem cells (ADMSCs) in vitro.

Spheroid culture systems have been extensively used to model the three-dimensional (3D) behavior of cells in vitro. Traditionally, spheroids consist of a single cell type, limiting their ability to fully recapitulate the complex inter-cellular interactions observed in vivo. Here we describe a protocol for generating cocultured spheroids composed of two distinct cell types, embedded within a 3D extracellular matrix (ECM) to better study cellular interactions. Fluorescent labeling of each cell type enables clear distinction and visualization, facilitating the analysis of cell invasion, proliferation, and behavior within the matrix. This method is particularly suited for studying matrix invasion, an essential process in cancer metastasis, using both fixed and live cell microscopy. The protocol is versatile and can be adapted for various cell types, providing a robust platform for investigating cell-cell interactions in cancer research, tissue remodeling, and drug screening.

In this chapter, we provide a method for silencing target genes in epidermal cells via RNA interference. Specifically, we describe a protocol for transfection-mediated delivery of small interfering RNA oligonucleotides (siRNA). Functional assays are indispensable to characterize the biological consequences of gene knockdowns, and we also provide a method to analyze alterations in cell adhesion properties, consequent to knockdown of genes involved in this process.

Human liver organoids (HLOs) derived from pluripotent stem cells hold potential for disease modeling and high-throughput compound screening due to their architectural and functional resemblance to human liver tissues. However, reproducible, scale-up production of HLOs for high-throughput screening (HTS) presents challenges. These include the high costs of additives and growth factors required for cell differentiation, variability in organoid size and function from batch to batch, suboptimal maturity of HLOs compared to primary hepatocytes, and low assay throughput due to excessive manual processes and the absence of assay-ready plates with HLOs. To address some of these issues, here we present standard operating procedures (SOPs) for the scale-up production of HLOs using a pillar plate through microarray 3D bioprinting. This technology facilitates the rapid, uniform seeding of foregut cells onto the pillar plate, maintaining cell viability and enabling the scale-up generation of HLOs. The assay-ready pillar plate with HLOs is suitable for compound testing, as well as in situ organoid staining and analysis.