Microarrays of lentiviruses for gene function screens in immortalized and primary cells

Here we describe lentivirus-infected cell microarrays for the high-throughput screening of gene function in mammalian cells. To create these arrays, we cultured mammalian cells on glass slides 'printed' with lentiviruses pseudotyped as vesicular stomatitis virus glycoprotein, which encode short hairpin RNA or cDNA. Cells that land on the printed 'features' become infected with lentivirus, creating a living array of stably transduced cell clusters within a monolayer of uninfected cells. The small size of the features of the microarrays (300 microm in diameter) allows high-density spotting of lentivirus, permitting thousands of distinct parallel infections on a single glass slide. Because lentiviruses have a wide cellular tropism, including primary cells, lentivirus-infected cell microarrays can be used as a platform for high-throughput screening in a variety of cell types.     

Mammalian cell-seeded hydrogel microarrays printed via dip-pin technology

Although significant advances have been made in the development of DNA and protein microarrays, less effort has been put toward developing mammalian cell microarrays. Such cellular microarrays may be useful in examining the effects of biological or chemical agents on cells, particularly in drug development and toxicological applications. Here, mammalian cell-seeded hydrogel microarrays were created using two different commercial microarrayers, with four different pin types. Human dermal fibroblasts were used here as a model cell type, seeded within polyethylene glycol-based hydrogels similar to those under investigation as tissue engineering scaffolds, which serve as synthetic extracellular matrices for the cells. Spot sizes of the hydrogels were found to vary with pin type. Multiple touches on a slide following a single dip in the reservoir print solution led to decreasing spot size with each touch; therefore, subsequent microarrays were printed with single touches after a dip. Individual pins of the same type and tip diameter had significantly different spot sizes, likely due to wear of the pins at the tip. However there was high run-to-run reproducibility between subsequent microarrays. Cell viability varied with pin type, and the number of cells per spot varied with cell density in the print solution, as expected.     

The phase behavior of cholesteryl esters in intracellular inclusions.

Differential scanning calorimetry and polarizing light microscopy have been used to investigate kinetic and thermodynamic properties of the phase behavior of cholesteryl ester contained in Fu5AH rat hepatoma cells and J774 murine macrophages. These cultured cells store cholesteryl esters as cytoplasmic inclusions of approximately 1-micron diameter and thus are models of the foam cells characteristic of atherosclerotic plaque. Simple binary mixtures of cholesteryl palmitate and cholesteryl oleate, the predominant cholesteryl esters in cellular inclusions in both cell types serve as models to explain important aspects of the phase behavior of these inclusions. Although inclusions should exist as stable crystals at 37 degrees C under conditions of thermodynamic equilibrium, microscopic examination of cells indicates that inclusions exist as metastable liquid crystals at 37 degrees C for extended periods of time. Using an analytical model based on nucleation theory, we predict that the cholesteryl ester inclusions should be liquid-crystalline in the cytoplasm of living cells. This may not be true either for lysosomal cholesteryl ester or for extracellular cholesteryl ester present in advanced atherosclerotic plaque where fusion of droplets can enhance the possibility of crystallization. The enhanced metastability of the relatively fluid liquid-crystalline state in cellular inclusions should result in increased activity of the neutral cholesteryl ester hydrolase in living cells.     

Quantitative reconstruction of leukocyte subsets using DNA methylation

Background

Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune modulations in virtually any blood sample including archived samples previously precluded from such analysis. Here we assess the performance characteristics and validity of this approach.

Results

Using Illumina Infinium HumanMethylation27 and VeraCode GoldenGate Methylation Assay microarrays, we measure DNA methylation in leukocyte subsets purified from human whole blood and identify cell lineage-specific DNA methylation signatures that distinguish human T cells, B cells, NK cells, monocytes, eosinophils, basophils and neutrophils. We employ a bioinformatics-based approach to quantify these cell types in complex mixtures, including whole blood, using DNA methylation at as few as 20 CpG loci. A reconstruction experiment confirms that the approach could accurately measure the composition of mixtures of human blood leukocyte subsets. Applying the DNA methylation-based approach to quantify the cellular components of human whole blood, we verify its accuracy by direct comparison to gold standard immune quantification methods that utilize physical, optical and proteomic characteristics of the cells. We also demonstrate that the approach is not affected by storage of blood samples, even under conditions prohibiting the use of gold standard methods.

Conclusions

Cell mixture distributions within peripheral blood can be assessed accurately and reliably using DNA methylation. Thus, precise immune cell differential estimates can be reconstructed using only DNA rather than whole cells.     

Protein and cell micropatterning and its integration with micro/nanoparticles assembly

Micropatterning of proteins and cells has become very popular over the past decade due to its importance in the development of biosensors, microarrays, tissue engineering and cellular studies. This article reviews the techniques developed for protein and cell micropatterning and its biomedical applications. The prospect of integrating micro and nanoparticles with protein and cell micropatterning is discussed. The micro/nanoparticles are assembled into patterns and form the substrate for proteins and cell attachment. The assembled particles create a micro or nanotopography, depending on the size of the particles employed. The nonplanar structure can increase the surface area for biomolecules attachment and therefore enhance the sensitivity for detection in biosensors. Furthermore, a nanostructured substrate can influence the conformation and functionality of protein attached to it, while cellular response in terms of morphology, adhesion, proliferation, differentiation, etc. can be affected by a surface expressing micro or nanoscale structures. Proteins and cells tend to lose their normal functions upon attachment to substrate. By recognizing the types of topography that are favourable for preserving proteins and cell behaviour, and integrating it with micropattering will lead to the development of functional protein and cell patterns.     

Arrayed cellular microenvironments for identifying culture and differentiation conditions for stem, primary and rare cell populations

During the development of an organism, cells are exposed to a myriad of signals, structural components and scaffolds, which collectively make up the cellular microenvironment. The majority of current developmental biology studies examine the effect of individual or small subsets of molecules and parameters on cellular behavior, and they consequently fail to explore the complexity of factors to which cells are exposed. Here we describe a technology, referred to as arrayed cellular microenvironments (ACMEs), that allows for a high-throughput examination of the effects of multiple extracellular components in a combinatorial manner on any cell type of interest. We will specifically focus on the application of this technology to human pluripotent stem cells (hPSCs), a population of cells with tremendous therapeutic potential, and one for which growth and differentiation conditions are poorly characterized and far from defined and optimized. A standard ACME screen uses the technologies previously applied to the manufacture and analysis of DNA microarrays, requires standard cell-culture facilities and can be performed from beginning to end within 5-10 days.     

Peptide-MHC Cellular Microarray with Innovative Data Analysis System for Simultaneously Detecting Multiple CD4 T-Cell Responses

Background

Peptide:MHC cellular microarrays have been proposed to simultaneously characterize multiple Ag-specific populations of T cells. The practice of studying immune responses to complicated pathogens with this tool demands extensive knowledge of T cell epitopes and the availability of peptide:MHC complexes for array fabrication as well as a specialized data analysis approach for result interpretation.

Methodology/Principal Findings

We co-immobilized peptide:DR0401 complexes, anti-CD28, anti-CD11a and cytokine capture antibodies on the surface of chamber slides to generate a functional array that was able to detect rare Ag-specific T cell populations from previously primed in vitro T cell cultures. A novel statistical methodology was also developed to facilitate batch processing of raw array-like data into standardized endpoint scores, which linearly correlated with total Ag-specific T cell inputs. Applying these methods to analyze Influenza A viral antigen-specific T cell responses, we not only revealed the most prominent viral epitopes, but also demonstrated the heterogeneity of anti-viral cellular responses in healthy individuals. Applying these methods to examine the insulin producing beta-cell autoantigen specific T cell responses, we observed little difference between autoimmune diabetic patients and healthy individuals, suggesting a more subtle association between diabetes status and peripheral autoreactive T cells.

Conclusions/Significance

The data analysis system is reliable for T cell specificity and functional testing. Peptide:MHC cellular microarrays can be used to obtain multi-parametric results using limited blood samples in a variety of translational settings.     

Profiling of differential protein expression in angiogenin-induced HUVECs using antibody-arrayed ProteoChip

ProteoChip has been developed as a novel protein microarray technology. So far it has been applied in new lead screening and molecular diagnostics and we expect its role to grow in the field of biology. Here, we investigated the application of ProteoChip for the study of differential protein expression profiles in angiogenin-induced human umbilical vein endothelial cells (HUVECs). Antibody microarrays constructed by immobilizing 60 distinct antibodies against signal-transducing proteins on ProteoChip base plates were used to analyze the expression pattern of cell-signaling proteins in HUVECs treated with angiogenin. The antibody microarray approach showed that angiogenin induced the up- and down-regulation of several cellular regulators related with cell proliferation. Changes in the expression of signaling proteins determined by antibody microarray were validated by Western blot analysis. In this experiment, ten up-regulated proteins and six down-regulated proteins were identified and confirmed by immunoblot analysis. Taken together, these data suggest that antibody microarrays using ProteoChip technology can be a powerful tool for high-throughput analysis of proteomes in biological samples.     

Cytodifferentiation in the accessory glands of Tenebrio molitor. XI. Transitional cell types during establishment of pattern

The bean-shaped accessory glands of male Tenebrio consist of a single-layered epithelium which is surrounded by a muscular coat. The epithelial layer, which produces precursors of the wall of the spermatophore, contains eight secretory cell types. Each secretory cell type is in one or more homogenous patches, and discharges granules which form one layer of the eight-layered secretory plug. Maturation begins in cell types 4, 7, and 6 on the last pupal day. A newly identified cell (type 8) in the posterolateral epithelium matures last. Cells of individual types mature in synchrony, and their secretory granules “ripen” in a sequence that is characteristic for each type. As the secretory cells of each patch mature, unusual short-lived cells appear at interfaces between patches. In some cases the secretory granules in these boundary cells have ultrastructural features which are mixtures of the definitive characteristics of granules in adjacent cell types. The transitional cell types disappear at 3–4 days after eclosion. Intermediate cell types are absent in the mature gland and boundaries between the patches are distinct. The transitional cells may form granules of intermediate structural characteristics as a dual response to cellular interaction with adjacent and previously differentiated secretory cells.     

Analysis of Cell Migration within a Three-dimensional Collagen Matrix

The ability to migrate is a hallmark of various cell types and plays a crucial role in several physiological processes, including embryonic development, wound healing, and immune responses. However, cell migration is also a key mechanism in cancer enabling these cancer cells to detach from the primary tumor to start metastatic spreading. Within the past years various cell migration assays have been developed to analyze the migratory behavior of different cell types. Because the locomotory behavior of cells markedly differs between a two-dimensional (2D) and three-dimensional (3D) environment it can be assumed that the analysis of the migration of cells that are embedded within a 3D environment would yield in more significant cell migration data. The advantage of the described 3D collagen matrix migration assay is that cells are embedded within a physiological 3D network of collagen fibers representing the major component of the extracellular matrix. Due to time-lapse video microscopy real cell migration is measured allowing the determination of several migration parameters as well as their alterations in response to pro-migratory factors or inhibitors. Various cell types could be analyzed using this technique, including lymphocytes/leukocytes, stem cells, and tumor cells. Likewise, also cell clusters or spheroids could be embedded within the collagen matrix concomitant with analysis of the emigration of single cells from the cell cluster/ spheroid into the collagen lattice. We conclude that the 3D collagen matrix migration assay is a versatile method to analyze the migration of cells within a physiological-like 3D environment.     

Isolation and characterization of mouse and human esophageal epithelial cells in 3D organotypic culture

This protocol describes the isolation and characterization of mouse and human esophageal epithelial cells and the application of 3D organotypic culture (OTC), a form of tissue engineering. This model system permits the interrogation of mechanisms underlying epithelial-stromal interactions. We provide guidelines for isolating and cultivating several sources of epithelial cells and fibroblasts, as well as genetic manipulation of these cell types, as a prelude to their integration into OTC. The protocol includes a number of important applications, including histology, immunohistochemistry/immunofluorescence, genetic modification of epithelial cells and fibroblasts with retroviral and lentiviral vectors for overexpression of genes or RNA interference strategies, confocal imaging, laser capture microdissection, RNA microarrays of individual cellular compartments and protein-based assays. The OTC (3D) culture protocol takes 15 d to perform.     

Network analysis of epidermal growth factor signaling using integrated genomic, proteomic and phosphorylation data

To understand how integration of multiple data types can help decipher cellular responses at the systems level, we analyzed the mitogenic response of human mammary epithelial cells to epidermal growth factor (EGF) using whole genome microarrays, mass spectrometry-based proteomics and large-scale western blots with over 1000 antibodies. A time course analysis revealed significant differences in the expression of 3172 genes and 596 proteins, including protein phosphorylation changes measured by western blot. Integration of these disparate data types showed that each contributed qualitatively different components to the observed cell response to EGF and that varying degrees of concordance in gene expression and protein abundance measurements could be linked to specific biological processes. Networks inferred from individual data types were relatively limited, whereas networks derived from the integrated data recapitulated the known major cellular responses to EGF and exhibited more highly connected signaling nodes than networks derived from any individual dataset. While cell cycle regulatory pathways were altered as anticipated, we found the most robust response to mitogenic concentrations of EGF was induction of matrix metalloprotease cascades, highlighting the importance of the EGFR system as a regulator of the extracellular environment. These results demonstrate the value of integrating multiple levels of biological information to more accurately reconstruct networks of cellular response.     

Using protein microarrays to study phosphorylation-mediated signal transduction

Unraveling the complexity of cell regulatory systems and monitoring their operations under normal and pathological circumstances is one of the major outstanding biomedical challenges. The phosphoproteome has emerged as a rich source of biomarkers for tracking cell signaling and disease, and many of the kinases that phosphorylate proteins represent attractive targets for drug development. Over 100,000 phosphorylation sites distributed in most of the 23,000 proteins encoded by the human genome have already been identified in a non-targeted fashion by mass-spectrometry. Antibody microarrays permit ultra-sensitive, semi-quantitative measurements of the levels of hundreds of target proteins and their phosphorylation in parallel with specimens from cells and tissues. Conversely, reverse-phase protein microarrays (RPPMs) that are printed with crude cell/tissue lysates allow tracking of a target protein with a probing antibody in hundreds to thousands of cell and tissue samples simultaneously. While more than half a million commercial antibodies are available, the identification of highly specific and potent antibodies for use in microarrays remains a major impediment. Antibody cross-reactivity is an issue for both antibody microarrays and RPPMs. The low abundance of signal transduction proteins and their substoichiometric levels of phosphorylation are also problematic. Finally, non-denaturing conditions used with standard antibody microarrays permit protein complexes, which can produce false positives and false negatives. Changes in the level of an interacting protein may be misinterpreted as alterations in the amount of a target protein or its phosphorylation state. It is critical that leads from both types of microarrays are validated by complementary approaches such as immunoblotting and ELISA. More than a hundred reports have appeared in the scientific literature that have benefited from utilization of antibody and protein lysate microarrays. We have highlighted some of the pioneering works in this field and provided recent examples of their successful deployment as tools for broad-based, targeted proteomics research.     

BEHAVIOR OF SECONDARY SPERMATOGONIA OF THE NEWT, CYNOPS PYRRHOGASTER, IN IN VITRO CULTURE

Several cell types migrated cut from small pieces of newt testes cultivated in vitro. Flat fibroblastic cells migrated out within a few days. Then, secondary spermatogonia, identified by the presence of germ cell-specific substances and by the shape and appearance of their nucleus and subcellular organelles, migrated out over the sheet of fibroblastic cells. Sertoli cells co-migrated with secondary spermatogonia, maintaining a similar cellular arrangement to that of testicular cells in vivo. Mitosis of secondary spermatogonia both in clusters and as single cells was frequent from the third day until about 2 weeks after inoculation. During mitosis, active and periodic rotation of chromosomes was observed. Identification of the cell types and studies on their behavior were performed by electron microscopy and phase contrast microscopy.     

RNAi living-cell microarrays for loss-of-function screens in Drosophila melanogaster cells

RNA interference (RNAi)-mediated loss-of-function screening in Drosophila melanogaster tissue culture cells is a powerful method for identifying the genes underlying cell biological functions and for annotating the fly genome. Here we describe the development of living-cell microarrays for screening large collections of RNAi-inducing double-stranded RNAs (dsRNAs) in Drosophila cells. The features of the microarrays consist of clusters of cells 200 mum in diameter, each with an RNAi-mediated depletion of a specific gene product. Because of the small size of the features, thousands of distinct dsRNAs can be screened on a single chip. The microarrays are suitable for quantitative and high-content cellular phenotyping and, in combination screens, for the identification of genetic suppressors, enhancers and synthetic lethal interactions. We used a prototype cell microarray with 384 different dsRNAs to identify previously unknown genes that affect cell proliferation and morphology, and, in a combination screen, that regulate dAkt/dPKB phosphorylation in the absence of dPTEN expression.     

Cell-biological applications of transfected-cell microarrays

Cell microarrays are a recent addition to the set of tools available for functional genomic studies. Each cell microarray is a slide with thousands of cell clusters that are each transfected with a defined DNA, which directs either the overproduction or the inhibition of a particular gene product. By using a range of detection assays, the phenotypic consequences of perturbing each gene in mammalian cells can be probed in a systematic, high-throughput fashion. Combining well-established methods for cellular investigation with the miniaturization and multiplexing capabilities of microarrays, cell arrays are a versatile tool that can be useful in many cell-biological applications.