Cell Surface Profiling Using High-Throughput Flow Cytometry: A Platform for Biomarker Discovery and Analysis of Cellular Heterogeneity

Cell surface proteins have a wide range of biological functions, and are often used as lineage-specific markers. Antibodies that recognize cell surface antigens are widely used as research tools, diagnostic markers, and even therapeutic agents. The ability to obtain broad cell surface protein profiles would thus be of great value in a wide range of fields. There are however currently few available methods for high-throughput analysis of large numbers of cell surface proteins. We describe here a high-throughput flow cytometry (HT-FC) platform for rapid analysis of 363 cell surface antigens. Here we demonstrate that HT-FC provides reproducible results, and use the platform to identify cell surface antigens that are influenced by common cell preparation methods. We show that multiple populations within complex samples such as primary tumors can be simultaneously analyzed by co-staining of cells with lineage-specific antibodies, allowing unprecedented depth of analysis of heterogeneous cell populations. Furthermore, standard informatics methods can be used to visualize, cluster and downsample HT-FC data to reveal novel signatures and biomarkers. We show that the cell surface profile provides sufficient molecular information to classify samples from different cancers and tissue types into biologically relevant clusters using unsupervised hierarchical clustering. Finally, we describe the identification of a candidate lineage marker and its subsequent validation. In summary, HT-FC combines the advantages of a high-throughput screen with a detection method that is sensitive, quantitative, highly reproducible, and allows in-depth analysis of heterogeneous samples. The use of commercially available antibodies means that high quality reagents are immediately available for follow-up studies. HT-FC has a wide range of applications, including biomarker discovery, molecular classification of cancers, or identification of novel lineage specific or stem cell markers.     

Apoptotic myocytes generate monocyte chemoattractant protein-1 and mediate macrophage recruitment.

The mechanisms by which apoptotic myocytes are removed by macrophages have not been fully elucidated. This study examined whether apoptotic myocytes actively recruit macrophages by generating monocyte chemoattractant protein-1 (MCP-1) in experiments in vitro and in vivo. Neonatal rat cardiac myocytes were incubated for 4 h in the presence or absence of staurosporine (STS, 0.2-1 mumol/l), an apoptosis inducer. Nuclear staining with DAPI showed that STS induced apoptosis in a dose-dependent fashion. STS (1 mumol/l) caused extensive DNA fragmentation and increased caspase-3 activity compared with a serum-deprived control. MCP-1 mRNA and protein levels in myocytes increased twofold and fourfold, respectively, on STS treatment, and immunochemical staining revealed that apoptotic myocytes expressed MCP-1. To elucidate the role of MCP-1 expressed in apoptotic myocytes to recruit macrophages/monocytes, rat monocytes were incubated in the supernatant of STS-treated myocytes using a trans-well system. The culture medium of STS-treated myocytes recruited monocytes in a MCP-1-dependent fashion. In addition, experiments were performed in vivo using ischemia-reperfused rat hearts. Rats were subjected to 30 min of ligation of the left coronary artery followed by 24 h of reperfusion. After the reperfusion, in the ischemic border myocardium, 17.1 +/- 1.1% of myocytes were terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) positive. Moreover, double staining using the TUNEL technique and immunohistochemistry with MCP-1 antibody showed that 69.8 +/- 3.9% of TUNEL-positive myocytes expressed MCP-1 protein. Concomitantly, activated macrophages infiltrated the areas of apoptosis remarkably. These results suggest that apoptotic myocytes produce MCP-1, which have a critical role in the active recruitment of macrophages.     

Nitric oxide-cGMP pathway is involved in endotoxin-induced contractile dysfunction in rat hearts.

The mechanisms by which endotoxemia causes cardiac depression have not been fully elucidated. The present study examined the involvement of nitric oxide (NO) in this pathology. Rats were infused with lipopolysaccharide (LPS) or saline, and the plasma and myocardial NO(2)(-) and NO(3)(-) (NOx) concentrations were measured before or 3, 6, and 24 h after treatment. The hearts were then immediately isolated and mounted in a Langendorff apparatus, and left ventricular developed pressure (LVDP) was determined before biochemical analysis of the myocardium. LPS injection effected the expression of inducible NO synthase (iNOS) in the myocardium, a marked increase in plasma and myocardial NOx levels, and a significant decline in LVDP compared with saline controls. The LPS-induced NO production and concomitant cardiac depression were most pronounced 6 h after LPS injection and were accompanied by a significant increase in myocardial cGMP content. Myocardial ATP levels were not significantly altered after LPS injection. Significant negative correlation was observed between LVDP and myocardial cGMP content, as well as between LVDP and plasma NOx levels. Aminoguanidine, an inhibitor of iNOS, significantly attenuated the LPS-induced NOx production and contractile dysfunction. Furthermore, 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one, an inhibitor of soluble guanylate cyclase, significantly decreased myocardial cGMP content and attenuated the contractile depression, although aminoguanidine or 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one was not able to completely reverse myocardial dysfunction. Our data suggest that endotoxin-induced contractile dysfunction in rat hearts is associated with NO production by myocardial iNOS and a concomitant increase in myocardial cGMP.     

The cytoprotective properties of prostaglandin E2 against the toxic effects of actinomycin C on embryonic neural retina cells.

Prostaglandins (PGs) have been shown to cytoprotect various tissue types against the toxic effects of many chemicals. The mechanism of this protection is poorly understood, but the involvement of cAMP is often implied. Only one previous study examined nervous tissue and PG protection. The present study was designed to determine if PGE2 affords cytoprotection to a more specific nervous tissue (embryonic neural retina) from the toxicity of actinomycin C (AMC) using a trypan blue exclusion assay. The lowest concentration of PGE2 (2 x 10(-5)M) had no effect, but as the concentration increased (3 x 10(-5)M and 5 x 10(-5)M), PGE2 did afford protection against AMC in a dose dependent fashion. Theophylline treated cells were not protected, suggesting that cAMP may not be the primary mechanism of protection.     

Future Spruce Budworm Outbreak May Create a Carbon Source in Eastern Canadian Forests

Spruce budworm (Choristoneura fumiferana Clem.) is an important and recurrent disturbance throughout spruce (Picea sp.) and balsam fir (Abies balsamea L.) dominated forests of North America. Forest carbon (C) dynamics in these ecosystems are affected during insect outbreaks because millions of square kilometers of forest suffer growth loss and mortality. We tested the hypothesis that a spruce budworm outbreak similar to those in the past could switch a forest from a C sink to a source in the near future. We used a model of ecosystem C to integrate past spruce budworm impact sequences with current forest management data on 106,000 km² of forest in eastern Québec. Spruce budworm-caused mortality decreased stand-level merchantable C stocks by 11–90% and decreased ecosystem C stocks by 2–10% by the end of the simulation. For the first 13 years (2011–2024), adding spruce budworm significantly reduced ecosystem C stock change for the landscape from a sink (4.6 ± 2.7 g C m⁻² y⁻¹ in 2018) to a source (−16.8 ± 3.0 g C m⁻² y⁻¹ in 2018). This result was mostly due to reduced net primary production. The ecosystem stock change was reduced on average by 2 Tg C y⁻¹ for the entire simulated area. This study provides the first estimate that spruce budworm can significantly affect the C sink or source status of a large landscape. These results indicate that reducing spruce budworm impacts on timber may also provide an opportunity to mitigate a C source.     

Humanized Mouse Model to Study Bacterial Infections Targeting the Microvasculature

Neisseria meningitidis causes a severe, frequently fatal sepsis when it enters the human blood stream. Infection leads to extensive damage of the blood vessels resulting in vascular leak, the development of purpuric rashes and eventual tissue necrosis. Studying the pathogenesis of this infection was previously limited by the human specificity of the bacteria, which makes in vivo models difficult. In this protocol, we describe a humanized model for this infection in which human skin, containing dermal microvessels, is grafted onto immunocompromised mice. These vessels anastomose with the mouse circulation while maintaining their human characteristics. Once introduced into this model, N. meningitidis adhere exclusively to the human vessels, resulting in extensive vascular damage, inflammation and in some cases the development of purpuric rash. This protocol describes the grafting, infection and evaluation steps of this model in the context of N. meningitidis infection. The technique may be applied to numerous human specific pathogens that infect the blood stream.     

Damaged forests provide an opportunity to mitigate climate change

British Columbia (BC) forests are estimated to have become a net carbon source in recent years due to tree death and decay caused primarily by mountain pine beetle (MPB) and related post‐harvest slash burning practices. BC forest biomass has also become a major source of wood pellets, exported primarily for bioenergy to Europe, although the sustainability and net carbon emissions of forest bioenergy in general are the subject of current debate. We simulated the temporal carbon balance of BC wood pellets against different reference scenarios for forests affected by MPB in the interior BC timber harvesting area using the Carbon Budget Model of the Canadian Forest Sector (CBM‐CFS3). We evaluated the carbon dynamics for different insect‐mortality levels, at the stand‐ and landscape level, taking into account carbon storage in the ecosystem, wood products and fossil fuel displacement. Our results indicate that current harvesting practices, in which slash is burnt and only sawdust used for pellet production, require between 20–25 years for beetle‐impacted pine and 37–39 years for spruce‐dominated systems to reach pre‐harvest carbon levels (i.e. break‐even) at the stand‐level. Using pellets made from logging slash to replace coal creates immediate net carbon benefits to the atmosphere of 17–21 tonnes C ha^?1, shortening these break‐even times by 9–20 years and resulting in an instant carbon break‐even level on stands most severely impacted by the beetle. Harvesting pine dominated sites for timber while using slash for bioenergy was also found to be more carbon beneficial than a protection reference scenario on both stand‐ and landscape level. However, harvesting stands exclusively for bioenergy resulted in a net carbon source unless the system contained a high proportion of dead trees (>85%). Systems with higher proportions of living trees provide a greater climate change mitigation if used for long lived wood products.     

Peptide mixtures can self-assemble into large amyloid fibers of varying size and morphology

Peptide mixtures spontaneously formed micrometer-sized fibers and ribbons from aqueous solution. Hydrolyzed gliadin produced short, slightly elliptical fibers while hydrolyzed wheat gluten, a mixture of gliadin and glutenin, formed round fibers of similar size. Mixing hydrolyzed gliadin with increasing molar amounts of myoglobin or amylase resulted in longer, wider fibers that transitioned from round to rectangular cross section. Fiber size, morphology, and modulus were controlled by peptide mixture composition. Fourier transform infrared (FT-IR) spectroscopy results showed that peptides experienced α to β transitions forming an elementary cross-β peptide secondary structure, indicative of amyloids. Large fiber formation was observed to be dependent on hydrophobic packing between constituent peptides. A model was developed to show how the fiber morphology was influenced by the peptides in the mixture.