Construction of a cross-species cell landscape at single-cell level

Individual cells are basic units of life. Despite extensive efforts to characterize the cellular heterogeneity of different organisms, cross-species comparisons of landscape dynamics have not been achieved. Here, we applied single-cell RNA sequencing (scRNA-seq) to map organism-level cell landscapes at multiple life stages for mice, zebrafish and Drosophila. By integrating the comprehensive dataset of > 2.6 million single cells, we constructed a cross-species cell landscape and identified signatures and common pathways that changed throughout the life span. We identified structural inflammation and mitochondrial dysfunction as the most common hallmarks of organism aging, and found that pharmacological activation of mitochondrial metabolism alleviated aging phenotypes in mice. The cross-species cell landscape with other published datasets were stored in an integrated online portal—Cell Landscape. Our work provides a valuable resource for studying lineage development, maturation and aging.     

Effects of glycosylation on heparin binding and antithrombin activation by heparin

Antithrombin (AT), a serine protease inhibitor, circulates in blood in two major isoforms, α and β, which differ in their amount of glycosylation and affinity for heparin. After binding to this glycosaminoglycan, the native AT conformation, relatively inactive as a protease inhibitor, is converted to an activated form. In this process, β‐AT presents the higher affinity for heparin, being suggested as the major AT glycoform inhibitor in vivo. However, either the molecular basis demonstrating the differences in heparin binding to both AT isoforms or the mechanism of its conformational activation are not fully understood. Thus, the present work evaluated the effects of glycosylation and heparin binding on AT structure, function, and dynamics. Based on the obtained data, besides the native and activated forms of AT, an intermediate state, previously proposed to exist between such conformations, was also spontaneously observed in solution. Additionally, Asn135‐linked oligosaccharide caused a bending in AT‐bounded heparin, moving such polysaccharide away from helix D, which supports its reduced affinity for α‐AT. The obtained data supported the proposal of an atomic‐level, solvent and amino acid residues accounting, putative model for the transmission of the conformational signal from heparin binding exosite to β‐sheet A and the reactive center loop, also supporting the identification of differences in such transmission between the serpin glycoforms involving helix D, where the Asn135‐linked oligosaccharide stands. Such intramolecular rearrangements, together with heparin dynamics over AT surface, may support an atomic‐level explanation for the Asn135‐linked glycan influence over heparin binding and AT activation. Proteins 2011; © 2011 Wiley‐Liss, Inc.     

EDTA improves stability of whole blood C-Peptide and insulin to over 24 hours at room temperature

Introduction

C-peptide and insulin measurements in blood provide useful information regarding endogenous insulin secretion. Conflicting evidence on sample stability and handling procedures continue to limit the widespread clinical use of these tests. We assessed the factors that altered the stability of insulin and C-peptide in blood.

Methods

We investigated the impact of preservative type, time to centrifugation, storage conditions and duration of storage on the stability of C-peptide and insulin on three different analytical platforms.

Results

C-peptide was stable for at least 24 hours at room temperature in both centrifuged and whole blood collected in K⁺-EDTA and serum gel tubes, with the exception of whole blood serum gel, which decreased to 78% of baseline at 24 hours, (p = 0.008). Insulin was stable at room temperature for 24 hours in both centrifuged and whole blood collected in K⁺-EDTA tubes. In contrast insulin levels decreased in serum gel tubes both centrifuged and whole blood (66% of baseline, p = 0.01 and 76% of baseline p = 0.01, by 24 hours respectively). C-peptide and insulin remained stable after 6 freeze-thaw cycles.

Conclusions

The stability of C-peptide and insulin in whole blood K⁺-EDTA tubes negates the need to conform to strict sample handling procedures for these assays, greatly increasing their clinical utility.     

Characterization at the single-cell level of naive and primed CD8 T cell cytokine responses

The aim of this study was to characterize differences between naive and primed CD8 T cells. Our results show that (i) naive and primed CD8 T cells display similar activation thresholds, with no direct evidence for a difference in their TCR signals, and (ii) primed cells differ mainly in their capacity to secrete IFN-gamma. A comparison of the two populations at the single-cell level demonstrated that the increased production of IFN-gamma by the primed cell subset is due to a larger proportion of single cells that are able to synthesize this cytokine early following activation. These results indicate that the intrinsic effector capabilities of individual CD8 T cells expressing the same TCR are heterogeneous and that cells with identical antigen specificity but increased effector capacities are generated or selected during the primary response.     

Role of arginine 129 in heparin binding and activation of antithrombin

The contribution of Arg(129) of the serpin, antithrombin, to the mechanism of allosteric activation of the protein by heparin was determined from the effect of mutating this residue to either His or Gln. R129H and R129Q antithrombins bound pentasaccharide and full-length heparins containing the antithrombin recognition sequence with similar large reductions in affinity ranging from 400- to 2500-fold relative to the control serpin, corresponding to a loss of 28-35% of the binding free energy. The salt dependence of pentasaccharide binding showed that the binding defect of the mutant serpin resulted from the loss of approximately 2 ionic interactions, suggesting that Arg(129) binds the pentasaccharide cooperatively with other residues. Rapid kinetic studies showed that the mutation minimally affected the initial low affinity binding of heparin to antithrombin, but greatly affected the subsequent conformational activation of the serpin leading to high affinity heparin binding, although not enough to disfavor activation. Consistent with these findings, the mutant antithrombin was normally activated by heparin for accelerated inhibition of factor Xa and thrombin. These results support an important role for Arg(129) in an induced-fit mechanism of heparin activation of antithrombin wherein conformational activation of the serpin positions Arg(129) and other residues for cooperative interactions with the heparin pentasaccharide so as to lock the serpin in the activated state.     

Comparative analysis of cell lineage differentiation during hepatogenesis in humans and mice at the single-cell transcriptome level

During embryogenesis, the liver is the site of hepatogenesis and hematopoiesis and contains many cell lineages derived from the endoderm and mesoderm. However, the characteristics and developmental programs of many of these cell lineages remain unclear, especially in humans. Here, we performed single-cell RNA sequencing of whole human and mouse fetal livers throughout development. We identified four cell lineage families of endoderm-derived, erythroid, non-erythroid hematopoietic, and mesoderm-derived non-hematopoietic cells, and defined the developmental pathways of the major cell lineage families. In both humans and mice, we identified novel markers of hepatic lineages and an ID3⁺ subpopulation of hepatoblasts as well as verified that hepatoblast differentiation follows the “default-directed” model. Additionally, we found that human but not mouse fetal hepatocytes display heterogeneity associated with expression of metabolism-related genes. We described the developmental process of erythroid progenitor cells during human and mouse hematopoiesis. Moreover, despite the general conservation of cell differentiation programs between species, we observed different cell lineage compositions during hematopoiesis in the human and mouse fetal livers. Taken together, these results reveal the dynamic cell landscape of fetal liver development and illustrate the similarities and differences in liver development between species, providing an extensive resource for inducing various liver cell lineages in vitro.Subject terms: Developmental biology, Stem-cell differentiation, Stem-cell differentiation, Developmental biology     

The kinetics and stimulant dependence of cytokine production by blood and bronchoalveolar lavage T cells evaluated at the single cell level.

We have previously shown that bronchoalveolar lavage (BAL) T cells from human airways predominantly produce interferon gamma (IFN-gamma) and interleukin 2 (IL-2) when stimulated ex vivo. The kinetics of TH1 and TH2 cell cytokine production by T cells from both blood and BAL were studied to establish the optimal time after stimulation either with pharbol myristate (PMA) and ionomycin or with the more physiological stimulus of anti-CD3 for intracellular cytokine detection of IFN-gamma, IL-2, IL-4 and IL-5 in both blood and BAL T cells. The optimal time for positive identification of IL-2 in both blood and BAL was 5 h after PMA/ionomycin stimulation, whereas the first peak for IFN-gamma was found after 5 h in blood but after only 3 h in BAL. T cells from different biological compartments responded differently to each of the stimuli. Whilst anti-CD3 stimulation did not induce TH1 cytokine production in blood T cells, it readily induced both IFN-gamma and IL-2 production in BAL T cells. The kinetics of cytokine production were found to be stimulus dependent. Whilst IL-2 production showed similar kinetics with both stimuli, the kinetics of IFN-gamma production differed between stimuli. We have also examined the effect of five different stimuli on cytokine production by T cells to determine whether different forms of stimulation may selectively stimulate or inhibit different cytokines. Not surprisingly, PMA/ionomycin induced a greater percentage of BAL T cells to produce TH1 cytokines. However, other than modest amounts of the TH2 cytokines IL-4 and IL-5 were not induced by any of the five stimuli.     

Viscoelastic properties of whole blood. Influence of fast sedimenting red blood cell aggregates

Red blood cell (RBC) aggregation is known to be of deciding influence on erythrocyte sedimentation-rate (ESR) and on whole blood viscoelastic properties. The rheological behaviour of blood collected from a control-group with normal ESR is compared to the viscoelastic behaviour of blood collected from two groups with high to very high ESR, whose individuals are suffering from chronical polyarthritis and Morbus Bechterew, respectively. The rheological properties are evaluated by means of an oscillating-flow capillary-rheometer where the viscous (eta') and elastic (eta") component of the complex viscosity (eta) is measured at a constant frequency of 2 Hz. Correcting for the varying hematocrit of the different blood samples according to an exponential equation, the viscoelastic data are found to be elevated in the groups with high ESR. For the viscous properties this is only due to the increase of the plasma viscosity. A correction for the plasma viscosity, however, shows that the viscous properties at low shear- rates (2s-1) are significantly reduced, whereas elastic properties in a range of medium shear-rates (10s-1 to 50s-1) are significantly increased (P less than 0.001, t-test of Student). This result is discussed to be due to the high packing density of the RBC in fast sedimenting aggregates. High packing density reduces the effective volume of the RBC but increases the stiffness of the aggregates.     

Importance of tryptophan 49 of antithrombin in heparin binding and conformational activation

Tryptophan 49 of antithrombin, the primary inhibitor of blood clotting proteinases, has previously been implicated in binding the allosteric activator, heparin, by chemical modification and mutagenesis studies. However, the X-ray cocrystal structure of the antithrombin-pentasaccharide complex shows that Trp49 does not contact the bound saccharide. Here, we provide a detailed thermodynamic and kinetic characterization of heparin binding to a Trp49 to Lys variant of antithrombin and suggest a model for how Trp49 participates in heparin binding and activation. Mutation of Trp49 to Lys resulted in substantial losses of 16-24% in heparin-binding energy at pH 7.4, I 0.15, and 25 degrees C. These losses were due to both the loss of one ionic interaction ( approximately 30%) and the loss of nonionic interactions ( approximately 70%). Rapid kinetics analyses showed that the mutation minimally affected the initial weak binding of heparin to antithrombin or the rate constant for the subsequent conformational activation of the serpin. Rather, the principal effect of the mutation was to increase the rate constant for reversal of the conformational activation step by 70-100-fold, thereby destabilizing the activated conformation. This destabilization could be accounted for by the disruption of a network of interactions involving Trp49, Glu50, and Lys53 of helix A and Ser112 of helix P, which stabilizes the activated conformation.     

Analysis of the binding and postbinding activities of an inducible cloned CTL line at the population and the single-cell level

We have analyzed the binding and lytic properties of a cloned CTL line before and after induction with MLC SN. Functional, specific binding by both effector populations could be demonstrated to occur at 20 degrees C; however, lysis required temperatures greater than or equal to 30 degrees C. Approximately 50% of noninduced cells and 70% of induced cells formed specific conjugates with P815 target cells. Conjugate formation approached maximum levels by 30 min at 20 degrees C for both populations. When low cell concentrations were employed for conjugate formation, the difference between SN-induced cells and noninduced cells was more pronounced. Analysis of the postbinding abilities of these populations at the single-cell level revealed that SN-induced cells were considerably more efficient in lysing attached target cells than were noninduced cells; however, significant lysis by the latter could be demonstrated after long periods. When populations which had intermediate cytolytic activity were compared to optimally induced or noninduced cells, apparent dissociation of the binding and postbinding capacities was observed. Cells harvested 4 days after stimulation with allogeneic cells plus SN displayed maximal binding but low postbinding activities. These results are consistent with the possibility that multiple components of the lytic mechanism are affected following induction and that these components may be asynchronously modulated.     

Importance of lysine 125 for heparin binding and activation of antithrombin

The anticoagulant sulfated polysaccharide, heparin, binds to the plasma coagulation proteinase inhibitor, antithrombin, and activates it by a conformational change that results in a greatly increased rate of inhibition of target proteinases. Lys125 of antithrombin has previously been implicated in this binding by chemical modification and site-directed mutagenesis and by the crystal structure of a complex between antithrombin and a pentasaccharide constituting the antithrombin-binding region of heparin. Replacement of Lys125 with Met or Gln in this work reduced the affinity of antithrombin for full-length heparin or the pentasaccharide by 150-600-fold at I = 0.15, corresponding to a loss of 25-33% of the total binding energy. The affinity decrease was due both to disruption of approximately three ionic interactions, indicating that Lys125 and two other basic residues of antithrombin act cooperatively in binding to heparin, and to weakened nonionic interactions. The mutations caused a 10-17-fold decrease in the affinity of the initial, weak binding step of the two-step mechanism of heparin binding to antithrombin. They also increased the reverse rate constant of the second, conformational change step by 10-50-fold. Lys125 is thus a major heparin-binding residue of antithrombin, contributing an amount of binding energy comparable to that of Arg129, but less energy than Lys114. It is the first residue identified so far that has a critical role in the initial recognition of heparin by antithrombin, but also appreciably stabilizes the heparin-induced activated state of the inhibitor. These effects are exerted by interactions of Lys125 with the nonreducing end of the heparin pentasaccharide.     

Glucocorticoid effects on immune cell activation by staphylococcal exotoxins and lipopolysaccharide

Experiments were conducted to determine the effects of physiologically elevated corticosterone on the activation of macrophages and T cells. These studies find that the elevation of corticosterone does not affect the expression of membrane receptors on macrophages and does not affect the activation of macrophages to produce cytokines. In contrast, elevated corticosterone levels correlate with enhanced T cell proliferation to both mitogens and superantigens.     

Simultaneous detection of miRNA and mRNA at the single-cell level in plant tissues

Detecting the simultaneous presence of a microRNA (miRNA) and a mRNA in a specific tissue can provide support for the prediction that the miRNA regulates the mRNA. Although two such methods have been developed for mammalian tissues, they have a low signal-noise ratio and/or poor resolution at the single-cell level. To overcome these drawbacks, we develop a method that uses sequence-specific miRNA-locked nucleic acid (LNA) and mRNA-LNA probes. Moreover, it augments the detection signal by rolling circle amplification, achieving a high signal-noise ratio at the single-cell level. Dot signals are counted for determining the expression levels of mRNA and miRNA molecules in specific cells. We show a high sequence specificity of our miRNA-LNA probe, revealing that it can discriminate single-base mismatches. Numerical quantification by our method is tested in transgenic rice lines with different gene expression levels. We conduct several applications. First, the spatial expression profiling of osa-miR156 and OsSPL12 in rice leaves reveals their specific expression in mesophyll cells. Second, studying rice and its mutant lines with our method reveals opposite expression patterns of miRNA and its target mRNA in tissues. Third, the dynamic expression profiles of ZmGRF8 and zma-miR396 during maize leaf development provide evidence that zma-miR396 regulates the preferential spatial expression of ZmGRF8 in bundle sheath cells. Finally, our method can be scaled up to simultaneously detect multiple miRNAs and mRNAs in a tissue. Thus, it is a sensitive and versatile technique for studying miRNA regulation of plant tissue development.     

Influence of substitution pattern and cation binding on conformation and activity in heparin derivatives

As model compounds for the biologically important heparan sulfate, eight systematically modified heparin derivatives were studied by synchrotron radiation circular dichroism (SRCD), which is sensitive to uronic acid conformation. Substitution pattern altered uronic acid conformation, even when structural changes were made in adjacent glucosamine residues (e.g. 6-O-desulfation) and did not involve a chromophore. SRCD spectra of these derivatives following conversion to the Na+, K+, Mg2+, Ca2+, Mn2+, Cu2+ and Fe3+ cation forms revealed that almost all substitution/cation combinations resulted in unique spectra, showing that each was structurally distinct. The detailed effects that binding Na+, K+, Mg2+ and Ca2+ ions had on a 2-de-O-sulfated derivative was also studied by NMR, revealing that subtle changes in conformation (by NOE) and flexibility (by T2 measurements) resulted. Conversion to the K+ and Cu2+ ion forms also drastically modified biological activity, from inactive to active, in a cell-based assay of fibroblast growth factor-receptor (FGF2/FGFR1c) signalling and this effect was not reproduced by free cations. These observations could explain the often-contradictory data concerning structure-activity relationships for these derivatives in the literature and, furthermore, argue strongly against the established trend of considering sequence as a complete structural definition. It also provides additional means of modifying the activity of these polysaccharides and suggests a possible additional level of control in biological systems. There are also obvious potential applications for these findings in the biotechnology sphere.     

Protease specificity and heparin binding and activation of recombinant protease nexin I

Structural and functional properties of alpha-protease nexin I (alpha-PNI) expressed in Chinese hamster ovary cells were studied. All three cysteines were in the reduced form, showing that the potential disulfide bridge between residues Cys117 and Cys131 was not formed. Heparin association rate enhancements were from ka = 8.3 x 10(5) to 0.7-1.6 x 10(9) M-1 s-1 for the interaction of PNI with thrombin, from ka = 5.1 x 10(3) to 3.5 x 10(5) M-1 s-1 for interaction with Factor Xa, and from ka = 2.2 x 10(6) to 1.0 x 10(7) M-1 s-1 for interaction with trypsin; there was no rate enhancement of the plasmin interaction (ka = 1.0 x 10(5) M-1 s-1). The minimal heparin pentasaccharide had no effect on these interactions. Cleavage of the reactive center loop of PNI by three different proteases gave the typical stressed to relaxed change in thermal stability, but unlike with antithrombin III, there was no loss of heparin affinity. A similar difference from antithrombin was that PNI-thrombin complexes retained normal heparin affinity. These results are compatible with a role for protease nexin I as a cell-associated thrombin inhibitor that remains bound to the cell surface even after complexing with the protease, as compared with the role of antithrombin III as a circulating inhibitor of thrombin that becomes activated on binding to the microvasculature and is released on complex formation.     

Epidermal solute concentrations and osmolality in barley leaves studied at the single-cell level

The solute relations of the upper epidermis of the third leaf of barley (Hordeum vulgare L. cv. Klaxon) were studied by analysing vacuolar saps extracted from individual cells. Their osmolality (nanolitre osmometry) and the concentrations of K, Na, Ca, Cl, P, S (energy dispersive X-ray analysis) and NO ₃ ^– (microfluorometry) were measured. All of the osmotically important solutes were accounted for. These were K⁺, NO ₃ ^– , Cl^–, and Ca²⁺. The concentration of each solute varied along the leaf blade and changed with leaf age. Calcium in particular increased during leaf ageing, exceeding concentrations of 50 mM. Plants starved of Ca²⁺ during this period accumulated epidermal K⁺ instead of Ca²⁺. Leaf ageing was accompanied by an increase in epidermal osmolalities by about 100 mosmol · kg^–1. When compared to the bulk leaf extract, epidermal cell extracts exhibited significantly higher concentrations of NO ₃ ^– , Cl^– and Ca²⁺, similar concentrations of K⁺ and Na⁺, and lower concentrations of P. In plants subjected to various levels of NaCl stress (up to 200 mM), epidermal concentrations of Cl^– always exceeded those of the bulk extract, while Na⁺ concentrations were similar. Epidermal cells osmotically adjusted to the increase in the external salt concentration.Abbreviations EDX analysis energy dispersive X-ray analysis We wish to thank Paul Richardson, Jeremy Pritchard, Peter Hinde, Eirion Owen and Andrew Davies (Banger) for their helpfull discussion and technical advice. This work was financed by a grant (UR5/ 521) from the Agricultural and Food Research Council.     

Characterization of rhesus macaque natural killer activity against a rhesus-derived target cell line at the single-cell level

Natural killer (NK) cells and NK cell activities in the rhesus macaque have been incompletely characterized. Using a recently developed rhesus NK target cell line with down-regulated MHC-I (B116Lo) as stimulators and FACS-sorted cells as effectors in a 4-h [51Cr]-release assay we showed that the CD3-CD8lo subpopulation is the primary effector population for NK cell-mediated cytolysis. The majority of these cells co-express CD16, CD11b, NKG2D, and NKp46. To evaluate functional activity at the individual cell level, we employed intracellular cytokine staining and a flow cytometric assay for degranulation, based on cell surface CD107a expression. Flow cytometric analysis revealed that a greater proportion of NK cells degranulated than produced cytokines in response to B116Lo stimulation; the frequency of CD107a-expressing cells within the total NK cell population ranging from 5 to 39%. Somewhat surprisingly, we did not find a significant correlation between lysis, measured by [51Cr]-release assay, and the size of the degranulating NK cell population, implying that additional mechanisms may regulate lytic activity. Use of these approaches should facilitate an improved understanding of NK activity in the rhesus macaque.