An improved one-tube RT-PCR protocol for analyzing single-cell gene expression in individual mammalian cells

Target recognition assisted-primer exchange reaction (Ta-PER) for sensitive analysis of p53 gene and its application in analyzing amatoxin-treated samples

Sensitive and reliable detection of the p53 gene plays a significant role in precise cancer targeting and in fundamental research. However, the sensitivity of existing p53 gene detection approaches remains to be improved. Herein, we develop a target recognition assisted-primer exchange reaction (Ta-PER) for sensitive analysis of the p53 gene. Ta-PER was initiated by the recognition of a designed dumbbell structure probe by the p53 gene. In Ta-PER, the primer exchange reaction (PER) was combined with molecular beacon-based chain recycling to construct the signal amplification process. Through integrating target recognition with PER-based signal amplification, Ta-PER was established and exhibited a high detection sensitivity, with a limit of detection as low as 56 fM. In addition, the approach was also used to detect the p53 gene in normal HeLa cells and amatoxin-treated HeLa cells. The high level of the p53 gene in amatoxin-treated HeLa cells, which was approximately 1.67 times higher than that in HeLa cell extract, indicated the apoptosis of cells and suggested the promising prospect of the approach.

RNA cytometry of single-cells using semi-permeable microcapsules

Analytical tools for gene expression profiling of individual cells are critical for studying complex biological systems. However, the techniques enabling rapid measurements of gene expression on thousands of single-cells are lacking. Here, we report a high-throughput RNA cytometry for digital profiling of single-cells isolated in liquid droplets enveloped by a thin semi-permeable membrane (microcapsules). Due to the selective permeability of the membrane, the desirable enzymes and reagents can be loaded, or replaced, in the microcapsule at any given step by simply changing the reaction buffer in which the microcapsules are dispersed. Therefore, complex molecular biology workflows can be readily adapted to conduct nucleic acid analysis on encapsulated mammalian cells, or other biological species. The microcapsules support sequential multi-step enzymatic reactions and remain intact under different biochemical conditions, freezing, thawing, and thermocycling. Combining microcapsules with conventional FACS provides a high-throughput approach for conducting RNA cytometry of individual cells based on their digital gene expression signature.

Determination of elemental distribution and evaluation of elemental concentration in single Saccharomyces cerevisiae cells using single cell-inductively coupled plasma mass spectrometry

Single-cell analysis using inductively coupled plasma mass spectrometry (SC-ICP-MS) is a method to obtain qualitative and quantitative information of the elemental content and distribution of single cells. Six intrinsic target elements were analyzed in yeast cells at different cell growth phases cultured in medium with different phosphorus concentrations (0, 7, 14 mM) to study its effect on cell growth and composition. SC-ICP-MS results were compared with those obtained by the acid digestion and the average ratio was 0.81. The limits of detection of this method were 0.08, 2.54, 12.5, 0.02, 0.02, and 0.08 fg cell-1 for Mg, P, K, Mn, Cu, and Zn, respectively. During the exponential growth phase, the cells exhibited higher elemental contents, wider distribution for most elements, and larger cell size in comparison to the stationary growth phase. Phosphorus-free conditions reduced the average P content in single cells of stationary growth phase from 650 to 80 fg. Phosphorus deficiency led to decreasing intracellular concentrations not only of P but also of K and Cu, and to increasing Zn concentration after 48 h. Mg maintained its concentration at ∼0.11 fg µm-3 and did not change significantly under the three investigated conditions after 48 h. Accordingly, Mg content was successfully used to estimate the intracellular concentration of other intrinsic elements in single yeast cells. SC-ICP-MS is suited to determine target elements in single yeast cells, and allows the study of heterogeneity of cell composition and effects of stressors on the elemental content, distribution, and concentrations of intrinsic elements.

S100a8 silencing attenuates inflammation, oxidative stress and apoptosis in BV2 cells induced by oxygen‑glucose deprivation and reoxygenation by upregulating GAB1 expression

S100a8 serves an important role in cell differentiation and is abnormally expressed in common tumors, but there are few studies on the association between S100a8 and brain I/R injury. The present study aimed to investigate the role of S100a8 in oxygen-glucose deprivation and reoxygenation (OGD/R)-induced BV2 microglia cell injury, and to elucidate the potential underlying molecular mechanisms. BV2 cells were exposed to OGD/R to mimic ischemia/reperfusion (I/R) injury in vitro. S100a8 expression was detected via reverse transcription-quantitative PCR and western blot analyses. Following transfection with short hairpin RNAs targeting S100a8, the levels of inflammatory cytokines and oxidative stress-related factors were determined using commercial kits. Apoptosis was assessed using flow cytometric analysis and the expression levels of apoptosis-related proteins were determined using western blot analysis. Subsequently, the mRNA and protein levels of Grb2-associated binder 1 (GAB1) were assessed following S100a8 silencing. Immunoprecipitation (IP) was performed to verify the association between S100a8 and GAB1. The levels of inflammation, oxidative stress and apoptosis were assessed following GAB1 silencing, along with S100a8 silencing in BV2 cells subjected to OGD/R. The results indicated that exposure to OGD/R markedly upregulated S100a8 expression in BV2 cells. S100a8 silencing inhibited inflammation, oxidative stress and apoptosis, accompanied by changes in the expression of related proteins. The IP assay revealed a strong interaction between GAB1 and S100a8. In addition, GAB1 silencing reversed the inhibitory effects of S100a8 silencing on inflammation, oxidative stress and apoptosis in OGD/R-stimulated BV2 cells. Taken together, the results of the present study demonstrated that S100a8 silencing alleviated inflammation, oxidative stress and the apoptosis of BV2 cells induced by OGD/R, partly by upregulating the expression of GAB1. Thus, these findings may potentially provide a novel direction to develop therapeutic strategies for cerebral I/R injury.

Differential Microglial Morphological Response, TNFα, and Viral Load in Sedentary-like and Active Murine Models After Systemic Non-neurotropic Dengue Virus Infection

Peripheral inflammatory stimuli increase proinflammatory cytokines in the bloodstream and central nervous system and activate microglial cells. Here we tested the hypothesis that contrasting environments mimicking sedentary and active lives would be associated with differential microglial morphological responses, inflammatory cytokines concentration, and virus load in the peripheral blood. For this, mice were maintained either in standard (standard environment) or enriched cages (enriched environment) and then subjected to a single (DENV1) serotype infection. Blood samples from infected animals showed higher viral loads and higher tumor necrosis factor-α (TNFα) mRNA concentrations than control subjects. Using an unbiased stereological sampling approach, we selected 544 microglia from lateral septum for microscopic 3D reconstruction. Morphological complexity contributed most to cluster formation. Infected groups exhibited significant increase in the microglia morphological complexity and number, despite the absence of dengue virus antigens in the brain. Two microglial phenotypes (type I with lower and type II with higher morphological complexity) were found in both infected and control groups. However, microglia from infected mice maintained in enriched environment showed only one morphological phenotype. Two-way ANOVA revealed that environmental changes and infection influenced type-I and II microglial morphologies and number. Environmental enrichment and infection interactions may contribute to microglial morphological change to a point that type-I and II morphological phenotypes could no longer be distinguished in infected mice from enriched environment. Significant linear correlation was found between morphological complexity and TNFα peripheral blood. Our findings demonstrated that sedentary-like and active murine models exhibited differential microglial responses and peripheral inflammation to systemic non-neurotropic infections with DENV1 virus.

Single cell digital polymerase chain reaction on self-priming compartmentalization chip

Single cell analysis provides a new framework for understanding biology and disease, however, an absolute quantification of single cell gene expression still faces many challenges. Microfluidic digital polymerase chain reaction (PCR) provides a unique method to absolutely quantify the single cell gene expression, but only limited devices are developed to analyze a single cell with detection variation. This paper describes a self-priming compartmentalization (SPC) microfluidic digital polymerase chain reaction chip being capable of performing single molecule amplification from single cell. The chip can be used to detect four single cells simultaneously with 85% of sample digitization. With the optimized protocol for the SPC chip, we first tested the ability, precision, and sensitivity of our SPC digital PCR chip by assessing β-actin DNA gene expression in 1, 10, 100, and 1000 cells. And the reproducibility of the SPC chip is evaluated by testing 18S rRNA of single cells with 1.6%-4.6% of coefficient of variation. At last, by detecting the lung cancer related genes, PLAU gene expression of A549 cells at the single cell level, the single cell heterogeneity was demonstrated. So, with the power-free, valve-free SPC chip, the gene copy number of single cells can be quantified absolutely with higher sensitivity, reduced labor time, and reagent. We expect that this chip will enable new studies for biology and disease.

Hierarchical Cluster Analysis of Three-Dimensional Reconstructions of Unbiased Sampled Microglia Shows not Continuous Morphological Changes from Stage 1 to 2 after Multiple Dengue Infections in Callithrix penicillata

It is known that microglial morphology and function are related, but few studies have explored the subtleties of microglial morphological changes in response to specific pathogens. In the present report we quantitated microglia morphological changes in a monkey model of dengue disease with virus CNS invasion. To mimic multiple infections that usually occur in endemic areas, where higher dengue infection incidence and abundant mosquito vectors carrying different serotypes coexist, subjects received once a week subcutaneous injections of DENV3 (genotype III)-infected culture supernatant followed 24 h later by an injection of anti-DENV2 antibody. Control animals received either weekly anti-DENV2 antibodies, or no injections. Brain sections were immunolabeled for DENV3 antigens and IBA-1. Random and systematic microglial samples were taken from the polymorphic layer of dentate gyrus for 3-D reconstructions, where we found intense immunostaining for TNFα and DENV3 virus antigens. We submitted all bi- or multimodal morphological parameters of microglia to hierarchical cluster analysis and found two major morphological phenotypes designated types I and II. Compared to type I (stage 1), type II microglia were more complex; displaying higher number of nodes, processes and trees and larger surface area and volumes (stage 2). Type II microglia were found only in infected monkeys, whereas type I microglia was found in both control and infected subjects. Hierarchical cluster analysis of morphological parameters of 3-D reconstructions of random and systematic selected samples in control and ADE dengue infected monkeys suggests that microglia morphological changes from stage 1 to stage 2 may not be continuous.

Antibody-enhanced dengue disease generates a marked CNS inflammatory response in the black-tufted marmoset Callithrix penicillata

Severe dengue disease is often associated with long-term neurological impairments, but it is unclear what mechanisms are associated with neurological sequelae. Previously, we demonstrated antibody-enhanced dengue disease (ADE) dengue in an immunocompetent mouse model with a dengue virus 2 (DENV2) antibody injection followed by DENV3 virus infection. Here we migrated this ADE model to Callithrix penicillata. To mimic human multiple infections of endemic zones where abundant vectors and multiple serotypes co-exist, three animals received weekly subcutaneous injections of DENV3 (genotype III)-infected supernatant of C6/36 cell cultures, followed 24 h later by anti-DENV2 antibody for 12 weeks. There were six control animals, two of which received weekly anti-DENV2 antibodies, and four further animals received no injections. After multiple infections, brain, liver, and spleen samples were collected and tissue was immunolabeled for DENV3 antigens, ionized calcium binding adapter molecule 1, Ki-67, TNFα. There were marked morphological changes in the microglial population of ADE monkeys characterized by more highly ramified microglial processes, higher numbers of trees and larger surface areas. These changes were associated with intense TNFα-positive immunolabeling. It is unclear why ADE should generate such microglial activation given that IgG does not cross the blood-brain barrier, but this study reveals that in ADE dengue therapy targeting the CNS host response is likely to be important.

Single-cell PCR analysis of murine embryonic stem cells cultured on different substrates highlights heterogeneous expression of stem cell markers

BACKGROUND INFORMATION

In the last few years, recent evidence has revealed that inside an apparently homogeneous cell population there indeed appears to be heterogeneity. This is particularly true for embryonic stem (ES) cells where markers of pluripotency are dynamically expressed within the single cells. In this work, we have designed and tested a new set of primers for multiplex PCR detection of pluripotency markers expression, and have applied it to perform a single-cell analysis in murine ES cells cultured on three different substrates that could play an important role in controlling cell behaviour and fate: (i) mouse embryonic fibroblast (MEF) feeder layer, as the standard method for ES cells culture; (ii) Matrigel coating; (iii) micropatterned hydrogel.

RESULTS

Compared with population analysis, using a single-cell approach, we were able to evaluate not only the number of cells that maintained the expression of a specific gene but, most importantly, how many cells co-expressed different markers. We found that micropatterned hydrogel seems to represent a good alternative to MEF, as the expression of stemness markers is better preserved than in Matrigel culture.

CONCLUSIONS

This single-cell assay allows for the assessment of the stemness maintenance at a single-cell level in terms of gene expression profile, and can be applied in stem cell research to characterise freshly isolated and cultured cells, or to standardise, for instance, the method of culture closely linked to the transcriptional activity and the differentiation potential.

Single-cell analysis reveals early manifestation of cancerous phenotype in pre-malignant esophageal cells

Cellular heterogeneity plays a pivotal role in a variety of functional processes in vivo including carcinogenesis. However, our knowledge about cell-to-cell diversity and how differences in individual cells manifest in alterations at the population level remains very limited mainly due to the lack of appropriate tools enabling studies at the single-cell level. We present a study on changes in cellular heterogeneity in the context of pre-malignant progression in response to hypoxic stress. Utilizing pre-malignant progression of Barrett's esophagus (BE) as a disease model system we studied molecular mechanisms underlying the progression from metaplastic to dysplastic (pre-cancerous) stage. We used newly developed methods enabling measurements of cell-to-cell differences in copy numbers of mitochondrial DNA, expression levels of a set of mitochondrial and nuclear genes involved in hypoxia response pathways, and mitochondrial membrane potential. In contrast to bulk cell studies reported earlier, our study shows significant differences between metaplastic and dysplastic BE cells in both average values and single-cell parameter distributions of mtDNA copy numbers, mitochondrial function, and mRNA expression levels of studied genes. Based on single-cell data analysis, we propose that mitochondria may be one of the key factors in pre-malignant progression in BE.

Laser patterning for the study of MSC cardiogenic differentiation at the single-cell level

Mesenchymal stem cells (MSCs) have been cited as contributors to heart repair through cardiogenic differentiation and multiple cellular interactions, including the paracrine effect, cell fusion, and mechanical and electrical couplings. Due to heart-muscle complexity, progress in the development of knowledge concerning the role of MSCs in cardiac repair is heavily based on MSC-cardiomyocyte coculture. In conventional coculture systems, however, the in vivo cardiac muscle structure, in which rod-shaped cells are connected end-to-end, is not sustained; instead, irregularly shaped cells spread randomly, resulting in randomly distributed cell junctions. Consequently, contact-mediated cell-cell interactions (e.g., the electrical triggering signal and the mechanical contraction wave that propagate through MSC-cardiomyocyte junctions) occur randomly. Thus, the data generated on the beneficial effects of MSCs may be irrelevant to in vivo biological processes. In this study, we explored whether cardiomyocyte alignment, the most important phenotype, is relevant to stem cell cardiogenic differentiation. Here, we report (i) the construction of a laser-patterned, biochip-based, stem cell-cardiomyocyte coculture model with controlled cell alignment; and (ii) single-cell-level data on stem cell cardiogenic differentiation under in vivo-like cardiomyocyte alignment conditions.

Comparison of reverse transcription-quantitative polymerase chain reaction methods and platforms for single cell gene expression analysis

Single cell gene expression analysis can provide insights into development and disease progression by profiling individual cellular responses as opposed to reporting the global average of a population. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the "gold standard" for the quantification of gene expression levels; however, the technical performance of kits and platforms aimed at single cell analysis has not been fully defined in terms of sensitivity and assay comparability. We compared three kits using purification columns (PicoPure) or direct lysis (CellsDirect and Cells-to-CT) combined with a one- or two-step RT-qPCR approach using dilutions of cells and RNA standards to the single cell level. Single cell-level messenger RNA (mRNA) analysis was possible using all three methods, although the precision, linearity, and effect of lysis buffer and cell background differed depending on the approach used. The impact of using a microfluidic qPCR platform versus a standard instrument was investigated for potential variability introduced by preamplification of template or scaling down of the qPCR to nanoliter volumes using laser-dissected single cell samples. The two approaches were found to be comparable. These studies show that accurate gene expression analysis is achievable at the single cell level and highlight the importance of well-validated experimental procedures for low-level mRNA analysis.

Single-cell and regional gene expression analysis in Alzheimer's disease

The clinical manifestations of Alzheimer's disease (AD) are secondary to the substantial loss of cortical neurons. To be effective, neuroprotective strategies will need to target the primary pathogenic mechanisms of AD prior to cell loss. The differences between neurons are largely determined by their specific repertoire of mRNAs. Thus, transcriptomic analyses that do not assume a priori etiological hypotheses are potentially powerful tools that can be used to understand the pathogenesis of complex diseases, including AD. The human brain comprises thousands of different cell types of both neuronal and non-neuronal origins. Information about individual cell-type-specific gene expression patterns will allow for a better understanding of the mechanisms that govern the progression of AD, which may lead to new therapeutic targets for prevention and treatment of the disease. This review provides an overview of the current technologies in use and the developments for single-cell extraction and transcriptome analysis. Recent transcriptome profiling studies on individual AD-afflicted brain cells are also discussed.

Comprehensive qPCR profiling of gene expression in single neuronal cells

A major challenge in neuronal stem cell biology lies in characterization of lineage-specific reprogrammed human neuronal cells, a process that necessitates the use of an assay sensitive to the single-cell level. Single-cell gene profiling can provide definitive evidence regarding the conversion of one cell type into another at a high level of resolution. The protocol we describe uses Fluidigm Biomark dynamic arrays for high-throughput expression profiling from single neuronal cells, assaying up to 96 independent samples with up to 96 quantitative PCR (qPCR) probes (equivalent to 9,216 reactions) in a single experiment, which can be completed within 2-3 d. The protocol enables simple and cost-effective profiling of several hundred transcripts from a single cell, and it could have numerous utilities.