Quantitative Single-cell Analysis Research Articles

The multimodality cell segmentation challenge: toward universal solutions.

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in different experimental settings. Here, we present a multimodality cell segmentation benchmark, comprising more than 1,500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging.

Guidelines for application of high-content screening in traditional Chinese medicine: concept, equipment, and troubleshooting

High-content screening (HCS) technology combines automated high-speed imaging hardware and single-cell quantitative analysis. It can greatly accelerate data acquisition in cellular fluorescence imaging and is a powerful research technique in traditional Chinese medicine (TCM). An increasing number of laboratories and platforms, including TCM laboratories, have begun utilizing HCS systems. However, this technology is still in its infancy in TCM research and there is a lack of sufficient experience with the associated concepts, instrument configurations, and analysis methods. To improve the understanding of HCS among researchers in the field of TCM, this paper summarizes the concept of HCS, software and hardware configuration, the overall research process, as well as common problems and related solutions of HCS in TCM research based on our team’s previous research experience, providing several research examples and an outlook on future perspectives, aiming to provide a technical guide for HCS in TCM research.

Using MitER for 3D analysis of mitochondrial morphology and ER contacts.

We have developed an open-source workflow that allows for quantitative single-cell analysis of organelle morphology, distribution, and inter-organelle contacts with an emphasis on the analysis of mitochondria and mitochondria-endoplasmic reticulum (mito-ER) contact sites. As the importance of inter-organelle contacts becomes more widely recognized, there is a concomitant increase in demand for tools to analyze subcellular architecture. Here, we describe a workflow we call MitER (pronounced "mightier"), which allows for automated calculation of organelle morphology, distribution, and inter-organelle contacts from 3D renderings by employing the animation software Blender. We then use MitER to quantify the variations in the mito-ER networks of Saccharomyces cerevisiae, revealing significantly more mito-ER contacts within respiring cells compared to fermenting cells. We then demonstrate how this workflow can be applied to mammalian systems and used to monitor mitochondrial dynamics and inter-organelle contact in time-lapse studies.

Determination of carbon in microplastics and single cells by total consumption microdroplet ICP-TOFMS

Recently, spICP-MS analyses of microplastics have demonstrated that the detection capabilities of ICP-MS are sufficient to determine the size and composition of such materials. However, solution nebulization or microdroplet generation limits the sizes of droplets, microparticles, or cells that can be efficiently introduced into commonly used horizontal ICP-MS configurations. Therefore, we introduced the development of a downward-pointing ICP coupled to a time-of-flight mass spectrometer (ICP-TOFMS), which enables quantitative transport of large microdroplets (diameters up to 90 µm) into the ICP. Here, we report the capabilities of downward ICP-TOFMS for the quantitative analysis of single cells and microplastic particles. For calibration of element mass amount per particle or cell, microdroplets (70 µm diameter) composed of multielement solutions were measured by ICP-TOFMS. Microplastic beads (polystyrene) and spleenocyte cells were then also embedded in microdroplets and measured by ICP-TOFMS with ion optics optimized to determine the signals from 12C+ and other isotopes of interest, including 140Ce, 153Eu, 165Ho, and 175Lu from the REE beads and 31P for the cells. The results achieved using the prototype instrument of a vertical downward-pointing ICP-TOFMS demonstrate that such a plasma configuration is well suited to analyze microplastics and single cells. For single microbead and cell analyses, the critical mass for carbon was 4.8 pg, and the mean determined carbon mass amounts were 14 and 23 pg, respectively. For the microbead analysis, the detected carbon mass corresponds to a particle diameter of 2.93 ± 0.24 µm, which is consistent with the scanning (transmission) electron microscopy–determined diameter of 2.97 ± 0.04 µm. Furthermore, in the analysis of spleenocyte cells, carbon and phosphorus masses were determined to be correlated.Graphical abstract

High content screening miniaturization and single cell imaging of mature human feeder layer-free iPSC-derived neurons.

Human induced pluripotent stem cell (iPSC)-derived neurons are being increasingly used for high content imaging and screening. However, iPSC-derived neuronal differentiation and maturation is time-intensive, often requiring >8 weeks. Unfortunately, the differentiating and maturing iPSC-derived neuronal cultures also tend to migrate and coalesce into ganglion-like clusters making single-cell analysis challenging, especially in miniaturized formats. Using our defined extracellular matrix and low oxygen culturing conditions for the differentiation and maturation of human cortical neurons, we further modified neuronal progenitor cell seeding densities and feeder layer-free culturing conditions in miniaturized formats (i.e., 96 well) to decrease neuronal clustering, enhance single-cell identification and reduce edge effects usually observed after extended neuronal cell culture. Subsequent algorithm development refined capabilities to distinguish and identify single mature neurons, as identified by NeuN expression, from large cellular aggregates, which were excluded from image analysis. Incorporation of astrocyte conditioned medium during differentiation and maturation periods significantly increased the percentage (i.e., ∼10% to ∼30%) of mature neurons (i.e., NeuN+) detected at 4-weeks post-differentiation. Pilot, proof of concept studies using this optimized assay system yielded negligible edge effects and robust Z-factors in population-based as well as image-based neurotoxicity assay formats. Moreover, moxidectin, an FDA-approved drug with documented neurotoxic adverse effects, was identified as a hit using both screening formats. This miniaturized, feeder layer-free format and image analysis algorithm provides a foundational imaging and screening platform, which enables quantitative single-cell analysis of differentiated human neurons.

SPRY4-dependent ERK negative feedback demarcates functional adult stem cells in the male mouse germline†.

Niche-derived growth factors support self-renewal of mouse spermatogonial stem and progenitor cells through ERK MAPK signaling and other pathways. At the same time, dysregulated growth factor-dependent signaling has been associated with loss of stem cell activity and aberrant differentiation. We hypothesized that growth factor signaling through the ERK MAPK pathway in spermatogonial stem cells is tightly regulated within a narrow range through distinct intracellular negative feedback regulators. Evaluation of candidate extracellular signal-regulated kinase (ERK) mitogen-activated protein kinase (MAPK)-responsive genes known to dampen downstream signaling revealed robust induction of specific negative feedback regulators, including Spry4, in cultured mouse spermatogonial stem cells in response to glial cell line-derived neurotrophic factor or fibroblast growth factor 2. Undifferentiated spermatogonia in vivo exhibited high levels of Spry4 mRNA. Quantitative single-cell analysis of ERK MAPK signaling in spermatogonial stem cell cultures revealed both dynamic signaling patterns in response to growth factors and disruption of such effects when Spry4 was ablated, due to dysregulation of ERK MAPK downstream of RAS. Whereas negative feedback regulator expression decreased during differentiation, loss of Spry4 shifted cell fate toward early differentiation with concomitant loss of stem cell activity. Finally, a mouse Spry4 reporter line revealed that the adult spermatogonial stem cell population in vivo is demarcated by strong Spry4 promoter activity. Collectively, our data suggest that negative feedback-dependent regulation of ERK MAPK is critical for preservation of spermatogonial stem cell fate within the mammalian testis.

A sandwiched photoelectrochemical sensor for high-throughput single-cell analysis based on low-toxic and near-infrared AgInS2 microarray

High-throughput single-cell quantitative analysis is becoming increasingly important to elucidate cellular heterogeneity and further understand some related disease mechanisms. Various techniques including mass spectrometry, fluorescence detection, and electrochemiluminescence analysis have made significant progress in this area, but their dilemma is the destruction of cellular activity, the introduction of exogenetic probes and the resulting cellular metabolism perturbation, or the steric hindrance of the cells to the substrate. Here, we develop a non-destructive, probe-free, and hindrance-free photoelectrochemical (PEC) single-cell microsensor. First, a patterned PEC microelectrode with low-toxic and near-infrared AgInS2 microdots is simply fabricated by using a polydimethylsiloxane (PDMS) microstencil, exhibiting high photoelectric efficiency and low S2- detection limit (1.0 nM). Then, a PDMS microwell array is prepared for single cells trapping, matching the size of the microelectrode and with high single-cell occupancy (>93%). Finally, a sealed sandwiching platform is formed by aligning and clamping the two arrays, each microdot contacts with a single cell in one microwell and reacts with the secreted H2S, preventing the neighboring microwell’s cross-contamination, cellular analyte’s dilution, and cell’s steric effect. The different light-addressable recorded photocurrent signals of all single cells directly reflect the 55.6% cell-to-cell differences. This report provides a useful and powerful tool to study single-cell heterogeneity.

Application of Flow Cytometry in the Diagnosis of Bovine Epidemic Disease.

As science and technology continue to advance, the use of flow cytometry is becoming more widespread. It can provide important information about cells in the body by detecting and analysing them, thereby providing a reliable basis for disease diagnosis. In the diagnosis of bovine epidemic diseases, flow cytometry can be used to detect bovine viral diarrhoea, bovine leukaemia, bovine brucellosis, bovine tuberculosis, and other diseases. This paper describes the structure of a flow cytometer (liquid flow system, optical detection system, data storage and analysis system) and its working principles for rapid quantitative analysis and sorting of single cells or biological particles. Additionally, the research progress of flow cytometry in the diagnosis of bovine epidemic diseases was reviewed in order to provide a reference for future research and application of flow cytometry in the diagnosis of bovine epidemic diseases.

Unbiased Quantitative Single-Cell Morphometric Analysis to Identify Microglia Reactivity in Developmental Brain Injury.

Microglia morphological studies have been limited to the process of reviewing the most common characteristics of a group of cells to conclude the likelihood of a "pathological" milieu. We have developed an Imaris-software-based analytical pipeline to address selection and operator biases, enabling use of highly reproducible machine-learning algorithms to quantify at single-cell resolution differences between groups. We hypothesized that this analytical pipeline improved our ability to detect subtle yet important differences between groups. Thus, we studied the temporal changes in Iba1+ microglia-like cell (MCL) populations in the CA1 between P10-P11 and P18-P19 in response to intrauterine growth restriction (IUGR) at E12.5 in mice, chorioamnionitis (chorio) at E18 in rats and neonatal hypoxia-ischemia (HI) at P10 in mice. Sholl and convex hull analyses differentiate stages of maturation of Iba1+ MLCs. At P10-P11, IUGR or HI MLCs were more prominently 'ameboid', while chorio MLCs were hyper-ramified compared to sham. At P18-P19, HI MLCs remained persistently 'ameboid' to 'transitional'. Thus, we conclude that this unbiased analytical pipeline, which can be adjusted to other brain cells (i.e., astrocytes), improves sensitivity to detect previously elusive morphological changes known to promote specific inflammatory milieu and lead to worse outcomes and therapeutic responses.

Cell aggregation is associated with enzyme secretion strategies in marine polysaccharide-degrading bacteria

Polysaccharide breakdown by bacteria requires the activity of enzymes that degrade polymers either intra- or extra-cellularly. The latter mechanism generates a localized pool of breakdown products that are accessible to the enzyme producers themselves as well as to other organisms. Marine bacterial taxa often show marked differences in the production and secretion of degradative enzymes that break down polysaccharides. These differences can have profound effects on the pool of diffusible breakdown products and hence on the ecological dynamics. However, the consequences of differences in enzymatic secretions on cellular growth dynamics and interactions are unclear. Here we study growth dynamics of single cells within populations of marine Vibrionaceae strains that grow on the abundant marine polymer alginate, using microfluidics coupled to quantitative single-cell analysis and mathematical modelling. We find that strains that have low extracellular secretions of alginate lyases aggregate more strongly than strains that secrete high levels of enzymes. One plausible reason for this observation is that low secretors require a higher cellular density to achieve maximal growth rates in comparison with high secretors. Our findings indicate that increased aggregation increases intercellular synergy amongst cells of low-secreting strains. By mathematically modelling the impact of the level of degradative enzyme secretion on the rate of diffusive oligomer loss, we find that enzymatic secretion capability modulates the propensity of cells within clonal populations to cooperate or compete with each other. Our experiments and models demonstrate that enzymatic secretion capabilities can be linked with the propensity of cell aggregation in marine bacteria that extracellularly catabolize polysaccharides.

Quantitative single-cell analysis of Leishmania major amastigote differentiation demonstrates variably extended expression of the lipophosphoglycan (LPG) virulence factor in different host cell types.

Immediately following their deposition into the mammalian host by an infected sand fly vector, Leishmania parasites encounter and are engulfed by a variety of cell types. From there, parasites may transit to other cell types, primarily macrophages or dendritic cells, where they replicate and induce pathology. During this time, Leishmania cells undergo a dramatic transformation from the motile non-replicating metacyclic stage to the non-motile replicative amastigote stage, a differentiative process that can be termed amastigogenesis. To follow this at the single cell level, we identified a suite of experimental 'landmarks' delineating different stages of amastigogenesis qualitatively or quantitatively, including new uses of amastigote-specific markers that showed interesting cellular localizations at the anterior or posterior ends. We compared amastigogenesis in synchronous infections of peritoneal and bone-marrow derived macrophages (PEM, BMM) or dendritic cells (BMDC). Overall, the marker suite expression showed an orderly transition post-infection with similar kinetics between host cell types, with the emergence of several amastigote traits within 12 hours, followed by parasite replication after 24 hours, with parasites in BMM or BMDC initiating DNA replication more slowly. Lipophosphoglycan (LPG) is a Leishmania virulence factor that facilitates metacyclic establishment in host cells but declines in amastigotes. Whereas LPG expression was lost by parasites within PEM by 48 hours, >40% of the parasites infecting BMM or BMDC retained metacyclic-level LPG expression at 72 hr. Thus L. major may prolong LPG expression in different intracellular environments, thereby extending its efficacy in promoting infectivity in situ and during cell-to-cell transfer of parasites expressing this key virulence factor.

Trans-cellular tunnels induced by the fungal pathogen Candida albicans facilitate invasion through successive epithelial cells without host damage

The opportunistic fungal pathogen Candida albicans is normally commensal, residing in the mucosa of most healthy individuals. In susceptible hosts, its filamentous hyphal form can invade epithelial layers leading to superficial or severe systemic infection. Although invasion is mainly intracellular, it causes no apparent damage to host cells at early stages of infection. Here, we investigate C. albicans invasion in vitro using live-cell imaging and the damage-sensitive reporter galectin-3. Quantitative single cell analysis shows that invasion can result in host membrane breaching at different stages and host cell death, or in traversal of host cells without membrane breaching. Membrane labelling and three-dimensional ‘volume’ electron microscopy reveal that hyphae can traverse several host cells within trans-cellular tunnels that are progressively remodelled and may undergo ‘inflations’ linked to host glycogen stores. Thus, C. albicans early invasion of epithelial tissues can lead to either host membrane breaching or trans-cellular tunnelling.

Determination of protoplast growth properties using quantitative single-cell tracking analysis

BackgroundAlthough quantitative single-cell analysis is frequently applied in animal systems, e.g. to identify novel drugs, similar applications on plant single cells are largely missing. We have exploited the applicability of high-throughput microscopic image analysis on plant single cells using tobacco leaf protoplasts, cell-wall free single cells isolated by lytic digestion. Protoplasts regenerate their cell wall within several days after isolation and have the potential to expand and proliferate, generating microcalli and finally whole plants after the application of suitable regeneration conditions.ResultsHigh-throughput automated microscopy coupled with the development of image processing pipelines allowed to quantify various developmental properties of thousands of protoplasts during the initial days following cultivation by immobilization in multi-well-plates. The focus on early protoplast responses allowed to study cell expansion prior to the initiation of proliferation and without the effects of shape-compromising cell walls. We compared growth parameters of wild-type tobacco cells with cells expressing the antiapoptotic protein Bcl2-associated athanogene 4 from Arabidopsis (AtBAG4).ConclusionsAtBAG4-expressing protoplasts showed a higher proportion of cells responding with positive area increases than the wild type and showed increased growth rates as well as increased proliferation rates upon continued cultivation. These features are associated with reported observations on a BAG4-mediated increased resilience to various stress responses and improved cellular survival rates following transformation approaches. Moreover, our single-cell expansion results suggest a BAG4-mediated, cell-independent increase of potassium channel abundance which was hitherto reported for guard cells only. The possibility to explain plant phenotypes with single-cell properties, extracted with the single-cell processing and analysis pipeline developed, allows to envision novel biotechnological screening strategies able to determine improved plant properties via single-cell analysis.

Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma

There is increasing evidence that the spatial organization of cells within the tumor-immune microenvironment (TiME) of solid tumors influences survival and response to therapy in numerous cancer types. Here, we report results and demonstrate the applicability of quantitative single-cell spatial proteomics analyses in the TiME of primary and recurrent human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) tumors. Single-cell compositions of a nine patient, primary and recurrent (n = 18), HNSCC cohort is presented, followed by deeper investigation into the spatial architecture of the TiME and its relationship with clinical variables and progression free survival (PFS). Multiple spatial algorithms were used to quantify the spatial landscapes of immune cells within TiMEs and demonstrate that neoplastic tumor-immune cell spatial compartmentalization, rather than mixing, is associated with longer PFS. Mesenchymal (αSMA+) cellular neighborhoods describe distinct immune landscapes associated with neoplastic tumor-immune compartmentalization and improved patient outcomes. Results from this investigation are concordant with studies in other tumor types, suggesting that trends in TiME cellular heterogeneity and spatial organization may be shared across cancers and may provide prognostic value in multiple cancer types.

Quantitative single-cell analysis of immunofluorescence protein multiplex images illustrates biomarker spatial heterogeneity within breast cancer subtypes

BackgroundThe extent of cellular heterogeneity in breast cancer could have potential impact on diagnosis and long-term outcome. However, pathology evaluation is limited to biomarker immunohistochemical staining and morphology of the bulk cancer. Inter-cellular heterogeneity of biomarkers is not usually assessed. As an initial evaluation of the extent of breast cancer cellular heterogeneity, we conducted quantitative and spatial imaging of Estrogen Receptor (ER), Progesterone Receptor (PR), Epidermal Growth Factor Receptor-2 (HER2), Ki67, TP53, CDKN1A (P21/WAF1), CDKN2A (P16INK4A), CD8 and CD20 of a tissue microarray (TMA) representing subtypes defined by St. Gallen surrogate classification.MethodsQuantitative, single cell-based imaging was conducted using an Immunofluorescence protein multiplexing platform (MxIF) to study protein co-expression signatures and their spatial localization patterns. The range of MxIF intensity values of each protein marker was compared to the respective IHC score for the TMA core. Extent of heterogeneity in spatial neighborhoods was analyzed using co-occurrence matrix and Diversity Index measures.ResultsOn the 101 cores from 59 cases studied, diverse expression levels and distributions were observed in MxIF measures of ER and PR among the hormonal receptor-positive tumor cores. As expected, Luminal A-like cancers exhibit higher proportions of cell groups that co-express ER and PR, while Luminal B-like (HER2-negative) cancers were composed of ER+, PR- groups. Proliferating cells defined by Ki67 positivity were mainly found in groups with PR-negative cells. Triple-Negative Breast Cancer (TNBC) exhibited the highest proliferative fraction and incidence of abnormal P53 and P16 expression. Among the tumors exhibiting P53 overexpression by immunohistochemistry, a group of TNBC was found with much higher MxIF-measured P53 signal intensity compared to HER2+, Luminal B-like and other TNBC cases. Densities of CD8 and CD20 cells were highest in HER2+ cancers. Spatial analysis demonstrated variability in heterogeneity in cellular neighborhoods in the cancer and the tumor microenvironment. ConclusionsProtein marker multiplexing and quantitative image analysis demonstrated marked heterogeneity in protein co-expression signatures and cellular arrangement within each breast cancer subtype. These refined descriptors of biomarker expressions and spatial patterns could be valuable in the development of more informative tools to guide diagnosis and treatment.

Lysosomal subcellular distribution in neurons: Are there synaptic lysosomes?

Despite Alzheimer's disease's first description 114 years ago1 , the mechanisms driving the most common late-onset forms' molecular etiology and neuropathophysiology remain elusive. While considering its elaborate display of pathological hallmarks, recent advances have described synapse loss as the most accurate correlate of disease progression2 . A wide array of data, including insights from human genetics, preclinical AD models, clinical research, and trials, has continuously linked a dysfunctional lysosomal network to pathological aging and disease onset. However, evidence correlating lysosomal dysfunction with early synapse loss is still lacking. Here, we aim to characterize the subcellular distribution of neuronal lysosomes, hypothesizing that these complex organelles localize to both presynaptic and postsynaptic terminals. We have analyzed the subcellular distribution of synaptic and non-synaptic associated LAMP-1+ organelles in our established mature primary hippocampal and cortical mouse neuronal in vitro model and adult mouse brain synaptosomes. We applied quantitative single-cell analysis using ICY and ImageJ software for analytical purposes. Our results show that the subcellular distribution of (endo)lysosomes is highly compartmentalized and dynamic. Based on the % of (endo)lysosomes in the neuronal soma, we documented that roughly 42% of (endo)lysosomes distribute along dendrites and 37% along the axon initial segment (AIS). Remarkably, we report that close to 8% of the total (endo)lysosomal pool was associated with synapsin, a presynaptic compartment marker. We also reveal that about 26% of (endo)lysosomes colocalized with PSD-95, a postsynaptic compartment marker, constituting 60% of the dendritic (endo)lysosomes. Moreover, we found LAMP-1 enriched in mouse brain synaptosomes against nuclear, non-nuclear, non-synaptosomal and membrane fractions. We are currently pushing to characterize these synaptic (endo)lysosomes' function. These results suggest that (endo)lysosomes are present at synapses. In the future we would like to establish whether its dysfunctional activity and trafficking act as a catalyst in the very early stages of synaptic dysfunction in the aging brain, potentially contributing to LOAD etiology and development.

Cisplatin Uptake in Macrophage Subtypes at the Single-Cell Level by LA-ICP-TOFMS Imaging.

A high-throughput laser ablation–inductively coupled plasma–time-of-flight mass spectrometry (LA-ICP-TOFMS) workflow was implemented for quantitative single-cell analysis following cytospin preparation of cells. For the first time, in vitro studies on cisplatin exposure addressed human monocytes and monocyte-derived macrophages (undifferentiated THP-1 monocytic cells, differentiated M0 macrophages, as well as further polarized M1 and M2 phenotypes) at the single-cell level. The models are of particular interest as macrophages comprise the biggest part of immune cells present in the tumor microenvironment and play an important role in modulating tumor growth and progression. The introduced bioimaging workflow proved to be universally applicable to adherent and suspension cell cultures and fit-for-purpose for the quantitative analysis of several hundreds of cells within minutes. Both, cross-validation of the method with single-cell analysis in suspension for THP-1 cells and with LA-ICP-TOFMS analysis of adherent M0 cells grown on chambered glass coverslips, revealed agreeing platinum concentrations at the single-cell level. A high incorporation of cisplatin was observed in M2 macrophages compared to the M0 and M1 macrophage subtypes and the monocyte model, THP-1. The combination with bright-field images and monitoring of highly abundant endogenous elements such as phosphorus and sodium at a high spatial resolution allowed assessing cell size and important morphological cell parameters and thus straightforward control over several cell conditions. This way, apoptotic cells and cell debris as well as doublets or cell clusters could be easily excluded prior to data evaluation without additional staining.

Scaling Up Single-Cell Proteomics

Single-cell tandem MS has enabled analyzing hundreds of single cells per day and quantifying thousands of proteins across the cells. The broad dissemination of these capabilities can empower the dissection of pathophysiological mechanisms in heterogeneous tissues. Key requirements for achieving this goal include robust protocols performed on widely accessible hardware, robust quality controls, community standards, and automated data analysis pipelines that can pinpoint analytical problems and facilitate their timely resolution. Toward meeting these requirements, this perspective outlines both existing resources and outstanding opportunities, such as parallelization, for catalyzing the wide dissemination of quantitative single-cell proteomics analysis that can be scaled up to tens of thousands of single cells. Indeed, simultaneous parallelization of the analysis of peptides and single cells is a promising approach for multiplicative increase in the speed of performing deep and quantitative single-cell proteomics. The community is ready to begin a virtuous cycle of increased adoption fueling the development of more technology and resources for single-cell proteomics that in turn drive broader adoption, scientific discoveries, and clinical applications.

A Cascaded DNA Circuit in Bead Arrays for Quantitative Single-Cell MicroRNA Analysis.

Single-cell microRNA (miRNA) analysis helps people understand the causes of diseases and formulate new disease treatment strategies. However, miRNA from a single cell is usually very rare and requires signal amplification for accurate quantification. Here, to amplify the signal, we constructed the cascaded DNA circuits consisting of catalytic hairpin assembly and hybrid chain reaction into the bead array platform, on which the uniformly distributed beads were adopted for miRNA quantification. After exponential signal amplification, a consistent linear correlation between the percentage of fluorescent beads and the copy number of miRNA was detected. The proposed bead array can achieve ultrahigh sensitivity as low as 60 copies of miR-155 and high specificity for distinguishing single nucleotide differences. This method has been successfully applied to the quantitative detection of miRNA in a single cancer cell. The high sensitivity, programmability, and simple workflow of the bead array chip will give a huge advantage in basic and clinical research.

Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations.

Single-cell image analysis provides a powerful approach for studying cell-to-cell heterogeneity, which is an important attribute of isogenic cell populations, from microbial cultures to individual cells in multicellular organisms. This phenotypic variability must be explained at a mechanistic level if biologists are to fully understand cellular function and address the genotype-to-phenotype relationship. Variability in single-cell phenotypes is obscured by bulk readouts or averaging of phenotypes from individual cells in a sample; thus, single-cell image analysis enables a higher resolution view of cellular function. Here, we consider examples of both small- and large-scale studies carried out with isogenic cell populations assessed by fluorescence microscopy, and we illustrate the advantages, challenges, and the promise of quantitative single-cell image analysis.