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PubMed2004

Microtechnologies and nanotechnologies for single-cell analysis.

Many efforts are currently underway to try and mimic the properties of single cells with the aim of designing chips that are as efficient as cells. However, cells are nature's nanotechnology engineering at the scale of atoms and molecules, and it might be better to envision a microchip that utilizes a single cell as an experimentation platform. A novel, so-called laboratory-in-a-cell concept has been described, where advantage is taken of micro- and nanotechnological tools to enable precise control of the biochemical cellular environment; these tools also offer the possibility to analyse the composition of single cells. Methods for single-cell handling and analysis are being developed and will be required for this concept to progress further.

Animals↗
PubMed2000

A novel method for the simultaneous assessment of natural killer cell conjugate formation and cytotoxicity at the single-cell level by multi-parameter flow cytometry.

A flow cytometric assay for the combined measurement of cell-mediated cytotoxicity and conjugate formation has been developed. Cytolysis is detected by propidium iodide uptake. Target cells, effector cells and conjugates between targets and effectors are separated by post-culture immunophenotyping and their scatter profiles. Pre-assay staining of cells is thus not required. Each cluster of cells can be further examined at the single-cell level by simultaneously performed additional immunophenotyping. Two applications were established: the assessment of NK cell activity against K562 cells and the evaluation of LAK cell cytotoxicity against both K562 and Daudi cells. A comparison with the standard 51Cr release assay for the detection of NK cytotoxicity showed that the two assays were strongly correlated, but the sensitivity of the flow cytometric assay was significantly higher.

Chromium Radioisotopes↗
PubMed1979

Dissociation of adult mammalian heart into single cell suspension: an ultrastructural study.

Adult rat heart was dissociated into a single cell suspension by a perfusion technique which used 0.05% collagenase and 0.1% hyaluronidase in Krebs-Ringer phosphate buffer (KRP). The non-muscle cells of the suspension were separated from the myocytes by centrifugation through 3% Ficoll solution in KRP with 0.01 mM Ca2+. An approximately 90% pure suspension of isolated single muscle cells was obtained with this method. The effects of the successive steps in the dissociation procedure on the ultrastructure of the heart were studied by scanning and transmission electron microscopy. After 30 minutes of enzyme digestion, dissociation of the inner endothelial lining of the ventricle into single cells or small groups of cells became apparent. In addition, the underlying cardiac skeleton began to disintegrate and linear arrays of cardiac muscle cells were observed. After 45 minutes of enzyme digestion the number of released single cells was higher because of the separation of intercalated discs. The majority of non-muscle cells were by now dissociated from the surfaces of muscle cells. Widening of the lateral intercellular spaces between the myocardial cells was associated with separation of desmosomes. In some regions of the heart, intact desmosomes, fasciae adherentes and gap junctions were observed even though lateral intercellular spaces had widened greatly. The majority of myocardial cells had become separated from one another after 60 minutes of enzyme digestion. Separation of gap junctional sites took place in two ways: (1) by 'unzipping' them through enzyme action; (2) by tearing them mechanically. Gap junction remnants were sometimes observed in a vesiculated state within the cell. The dissociation of the heart was ineffective when perfused with media containing 1.0 or 2 mM Ca2+. Alcian blue treatment after 60 minutes of enzyme digestion revealed that the basement membrane, and its accompanying collagen fibrils, was still present on the plasma membrane of dissociated single cells. The isolated myocardial cells retained their normal morphological characteristics. This study has enabled us to understand in detail how dismantlement of highly ordered adult cardiac tissue into a single cell suspension takes place. Cell suspensions of this type should be invaluable in the study of metabolic and synthetic activities in adult myocardial cells.

Animals↗
PubMed1999

Detailed chromosomal and molecular genetic analysis of single cells by whole genome amplification and comparative genomic hybridisation.

Molecular genetic analysis of isolated single cells and other minute DNA samples is limited because there is insufficient DNA to perform more than one independent PCR amplification. One solution to this problem is to first amplify the entire genome, thus providing enough DNA for numerous subsequent PCRs. In this study we have investigated four different methods of whole genome amplification performed on single cells, and have identified a protocol that generates sufficient quantities of DNA for comparative genomic hybridisation (CGH) as well as more than 90 independent amplification reactions. Thus, numerous specific loci and the copy number of every chromosome can be assessed in a single cell. We report here the first reliable application of CGH to single cells from human preimplantation embryos (blastomeres) and to single fibroblasts, buccal cells and amniocytes.

Humans↗
PubMed2001

Predictions of the spontaneous symmetry-breaking theory for visual code completeness and spatial scaling in single-cell learning rules.

This article shows analytically that single-cell learning rules that give rise to oriented and localized receptive fields, when their synaptic weights are randomly and independently initialized according to a plausible assumption of zero prior information, will generate visual codes that are invariant under two-dimensional translations, rotations, and scale magnifications, provided that the statistics of their training images are sufficiently invariant under these transformations. Such codes span different image locations, orientations, and size scales with equal economy. Thus, single-cell rules could account for the spatial scaling property of the cortical simple-cell code. This prediction is tested computationally by training with natural scenes; it is demonstrated that a single-cell learning rule can give rise to simple-cell receptive fields spanning the full range of orientations, image locations, and spatial frequencies (except at the extreme high and low frequencies at which the scale invariance of the statistics of digitally sampled images must ultimately break down, because of the image boundary and the finite pixel resolution). Thus, no constraint on completeness, or any other coupling between cells, is necessary to induce the visual code to span wide ranges of locations, orientations, and size scales. This prediction is made using the theory of spontaneous symmetry breaking, which we have previously shown can also explain the data-driven self-organization of a wide variety of transformation invariances in neurons' responses, such as the translation invariance of complex cell response.

Animals↗
PubMed2026

Single-Cell Triomics Analysis of Tumor Cells Infiltrating Patient-Derived Breast Cancer Scaffolds.

Cellular heterogeneity plays a critical role in tissues and diseases, including cancer. Single-cell technologies are required to provide detailed information about the phenotype and genotype of individual cells. Despite several approaches to analyzing different analytes at the single-cell level, it is challenging to assess DNA, RNA, and protein simultaneously. Here, a single-cell triomics method to assess DNA, RNA, and proteins from the same cell using a targeted sequencing approach is shown. Breast cancer cells cultured in monolayers and in patient-derived scaffolds that mimic in vivo-like growth conditions, both with and without chemotherapy treatment, were analyzed. Data showed that DNA, RNA, and protein biomarkers could be reliably analyzed, providing biological insights into breast cancer cell heterogeneity. In addition, chemotherapy treatment caused changes in subpopulations and expressions of biomarkers. Furthermore, cells growing in patient-derived scaffolds generated from various breast cancers affected cell heterogeneity and drug resistance differently as a result of the unique tumor-specific microenvironments. The data show that single-cell triomics provides new means to assess cancer cell heterogeneity at DNA, RNA, and protein levels.

Humans↗
PubMed2025

Absolute copy number aware CNV calling of sub-megabase segments in ultra-low coverage single-cell DNA sequencing data.

Recent advances in ultra-low coverage whole-genome sequencing (WGS) of single cells have enabled detailed analysis of copy number variation at a throughput approaching that of single-cell RNA sequencing. However, downstream computational methods have not seen comparable advances and are largely adaptations of deep sequencing methodology with reduced precision. Here, we present ASCENT, a computational method built to take full advantage of modern direct tagmentation-based WGS at ultra-low depth. Using joint segmentation with high-resolution bins, we accurately detect small segments, achieving accurate copy number profiles even at 100 000 reads per cell. ASCENT implements true absolute copy state inference for single cells, based on statistical modeling of coverage rather than comparison to a reference, while taking variable segment copy state into account. Further, ASCENT implements per-segment copy-neutral loss of heterozygosity (LOH) calling without the need for non-tumor or bulk WGS reference. When applied to a pediatric B-ALL sample, ASCENT finds copy-neutral LOH in a small segment and a minor subclone defined by breakpoints missed in bulk WGS. Thus, by applying appropriate computational methods, single-cell WGS provides clear advantages over bulk, even at a relatively low cell number and sequencing depth.

DNA Copy Number Variations↗
PubMed1993

Single-cell transplantation determines the time when Xenopus muscle precursor cells acquire a capacity for autonomous differentiation.

We have used a single-cell transplantation technique to find out whether there is a stage in development when a single cell can reach and maintain its differentiated state in the absence of its neighbors. Muscle precursor cells from early, mid-, and late gastrula stages of Xenopus laevis embryos were isolated and transplanted singly into the ventral region of late gastrula hosts. Single cells from late gastrulae differentiated into muscle when surrounded by nonmuscle cells. Similar cells from early or mid-gastrulae did not, unless they were transplanted as a group of adjacent cells taken from the same region of an embryo. These results show that single embryonic cells in a tissue can complete their differentiation without interacting with their normal neighbors and that, in the case of Xenopus muscle precursor cells, they acquire this capacity at the late gastrula stage. Our results also suggest that, in addition to mesoderm induction, further cell interactions during gastrulation are required for Xenopus muscle cell differentiation.

Alkaline Phosphatase↗
PubMed2024

Protocol to perform integrative analysis of high-dimensional single-cell multimodal data using an interpretable deep learning technique.

The advent of single-cell multi-omics sequencing technology makes it possible for researchers to leverage multiple modalities for individual cells. Here, we present a protocol to perform integrative analysis of high-dimensional single-cell multimodal data using an interpretable deep learning technique called moETM. We describe steps for data preprocessing, multi-omics integration, inclusion of prior pathway knowledge, and cross-omics imputation. As a demonstration, we used the single-cell multi-omics data collected from bone marrow mononuclear cells (GSE194122) as in our original study. For complete details on the use and execution of this protocol, please refer to Zhou et al.1.

Deep Learning↗
PubMed2006

Intracellular labeling method for chip-based capillary electrophoresis fluorimetric single cell analysis using liposomes.

An intracellular derivatization method mediated by liposome was developed for single cell analysis with chip-based capillary electrophoresis (CE) and laser-induced fluorescence (LIF) detection. Liposomes with an average diameter of 100 nm were produced from phosphatidylcholine to encapsulate fluorescent dyes by an ultrasonic method. The encapsulation yield and the vesicle density were determined to be 46+/-5% and 8.8 x 10(14)/mL, respectively. The amount of fluorescent dye that entered the cells was dependent on the duration of incubating cells with liposomes, liposome density, and concentration of the dye solution encapsulated in liposomes. The described method introduced cell membrane nonpermeable fluorescent dyes into living cells without reducing cell viability. Single cell analysis using microfluidic chip-based CE revealed that liposome-membrane fusion occurred after entrance of liposomes into the cells, with release of encapsulated fluorescence dyes and labeling of intracellular species.

Cells↗
PubMed1986

Isolation of single cell suspensions from the rat mammary gland: separation, characterization, and primary culture of various cell populations.

Isolation and characterization of a single cell suspension from the rat mammary gland was achieved by combining selective enzymatic digestion and the mechanical agitation of a Stomacher laboratory blender with immunohistological identification of cell-specific markers. Utilizing this procedure we were able to isolate single cell suspensions of high yield (10 to 15 X 10(6) cells/rat) and viability (greater than 98%) with a concurrent decrease in isolation time and the amount of proteolytic enzymes required. Five distinct cell fractions were isolated from the mammary gland cell suspension after banding on discontinuous Percoll gradients. These populations were characterized both before and after primary cell culture by a combination of histological, immunohistological, and autoradiographic techniques. Fractions two and three were found to be enriched for mammary epithelial cells, as identified by their high binding of antikeratin antibodies. These populations also exhibited a minimal degree of binding to actin, myosin, and fibronectin antibodies. Fraction three also exhibited a high labeling index as measured by autoradiography following in vivo administration of [methyl-3H]thymidine. The remaining fractions were found to contain higher percentages of myoepithelial cells or other mammary cell types. Inasmuch as there is a direct correlation between mammary gland cell types and susceptibility to mammary gland carcinomas, further studies of these cell populations may provide new insights into the mechanisms underlying mammary gland carcinogenesis.

Actins↗
PubMed2005

Large-scale single-cell trapping and imaging using microwell arrays.

High-throughput single-cell measurements of cellular responses are of great importance for a variety of applications including drug testing, toxicology, and basic cell biology. We present an optimization study for trapping single cells with high efficiency in large arrays of microwells. The method is compatible with standard fluorescence microscopy equipment and is not dependent on, but is compatible with, cell adherence. We have characterized microwell occupancy by cells for a range of microwell dimensions and seeding parameters and optimized it for fibroblasts (as a model of adherent cell) and rat basophilic leukemia cells (as a model of nonadherent cell). We have been able to obtain phase-contrast and fluorescence micrographs with more than 18,000 single cells per image using a 4x objective.

Animals↗
PubMed1992

Single cell assay of exocytosis from pancreatic islet B cells.

We have measured changes in membrane capacitance (delta Cm) in pancreatic B cells as a single cell assay of insulin secretion. Evidence that depolarization evoked delta Cm reflects exocytosis includes it's voltage, temperature and Ca2+ o dependence. Decreases in Cm, presumably reflecting endocytosis, occur on a variable time scale. Two features that make B cells unique among excitable cells are the large magnitude of delta Cm, when normalized to Ca2+ current, and the rapid "fatigue" of the response for even minimal stimulation, perhaps due to the depletion of a readily releasable pool of vesicles.

Animals↗
PubMed1982

Problems of the use of 2,2-dimethoxypropane as dehydrating agent in preparing single cells for transmission electron microscopy.

Dehydration with 2,2-dimethoxypropane acidified with 1 n HCl in an 1:100 volume ratio has been found to be unsuitable for the preservation of cell membranes in single cell preparations. Reducing the HCl concentration to 0.1 or 0.01 n results in an improvement of membrane structures. This effect is rather independent of different fixation modes, buffer concentrations, or embedding media. It is suggested that membrane destruction is caused by a proton concentration exceeding a suitable level.

1-Propanol↗
PubMed1986

A newly identified Ca2+ dependent K+ channel in the smooth muscle membrane of single cells dispersed from the rabbit portal vein.

We found a new type of Ca2+-dependent K+ channel in smooth muscle cell membranes of single cells of the rabbit portal vein. A slope conductance of the current was 180 pS when 142 mM K+ solution was exposed to both sides of the membrane (this channel was named the KM channel, in comparison to the known KL and KS channels from the same membrane patch; Inoue et al. 1985). This KM channel was less sensitive to the cytoplasmic Ca2+ concentration, [Ca2+]i, but was sensitive to the extracellular Ca2+, [Ca2+]o, e. g. in the outside-out membrane patch, lowering the [Ca2+]o in the bath markedly reduced the open probability of this channel, and also in cell-attached configuration, lowering of the [Ca2+]o using the internally perfused patch clamp electrode device reduced the opening of KM channel. TEA+ (1-10 mM) reduced the amplitude of the elementary current through the KM channel applied from each side of the membrane, but this agent inhibited the KM channel to a greater extent when applied to the inner than to the outer surface of the membrane. Furthermore, this KM channel had a weak voltage dependency, and the open probability of the channel remained much the same within a wide range of potential (from -60 mV to +60 mV). Whereas most Ca2+-dependent K+ channels are regulated mainly by [Ca2+]i and possess a voltage dependency, these properties of the KM channel differed from other Ca2+-dependent K+ channels.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1984

Selective inhibition of natural killer activity by the monoclonal antibodies OKT10 and VEP10 at the single cell level.

The monoclonal antibodies, VEP10 and OKT10, which have been shown to recognize determinants on human natural killer (NK) cells, inhibit large granular lymphocyte (LGL) NK activity against K562, MOLT4, and CEM tumor target cells in the single cell conjugate agarose assay. Inhibition of NK activity by monoclonal antibodies was expressed independently of effector-target cell binding, as inhibitory activity could be demonstrated when the monoclonal antibodies VEP10 and OKT10 were added to preformed conjugates or to the LGLs and targets prior to the binding event. In addition, this inhibition was exerted on the effector cell and not the target cell since VEP10 and OKT10 did not react with determinants on K562 target cells. Furthermore, the 4F2 monoclonal antibody, which reacted with determinants on the LGL and all of the targets used, effected no inhibition of NK activity. Inhibition of killing by OKT10 and VEP10 was specific to endogenous NK activity since the same antibodies did not inhibit antibody-dependent cellular cytotoxicity (ADCC), mixed lymphocyte-generated NK, or cytotoxic T lymphocyte (CTL) activities.

Antibodies, Monoclonal↗
PubMed1989

Measurement of cytoplasmic calcium in lymphocytes using flow cytometry. Kinetic studies and single cell analysis.

An increased level of cytoplasmic free ionized calcium [Ca2+]i after crosslinking of membrane receptors is a critical second messenger in the activation of T and B lymphocytes. The availability of fluorescent calcium chelators, such as quin-2 and indo-1, makes accurate measurement of [Ca2+]i possible. One of the major drawbacks of spectrofluorometry which is the generally used method in such studies is that the overall response of a cell suspension is recorded. Such data will be biased by the proportion of non-responding cells, which will differ according to the purity of cell populations and the nature of the stimulus applied. An accurate and reliable technique to measure intracellular free calcium responses in indo-1-loaded cells at the single cell level has been developed using a simple mercury arc lamp-based flow cytometer, the FACS analyzer. Using this technique we have found that the rapid increase in [Ca2+]i (within 30 s) in T cells following activation by ConA involves a minority of cells, whereas all T cells show increased [Ca2+]i levels within 2-3 min.

Antigens, Differentiation, T-Lymphocyte↗
PubMed2006

Measurement of cytokine release at the single cell level using the ELISPOT assay.

The enzyme-linked immunospot (ELISPOT) assay took its design concept from traditional ELISA techniques and evolved over the years from a method for detecting antibodies secreted from B cells to a method for detecting cytokines or other soluble mediators secreted from a variety of different cell types. The ELISPOT assay allows the quantitative measurement of frequency of cytokine secreting cells at the single cell level directly ex vivo without elaborate in vitro expansion or manipulation of cell populations. The function of cells can be inferred from the pattern of cytokines secreted by cells in response to diverse antigenic stimuli and thus the ELISPOT assay has become a powerful method for monitoring immune responses in health and disease. The ELISPOT assay like the ELISA assay is relatively easy to perform and it has the promise of robustness, reliability, and reproducibility of performance for use as a diagnostic tool. The history, applications, validation process, and future challenges of the ELISPOT assay are discussed in this chapter.

Animals↗