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Results for “single cell analysis”

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At least 19 recordsLinked to original sources

PubMed1988

Contextual analysis complements single-cell analysis in the diagnosis of breast cancer in fine needle aspirates.

Image analysis techniques were used to characterize individual nuclei of cells and entire clusters of cells in hematoxylin-and-eosin-stained smears of fine needle aspirates of the breast to determine the ability of these techniques to distinguish benign from malignant cases. Analysis of the individual nuclear features showed significant differences in nuclear area, shape (bending energy), texture and integrated darkness between benign and malignant samples. Analysis of the clusters demonstrated that the benign clusters were fewer in number, more cellular (average gray level) and larger than malignant clusters. A statistical classifier was constructed to test the discriminatory accuracy for benign and malignant cases. Good discrimination was found for both the individual nuclei and the clusters when analyzed separately, although a few cases were misclassified by each type of analysis. When combined, the two classifiers achieved a completely accurate classification. This suggests the complementary nature of high-resolution single-cell analysis and the more global cluster analysis techniques.

Adenofibroma↗

PubMed2025

ShortCake: an integrated platform for efficient and reproducible single-cell analysis.

SUMMARY: Recent advances in single-cell analysis have introduced new computational challenges. Researchers often need to use multiple analysis tools written in different programming languages while managing version conflicts between related packages within a single workflow. For the research community, minimizing the time spent on environment setup and installation issues is essential. We present ShortCake, a containerized platform that integrates a suite of single-cell analysis tools written in R and Python. ShortCake isolates competing Python tools into separate virtual environments that can be easily accessed within a Jupyter notebook. This enables users to effortlessly transition between various environments, including R, even within a single notebook. Additionally, ShortCake offers multiple "flavors," enabling users to select container images tailored to their specific needs. ShortCake provides a unified environment with fixed versions of various tools, thus streamlining workflows, reducing setup time, and improving reproducibility. AVAILABILITY AND IMPLEMENTATION: The ShortCake image is available on DockerHub (https://hub.docker.com/r/rnakato/shortcake) and Zenodo (DOIs: 10.5281/zenodo.17116765 and 10.5281/zenodo.17118158). The source code is available on GitHub (https://github.com/rnakato/ShortCake).

Single-Cell Analysis↗

PubMed2006

Sugar concentrations along and across the Ricinus communis L. hypocotyl measured by single cell sampling analysis.

Single cell sap sampling and analysis were used to measure the longitudinal and radial distribution of sucrose, glucose and fructose in the apical cell division zone and in the basal, elongated zone of the Ricinus hypocotyl. Sucrose and hexose increased in concentration from the apex to the base of the seedling axis. In the cell division zone low hexose and sucrose concentrations prevailed in cortex and pith, with a slightly higher hexose concentration in pith cells. The sucrose concentrations in sieve tubes and in phloem were much higher than in the cortex and pith cells. In the basal zone of the hypocotyl high levels of sucrose in phloem, cortex and pith were found, therefore radial, diffusional sucrose flow away from the phloem was considered unlikely. It is proposed that radial flow of growth-water to the hypocotyl periphery together with the down-regulation of a sucrose transporter at the phloem leads to a preferential sucrose flow to the expanding cortex. The pith cells, which do not experience flow of growth-water, are probably insufficiently supplied with sucrose from the phloem resulting eventually in cell death as the plant grows. Shortage of sucrose supply, experimentally achieved by removal of the endosperm, led to sucrose hydrolysis in the pith. The sucrose levels in the other tissues decreased less. It appears that the hydrolysis to hexose was initiated to maintain the osmotic value in the pith cell sap. It is speculated that high hexose levels in the cells are indicative of insufficient sucrose supply via the phloem and that the pith cells are confronted with that situation during early seedling development.

Carbohydrate Metabolism↗

PubMed2000

Single-cell analysis avoids sample processing bias.

Microscale separation tools such as capillary chromatography and capillary electrophoresis (CE) allow the study of metabolism in individual cells. In this work, we demonstrate that single-cell analysis describes metabolism more accurately than analysis of cellular extracts. We incubated HT29 cells (human colon adenocarcinoma) with a fluorescently labeled metabolic probe. This disaccharide, LacNAc, was labeled with a fluorescent dye, tetramethylrhodamine (TMR). The probe was taken up by the cells and metabolized to a number of products that retained the fluorescent label. We then split the cells into two batches. A cellular extract was prepared from one batch and analyzed by CE with laser-induced fluorescence (LIF) detection. The cells from the second batch were used for single-cell analysis by CE-LIF. Separation and detection conditions were identical for extract and single-cell analyses. We found that the electropherogram obtained by averaging the results from a number of single cells differed significantly from the cell extract electropherogram. Differences were due to sample processing during extract preparation. Disruption of the cells liberated enzymes that were compartmentalized within the cell, which allowed non-metabolic reactions to proceed. The accumulation of these non-metabolic products introduced a bias in the cell extract assay. During single-cell analysis, cells were lysed inside the capillary and the separation voltage was applied immediately to separate the enzymes from their substrates and prevent non-metabolic reactions. This paper is the first to report that CE analysis of single cells provides more accurate metabolic information than the CE analysis of a cellular extract.

Electrophoresis, Capillary↗

PubMed2006

Improved native UV laser induced fluorescence detection for single cell analysis in poly(dimethylsiloxane) microfluidic devices.

Single cell analytics is a key method in the framework of proteom research allowing analyses, which are not subjected to ensemble-averaging, cell-cycle or heterogeneous cell-population effects. Our previous studies on single cell analysis in poly(dimethylsiloxane) microfluidic devices with native label-free laser induced fluorescence detection [W. Hellmich, C. Pelargus, K. Leffhalm, A. Ros, D. Anselmetti, Electrophoresis 26 (2005) 3689] were extended in order to improve separation efficiency and detection sensitivity. Here, we particularly focus on the influence of poly(oxyethylene) based coatings on the separation performance. In addition, the influence on background fluorescence is studied by the variation of the incident laser power as well as the adaptation of the confocal volume to the microfluidic channel dimensions. Last but not least, the use of carbon black particles further enhanced the detection limit to 25 nM, thereby reaching the relevant concentration ranges necessary for the label-free detection of low abundant proteins in single cells. On the basis of these results, we demonstrate the first electropherogram from an individual Spodoptera frugiperda (Sf9) cell with native label-free UV-LIF detection in a microfluidic chip.

Animals↗

PubMed2003

Enzymatic amplification staining for single cell analysis: applied to in situ hybridization.

Single cell analysis by flow cytometry is a powerful modality for analyzing the expression of a set of molecules. Nevertheless, the most significant deficiency of this technology has been the poor sensitivity of flow cytometry compared to other techniques such as immunoblotting. In order to address this deficiency, we have developed an enzymatic amplification system for flow cytometry that enhances the specific signal by 10-100-fold. Using enzymatic amplification staining (EAS), we and others have been able to assess the expression of molecules that could not be detected otherwise. In this review, we show the capability of this new technology to detect specific RNA expression.

Enzyme Multiplied Immunoassay Technique↗

PubMed2004

Single-cell analysis of yeast, mammalian cells, and fungal spores with a microfluidic pressure-driven chip-based system.

BACKGROUND: Cytomics aims at understanding the function of cellular systems by analysis of single cells. Recently, there has been a growing interest in single cell measurements being performed in microfluidic systems. These systems promise to integrate staining, measurement, and analysis in a single system. One important aspect is the limitation of allowable cell sizes due to microfluidic channel dimensions. Here we want to demonstrate the broad applicability of microfluidic chip technology for the analysis of many different cell types. METHODS: We have developed a microfluidic chip and measurement system that allows flow cytometric analysis of fluorescently stained cells from different organisms. In this setup, the cells are moved by pressure-driven flow inside a network of microfluidic channels and are analyzed individually by fluorescence detection. RESULTS: We have successfully applied the system to develop a methodology to detect viable and dead cells in yeast cell populations. Also, we have measured short interfering RNA (siRNA) mediated silencing of protein expression in mammalian cells. In addition, we have characterized the infection state of Magnaportae grisea fungal spores. CONCLUSIONS: Results obtained with the microfluidic system demonstrate a broad applicability of microfluidic flow cytometry to measurement of various cell types.

Cell Line↗

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↗

PubMed2003

Microfluidic device for single-cell analysis.

We have developed a novel microfluidic device constructed from poly(dimethylsiloxane) using multilayer soft lithography technology for the analysis of single cells. The microfluidic network enables the passive and gentle separation of a single cell from the bulk cell suspension, and integrated valves and pumps enable the precise delivery of nanoliter volumes of reagents to that cell. Various applications are demonstrated, including cell viability assays, ionophore-mediated intracellular Ca2+ flux measurements, and multistep receptor-mediated Ca2+ measurements. These assays, and others, are achieved with significant improvements in reagent consumption, analysis time, and temporal resolution over macroscale alternatives.

Calcium↗

PubMed2005

Single-cell analysis by electrochemical detection with a microfluidic device.

A novel electrochemical method with a microfluidic device was developed for analysis of single cells. In this method, cell injection, loading and cell lysis, and electrokinetic transportation and detection of intracellular species were integrated in a microfluidic chip with a double-T injector coupled with an end-channel amperometric detector. A single cell was loaded at the double-T injector on the microfluidic chip by using electric field. Then, the docked cell was lysed by a direct current electric field strength of 220 V/cm. The analyte of interest inside the cell was electrokinetically transported to the detection end of separation channel and was electrochemically detected. External standardization was used to quantify the analyte of interest in individual cells. Ascorbic acid (AA) in single wheat callus cells was chosen as the model compound. AA could be directly detected at a carbon fiber disk bundle electrode. The selectivity of electrochemical detection made the electropherogram simple. The technique described here could, in principle, be applied to a variety of electroactive species within single cells.

Ascorbic Acid↗

PubMed2005

Identification of tick periviscerokinin, the first neurohormone of Ixodidae: single cell analysis by means of MALDI-TOF/TOF mass spectrometry.

The first peptidergic neurohormone from the ticks Ixodes ricinus and Boophilus microplus has been identified by using a combination of immunocytochemistry and mass spectrometric analysis of single cells. The novel peptide (Ixori-PVK, PALIPFPRV-NH2) shows a high sequence homology with members of the insect periviscerokinin/CAP2b peptides that in insects are involved in the regulation of water balance. The function of this peptide in ticks is still unknown, but these pests consume large amounts of blood in a single blood meal which is a challenge for the regulation of diuretic processes. Thus, the novel peptide may be involved in one of the key physiological processes in ticks. High energy collision-induced dissociation was successfully used to distinguish between Leu/Ile ambiguities in single cell preparations. This is the first successful de novo sequencing of a peptide from single cell preparations of arthropods.

Amino Acid Sequence↗

PubMed2002

Direct and quantitative single-cell analysis of human immunodeficiency virus type 1 reactivation from latency.

The ability of human immunodeficiency virus type 1 (HIV-1) to establish latent infections in cells has received renewed attention owing to the failure of highly active antiretroviral therapy to eradicate HIV-1 in vivo. Despite much study, the molecular bases of HIV-1 latency and reactivation are incompletely understood. Research on HIV-1 latency would benefit from a model system that is amenable to rapid and efficient analysis and through which compounds capable of regulating HIV-1 reactivation may be conveniently screened. We describe a novel reporter system that has several advantages over existing in vitro systems, which require elaborate, expensive, and time-consuming techniques to measure virus production. Two HIV-1 molecular clones (NL4-3 and 89.6) were engineered to express enhanced green fluorescent protein (EGFP) under the control of the viral long terminal repeat without removing any viral sequences. By using these replication-competent viruses, latently infected T-cell (Jurkat) and monocyte/macrophage (THP-1) lines in which EGFP fluorescence and virus expression are tightly coupled were generated. Following reactivation with agents such as tumor necrosis factor alpha, virus expression and EGFP fluorescence peaked after 4 days and over the next 3 weeks each declined in a synchronized manner, recapitulating the establishment of latency. Using fluorescence microscopy, flow cytometry, or plate-based fluorometry, this system allows immediate, direct, and quantitative real-time analysis of these processes within single cells or in bulk populations of cells. Exploiting the single-cell analysis abilities of this system, we demonstrate that cellular activation and virus reactivation following stimulation with proinflammatory cytokines can be uncoupled.

Cell Cycle↗

PubMed2005

Single cell analysis of G1 check points-the relationship between the restriction point and phosphorylation of pRb.

Single cell analysis allows high resolution investigation of temporal relationships between transition events in G1. It has been suggested that phosphorylation of the retinoblastoma tumor suppressor protein (pRb) is the molecular mechanism behind passage through the restriction point (R). We performed a detailed single cell study of the temporal relationship between R and pRb phosphorylation in human fibroblasts using time lapse video-microscopy combined with immunocytochemistry. Four principally different criteria for pRb phosphorylation were used, namely (i) phosphorylation of residues Ser795 and Ser780, (ii) degree of pRb-association with the nuclear structure, a property that is closely related with pRb phosphorylation status, (iii) release of the transcription factor E2F-1 from pRb, and (iv) accumulation of cyclin E, which is dependent on phosphorylation of pRb. The analyses of individual cells revealed that passage through R preceded phosphorylation of pRb, which occurs in a gradually increasing proportion of cells in late G1. Our data clearly suggest that pRb phosphorylation is not the molecular mechanism behind the passage through R. The restriction point and phosphorylation of pRb thus seem to represent two separate check point in G1.

Cell Cycle Proteins↗

PubMed2005

Single-cell analysis by intracellular immuno-reaction and capillary electrophoresis with laser-induced fluorescence detection.

A novel method for single-cell analysis was developed by combining electroporation for intracellular immuno-reaction and capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection. Human interferon-gamma (IFN-gamma) in natural killer (NK) cells was chosen as the test antigen. Two forms of IFN-gamma in single cells could be well separated and detected with a limit of detection of zeptomole. In this assay, the anti-IFN-gamma monoclonal antibody labeled with fluorescein isothiocyanate (Ab*) was introduced into NK cells by electrophoration for intracellular immuno-reaction. After completion of the intracellular immuno-reaction, the NK cells were chemically pre-perforated with digitonin to lyse easily. Then, one NK cell containing the complexes of IFN-gamma isoantigens with Ab* was electrokinetically injected into the capillary. The cell adsorbed on the tip of capillary was lysed by ultrasonication. Finally, the complexes of the different forms of IFN-gamma in the cell were separated and detected by CE-LIF detection.

Electrophoresis, Capillary↗

PubMed2000

Single cell analysis reveals that IL-4 receptor/Stat6 signaling is not required for the in vivo or in vitro development of CD4+ lymphocytes with a Th2 cytokine profile.

The concept that IL-4 is the primary signal for Th2 lymphocyte differentiation has recently been put in doubt by studies in which the production of Th2-associated cytokines was detected in mice deficient in IL-4 synthesis or IL-4R triggering. In this study, we formally demonstrate by single cell analysis that CD4+ lymphocytes with a classical Th2 phenotype (IL-4+, IL-5+, IFN-gamma-, IL-2-) develop in significant numbers in helminth-infected mice deficient in either IL-4R alpha-chain or Stat6. While an expanded population of Th1 (IL-4-, IL-5-, IFN-gamma+, IL-2+) lymphocytes was observed in the same animals, surprisingly, cells with a mixed Th0 cytokine pattern were rare. The cytokine production phenotypes of the Th1 and Th2 subpopulations generated in infected Stat6-deficient mice were unaffected by in vitro neutralization of endogenous IL-4 or IFN-gamma. Nevertheless, while addition of exogenous rIL-12 resulted in transitory IFN-gamma production by Th2 lymphocytes from both wild-type and Stat6-deficient mice, IL-4 synthesis was preserved in the former, but temporarily ablated in the latter cells. Importantly, IL-4+ IFN-gamma- and IL-4- IFN-gamma+ populations similar to those arising in helminth-infected Stat6-deficient mice could also be generated in vitro by repetitive polyclonal stimulation of CD4+CD62Lhigh lymphocytes from uninfected mice of the same strain. Together, the results of these single cell analysis experiments demonstrate that IL-4R/Stat6 signaling, while influencing the final frequency of Th2 lymphocytes, is not essential for Th2 cell development, and suggest that this pathway has a previously unrecognized function in stabilizing Th2 populations once they have emerged.

Animals↗

PubMed1996

Single cell analysis of tyrosine kinase dependent and independent Ca2+ fluxes in progesterone induced acrosome reaction.

In this study we developed a single cell analysis protocol with which protein tyrosine kinase (PTK)-dependent and independent Ca2+ fluxes occurring in human spermatozoa in response to progesterone were evaluated. By recording the fluorescence emitted by fluo-3-loaded spermatozoa using a confocal laser scanning microscopy system it was possible not only to monitor relative changes in the intracellular free Ca2+ concentration ([Ca2+]i) but also to determine the time at which the acrosomal exocytosis began. The addition of progesterone produced a rapid transient [Ca2+]i increase in 35% of spermatozoa. In approximately 10% of spermatozoa, this initial [Ca2+]i increase was followed by a secondary [Ca2+]i increase beginning 2-10 min after the progesterone addition and leading to the acrosomal exocytosis in most of these spermatozoa. On the other hand, a rapid triggering of exocytosis during the initial [Ca2+]i increase was a relatively infrequent observation. The inhibition of PTK with genistein or herbimycin A did not influence the initial progesterone-induced [Ca2+]i increase but inhibited the secondary [Ca2+]i increase and the ensuing acrosomal exocytosis. The initial PTK-independent Ca2+ response could be induced by progesterone in both non-capacitated and capacitated spermatozoa, whereas the ability to generate the secondary, PTK-dependent response developed during in-vitro capacitation.

Acrosome↗

PubMed2026

Integrative multi-omics and single-cell analysis identifies EGFR pathway activation and metabolic reprogramming as potential synthetic lethal vulnerabilities in resistance to the FGFR inhibitor AZD4547.

BACKGROUND: Although fibroblast growth factor receptor (FGFR) inhibitors (FGFRi) have demonstrated clinical promise, the inevitable emergence of acquired resistance remains a critical bottleneck, severely compromising their long-term clinical efficacy. The pan-cancer molecular landscape and heterogeneous mechanisms driving this resistance, ranging from genetic alterations to dynamic network rewiring, remain poorly understood. METHODS: We integrated large-scale pharmacogenomic profiling of the FGFR inhibitor AZD4547 from the GDSC2 and PRISM databases with single-cell RNA sequencing to dissect the multi-omics landscape of FGFRi resistance across 312 cell lines from 8 cancer types. This multi-omics framework was further extended by machine learning modeling and systematic synthetic lethality screening to uncover actionable therapeutic targets. In vitro viability assays and western blot analysis were subsequently conducted to experimentally evaluate the predicted FGFR-EGFR synthetic lethality. RESULTS: Our dual-database analysis unveiled a multi-dimensional atlas of FGFRi resistance. We identified cancer-specific genomic drivers, such as ELF4 amplification in glioblastoma, alongside key transcriptomic markers including UCP2 and FSCN1, highlighting a shift towards metabolic reprogramming and epithelial-mesenchymal transition (EMT). Single-cell analysis unveiled that resistance is linked to the heterogeneous enrichment of baseline subpopulations characterized by distinct metaprograms, including cell-cycle dysregulation. Furthermore, a random forest model built on a LASSO-derived transcriptomic signature was constructed, demonstrating promising predictive capability for AZD4547 sensitivity (mean test-set AUC = 0.73, 95% CI [0.63, 0.80]); the signature generalized well to erdafitinib but showed limited transferability to some other FGFR inhibitors (e.g. pemigatinib, BGJ398). Most notably, our synthetic lethal screening revealed a convergent reliance on compensatory RTK signaling (specifically EGFR pathway enrichment) and downstream MAPK/PI3K cascades in resistant phenotypes, providing converging computational evidence for EGFR pathway activation as an adaptive bypass mechanism. This predicted synthetic lethality was experimentally supported in two FGFR-dependent cell line models (RT112 and CCLP1), in which combined FGFR-EGFR inhibition produced marked synergistic antiproliferative effects. CONCLUSIONS: This study establishes a comprehensive multi-omics atlas of resistance to the FGFR inhibitor AZD4547, delineating convergent mechanisms of metabolic reprogramming and EGFR-mediated bypass signaling. Our findings characterize the resistance as a dynamic network rewiring and nominate rational combination strategies to overcome this therapeutic bottleneck. While FGFR-EGFR co-inhibition is experimentally supported, metabolic co-targeting remains a computationally derived, hypothesis-generating strategy.

Benzamides↗

PubMed1995

Single cell analysis demonstrating somatic mosaicism involving 11p in a patient with paternal isodisomy and Beckwith-Wiedemann syndrome.

Partial isodisomy of 11p has been observed in some patients with Beckwith-Wiedemann syndrome. In this study, we demonstrate somatic mosaicism directly through PCR and single cell analysis on blood lymphocytes from a patient with Beckwith-Wiedemann syndrome. Whole genome amplification was performed on single cells and the resultant product was subjected to locus specific microsatellite marker analysis using PCR. Two populations of cells were detected, a population of cells with normal biparental inheritance for chromosome 11 and a population of cells with partial paternal isodisomy of 11p between markers D11S922 (11p15.5) and D11S904 (11p14-p13). These results are consistent with somatic recombination resulting in mosaicism for paternal isodisomy. The use of single cell PCR is ideal for studying the distribution of mosaicism within and between tissues and has been used in this study to identify a cell line with uniparental disomy in a patient with Beckwith-Wiedemann syndrome.

Adult↗