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Results for “single cell analysis”

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At least 271 records · Page 15Linked to original sources
PubMed1991

Single cell endocrinology: analysis of P-450scc activity by fluorescence detection methods.

A mechanism-based, fluorogenic probe for the cytochrome P-450scc (cholesterol side chain cleavage) enzyme, rate-limiting for the conversion of cholesterol to steroid hormones, is introduced and its application to the study of enzyme activity and regulation in single steroidogenic cells by several fluorescence detection methods is demonstrated. Reaction of the probe with P-450scc gives pregnenolone and the highly fluorescent resorufin anion. Spectroscopic changes in probe fluorescence, indicative of P-450scc activity, were monitored by steady-state fluorescence spectroscopy, flow cytometry, and microspectrofluorometry. This unique probe provides a nonradiometric indicator for real-time measurement of P-450scc activity in single living cells.

Animals↗
PubMed2026

Capturing gene-cell duality in a cat's cradle.

SUMMARY: CatsCradle is an R package for single-cell analysis that exploits the duality between cells and the genes they express. Our package provides tools to cluster genes, visualize relationships between them, and to explore relationships between gene clusters (programmes) and cell clusters (cell types). AVAILABILITY AND IMPLEMENTATION: CatsCradle is available freely as an R Bioconductor package (https://bioconductor.org/packages/CatsCradle) and interfaces directly with Seurat (Hao et al. 2024) and SingleCellExperiment (Amezquita et al. 2020) data structures.

Software↗
PubMed1997

A simple approach to single-cell microdissection and molecular analysis.

OBJECTIVE: To develop a simple approach to single-cell microdissection from Papanicolaou-stained smears and to determine its usefulness in molecular diagnosis using archival cytologic material. STUDY DESIGN: Culture cells from three cell lines (TT, A549 and Lu65) were used to prepare Papanicolaou-stained smears. Mount-Quick, a mounting medium, was used to establish the method of sorting target single cells from smear slides under direct microscopic observation. Calcitonin receptor gene and codon 12 of the K-ras oncogene were amplified to check the application of single-cell genetic analysis in cytology. RESULTS: The target single cell could be simply sorted from Papanicolaou-stained smears using the Mount-Quick microdissection technique. Boiling in water was more suitable for preparing DNA from a single cell or from fewer than five cells versus other methods. Analysis of calcitonin receptor gene and K-ras codon 12 demonstrated that molecular analysis was applicable to a single cell or a few cells from archival Papanicolaou-stained smears. CONCLUSION: This approach has significant implications for cytology: (1) it circumvents the limitations of molecular analysis in cytology and makes the combination of molecular analysis and morphologic diagnosis possible in cases with limited materials; (2) the remaining part of the smear is still preserved well for additional analysis; and (3) the approach is simple, economical and practical for cytology as well as histology.

DNA, Neoplasm↗
PubMed2000

Follow-up study of the genetic damage in lymphocytes of pharmacists and nurses handling antineoplastic drugs evaluated by cytokinesis-block micronuclei analysis and single cell gel electrophoresis assay.

A follow-up study was carried out 4 years after an initial evaluation of the micronucleus frequency in 10 healthy individuals who had been occupationally exposed to antineoplastic drugs in a Brazilian hospital. Upon the first evaluation, these 10 exposed individuals were compared with 10 non-exposed individuals matched for age, sex and smoking habits; the results revealed that the frequency of micronucleated lymphocytes in individuals exposed to antineoplastic drugs was significantly higher (P=0.038) than in controls. The frequency of dicentric bridges was also increased, although not significantly (P=0.0545). After the first analysis, the workers handling antineoplastic drugs were advised to modify their work schedule to limit exposure, and the number of workers in the group was increased from 10 to 12 individuals. In the follow-up study, 12 individuals from the same work area were assessed. In addition to micronucleus frequency, alkaline single cell gel electrophoresis was also used to monitor genetic hazard. This exposed group was compared to 12 non-exposed workers from the same hospital, matched for age, sex and smoking habits. In the follow-up study, no statistical difference was found between exposed workers and controls in terms of micronucleus and dicentric bridge frequency with the Mann--Whitney U-test (P=0.129 and 0.373, respectively). However, the mean value of SCGE analysis was significantly higher in the exposed group than in the controls (P=0.0006). Although the micronucleus analysis seems to be less sensitive to assess DNA damage, it detects chromosome aberrations and not just repairable DNA breakage and alkali-labile sites. Combination of the alkaline single cell gel electrophoresis and cytokinesis blocked micronucleus assay appears to be commendable to monitor populations chronically exposed to genotoxic agents.

Adult↗
PubMed2006

Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise.

A major goal of biology is to provide a quantitative description of cellular behaviour. This task, however, has been hampered by the difficulty in measuring protein abundances and their variation. Here we present a strategy that pairs high-throughput flow cytometry and a library of GFP-tagged yeast strains to monitor rapidly and precisely protein levels at single-cell resolution. Bulk protein abundance measurements of >2,500 proteins in rich and minimal media provide a detailed view of the cellular response to these conditions, and capture many changes not observed by DNA microarray analyses. Our single-cell data argue that noise in protein expression is dominated by the stochastic production/destruction of messenger RNAs. Beyond this global trend, there are dramatic protein-specific differences in noise that are strongly correlated with a protein's mode of transcription and its function. For example, proteins that respond to environmental changes are noisy whereas those involved in protein synthesis are quiet. Thus, these studies reveal a remarkable structure to biological noise and suggest that protein noise levels have been selected to reflect the costs and potential benefits of this variation.

Culture Media↗
PubMed1984

DNA-Feulgen-cytophotometric analysis of single cells isolated from paraffin embedded tissue.

This study describes a method for the isolation of cells from paraffin embedded tissues for DNA-Feulgen-cytophotometric measurements. The relevance of the method used is demonstrated by the analysis of the DNA-distribution pattern of cells isolated from an alveolar sarcoma of the soft tissues of a 10-year old girl. The comparison between freshly prepared imprint preparations and specimens after pepsin--extraction clearly shows, that the preparation mode used did not influence the relative DNA-content. The mean values of DNA/nuclei did not show a decrease even after prolonged pepsin treatment (90 minutes). Therefore this method permits access to stored histopathological material for retrospective DNA-Feulgen-Cytophotometric investigations.

Child↗
PubMed2002

Single cell expression analysis--pharmacogenomic potential.

A fundamental challenge in biology is to correlate physiology with gene expression in specific cell types. This can only be achieved by understanding gene expression at the level of the single cell because, in many systems, each cell has the capacity to express a unique set of genes. Therefore, each cell can be considered to be functionally distinct. A clearer understanding of gene expression differences at such a discrete level provides an opportunity to develop drugs with more targeted pharmacologies or with decreased side effects.

Animals↗
PubMed1996

Single-cell mutation analysis of tumors from stained histologic slides.

Formalin-fixed and paraffin-embedded tissues are a valuable resource for diagnosis and research. PCR is one of the most powerful methods of retrospective analysis of the DNA present in fixed tissues. One major problem with the molecular analysis of tissue samples, however, is cellular heterogeneity, ie, the large variety of cell types usually present in these specimens can mask cell-specific genetic alterations associated with disease. Herein we describe a procedure for obtaining and analyzing single cells recovered from stained histologic tissue sections without risking contamination from neighboring cells. An ultraviolet laser microbeam was used to physically destroy the tissue surrounding the single cells of interest. These cells, now freed from adjacent cells, were then easily retrieved with a motorized, computer-controlled micromanipulator and molecularly characterized through the use of PCR-based microanalysis. This accurate microdissection technique, followed by DNA amplification and direct sequencing, revealed a novel mutation in the gene coding for the cell adhesion molecule E-cadherin in single tumor cells that was absent in the adjacent single epithelial cells of a patient with early gastric cancer of the diffuse type. In this form of malignancy, tumor cells lose homophilic cell-to-cell interactions and invade the connective tissue as single cells. E-cadherin gene mutations have previously been detected in advanced diffuse-type gastric cancer and gastric carcinoma cell lines. The present study suggests that E-cadherin gene mutations may be an early event in gastric tumorigenesis. The laser-based isolation and subsequent molecular characterization of individual cells, as described herein, allows for micrometer-sized precision and should prove useful in detecting the nucleic acid abnormalities that underlie cancer, infection, and genetic disease.

Base Sequence↗
PubMed2002

[WHO classification of Hodgkin's lymphoma and its molecular pathological relevance].

The current WHO classification of Hodgkin's lymphoma (HL) generally distinguishes the relatively rare variant (approximately 5% of all cases of HL) of nodular lymphocyte predominant type from a second group, which comprises classical HL and is separated into four subtypes: lymphocyte rich type, nodular sclerosis type, mixed cellularity type and lymphocyte depleted type. The classical lymphocyte rich subtype is a new entity and based on the typical morphology, can be recognized by definition only by the immunohistochemical characteristics of the Hodgkin and Reed/Sternberg cells (HRS) (CD30+, CD15+, CD20-). Molecular single cell studies are consistent with the dichotomy of HL in nodular lymphocyte predominant and classical types and stress the exceptional position of the former, which shows similarities with non-Hodgkin's lymphomas in several aspects. On the molecular biology level the tumor cells of all kinds of HL turn out to be clonal B cells derived from germinal center cells. However, tumor cells of nodular lymphocyte predominant HL differ from those of classical HL by the pattern of somatic mutations. Considering the inability of HRS cells of classical HL to express a B cell receptor, they should perish under normal conditions. However, they escape from apoptosis by mechanisms so far only partially understood, such as genomic mutations of the l-kappa B gene and the fas receptor gene or probably by down-regulation of B cell markers. In rare cases, HRS cells of HL can also be derived from T cells, as could be demonstrated by single cell analysis. Also, it could be shown by single cell PCR that HL and non-Hodgkin's lymphoma of both B and T cell types can arise from a common precursor. These results suggest that future classifications of HL will not only take into account the morphological and phenotypical profile, but also mechanisms of transformation yet to be discovered.

Biomarkers, Tumor↗
PubMed2026

transFusion: a novel comprehensive platform for integration analysis of single-cell and spatial transcriptomics.

MOTIVATION: Understanding spatial organization, intercellular interactions, and regulatory networks within the spatial context of tissues is crucial for uncovering complex biological processes and disease mechanisms. Spatial transcriptomics technologies have revolutionized this field by enabling the spatially resolved profiling of gene expression. 10× Visium has emerged as the predominant spatial technology, but its low resolution and the complexity of integrating multimodal datasets present significant analytical challenges, particularly for researchers with limited computational and statistical expertise. Current spatial transcriptomics analysis platforms generally fall short of effectively integrating multimodal data and maximizing the utility of spatial information-such as uncovering complex cellular spatial dependencies, multimodal gradient patterns, and spatial coexpression of ligand-receptor pairs and regulatory networks related to disease or biological states-thereby limiting their ability to provide comprehensive end-to-end analytical workflows when analyzing 10× Visium data. RESULTS: To address these limitations, we developed transFusion, a novel, advanced web-based platform specializing in the most comprehensive and effective integration analysis of scRNA-seq and 10× Visium spatial transcriptomics data. transFusion offers 12 key functions, from basic visualization to advanced analyses, including intercellular dependency analysis, ligand-receptor coexpression identification and visualization, and spatial multimodal gradient variation patterns. Two case studies were used to demonstrate transFusion's capabilities in exploring tissue architecture, intercellular communication, dependency networks, and multimodal gradient variation patterns with minimal computational skills and statistical expertise. transFusion provides a flexible and powerful framework for multimodal data integration analysis. AVAILABILITY AND IMPLEMENTATION: transFusion is freely available at https://github.com/WQLin8/transFusion.

Spatial Transcriptomics↗
PubMedDate not supplied

Multilineage gene expression in human bone marrow stromal cells as evidenced by single-cell microarray analysis.

The nonhematopoietic stromal cells of the bone marrow are critical for the development of hematopoietic stem cells into functionally competent blood cells. This study addresses the question of whether bone marrow stromal cell cultures in the Dexter system propagate multiple different mesenchymal stromal cell types or one stromal cell type that expresses multiple phenotypes. Results show that isolated single stromal cells simultaneously express transcripts associated with osteoblast, fibroblast, muscle, and adipocyte differentiation. Furthermore, isolated single stromal cells simultaneously express transcripts characteristic of epithelial cells, endothelial cells, and neural/glial cells. Isolated single stromal cells also express transcripts for CD45, CD19, CD10, CD79a, and representative proto-oncogenes and transcription factors, which are typically associated with normal and neoplastic hematopoietic cells. These findings suggest that the nonhematopoietic mesenchymal cells and the hematopoietic B-lymphocytes have a common progenitor. This is consistent with the idea that progenitor cells express genes that are characteristic of the multiple lineage paths that such cells may be capable of adopting. This study demonstrates the technical feasibility of transcriptome analysis of individual primary cell-culture grown stromal cells and supports the concept that bone marrow stromal cells are relatively homogeneous and show a phenotypic signature of potential multilineage differentiation capacity.

Adult↗
PubMed2004

Molecular single-cell PCR analysis of rearranged immunoglobulin genes as a tool to determine the clonal composition of normal and malignant human B cells.

Owing to the nearly limitless diversity of immunoglobulin (Ig) variable-region gene rearrangements, such rearrangements represent ideal clonal markers for B-lineage cells. This chapter describes an approach to isolate single cells from frozen tissue sections by microdissection using a hydraulic micromanipulator and the subsequent amplification of rearranged IgH and Igkappa genes from the cells in a seminested polymerase chain reaction (PCR) approach. The amplification of a priori unknown V-gene rearrangements is made possible by the usage of a collection of V-gene family-specific primers recognizing nearly all V-gene segments together with primer mixes for the J-gene segments. By sequence comparison of V-gene amplificates from distinct cells, the clonal relationship of the B-lineage cells can unequivocally be determined. As a large part of the V-gene rearrangements is amplified, the approach is also useful to address additional issues, such as V-, D-, and J-gene usage and the presence and pattern of somatic mutations.

Animals↗
PubMed2005

Laser printing of single cells: statistical analysis, cell viability, and stress.

Methods to print patterns of mammalian cells to various substrates with high resolution offer unique possibilities to contribute to a wide range of fields including tissue engineering, cell separation, and functional genomics. This manuscript details experiments demonstrating that BioLP Biological Laser Printing, can be used to rapidly and accurately print patterns of single cells in a noncontact manner. Human osteosarcoma cells were deposited into a biopolymer matrix, and after 6 days of incubation, the printed cells are shown to be 100% viable. Printing low numbers of cells per spot by BioLP is shown to follow a Poisson distribution, indicating that the reproducibility for the number of cells per spot is therefore determined not by the variance in printed volume per drop but by random sampling statistics. Potential cell damage during the laser printing process is also investigated via immunocytochemical studies that demonstrate minimal expression of heat shock proteins by printed cells. Overall, we find that BioLP is able to print patterns of osteosarcoma cells with high viability, little to no heat or shear damage to the cells, and at the ultimate single cell resolution.

Cell Count↗
PubMed1995

Interphase cytogenetic analysis of single cell suspensions prepared from previously formalin-fixed and paraffin-embedded tissues.

Fluorescence in situ hybridization (FISH) provides a rapid and accurate method for the detection of chromosomal aneuploidy. We have developed a technique for the use of FISH on single cell suspensions produced from either formalin-fixed or paraffin-embedded tissues. Preparation of such tissues involves sequential rehydration, enzymatic digestion to release single nuclei, and hybridization with a fluorescently labeled chromosome-specific centromeric probe. In a clinical setting formalin-fixed tissue from many tissue types is readily available for additional retrospective study. FISH on formalin-fixed tissues is especially beneficial in follow-up studies of cases involving termination after prenatal diagnosis or patients with a malignant disease where previous routine cytogenetics established the chromosomal aneuploidy. The use of this technique eliminates the biases of cytogenetic analysis due to clonal selection in tissue culture, the low number of cells analyzed, and the restriction to only dividing cell populations. We have demonstrated that this application of interphase cytogenetics to the study of various formalin-fixed tissues is amenable to the detection of chromosomal aneuploidies and has specific advantages over cytogenetic analysis.

Aneuploidy↗
PubMed2002

Single-cell cytokine analysis allows detection of cervical T-cell responses against human papillomavirus type 16 L1 in women infected with genital HPV.

Specific types of human papillomavirus (HPV) are known to play a causal role in the development of cervical cancer, with human papillomavirus type 16 (HPV-16) identified as the predominant type. Despite this, little is known about cervical immune responses to this pathogen. The aim of this study was to assess the feasibility of cervical cytobrush sampling and single-cell cytokine staining to investigate cervical lymphocyte-specific cytokine responses to HPV-16 antigens. Of eighteen women recruited into the study, five were HPV DNA positive at the cervix (current exposure) and a further five had circulating antibodies to HPV-16 (previous exposure). Cervical lymphocytes, isolated from the five HPV DNA-positive women, two HPV DNA-negative controls, and one woman with circulating HPV-16 antibodies were assessed for HPV-specific responses using intracellular staining for interferon-gamma (IFN-gamma) and interleukin-4 (IL-4). We demonstrate that both CD4(+) and CD8(+) cervical T lymphocytes, harvested from noninfected and infected subjects, produce these cytokines in response to nonspecific stimulation. However, antigen-specific (HPV-16 L1) IFN-gamma production by CD4(+) and CD8(+) cervical T lymphocytes is only detectable in women exposed currently or previously to HPV-16. This is the first time that antigen-specific cytokine responses of mucosal lymphocytes, obtained from a site of HPV infection, have been demonstrated. This finding clearly illustrates the use of intracellular cytokine staining for investigation of low precursor frequency single-cell antigen-specific responses in lymphocytes harvested from mucosal sites with HPV infection.

CD4-Positive T-Lymphocytes↗
PubMed2006

Elucidating the digital control mechanism for DNA damage repair with the p53-Mdm2 system: single cell data analysis and ensemble modelling.

Recent experimental evidence about DNA damage response using the p53-Mdm2 system has raised some fundamental questions about the control mechanism employed. In response to DNA damage, an ensemble of cells shows a damped oscillation in p53 expression whose amplitude increases with increased DNA damage--consistent with 'analogue' control. Recent experimental results, however, show that the single cell response is a series of discrete pulses in p53; and with increase in DNA damage, neither the height nor the duration of the pulses change, but the mean number of pulses increase--consistent with 'digital' control. Here we present a system engineering model that uses published data to elucidate this mechanism and resolve the dilemma of how digital behaviour at the single cell level can manifest as analogue ensemble behaviour. First, we develop a dynamic model of the p53-Mdm2 system that produces non-oscillatory responses to a stress signal. Second, we develop a probability model of the distribution of pulses in a cell population, and combine the two with the simplest digital control algorithm to show how oscillatory responses whose amplitudes grow with DNA damage can arise from single cell behaviour in which each single pulse response is independent of the extent of DNA damage. A stochastic simulation of the hypothesized control mechanism reproduces experimental observations remarkably well.

Cell Physiological Phenomena↗
PubMed2006

Gene expression analysis of myeloid and lymphoid lineage markers during mouse haematopoiesis.

Expression profiling of haematopoietic cells is hampered by the heterogeneous nature of haematopoietic tissues and the absolute rarity of early unrestricted progenitors. To overcome this, the expression profile of lymphoid and myeloid-associated genes (LEF1, EBF, CD19, Sox-4, B29, CD45, C-fms, lysozyme, PU.1 and CD5) were investigated in 40 mouse myeloid haematopoietic precursors covering the entire haematopoietic hierarchy from multipotential to committed single lineages. The lineage-specific expression seen in single-cell studies was confirmed by examining fractionated bone marrow, whole tissues and differentiation of the multipotent cell line FDCP (Factor Dependent Cell Paterson) mix. Analysis of the 40 single myeloid precursors failed to detect expression of lymphoid-associated genes, LEF1, EBF, CD19 and CD5, despite detection in lymphoid cell controls. Surprisingly, the lymphoid-associated genes, Sox-4 and B29 were detected in the single myeloid precursors, which was confirmed in bone marrow and a multipotential myeloid cell line. The pattern of Sox-4 and B29, is consistent with a potential role in the commitment of bipotential granulocytic/macrophage precursors towards the granulocyte or macrophage lineage. In addition to providing baseline values for myeloid and lymphoid lineage markers during mouse haematopoiesis, these results highlight the importance of single-cell analysis in the study of complex tissues.

Animals↗
PubMed1997

NPM/ALK fusion mRNA expression in Hodgkin and Reed-Sternberg cells is rare but does occur: results from single-cell cDNA analysis.

BACKGROUND: The translocation t(2;5)(p23;q35) leads to the fusion of the nucleophosmin gene (NPM) on chromosome 5q35 to the recently described receptor kinase ALK on 2p23. It is characteristic of a subgroup of CD30+ large-cell anaplastic non-Hodgkin's lymphoma (ALCL). Since some cases of Hodgkin's disease (HD) and ALCL share common features, a common pathogenesis has been proposed in a report of the expression of NPM/ALK fusion mRNA in 11/13 Hodgkin's lymphomas. PATIENTS AND METHODS: We approached this question by micro-manipulatory isolation of single Hodgkin and Reed-Sternberg (H-RS) cells and subsequent RT-PCR amplification of NPM/ALK fusion cDNA from these single cells. RESULTS: Specificity of cell selection was shown by the HD-specific pattern of EBV-gene expression in single H-RS cells. In 4 out of 7 cases, NPM/ALK fusion cDNA was detected in the RNA from whole lymph node tissue. In 2 out of 9 cases, NPM/ALK fusion sequences were amplified from single H-RS cells, albeit in a very low frequency (< 5%). CONCLUSIONS: These data indicate that NPM/ALK fusion transcripts do not play an early role in the pathogenesis of HD. Whether the rare expression of NPM/ALK is the result of clonal heterogeneity or an indication for clonal evolution and progression toward ALCL can only be answered by the repeated analysis of indicator cases during the course of the disease.

Adolescent↗