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At least 307 records · Page 17Linked to original sources
PubMed2001

DNA damage by cadmium and arsenic salts assessed by the single cell gel electrophoresis assay.

Human exposure to metals is frequent due to their ubiquity, wide use in industry, and environmental persistence. Direct and indirect genotoxic effects of cadmium (Cd) and arsenic (As) were reported. However, the mechanisms of induction of genetic damage are not well known. The aim of the present work was to evaluate the degree of damage induced by Cd and As salts in a human lung fibroblasts cell line using the single cell gel electrophoresis assay (SCGE). MRC-5 cells were treated with cadmium chloride (CdCl(2)), cadmium sulfate (CdSO(4)), sodium arsenite (NaAsO(2)) and cacodylic acid (C(2)H(7)AsO(2)). A significant dose-dependent increment in the extent of DNA migration as well as in the percentage of cells with tails was observed (P<0.001) after treatment with CdSO(4) and NaAsO(2). Treatment with CdCl(2) induced a relatively low level of DNA strand breaks in comparison with that induced by CdSO(4). The increase migration observed with the three compounds could be originated either by the direct induction of DNA lesions or by the inhibition of excision repair mechanisms. On the other hand, cells treated with C(2)H(7)AsO(2) showed a decrease in the migration length with the three doses employed (P<0.001). The decrease in the rate of DNA migration could be a consequence of the induction of DNA cross-links by organic arsenicals.Cd and As salts induced DNA damage in fibroblast cells, detected as DNA migration in the single cell gel (SCG) assay. The distribution of DNA migration among cells as a function of dose revealed that the majority of exposed cells showed more DNA damage than cells obtained from control cultures. The potential for human exposure to both metals has been increased over the years due to the increment in their use. For this reason, elucidation of carcinogenic mechanisms is very important.

Arsenic↗
PubMed2004

Microarrays and the gene expression profile of a single cell.

With completion of the human genome sequence, it is now possible to study the expression of the entire human gene complement of approximately 30,000-35,000 genes. To accomplish this goal, microarrays have become the leading methodology for the analysis of global gene expression. Improvements in technology have increased the sensitivity of microarrays to the point where it is feasible to study gene expression in a small number of cells and even at the single cell level. A summary of developments in the area of expression profiling in single cells will be described, and the rationale for these types of studies will be presented. In addition, from a biologist's point of view, some bioinformatic challenges of expression analysis of single cells will be discussed.

Cell Physiological Phenomena↗
PubMed2002

Radionuclide-antibody conjugates for single-cell cytotoxicity.

BACKGROUND: Radioimmunotherapy has primarily utilized high-energy beta-particles, which are intended to kill macroscopic tumor masses. Such conjugates do not kill single cells or micrometastases efficiently. For killing single cells, it may be preferable to use radiation with a much shorter path length, such as alpha-particles or Auger or conversion electrons. METHODS: This selective review focuses on the use of radiolabeled antibody (Ab) conjugates to achieve single-cell kill. The advantages and disadvantages of particular types of radionuclides, the significance of intracellular localization of the Ab, and the potential clinical application of this approach are discussed. Potentially useful radionuclides are listed. RESULTS: Auger and conversion electrons can kill cells effectively, with at least 6 logs of cell kill. Abs on the cell surface are only slightly less potent than Abs internalized into the cytoplasm, and this is consistent with theoretical considerations. alpha-Particles kill single cells very effectively, but the short half-lives of the available alpha-particle emitters are probably a disadvantage. High-energy beta-particles can also kill single cells if they bind in sufficient amounts, but their disadvantage appears to be greater nonspecific toxicity. CONCLUSIONS: Single-cell kill can be obtained with radionuclide-Ab conjugates. The selection of the optimal radionuclide may depend on the details of the clinical situation, such as the size and accessibility of the tumor burden, and the particular Ab to be used. Direct comparisons of various radionuclides are required in order to identify the optimal approach. However, for single-cell kill, as required for therapy of micrometastases, the use of Auger and conversion electron emitters appears to have substantial advantages. While current methods limit the applicability of this approach to Abs having a high level of binding, it may be applicable to lower-density antigens if higher specific activities or more potent radionuclides can be used. Tumor cure may require a mixture of radionuclides intended to kill both single cells and large tumor masses.

Alpha Particles↗
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↗
PubMed1991

Cytogenetic variability and kinetochore proteins. Comparison among populations derived from single-cell cultures.

This study reports comparative changes in five sub-lines obtained from a transformed culture of rat cerebral origin. Two of the lines were obtained from the original cell population while three others were raised from single-cell cultures. The comparative study was carried out on the DNA content and several cytogenetic parameters including variability in chromosome number, anaphase bridges, acentric fragments, chromosomes without detectable kinetochore proteins, and the frequency of micronuclei in these five lines. All cell lines, including the single-cell-derived clones expressed considerable variability in all aspects. One interesting aspect is the evolution of a chromosome with compound centromere, which is present only in two cell lines. The data indicate that the clone derived from a single cell does not maintain uniformity and even single cells have some sort of inherent potential to generate extreme variability. Some numerical variability may be attributed to a new phenomenon of a lack of kinetochore proteins seen on some chromosomes.

Anaphase↗
PubMed1995

Detection of DNA in single cells using an automated cell deposition unit and PCR.

A highly effective single-cell PCR method using a fluorescence-activated cell sorting (FACS)-based automated cell deposition unit (ACDU) that sorts single cells directly into PCR tubes was developed. To evaluate the sensitivity of this method, single ACH-2 cells (containing one HIV-1 genome per cell) were sorted, and 220 out of 228 samples (96.5%) were HIV DNA-positive by PCR. Furthermore, the number of samples accidentally containing more than one cell was determined by sorting single cells from a mixture of human cytomegalovirus (HCMV)-infected fibroblasts and ACH-2 cells. Multiplex nested PCR (nPCR) was then performed, detecting HCMV and HIV DNA simultaneously. From 66 sorted cells, 2 (3%) were double-positive for HIV and HCMV, 31 (47%) for HCMV alone, 30 (45.5%) for HIV alone and 3 (4.5%) were PCR-negative. The ACDU was then programmed to sort defined numbers of cells into PCR tubes. This is similar to classic dilution assays in that it allows the determination of the percentage of cells that was positive for a specific DNA. The accuracy of multiple cell deposition by the ACDU was evaluated by determining the percentage of HIV-positive cells in defined mixtures of ACH-2 and uninfected H9 cells. Infection rates determined by the ACDU correlated well with the rates expected from the given dilutions.

Autoanalysis↗
PubMed2006

Single-cell-derived mesenchymal stem cells overexpressing Csx/Nkx2.5 and GATA4 undergo the stochastic cardiomyogenic fate and behave like transient amplifying cells.

Bone marrow-derived stromal cells can give rise to cardiomyocytes as well as adipocytes, osteocytes, and chondrocytes in vitro. The existence of mesenchymal stem cells has been proposed, but it remains unclear if a single-cell-derived stem cell stochastically commits toward a cardiac lineage. By single-cell marking, we performed a follow-up study of individual cells during the differentiation of 9-15c mesenchymal stromal cells derived from bone marrow cells. Three types of cells, i.e., cardiac myoblasts, cardiac progenitors and multipotent stem cells were differentiated from a single cell, implying that cardiomyocytes are generated stochastically from a single-cell-derived stem cell. We also demonstrated that overexpression of Csx/Nkx2.5 and GATA4, precardiac mesodermal transcription factors, enhanced cardiomyogenic differentiation of 9-15c cells, and the frequency of cardiomyogenic differentiation was increased by co-culturing with fetal cardiomyocytes. Single-cell-derived mesenchymal stem cells overexpressing Csx/Nkx2.5 and GATA4 behaved like cardiac transient amplifying cells, and still retained their plasticity in vivo.

Animals↗
PubMed2026

Single-cell expression quantitative trait locus Mendelian randomization reveals immune cell-specific causal regulatory networks and actionable targets in polycystic ovary syndrome.

ObjectiveTo systematically investigate whether the pathogenesis of polycystic ovary syndrome (PCOS) is causally related to dysregulated gene expression in specific immune cell subsets, and to evaluate the potential of these causal genes as actionable drug targets.MethodsThis study employed a two-sample Mendelian randomization (MR) framework using publicly available genome-wide association study (GWAS) summary statistics. The participant data included 797 PCOS cases and 140,558 controls (no direct patient recruitment was involved). Instrumental variables were derived from high-resolution immune cell-specific single-cell expression quantitative trait locus (sc-eQTL) data (OneK1K project) across 14 immune cell types. Primary analyses utilized the inverse-variance weighted (IVW) method. Shared causal variants were validated using Bayesian colocalization. Phenome-wide association analysis (PheWAS), external transcriptomic dataset validation (GSE8157), and DrugBank database screening were conducted for pleiotropy assessment and drug repositioning.ResultsMR analysis revealed genome-wide significant causal associations for GLIPR1 in non-classical monocytes (Mono NC) and XBP1 in CD4+ effector memory T cells (CD4 ET) with PCOS risk. Higher GLIPR1 expression was associated with a decreased PCOS risk (OR = 0.669, P = 4.34&#xd7;10-6), whereas higher XBP1 expression was associated with an increased risk (OR = 1.406, P = 9.53&#xd7;10-8). Colocalization analysis confirmed that GLIPR1 shares a causal variant with PCOS (PP.H4 = 96.73%). PheWAS and external validation confirmed the safety profile and significant upregulation (P = 0.03) of GLIPR1. Drug repositioning identified SOT-107, a Phase III protein therapy drug, as a potential interacting agent for GLIPR1.ConclusionsThis sc-eQTL MR study reveals immune cell-specific causal regulatory networks in PCOS. GLIPR1 in non-classical monocytes represents a high-confidence protective target, while XBP1 provides suggestive evidence for immune-mediated pathogenesis. The candidate drug SOT-107 highlights theoretical repositioning opportunities, though rigorous preclinical validation remains required.

Female↗
PubMed2002

Alkylator-induced DNA excision repair in human leukemia CCRF-CEM cells in vitro, measured using the single-cell gel electrophoresis (comet) assay.

The capacity to repair DNA damage is an important factor that affects the therapeutic outcome in cancer treatment. To clarify the cellular repair response, we investigated the kinetics of DNA excision repair initiated by 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) in human leukemia CCRF-CEM cells at an exponential growth phase in vitro. Using the alkaline single-cell gel electrophoresis (comet) assay, we quantitated the repair kinetics as the amount of DNA single-strand breaks that were generated from the incision and were diminished by the rejoining in the repair process. CEM cells could initiate DNA excision repair in response to BCNU by starting an incision reaction. However, the incision capacity came to a plateau at a concentration of 80 to 100 microM or after an incubation time of 90 to 120 minutes. When the cells were pulsed with 40 microM BCNU, the maximal incision occurred at the end of the incubation period, and the repair process was completed within 4 hours When cells were treated with 100 microM BCNU, the incised DNA was not rejoined at 4 hours, suggesting that the repair was not completed. Higher concentrations might surpass the cellular capacity for repair and would be associated with increased cell death. Evaluation of the repair process may provide a clue for therapeutic strategies to improve clinical efficacy if accelerated DNA repair is responsible for the drug resistance.

Antineoplastic Agents, Alkylating↗
PubMed2003

Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity.

Laser capture microdissection in combination with microarrays allows for the expression analysis of thousands of genes in selected cells. Here we describe single-cell gene expression profiling of CA1 neurons in the rat hippocampus using a combination of laser capture, T7 RNA amplification, and cDNA microarray analysis. Subsequent cluster analysis of the microarray data identified two different cell types: pyramidal neurons and an interneuron. Cluster analysis also revealed differences among the pyramidal neurons, indicating that even a single cell type in vivo is not a homogeneous population of cells at the gene expression level. Microarray data were confirmed by quantitative RT-PCR and in situ hybridization. We also report on the reproducibility and sensitivity of this combination of methods. Single-cell gene expression profiling offers a powerful tool to tackle the complexity of the mammalian brain.

Animals↗
PubMed2023

Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins.

Assessment of single-cell gene expression (single-cell RNA sequencing) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here we introduce Dandelion, a computational pipeline for scVDJ-seq analysis. It enables the application of standard V(D)J analysis workflows to single-cell datasets, delivering improved V(D)J contig annotation and the identification of nonproductive and partially spliced contigs. We devised a strategy to create an AIR feature space that can be used for both differential V(D)J usage analysis and pseudotime trajectory inference. The application of Dandelion improved the alignment of human thymic development trajectories of double-positive T cells to mature single-positive CD4/CD8 T cells, generating predictions of factors regulating lineage commitment. Dandelion analysis of other cell compartments provided insights into the origins of human B1 cells and ILC/NK cell development, illustrating the power of our approach. Dandelion is available at https://www.github.com/zktuong/dandelion .

Humans↗
PubMed2006

High-throughput and real-time study of single cell electroporation using microfluidics: effects of medium osmolarity.

Electroporation has been widely accepted as an important tool for the delivery of exogenous molecules into cells. Previous mechanistic studies have been carried out by observing either the average behavior from a large population of cells or the response from a small number of single cells. In this study, we demonstrated a novel microfluidic method with high throughput (up to 30 Hz) for real-time studies of single cell electroporation events. Electroporation occurred when cells flowed through a section of a microfluidic channel defined by special geometry. A CCD camera was used to monitor the response of cells starting from the onset of the electroporation. We studied the swelling of Chinese hamster ovary cells and the rupture of cell membrane during electroporation using this technique. We applied buffers with different osmolarities to investigate the effects of medium osmolarity, based on results from a population of single cells. We were able to establish the distributions of the rates of swelling and membrane rupture in the cell population. We also explored establishing the correlation between the property (the cell diameter) and the behavior (the swelling rate) of single cells. Our results indicated that the processes of swelling and rupture occurred more rapidly in the hypotonic or hypertonic buffers than in the isotonic buffer. Statistical analysis did not reveal strong linear correlation between the cell size and the swelling rate. These proof-of-concept studies reveal the potential of applying microfluidics to study electroporation of a cell population at single cell level in real time with high throughput. The limitations associated with this approach were also addressed.

Animals↗
PubMed1999

Four of five RAG-expressing JCkappa-/- small pre-BII cells have no L chain gene rearrangements: detection by high-efficiency single cell PCR.

Single cell PCR assays have been further developed that detect over 80% of all VkappaJkappa, VkappaRS, and VlambdaJlambda rearrangements at efficiencies between 70% and 90%. These IgL chain gene rearrangement assays were used with small pre-BII cells that develop in comparably high numbers in the bone marrow of wild-type, Ckappa-deficient, and JCkappa-deficient homozygous and heterozygous mice. In all of these mice, only 15%-25% of all small pre-BII cells carry VlambdaJlambda rearrangements. These results confirm that lambdaL chain gene rearrangements occur independently of kappaL chain gene rearrangement and expression. They also show that a large part of the small pre-BII cells that express the rearrangement machinery can develop without IgL chain gene rearrangements.

Animals↗
PubMed2025

Droplet-Based Single-Cell 3' mRNA Sequencing of Marburg Virus-Infected Samples.

Single-cell technologies are continually evolving with emerging methods that are gradually uncovering the central DNA-RNA-protein dogma. Single-cell RNA sequencing is one arm of a multi-omic approach that achieves an astounding level of granularity to reveal the complexity of virus-host interactions at the transcriptomic level. Cell tropism, virus replication, pathogenesis, and gene expression changes mediated by the virus and the host's immune response to infection are just some areas of study that are gaining better clarity due to the high-resolution analysis afforded by the technology.We describe a single-cell sequencing protocol for Marburg virus infection in vivo using nonhuman primate blood and the 10&#xd7; Chromium Next GEM single-cell genomics methodology. Working with pathogens of high consequence is logistically complicated, requiring containment in biosafety level (BSL)-4 laboratories and harsh inactivation procedures before samples can safely be removed to lower biosafety conditions. We provide procedural insight into sample isolation and processing conducted in BSL-4 and describe the requirements for safe sample removal without jeopardizing quality for down-stream sequencing and analysis in BSL-2 conditions. Characterization of complicated biological processes mediated by high-containment pathogens, typically restricted to analogous model systems, e.g., minigenome, can be achieved using live virus.

Animals↗
PubMed1992

Dissociation of unintegrated viral DNA accumulation from single-cell lysis induced by human immunodeficiency virus type 1.

Acute cytopathic retroviral infections are accompanied by the accumulation, due to superinfection, of large amounts of unintegrated viral DNA in the cells. The cytopathic effects of human immunodeficiency virus type 1 (HIV-1) infection are specific for cells that express the CD4 viral receptor and consist of syncytium formation and single-cell lysis. Here we investigated the relationship between superinfection and single-cell lysis by HIV-1. Antiviral agents were added to C8166 or Jurkat lymphocytes after HIV-1 infection had occurred. Treatment with azidothymidine or a neutralizing anti-gp120 monoclonal antibody reduced or eliminated, respectively, the formation of unintegrated viral DNA but did not inhibit single-cell killing. Furthermore, in the infected Jurkat cells, the levels of unintegrated viral DNA peaked several days before significant single-cell lysis was observed. Essentially complete superinfection resistance was established before the occurrence of single-cell killing. These results demonstrate that single-cell lysis by HIV-1 can be dissociated from superinfection and unintegrated viral DNA accumulation. These results also indicate that single-cell killing may involve envelope glycoprotein-receptor interactions not accessible to the exterior of the cell.

Antibodies, Monoclonal↗
PubMed2004

On-column labeling reaction for analysis of protein contents of a single cell using capillary electrophoresis with laser-induced fluorescence detection.

This chapter presents methods for capillary electrophoresis (CE) fingerprinting of proteins in a cell extract and in single cells. A custom-made CE instrument with laser-induced fluorescence (LIF) detection, used for the analyses, is described. Detailed procedures are given for: (1) on column labeling of proteins with a fluorogenic reagent, 5-furoyl quinoline-3-carboxaldehyde, (2) CE separation of labeled proteins, (3) preparation of a protein extract from cultured cells, and (4) manipulations associated with analyses of proteins in single cells. More than 20 relevant publications are cited in this chapter to assist the reader with adopting the presented methods.

Animals↗
PubMed2026

FIERCE: reconstructing dynamic trajectories from the differentiation potency of single cells.

MOTIVATION: Since the introduction of single-cell RNA sequencing (scRNA-seq), numerous computational approaches have been developed to reconstruct dynamic cellular processes from static transcriptional profiles. These methods order cells along continuous trajectories by assessing their similarity in the gene-expression space. However, they rely on several assumptions, such as prior knowledge of the structure and directionality of the expected genealogy. These assumptions can limit their application to complex cellular systems with poorly understood developmental paths. RESULTS: To address this challenge, we introduce FIERCE (Framework for InfERence of the veloCity of Entropy), a novel computational pipeline designed to predict the changes in the differentiation potency of single cells during dynamic processes. Through a fully unsupervised approach, FIERCE enables the inference of cell lineages directly on the differentiation landscape of the biological system, thus eliminating the need for prior specification of developmental parameters. We demonstrate the efficacy of FIERCE by reconstructing three well-known mouse differentiation systems and by quantifying its accuracy on simulated data. AVAILABILITY AND IMPLEMENTATION: The FIERCE R package is available on GitHub at https://github.com/bicciatolab/FIERCE.

Cell Differentiation↗
PubMed1979

Dynamic assay of enzyme activities in single cells by flow cytometry.

Three enzymes in single cells were assayed dynamically by flow cytometry using four fluorogenic substrates. Acid phosphatase was determined with 7-bromo-3-hydroxy-2-naphtho-o-anisidine (naphthol AS-BI) phosphate and 4-methylumbelliferone (MU) phosphate, neutral esterase with fluorescein diacetate, and lactic dehydrogenase with NAD-sodium lactate. Fluorescence measurements obtained with the flow cytometer were converted into relative specific enzyme activities for single cells with molar fluorescence coefficients determined with a spectrofluorometer. Specific activities obtained from spectrofluorometric data were compared with activities calculated from flow cytometeric data. Flow cytometric assays gave lower specific single cell activities for 4-methylumbelliferone phosphate hydrolysis and for lactic dehydrogenase than did similar assays by standard spectrofluorometry. Product diffusion may be the greatest cause for this discrepancy.

Acid Phosphatase↗