Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “single cell analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3Linked to original sources
PubMed2004

Obtaining single cells: analysis and evaluation of an experimental protocol by means of a simulation model.

The research presented in this paper analyses a newly developed experimental protocol for isolating single cells by constructing a simulation model of the process. The protocol involves sequential 50% dilutions of a cell suspension in a microtiter plate, so that eventually, wells are obtained containing exactly one cell. The aim of this modelling study is (i) to gain insight in the governing mechanisms of the dilution process, (ii) to confirm experimental findings and (iii) to enable the prediction of an average outcome for future experiments. The model construction process is presented chronologically. The initial basic model simulates the experiment as a sequence of binomial processes, using Monte Carlo techniques. Statistical analysis of the results shows that aggregational factors need to be taken into account in the form of a lognormal distribution. Several issues involved in this adaptation are discussed. To fully account for cell aggregation in the dilution process, a cell clumping algorithm is built into the simulation model. Simulation data from the resulting model show similar statistical characteristics as the experimental data and yield reliable prediction intervals for the available experimental data. The simulation model is a useful tool to support experimental findings and predict the outcome of future experiments. Even more importantly, this study emphasises the importance of careful statistical analysis in single cell research. The impact of stochastic effects is considerably amplified at the low cell concentrations involved and needs to be taken into account in any modelling effort.

Bacteria↗
PubMed2003

Single-cell analysis of the murine chemokines MIP-1alpha, MIP-1beta, RANTES and ATAC/lymphotactin by flow cytometry.

Upon stimulation, leukocytes secrete chemokines to attract distinct effector cell populations to the site of inflammation. Only a few data are available about the phenotype and the frequencies of cells expressing particular chemokines. To date, the expression of individual chemokines is mainly analyzed at the mRNA level or via ELISA. Both techniques do not allow the analysis of chemokines at the level of single cells. We have established the intracellular flow-cytometric detection of the murine chemokines macrophage inflammatory protein-1alpha (MIP-1alpha), MIP-1beta, regulated on activation normal T cell expressed and secreted (RANTES) and activation-induced, T cell-derived and chemokine-related cytokine (ATAC)/lymphotactin. For detection of the nonclassical chemokine ATAC, we generated the novel mAb MTAC-2. Using this assay, we analyzed for the first time the frequency and kinetics of the expression of these murine chemokines in lymphocyte subpopulations. We show that these chemokines are differentially expressed by NK cells, naive and memory CD4(+) and CD8(+) T cells. Our results emphasize that the analysis of chemokine expression at the single-cell level is required to understand the functional role of specialized lymphocyte subpopulations in vivo.

Animals↗
PubMed2003

Single-cell analysis of lambda immunity regulation.

We have examined expression of the lambdacI operon in single cells via a rex Colon, two colons gfp substitution. Although average fluorescence agreed with expectations for expression of lambda-repressor, fluorescence fluctuated greatly from cell-to-cell. Fluctuations in repressor concentration are not predicted by previous models and are tolerated in part by a regulatory response to DNA damage.

Artificial Gene Fusion↗
PubMed2005

Distinguishing between proliferating nodal lymphoid blasts in chronic myelogenous leukemia and non-Hodgkin lymphoma: report of three cases and detection of a bcr/abl fusion signal by single-cell analysis.

Lymph node biopsies were analyzed from three patients with chronic myelogenous leukemia (CML) showing nodal blast proliferation. Immunohistochemically, the blasts from all three patients had an immature marker profile with a T-blast population (cCD3+, CD4-, CD7+, CD8-, CD99+, terminal deoxynucleotidyl transferase +) and a hematopoietic progenitor cell marker (CD34). In two patients, the blasts also expressed myeloid lineage specificity (naphthol AS-D chloroacetate esterase activity and myeloperoxidase positivity). However, it was difficult to distinguish between blast proliferation in CML and non-Hodgkin lymphoma from these immunohistopathological findings alone. Subsequently, bcr gene rearrangement and bcr/abl mRNA expression were detected by Southern blot and reverse transcription-polymerase chain reaction analysis of the lymph nodes. Fluorescence in situ hybridization (FISH) analysis of lymph node touch smears also disclosed bcr/abl gene fusion signals in the blasts of all patients, confirming that the blasts were derived from Philadelphia chromosome-positive CML. Accurate discrimination between the proliferating nodal blasts of CML and non-Hodgkin lymphoma is essential for determining subsequent therapy. FISH analysis of bcr/abl in single-cell blast preparations is an efficient tool that allows rapid, accurate cytopathological diagnosis of extramedullary blast-phase CML and its discrimination from non-Hodgkin lymphoma.

12E7 Antigen↗
PubMed2002

DNA damage profiling in motor neurons: a single-cell analysis by comet assay.

We developed a method to measure DNA damage in single motor neurons (MN). A cell fraction enriched in viable alpha-motor neurons was isolated from adult rat spinal cord. This cell preparation was used to measure the vulnerability of the MN genome to different reactive oxygen species (ROS). MN were exposed in vitro to hydrogen peroxide, nitric oxide and peroxynitrite. Specific types of DNA lesions (e.g., abasic sites, single-strand breaks, and double-strand breaks) were measured using single-cell gel electrophoresis (comet assay). The MN genome was very susceptible to attack by ROS. Different ROS induced different DNA damage profiles in MN. MN were also isolated from adult rats with sciatic nerve avulsions to show that DNA damage emerges early during their degeneration in vivo. This study demonstrates that the comet assay is a feasible method for profiling DNA lesions in the genome of single MN. Viable mature MN can be isolated and used for in vitro models of MN genotoxicity and can be isolated from in vivo models of MN degeneration for profiling DNA damage on a single-cell basis.

Animals↗
PubMed1997

Single-cell analysis of regulatory gene expression in quiescent and activated mouse skeletal muscle satellite cells.

Repair and regeneration of adult skeletal muscle are mediated by satellite cells. In healthy muscle these rare mononucleate muscle precursor cells are mitotically quiescent. Upon muscle injury or degeneration, members of this self-renewing pool are activated to proliferate and then differentiate. Here we analyzed in single satellite cells the expression of a set of regulatory genes that are candidates for causal roles in satellite cell activation, maturation, and differentiation. Individual cells were identified as satellite cells and selected for analysis based on their physical association with single explanted myofibers or their position beneath the basal lamina in unperturbed muscle tissue. Using a multiplex single-cell RT-PCR assay we simultaneously monitored expression of all four MyoD family regulators of muscle determination and differentiation (MRFs) together with two candidate markers of satellite cell identity, c-met and m-cadherin. By making these measurements on large numbers of individual cells during the time course of satellite cell activation, we were able to define which expression states (possible combinations of the six genes) were represented and to specify how the representation of each state changed with time. Activated satellite cells began to express either MyoD or myf5 first among the MRFs; most cells then expressed both myf-5 and MyoD simultaneously; myogenin came on later in cells expressing both MyoD and myf5; and many cells ultimately expressed all four MRFs simultaneously. The results for fiber-associated satellite cells from either predominantly fast or slow muscles were indistinguishable from each other. The c-met receptor tyrosine kinase was also monitored because it is a candidate for mediating activation of quiescent satellite cells (Allen et al., 1995) and because it might also be a candidate molecular marker for satellite cells. A significant difficulty in studying mouse satellite cells has been the absence of molecular markers that could identify them in the quiescent state before expression of MRFs or desmin and distinguish them from fibroblasts. We show here that c-met receptor is present beneath the basal lamina on presumptive satellite cells in intact muscle and that c-met mRNA and protein are expressed by all myofiber-associated satellite cells from the time of explant through the course of activation, proliferation, and differentiation. c-met was not detected in muscle-derived fibroblasts or in other mononucleate cells from healthy muscle explants. When compared directly with m-cadherin, which has previously been suggested as a marker for quiescent satellite cells, m-cadherin mRNA was detected only in a small subset of satellite cells at early times after myofiber explant. However, at late times following activation (by 96 hr in this fiber culture system), c-met and m-cadherin were uniformly coexpressed. From the individual satellite cell expression types observed, a model of the satellite cell population at rest and during the time course of activation was generated.

Animals↗
PubMed1994

Preimplantation single-cell analysis of multiple genetic loci by whole-genome amplification.

Due to the limited amount of DNA in a single diploid cell, preimplantation genetic diagnosis has relied on single- or dual-locus analyses in biopsied blastomers. We have applied single-cell whole-genome preamplification to PCR-based analysis of multiple disease loci from the same diploid cell. This method allows diagnosis of multiple disease genes, analysis of multiple exons/introns within a gene, or corroborative embryo-sex assignment and specific mutation detection at sex-linked loci. A blinded study of six genetic loci was performed with whole-genome preamplification followed by nested PCR. Amplification was observed in 103 of 105 assays (98%) and a correct diagnosis was made in 98%. All human blastomeres were correctly diagnosed (100%) at loci where the genotype could be confirmed, attesting to the reliability of the technique. Preamplification has now been applied successfully to the analysis of the two major mutations responsible for Tay-Sachs disease and of a common restriction polymorphism in the gene responsible for hemophilia A. The fidelity and length of product derived from this preamplification step make it an appealing technique for preimplantation genetic diagnoses requiring analyses at more than one locus.

Base Sequence↗
PubMed1993

Cytokine-specific ELISPOT assay. Single cell analysis of IL-2, IL-4 and IL-6 producing cells.

In order to assess cytokine-producing cells at the single cell level, the cytokine-specific ELISPOT assay has proven to be an important and sensitive method. The purpose of this study was to adapt this method to elucidate individual cells producing murine IL-2, IL-4 or IL-6. In order to establish these cytokine-specific ELISPOT assays, IL-2-, IL-4- and IL-6-specific cDNA transfected myeloma cell lines, e.g., X63-Ag8-653 X2, X63-Ag8-653 X4 and X63-Ag8-653 X6, respectively, were used as specific cytokine-producing cells. In the IL-2 ELISPOT assay, the coating reagent, monoclonal antibody (mAb) rat IgG2a anti-mouse IL-2 (CR #40014) was used while rabbit IgG polyclonal anti-mouse IL-2 was employed for detection of IL-2 spot forming cells (SFC). The mAbs anti-mouse IL-4, BVD4-1D11 and BVD6-24G2 were selected as capture and detection antibodies for enumeration of IL-4 SFC. For the IL-6 ELISPOT assay, anti-mouse IL-6 (MP5-20F3) mAb was used for coating and MP5-32C11 mAb was used for detection of IL-6 SFC. When IL-2 producing X63-Ag8-653 X2 cells were subjected to these three different ELISPOT assays, IL-2-specific SFC were only noted with the IL-2 ELISPOT system. In the case of IL-4 SFC, only X63-Ag8-653 X4 cells formed specific spots using the tandem of BVD4-1D11 and BVD6-24G2 mAbs. IL-6-specific spots developed in MP5-20F3 mAb pre-coated wells containing X63-Ag8-653 X6 cells, when developed with mAb anti-IL-6 (MP5-32C11). Addition of cycloheximide (50 micrograms/ml) inhibited formation of IL-2, IL-4 and IL-6 SFC by approximately 90%. When an unrelated mAb was used as detection antibody in these three different cytokine-specific ELISPOT assays, IL-2-, IL-4- and IL-6-specific SFC were not detected. Further, when concanavalin A stimulated T cells from Peyer's patch of normal mice were subjected to the respective cytokine-specific ELISPOT assay, IL-2, IL-4 and IL-6 SFC were enumerated. These results have shown that cytokine-specific IL-2, IL-4 and IL-6 ELISPOT assays have now been established and will allow analysis of the frequency of cytokine-secreting cells at the single cell level.

Animals↗
PubMed1989

Single-cell analysis of the mitogen-induced calcium responses of normal and protein kinase C-depleted Swiss 3T3 cells.

Single-cell fluorescence image analysis has been used to characterize the mitogen-induced increases in intracellular free [Ca2+] ([Ca2+]i) in control and protein kinase C-depleted Swiss 3T3 cells. More than 80% of the control cells exhibited fast, transient responses to bombesin, vasopressin, or prostaglandin F2 alpha (PGF2 alpha). In contrast, the [Ca2+]i responses induced by platelet-derived growth factor (PDGF) were markedly more heterogeneous, slower, and often biphasic, with fewer cells (60-70%) responding. The peak [Ca2+]i values obtained in response to each mitogen showed substantial variation between cells. Brief pretreatment of the cells with 12-O-tetradecanoyl phorbol 13-acetate (TPA) reduced the [Ca2+]i responses to bombesin, but did not affect the responses to PDGF. Long-term pretreatment of the cells with TPA to down-modulate protein kinase C resulted in substantially prolonged [Ca2+]i responses to bombesin, vasopressin, and PGF2 alpha, but had no such effect on the responses to PDGF. We conclude that differences between the [Ca2+]i responses to bombesin and PDGF, previously reported using cell populations, reflect differences occurring in individual cells, and that the [Ca2+]i responses to bombesin, vasopressin, and PGF2 alpha (but not PDGF) are subject to feedback inhibition via protein kinase C.

3T3 Cells↗
PubMed1996

Single-cell analysis of unstable genes.

PURPOSE: We have developed sensitive diagnostic procedures for studies on the normal and mutant alleles of the triplet repeat genes associated with myotonic dystrophy and fragile X in single human somatic cells, gametes and embryos. METHODS: Polymerase chain reaction (PCR) assays for the normal alleles of the myotonic dystrophy and fragile X loci have been refined to the sensitivity of the single cell. In addition, we have developed a simple PCR-based technique, termed ¿Repeat Primer PCR', which can detect the full fragile X expansion in small samples of buccal cells. CONCLUSIONS: The assay for the triplet repeat sequence in the myotonic dystrophy locus could not be used to study stability since we observed additional PCR products derived from in vitro expansion of the triplet repeat sequence during the PCR reaction itself. The implications of in vitro expansion and allele drop-out for studies on the timing of the expansion in development and preimplantation diagnosis of triplet repeat diseases are discussed. The development of a new PCR procedure to identify the expanded alleles of the fragile X locus could prove invaluable for monitoring the timing of repeat expansion in early embryonic development. Triplet repeat polymorphisms provide a means of identifying the maternally and paternally-derived alleles of the myotonic dystrophy gene. Using single cell reverse transcriptase PCR analysis, we have monitored the onset of the myotonic dystrophy gene transcription in early preimplantation embryos. Transcripts from the paternally-inherited allele of the myotonic dystrophy gene are already detectable in the 1-cell stage human embryo.

Alleles↗
PubMed2006

High-throughput single-cell analysis for enzyme activity without cytolysis.

A novel high-throughput method without cytolysis for determination of enzyme activity inside single cells was developed by a combination of chemical cell perforation and an intracellular enzyme-catalyzed reaction. Peroxidase (PO) inside human neutrophils was chosen as the model system. Cells were perforated with digitonin to form micropores on the cell membrane. The perforated cells, with physiological buffer saline of pH 7.4 containing hydroquinone (H2Q) and H2O2, were continuously propelled by pressure through a capillary as the microsampler and microreactor. Small molecules H2Q and H2O2 could diffuse into the cell interior through the micropores on the cell membrane, and the large molecule PO remained in the cell interior. Intracellular PO converted H2Q into benzoquinone (BQ). BQ diffused out from the cell interior to the cell surface through the micropores and formed a BQ zone around the cell. The process proceeded in the capillary during cell movement. The BQ zones around every moving perforated cell were continuously delivered to the capillary outlet by hydraulic flow and detected. An average detection rate of >1 cell/min was obtained.

Catalysis↗
PubMed2025

Single-cell analysis of dup15q syndrome reveals developmental and postnatal molecular changes in autism.

Duplication 15q (dup15q) syndrome is a leading genetic cause of autism spectrum disorder, offering a key model for studying autism-related mechanisms. Using single-cell and single-nucleus RNA sequencing of cortical organoids from dup15q patient-derived iPSCs and post-mortem brain samples, we identify increased glycolysis, disrupted layer-specific marker expression, and aberrant morphology in deep-layer neurons during fetal-stage organoid development. In adolescent-adult postmortem brains, upper-layer neurons exhibit heightened transcriptional burden related to synaptic signaling, a pattern shared with idiopathic autism. Using spatial transcriptomics, we confirm these cell-type-specific disruptions in brain tissue. By gene co-expression network analysis, we reveal disease-associated modules that are well preserved between postmortem and organoid samples, suggesting metabolic dysregulation that may lead to altered neuron projection, synaptic dysfunction, and neuron hyperexcitability in dup15q syndrome.

Humans↗
PubMed1998

Laser-micropipet combination for single-cell analysis.

Due to its potential for exquisite mass detection limits and resolving power, capillary electrophoresis is used for biochemical measurements on single cells; however, accurate measurements of many physiological parameters require sampling strategies that are considerably faster than those presently available. We have developed a laser-based technique to lyse single, adherent, mammalian cells on millisecond time scales. The cellular contents are then introduced into a capillary where electrophoretic separation and detection are performed. Improved temporal resolution of biological measurements results from the extremely rapid lysis made possible by this method. Additionally, the cell is not perturbed by mechanical or electrical stresses prior to sampling. Such disturbances can alter cellular physiology, resulting in inaccurate measurements. The fast cell lysis, the absence of cellular stresses prior to lysis, and the application to adherent mammalian cells are significant refinements to CE-based measurements on single cells. With this laser-micropipet combination, it will be possible to measure the intracellular concentration of molecules that change on subsecond to second time scales, for example, substrates of many cellular enzymes.

Animals↗
PubMed2000

Clonal evolution in a primary cutaneous follicle center B cell lymphoma revealed by single cell analysis in sequential biopsies.

B cell neoplasias descending from germinal center cells harbor the hallmark of intraclonal diversity resulting from ongoing mutation in the variable parts of their immunoglobulin-encoding genes. To characterize a primary cutaneous follicle center B cell lymphoma in more detail, we analyzed the respective VH and VL genes in single cells mobilized from four sequential biopsies, three taken from the skin and one obtained after internal dissemination from a retrobulbar infiltrate. The lymphoma cells were found to contain V5-51/D6-12/JH5b (heavy chain) and A27/Jkappa2 (light chain) gene rearrangements detected on both the genomic and the transcriptional level. To provide an accurate mutation analysis, the specific VH gene counterpart (V5-51UK) was cloned from the patient's germline. Analyzing 226 single cells, we found: (i) complete nucleotide identity when VH and VL genes of lymphoma cells from one particular biopsy were compared among each other; (ii) intraclonal diversity due to ongoing mutation comparing the sequences obtained from sequential biopsies; (iii) both VH and VL genes to be highly mutated. Deducing from the sequence data, we propose a scenario of the clonal evolution of the B cell tumor in this patient. From the molecular-biological point of view, this primary cutaneous follicle center B cell lymphoma shows the features of a germinal center cell lymphoma. To draw this conclusion from single cell PCR data, however, a sample of sequential biopsies had to be analyzed.

B-Lymphocytes↗
PubMed2005

Simultaneous detection of double-stranded RNA-induced protein kinase and its specific mRNA by single cell analysis.

Fluorescent in situ hybridization was combined with flow cytometry to detect the expression of the double-stranded-RNA-induced protein kinase (PKR) in single cells. Labeled anti-sense oligonucleotide was used to target the specific mRNA while the protein was targeted with an antibody. It was demonstrated that the PKR-mRNA signal could be protected through a lengthy immunostaining procedure. The expression pattern of the PKR-mRNA with respect to DNA content was shown to be comparable to that of 18S ribosomal RNA.

Cell Line, Tumor↗
PubMed1995

Molecular single-cell analysis of Hodgkin and Reed-Sternberg cells.

In Hodgkin's disease, the malignant Hodgkin and Reed-Sternberg (HRS) cells are present in very small numbers in the diseased tissue, thus making molecular analysis of these cells very difficult. Using micromanipulation and single-cell polymerase chain reaction (PCR), rearranged immunoglobulin genes can be amplified and sequenced from single HRS cells. Oligonucleotides chosen from the variable (V)-gene sequences identified in the HRS cells can be used as specific markers for the tumour clone. This technique will allow one to search for members of the tumour clone in various compartments of the patient's body, to follow disease progression during therapy, and to analyse stem-cell populations for contamination by tumour cells before autologous bone-marrow transplantation.

Animals↗
PubMed2003

Real-time single cell analysis of Smac/DIABLO release during apoptosis.

We examined the temporal and causal relationship between Smac/DIABLO release, cytochrome c (cyt-c) release, and caspase activation at the single cell level during apoptosis. Cells treated with the broad-spectrum caspase inhibitor z-VAD-fmk, caspase-3 (Casp-3)-deficient MCF-7 cells, as well as Bax-deficient DU-145 cells released Smac/DIABLO and cyt-c in response to proapoptotic agents. Real-time confocal imaging of MCF-7 cells stably expressing Smac/DIABLO-yellow fluorescent protein (YFP) revealed that the average duration of Smac/DIABLO-YFP release was greater than that of cyt-c-green fluorescent protein (GFP). However, there was no significant difference in the time to the onset of release, and both cyt-c-GFP and Smac/DIABLO-YFP release coincided with mitochondrial membrane potential depolarization. We also observed no significant differences in the Smac/DIABLO-YFP release kinetics when z-VAD-fmk-sensitive caspases were inhibited or Casp-3 was reintroduced. Simultaneous measurement of DEVDase activation and Smac/DIABLO-YFP release demonstrated that DEVDase activation occurred within 10 min of release, even in the absence of Casp-3.

Apoptosis↗
PubMed1995

Molecular single-cell analysis identifies somatostatin type 1 (sst1) receptors to block inwardly rectifying K+ channels in rat brain oligodendrocytes.

For the first time whole-cell patch-clamp recordings were performed together with a molecular analysis of mRNA expression on single rat cortical oligodendrocytes. The neuropeptide somatostatin (3 microM) was found to rapidly (< 1s) induce a 58 +/- 33% block of the inwardly rectifying K+ current (IKIR). Following recording, the cells' cytoplasm was harvested through the patch pipette and processed for RNA amplification. Polymerase chain reactions on the amplified products showed that of the primers specific for all five somatostatin receptor subtypes (sst1-sst5), only those derived from sst1 amplified cDNA fragments. Sequence analysis of these fragments revealed complete identity to rat sst1 receptors; thus they are probably the major subtype of somatostatin receptors that control IKIR in rat brain oligodendrocytes.

Animals↗