Studies of human natural killer cells. II. Analysis at the single cell level.
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Basal Cell Carcinoma↗
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A quantitative, single-cell PCR analysis of an antigen-specific TCR repertoire selected during an in vivo CD8 response: direct evidence for a wide range of clone sizes with uniform tissue distribution.
The development of T cell effector and memory responses against foreign antigens (Ags) involves the activation, differentiation and proliferation of naive T cells expressing distinct Ag-specific TCRs. Understanding the complexity of Ag-selected TCR repertoires in individual responders in terms of the sequences selected and their relative frequencies may provide indications about how a repertoire is established and suggest ways to influence the outcome of an immune response. Most methods of repertoire analysis are unsuitable for calculating the relative in vivo frequencies of Ag-specific clones (expressing distinct TCRs) selected during an immune response, whereas sequence data obtained by single-cell PCR analysis directly reflect cell frequencies if a sufficiently large number of cells is sampled. Using a CD8 T cell response in normal mice in which Ag-selected cells are identified by cell surface phenotype and rearranged TCRBV sequences are determined by PCR amplification of genomic DNA directly from single cells, we have analyzed a large number (>200 per animal) of structurally-related Ag-specific TCRs to calculate the frequencies of distinct TCRs selected by individual mice. We found that each responder selects a unique Ag-specific TCR repertoire in which the various TCRBV sequences are present in a wide range of frequencies. However, the overall distribution of sequences is quite similar for different responder animals. Moreover, an individual's selected TCR repertoire is uniformly represented among Ag-specific CD8 cells circulating in the blood or localized in the spleen or liver. Relatively few sequences make up the bulk of the repertoire and account for the oligoclonality observed in earlier studies. We discuss various models that could account for this skewed distribution of an Ag-selected TCR repertoire.
Animals↗
[Single cell photometry analysis of nuclear DNA in treated undifferentiated prostate cancer and its clinical significance].
Based on 67 specimens from 20 conservatively treated undifferentiated prostate cancer patients cell nucleic acid analysis combined with a prospective clinical study was attempted using single cell scanning-cytophotometry. Regardless of therapy type a statistically significant difference in nuclear DNA-content was evident between successfully treated prostate cancers and therapy-resistant cancers. Good prognosis was suggested by a significant decline from aneuploid or polyploid to diploid nuclear-DNA-content with a narrow peak in 2c, especially within the first 12 weeks of treatment. Lack of DNA-content alteration or a DNA-frequency distribution change to the right were correlated with rapid clinical regression. Although all had undifferentiated prostate cancer morphology statistically significant differences in nuclear DNA-content were found. The prognostic value of this remains unknown.
DNA, Neoplasm↗
Steroid analysis in single cells by capillary electrophoresis with collinear laser-induced fluorescence detection.
Capillary electrophoresis with collinear laser-induced fluorescence detection was used for the analysis of steroids in single R2C cells. Progesterone secretion was monitored from cultured cells and subsequently detected in single cells. Mass detection limit of 10(-18) mol for dansylated steroids was achieved with the 325-nm line of a helium-cadmium laser. Dansylhydrazine proved to be an effective fluorescent tag for derivatization of steroids outside and inside the biological cell. Fluorescence microscopy indicates that a dimethyl sulfoxide-containing physiological buffer was sufficient to incorporate the tag inside the cell for subsequent steroid derivatization.
Animals↗
RhD genotype determination by single sperm cell analysis.
OBJECTIVE: An Rh-negative woman with preexisting anti-D antibodies may affect some or all subsequent fetuses, depending on the genotype of her Rh-positive partner. Currently, a reliable technique for an absolute determination of RhD genotype is not available. This study was initiated to develop an accurate method for RhD genotyping in men. STUDY DESIGN: RhD genotype was determined by deoxyribonucleic acid amplification of a D-specific sequence in single sperm cell samples. Micromanipulation techniques were used for sampling of single sperm cells, which were further amplified by multiplex nested polymerase chain reaction at the RhD locus. A RhD sequence amplification product was expected in all of the successfully amplified samples from Rh-positive homozygotes, in some of the samples from heterozygotes, and in none of the samples form Rh-negative subjects. RESULTS: RhD genotype was accurately determined in 10 of 10 donors. A total of 132 single sperm cells were analyzed (8 to 17 samples per donor), of which 96 were successfully amplified as assessed by an internal control. As expected, the specific region of the RhD gene was amplified in all, some, and none of the signal-positive sperm samples from Rh-positive homozygotes, heterozygotes, and Rh-negative subjects, respectively, allowing accurate determination of the genotype. CONCLUSION: An accurate diagnosis of the RhD genotype can be attained from single sperm cell analysis by means of polymerase chain reaction and may have major clinical applications in the management of Rh isoimmunization.
Base Sequence↗
Single-cell image analysis to assess ABC-transporter-mediated efflux in highly purified hematopoietic progenitors.
BACKGROUND: Normal and malignant hematopoietic stem cells are characterized by their capacity to actively extrude fluorescent dyes. The contribution of different ATP-binding cassette (ABC) transporters to this phenomenon is largely unknown due to the small stem cell numbers limiting the use of standard methods to assess functional efflux. METHODS: We used epifluorescence microscopy (EFM) in combination with single-cell image analysis to study ABC-transporter-mediated efflux in highly purified, viable, CD34+CD38- cells sorted on an adhesive biolayer. P-glycoprotein and multidrug-resistant protein (MRP)-mediated efflux were quantitated using fluorescent substrates (rhodamine-123 and calcein acetoxymethyl ester [calcein-AM]) and specific inhibitors (verapamil and probenecid, respectively). RESULTS: The feasibility, sensitivity, and reproducibility of rhodamine-123 efflux quantitation using single-cell EFM was shown in cell lines and compared with standard flow cytometric assessment. P-glycoprotein-mediated transport was higher in CD34+CD38- cells than in more differentiated progenitors (mean efflux index = 2.24 +/- 0.35 and 1.14 +/- 0.11, respectively; P = 0.01). P-glycoprotein-mediated transport was the main determinant of the rhodamine "dull" phenotype of these cells. In addition, significant MRP-mediated efflux was demonstrated in CD34+CD38- and CD38+ cells (mean efflux index = 1.42 +/- 0.19 and 1.28 +/- 0.18, respectively). CONCLUSION: The described method is a valuable tool for assessing ABC-transporter-mediated efflux in highly purified single cells. Both P-glycoprotein and MRP-mediated efflux are present in human CD34+CD38- hematopoietic stem cells.
ADP-ribosyl Cyclase↗
Microfluidics device for single cell gene expression analysis in Saccharomyces cerevisiae.
We have measured single-cell gene expression over time using a microfluidics-based flow cell which physically traps individual yeast using microm-sized structures (yeast jails). Our goal was to determine variability of gene expression within a cell over time, as well as variability between individual cells. In our flow cell system, yeast jails are fabricated out of PDMS and gene expression is visualized using fluorescently-tagged proteins of interest. Previously, single-cell yeast work has been done using micromanipulation on agar, or FACS. In the present device agar is eliminated, resulting in a superior optical system. The flow of media through the flow cell washes daughter cells away, eliminating the need for micromanipulation. Unlike FACS, the described device can track individual yeast over a time course of many hours. The flow cells are compatible with the needs of quantitative fluorescence microscopy, and allow simultaneous measurements to be done on a large number of individual yeast. We used these flow cells to determine the expression of HSP104-GFPand RAS2-YFP, genes known to affect yeast life span. The results demonstrate inter-cell variation in expression of both genes that could not have been detected without this single-cell analysis.
Bacterial Proteins↗
QCatch: a framework for quality control assessment and analysis of single-cell sequencing data.
MOTIVATION: Single-cell sequencing data analysis requires robust quality control (QC) to mitigate technical artifacts and ensure reliable downstream results. While tools like alevin-fry and simpleaf (and augmented execution context for the alevin-fry), offer flexibility and computational efficiency to process single-cell data, this ecosystem will further benefit from a standardized QC reporting tailored for its outputs. RESULTS: We introduce QCatch, a Python-based command-line tool that generates comprehensive and interactive HTML QC reports designed specifically for single-cell quantification results. Taking the output directory of alevin-fry or simpleaf as the input, QCatch is able to perform essential processing steps, like cell calling, and generate detailed QC reports that contain informative visualizations and statistics, including unique molecular identifier (UMI) count distributions, sequencing saturation estimates, and splicing status information, for QC assurance. Built for seamless integration into downstream analysis workflows, QCatch exports the processed results in a richly-annotated H5AD format file, a widely used data format common among many downstream single-cell data analysis tools. AVAILABILITY AND IMPLEMENTATION: The source code and documentation of QCatch are available on GitHub at https://github.com/COMBINE-lab/QCatch. QCatch can be installed via both Bioconda and PyPI.
Single-Cell Analysis↗
Detection of doxorubicin and metabolites in cell extracts and in single cells by capillary electrophoresis with laser-induced fluorescence detection.
Capillary electrophoresis with laser-induced fluorescence detection was used to separate and detect doxorubicin and at least five metabolites from NS-1 cells that were treated with 25 microM doxorubicin for 8 h. Using 10 mM borate, 10 mM sodium dodecyl sulfate (pH 9.3) as separation buffer, the 488-nm argon-ion laser line for fluorescence excitation, and a 635 +/- 27.5 nm bandpass filter for detection, the limit of detection (S/N=3) for doxorubicin is 61 +/- 13 zmol. This low limit of detection allows for the detection of a larger number of metabolites than previously reported. Two extraction procedures were performed: a bulk liquid-liquid extraction and an in-capillary single-cell lysis. While in the bulk liquid-liquid extraction procedure, recovery for doxorubicin range from 50 to 99%, in single cell analysis the recovery is expected to be complete. Furthermore performing lysis of a single cell inside the separation capillary prevents doxorubicin or metabolite loss or degradation during handling. Based on the bulk method the calculated metabolite abundance is in the sub-amol per cell range while it varies from 0.1 to 1.1 fmol per cell in single cell analysis confirming metabolite loss during handling. Each metabolite was found at a level less than 0.1% of the doxorubicin content in either method, suggesting a slow metabolism in the NS-1 cell system or effective removal of metabolites by the cell.
Antibiotics, Antineoplastic↗
Cryopreserved human B cells as an alternative source for single cell mRNA analysis.
Reverse transcription-polymerase chain reaction (RT-PCR) of individual B-lymphocytes has been shown to be a powerful tool for the simultaneous analysis of different mRNA specificities in both malignant and non-malignant B cell subpopulations. However, especially for longitudinal studies, this may also require analyses of cryopreserved cells. Therefore, the current study assessed whether cryopreserved (liquid nitrogen, dimethyl sulfoxide [DMSO]-stored) viable B cells are an alternative source for single cell RT-PCR analysis. Fresh (non-frozen) and post-thawed human peripheral blood B cells were analyzed by fluorescence-activated cell sorting (FACS). As a result, different B cell subpopulations could be reliably stained and separated from both fresh and post-thawed cells by four-color flow cytometry, although slightly diminished fluorescence intensities of some subpopulation markers were observed when analyzing cryopreserved cells. Subsequently, viable individual CD19+CD27+ memory B cells were sorted into single wells and analyzed for the expression of mRNA transcripts of the 'house-keeping gene' glyceraldehyde phosphate dehydrogenase (GAPD), the constitutive B cell homing receptor CXCR4, and immunoglobulin heavy chain variable region (IgVH) genes by nested RT-PCR protocols. Comparing both B cell sources, RT-PCR analysis revealed comparable yields of cells expressing transcripts for the three mRNA specificities tested (GAPD, CXCR4, IgVH) indicating the integrity of the respective mRNAs in cryopreserved B cells. In conclusion, these data indicate that optimally cryopreserved B cells may be an alternative source for single-cell RT-PCR analysis, especially in longitudinal B cell studies. However, the settings for both FACS analysis and RT-PCR should be re-evaluated for each distinct subpopulation and target mRNA of interest when analyzing post-thawed cells.
Antigens, Surface↗
[The latest development in preimplantation genetic diagnosis].
Preimplantation genetic diagnosis is the integration of both assisted reproductive technologies and molecular genetic technologies. Since the birth of the first healthy females after PGD in 1990, remarkable advances have been achieved in this field. Most research in PGD is focused on new methods to improve the sensitivity and accuracy of single cell analysis. The principal problems in single cell PCR include amplification failure, ADO and contamination. Fluorescent PCR with multiplex amplifications of highly polymorphic markers is a highly effective strategy to avoid contamination and detect ADO. The advantages and disadvantages of fluorescence in situ hybridization to detect age-related aneuploidy are still under debate. We summarize the most recent developments in this review, and also introduce our own experiences in PGD.
Blastocyst↗
Single-cell PCR analysis of TCR repertoires selected by antigen in vivo: a high magnitude CD8 response is comprised of very few clones.
Taking advantage of a potent MHC class I-restricted response that allows the identification of antigen-selected CD8 T cells directly ex vivo, we characterized the antigen-specific T cell repertoires that develop in individual mice by single-cell PCR analysis. Each of the immune mice displayed distinct yet structurally similar TCR repertoires. The overall repertoire size was estimated to be in the range of 15-20 for most mice. No major differences were observed between primary and secondary responses. Moreover, for a hyperimmunized mouse the antigen-specific TCR repertoire expressed 8 months after the initial immunization was very similar to that found at the peak of the primary response. Our results demonstrate that a high magnitude immune response may be composed of very few clones, and that at least in the system analyzed, the memory response largely reflects the repertoire selected by the peak of the primary response.
Amino Acid Sequence↗
Single-cell PCR analysis of the immunoglobulin heavy-chain CDR3 region for the diagnosis of leptomeningeal involvement of B-cell malignancies using standard cerebrospinal fluid cytospins.
The diagnosis of leptomeningeal B-cell malignancies is based on the identification of malignant B cells in the cerebrospinal fluid (CSF). We have established a polymerase chain reaction (PCR) approach to characterize the clonally diverse gene encoding the immunoglobulin heavy-chain (IgH) third complementarity determining region (CDR3) of single B cells. We demonstrate that single-cell PCR is readily applicable to individual cells derived from routine CSF cytospins and is a powerful method to discriminate monoclonal neoplastic from polyclonal reactive B-cell responses. Single-cell PCR analysis, as a new tool for the diagnosis and monitoring of neoplastic meningitis associated with B-cell malignancies, is particularly important if cytology, immunocytochemistry, flow cytometry and automated gene scanning of CSF samples are unable to detect malignant monoclonal proliferation.
B-Lymphocytes↗
[Single cell DNA analysis: possibilities, methods, implications in relation to stem cell therapy].
In the analysis of circulating tumor cells or in the preimplantation genetic diagnosis it is frequently necessary to examine one single cell. Some methods are appropriate to isolate single cells: Laser Assisted Microdissection, magnetic cell separation or FACS. The use of the whole genome amplification methods are needful, because the amount of the DNA extracted from the isolated cells is very low and inappropriate for additional examinations. With different molecular biological methods (e.g. sequencing, chip-technology) it is possible to determine genetic alterations in the analysed cells, and to return the modified cells with in vitro gene technological methods (viral vectors, non viral methods). Our aim is to summarize the methods and the possible technical problems developing during the process of the single cell molecular biological analysis.
DNA Mutational Analysis↗
Applications and technical challenges of fluorescence in situ hybridization in stem cell research.
Stem cell research, maintenance, and manipulations have advanced significantly in recent years, and we now witness successful clinical applications of stem therapies. However, challenges in regard to karyotypic stability and the ploidy status of stem cell lines have been addressed only marginally. Our approach to develop technology to address these highly relevant issues is based on fluorescence in situ hybridization (FISH) using nonisotopically labeled DNA probes. As a single cell analysis technique, FISH is expected to be applicable to a variety of cells and tissues including interphase and metaphase cell preparations as well as tissue sections and biopsy material. Over the last decade, our laboratories generated a large number of probes and probe sets for the molecular cytogenetic analyses of stem cells derived from different species. These probes and the introduction of spectral imaging bring us close to be able to perform a comprehensive karyotype analysis of single interphase cell nuclei. It should furthermore be possible to couple cytogenetic investigations of the cellular genotype with analysis of gene expression. This report summarizes our technical achievements relevant to stem cell research and outlines plans for future research and developments.
DNA Probes↗
A simultaneous three-color T cell subsets analysis with single laser flow cytometers using T cell gating protocol. Comparison with conventional two-color immunophenotyping method.
We describe a method for simultaneous analysis of CD3, CD4, and CD8 positive cells from whole blood utilizing single laser flow cytometers. All three T cell values are attained from a single test tube. CD4 and CD8 positive cells are identified only if they are CD3 positive. Thus the values obtained by this method for T helper/inducer and T cytotoxic/suppressor cells can be reported directly as a percentage of T lymphocytes. Analysis for CD4 and CD8 positive cells is accomplished, by first gating on CD3 positive T lymphocytes, hence the approach is referred to as a T gating method. As the third dye, conjugated to anti-CD3 monoclonal antibodies (MAbs), we utilized peridinin chlorophyll protein (PerCP), a new red fluorochrome. The proposed method may prove to be practical for monitoring disease progression in AIDS, where longitudinal T helper/inducer and T cytotoxic/suppressor cell enumeration must be performed unambiguously by a simple, reproducible, and fast method.
CD3 Complex↗
Single-cell repertoire analysis demonstrates that clonal expansion is a prominent feature of the B cell response in multiple sclerosis cerebrospinal fluid.
Single-cell RT-PCR was used to sample CD19(+) B cell repertoires in cerebrospinal fluid (CSF) of patients with multiple sclerosis (MS) or viral meningitis. Analysis of amplified Ab H and L chain products served to identify the rearranged germline segment and J segment, and to determine the degree of homology for the H and L chain sequence of individual B cells. The B cell repertoire of viral meningitis CSF was predominantly polyclonal, whereas B cell clonal expansion was a prominent feature of the IgG repertoire in three of four MS patients. Two dominant clonal populations in one MS CSF accounted for approximately 70% of the IgG H chain V regions sequenced, while the corresponding IgM repertoires were more heterogeneous. One clonal B cell population revealed multiple L chain rearrangements, raising the possibility of a role for receptor editing in shaping the B cell response in some MS patients. The most immediate implications of identifying rearranged Ig sequences in MS B cells is the potential to accurately recreate recombinant Abs from these overrepresented H and L chains that can be used to discover the relevant Ag(s) in MS.
Acute Disease↗
Gene expression analysis of single neoplastic cells and the pathogenesis of Hodgkin's lymphoma.
The origin of the Reed-Sternberg cell of Hodgkin's disease remained clouded in mystery for almost a century after its discovery in 1898. The major obstacle to its understanding is that, unlike other cancers, the malignant cell of Hodgkin's disease is vastly outnumbered by surrounding non-neoplastic cells at approximately 1000:1. We have devised several strategies to isolate Reed-Sternberg T-cells to determine their origin, global gene expression and, ultimately, their pathogenesis. This has increased the number of genes known to be expressed in Reed-Sternberg cells by >100-fold to over 12,000. Approaches such as density gradients, microdissection, and cell sorting help to enrich Reed-Sternberg cells for genomic DNA analysis. However, single-cell micromanipulation of living Reed-Sternberg cells was required to determine the genome-wide gene expression profile of these cells. Combined analysis of single cells and cell lines revealed the expression of 2666 named genes. Further analysis with high-density gene expression microarrays has demonstrated the expression of approximately 12,000 genes by Reed-Sternberg cells. The gene expression profile is that of an aberrant germinal center B-lymphocyte that resists apoptosis through CD40 signaling and NFkappaB activation. Gene expression analysis of Hodgkin's disease is an extreme test case demonstrating the application of high-throughput gene expression studies even to individual cells from clinical samples.
B-Lymphocytes↗