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1.  Laser Scanning Cytometry 
The laser scanning cytometer (LSC) is the microscope-based cytofluorometer that offers a plethora of analytical capabilities. Multilaser-excited fluorescence emitted from individual cells is measured at several wavelength ranges, rapidly (up to 5000 cells/min), with high sensitivity and accuracy. The following applications of LSC are reviewed: (1) identification of cells that differ in degree of chromatin condensation (e.g., mitotic or apoptotic cells or lymphocytes vs granulocytes vs monocytes); (2) detection of translocation between cytoplasm vs nucleus or nucleoplasm vs nucleolus of regulatory molecules such as NF- κB, p53, or Bax; (3) semiautomatic scoring of micronuclei in mutagenicity assays; (4) analysis of fluorescence in situ hybridization; (5) enumeration and morphometry of nucleoli; (6) analysis of phenotype of progeny of individual cells in clonogenicity assay; (7) cell immunophenotyping; (8) visual examination, imaging, or sequential analysis of the cells measured earlier upon their relocation, using different probes; (9) in situ enzyme kinetics and other time-resolved processes; (10) analysis of tissue section architecture; (11) application for hypocellular samples (needle aspirate, spinal fluid, etc.); (12) other clinical applications. Advantages and limitations of LSC are discussed and compared with flow cytometry.
PMCID: PMC3892962  PMID: 16719355
Cytometry; fluorescence; cell cycle; apoptosis; nucleus; nucleolus; micronucleus cytoplasm; enzyme kinetics
2.  Laser Scanning Cytometry: Principles and Applications—An Update 
Laser scanning cytometer (LSC) is the microscope-based cytofluorometer that offers a plethora of unique analytical capabilities, not provided by flow cytometry (FCM). This review describes attributes of LSC and covers its numerous applications derived from plentitude of the parameters that can be measured. Among many LSC applications the following are emphasized: (a) assessment of chromatin condensation to identify mitotic, apoptotic cells, or senescent cells; (b) detection of nuclear or mitochondrial translocation of critical factors such as NF-κB, p53, or Bax; (c) semi-automatic scoring of micronuclei in mutagenicity assays; (d) analysis of fluorescence in situ hybridization (FISH) and use of the FISH analysis attribute to measure other punctuate fluorescence patterns such as γH2AX foci or receptor clustering; (e) enumeration and morphometry of nucleoli and other cell organelles; (f) analysis of progeny of individual cells in clonogenicity assay; (g) cell immunophenotyping; (h) imaging, visual examination, or sequential analysis using different probes of the same cells upon their relocation; (i) in situ enzyme kinetics, drug uptake, and other time-resolved processes; (j) analysis of tissue section architecture using fluorescent and chromogenic probes; (k) application for hypocellular samples (needle aspirate, spinal fluid, etc.); and (l) other clinical applications. Advantages and limitations of LSC are discussed and compared with FCM.
PMCID: PMC3488462  PMID: 23027005
Cytometry; Fluorescence; Cell cycle; Apoptosis; Nucleus; Nucleolus; Micronucleus; Cytoplasm; Enzyme kinetics
3.  New Biomarkers Probing Depth of Cell Senescence Assessed by Laser Scanning Cytometry 
Cytometry  2010;77A(11):999-1007.
The imaging analytical capabilities of laser scanning cytometer (LSC) have been used to assess morphological features considered to be typical of the senescent phenotype. The characteristic “flattening” of senescent cells was reflected by the decline in the density of staining (intensity of maximal pixel) of DNA-associated fluorescence [4,6-diamidino-2-phenylindole (DAPI)] paralleled by an increase in nuclear size (area). The decrease in ratio of maximal pixel to nuclear area was even more sensitive senescence biomarker than the change in maximal pixel or nuclear area, each alone. The saturation cell density at plateau phase of growth recorded by LSC was found to be dramatically decreased in cultures of senescent cells, thereby also serving as an additional marker. The induction of cyclin dependent kinase inhibitors p21WAF1 and p27KIP1 and γH2AX and activation of ATM markers of DNA damage response were measured in parallel with DNA/DAPI maximal pixel and nuclear area. These biomarker indices were expressed in quantitative terms by reporting them as a fraction of the respective controls. The effect of treatment of A549 and WI-38 cells with different concentrations of mitoxantrone (Mxt) and trichostatin A for various time periods was studied to assess the degree (depth) of cell senescence. Also assessed was the effect of 2-deoxy-d-glucose, the agent attenuating metabolic cell activity, on the depth of senescence induced by Mxt. A relationship between the ability of cells to synthesize RNA (incorporate 5-ethynyluridine) that leads to growth imbalance and induction of cell senescence was also studied. The data show that morphometric analysis of cellular attributes by LSC offers an attractive tool to detect cell senescence and measure its degree particularly in assessing effects of the factors that enhance or attenuate this process. This methodology is of importance in light of the evidence that cellular senescence is not only a biological process that is fundamental for organismal aging but also impedes formation of induced-pluripotent stem cells providing the barrier for neoplastic transformation and is the major mechanism of induction of reproductive cell death during treatment of solid tumors. © 2010 International Society for Advancement of Cytometry.
PMCID: PMC2977923  PMID: 20939035
image analysis; trichostatin A; maximal pixel of fluorescence intensity; nuclear area; EU incorporation; growth imbalance; cell morphometry; chromatin condensation; cell cycle; apoptosis; p21WAF1
4.  Cytometric Assessment of Cytostatic and Cytotoxic Effects of Topical Glaucoma Medications on Human Epithelial Corneal Line Cells 
The long-term-treatment of glaucoma with topical medications is associated with side effects involving cornea damage. We examined the effect of glaucoma topical medications (bimatoprost, travoprost, latanoprost, timolol, betaxolol, dorzolamide, brinzolamide, brimonidine) on growth of cells of three human epithelial corneal lines.
The cells were cultured in 8-chamber slides, treated with different concentrations of the medications, and fixed at 24, 48, and 72 h. Cell number on slides to estimate viability and growth curves, frequency of apoptosis (FLICA and caspase-3 activation probes), and proliferation (BrdU incorporation assay) were measured by laser scanning cytometry (LSC).
Depending on concentration all examined medications induced cell necrosis or apoptosis and suppressed proliferation. Significant variability in proliferation and apoptosis was observed within the same cultures depending on local cell density, with cells in high density areas being more resistant. The data indicate that commonly used topical medications exert cytostatic and cytotoxic effects in cultures of corneal cells and suggest that caution should be exercised in their use, particularly, when the corneal diseases are accompanied by cell proliferation and regeneration, in long-term-treatment.
The present approach of using LSC makes it possible to assess and compare cytostatic and cytotoxic effects of different topical medications on the respective target cells.
PMCID: PMC3003611  PMID: 19834965
cell proliferation; cell death; cell cycle; apoptosis; antiglaucoma topical medications
5.  Activation of Nuclear Factor Kappa B (NF-κB) Assayed by Laser Scanning Cytometry (LSC) 
Cytometry  1998;33(3):376-382.
Nuclear factor kappa B (NF-κB)/rel is the family of ubiquitous transcriptional activators involved in regulation of diverse immune and inflammatory responses. It also plays a role in control of cell growth and apoptosis. In its inactive form NF-κB remains in the cytoplasm sequestered through interaction with IκB protein. Rapid translocation of NF-κB from cytoplasm to nucleus that occurs in response to extracellular signals is considered to be a hallmark feature of its activation. The translocation of NF-κB in HL-60, U-937 and Jurkat leukemic cells as well as in human fibroblasts induced by tumor necrosis factor α (TNF-α) or phorbol myristate acetate (PMA) was presently measured by laser scanning cytometry (LSC). NF-κB was detected immunocytochemically with FITC-tagged antibody and its presence in the nucleus vis-a-vis cytoplasm was monitored by measuring the green fluorescence integrated over the nucleus, which was counter-stained with propidium iodide (PI), and over the cytoplasm, respectively. Activation of NF-κB led to a rapid increase in NF-κB-associated fluorescence measured over the nucleus (FN) concomitant with a decrease in fluorescence over the cytoplasm (FC), which was reflected by an increase in FN/FC ratio. This rapid assay of NF-κB activation can be combined with morphological identification of the activated cells or with their immunophenotype. Bivariate analysis of NF-κB expression versus cellular DNA content makes it possible to correlate its activation with the cell cycle position. The described method has a potential to be used as a functional assay to monitor intracellular translocation of other transcriptional activators such as p53 tumor suppressor protein or signal transduction molecules.
PMCID: PMC3874872  PMID: 9822350
nucleus; cytoplasm; tumor necrosis factor
6.  Biomarkers of Cell Senescence Assessed by Imaging Cytometry 
The characteristic features of senescent cells such as their “flattened” appearance, enlarged nuclei and low saturation density at the plateau phase of cell growth, can be conveniently measured by image-assisted d cytometry such as provided by the laser scanning cytometry (LSC). The “flattening” of senescent cells is reflected by the decline in local density of staining (intensity of maximal pixel) of DNA-associated fluorescence [4,6-diamidino-2- phenylindole (DAPI)] paralleled by an increase in nuclear size (area). Thus, the ratio of the maximal pixel of DAPI fluorescence per nucleus to the nuclear area provides a very sensitive morphometric biomarker of “depth” of senescence, which progressively declines during induction of senescence. Also recorded is cellular DNA content revealing cell cycle phase, as well as the saturation cell density at plateau phase of growth, which is dramatically decreased in cultures of senescent cells. Concurrent immunocytochemical analysis of expression of p21WAF1, p16INK4a or p27KIP1 cyclin kinase inhibitor provides additional markers of senescence. These biomarker indices can be expressed in quantitative terms (“senescence indices”) as a fraction of the same markers of the exponentially growing cells in control cultures.
PMCID: PMC3541526  PMID: 23296652
Cell aging; chromatin structure; cell cycle; apoptosis; nuclear size; laser scanning cytometry; p21WAF1; p16INK4a; p27KIP1; premature cell senescence
7.  New Biomarkers Probing the Depth of Cell Senescence Assessed by Laser Scanning Cytometry 
The imaging analytical capabilities of laser scanning cytometer (LSC) have been used to assess morphological features considered to be typical of the senescent phenotype. The characteristic “flattening” of senescing cells was reflected by the decline in the density of staining (intensity of maximal pixel) of DNA-associated fluorescence (DAPI) paralleled by an increase in nuclear size (area). The decrease in ratio of maximal pixel to nuclear area was even more sensitive senescence biomarker than the change in maximal pixel or nuclear area, each alone. The saturation density at plateau phase of growth recorded by LSC was found to be dramatically decreased in cultures of senescent cells thereby also serving as a convenient marker. The induction of cyclin dependent kinase inhibitors p21WAF1 and p27KIP1 as well as γH2AX and activation of ATM, markers of DNA damage response were measured in parallel with DNA/DAPI maximal pixel and nuclear area. These biomarker indices were expressed in quantitative terms by reporting them as a fraction of the respective markers in control cultures. The effect of treatment of A549 cells with different concentrations of mitoxantrone and trichostatin A for various time periods was studied to assess the degree (depth) of induction of senescence by these biomarkers. Induction of senescence in WI-38 fibroblasts by mitoxantrone and in HT-p21-a cells by enforced expression of p21WAF1 was also studied. The effects of 2-deoxy-D-glucose and rapamycin, the factors attenuating metabolic cell activity, were found to decrease the depth of senescence. The morphometric analysis of cellular attributes by LSC offers an attractive tool to detect cell senescence and measure its degree particularly in assessing effects of the factors that enhance or attenuate this process.
PMCID: PMC2977923  PMID: 20939035
8.  A Leukemic Stem Cell Gene Expression Signature is Associated with Clinical Outcomes in Acute Myeloid Leukemia 
In many cancers, specific subpopulations of cells appear to be uniquely capable of initiating and maintaining tumors. The strongest support for this cancer stem cell model comes from transplantation assays in immune-deficient mice, which indicate that human acute myeloid leukemia (AML) is driven by self-renewing leukemia stem cells (LSC). This model has significant implications for the development of novel therapies, but its clinical relevance has yet to be determined.
To identify a leukemic stem cell gene expression signature and test its association with clinical outcomes in AML.
Design, Setting, and Patients
Global gene expression (microarray) profiles of LSC-enriched subpopulations from primary AML and normal patient samples were analyzed. Patient samples were obtained at Stanford University Medical Center between April 2005 and July 2007. Validation datasets of global transcriptional profiles of AML tumors from four independent cohorts totaling 1047 patients were analyzed retrospectively.
Main Outcome Measures
Identification of genes discriminating LSC-enriched from other subpopulations in AML tumors; association of the LSC-specific genes with overall, event-free, and relapse-free survival, and with therapeutic response.
Expression levels of 52 genes distinguished LSC-enriched from other subpopulations in cell-sorted AML samples. An LSC score summarizing expression of these genes in bulk primary AML tumor samples was defined and found to be associated with clinical outcomes in four independent patient cohorts. High LSC scores were associated with worse overall (OS), event-free (EFS), and relapse-free (RFS) survival, among patients with either a normal karyotype (NKAML), or with chromosomal abnormalities. For the largest cohort of patients with NKAML (n=163), the LSC score was significantly associated with OS as a continuous variable (hazard ratios [HR] 1.15, 95% Confidence Interval [CI] 1.08-1.22, log-likelihood p<0.001). When patients were split into high and low LSC score groups, the absolute risk of death by 3 years was 57% (95% CI 43-67%) for the low LSC score group, versus 78% (95% CI 66-86%) in the high LSC score group (HR 1.9, 95% CI 1.3-2.7, log-rank p=0.002). In another cohort with available data on EFS for 70 patients with NKAML, the risk of an event by 3 years was 48% (95% CI 27-63%) in the low LSC score group vs. 81% (95% CI 60-91%) in the high LSC score group (HR 2.4, 95% CI 1.3-4.5, log-rank p=0.006). The LSC score was associated with poorer outcomes, independently of known prognostic factors including age, FLT3 or NPM1 mutations, and cytogenetic risk group, and added to their prognostic value. For OS in three cohorts that included patients with cytogenetic abnormalities, the HRs of the continuous LSC score in multivariate Cox regression with FLT3/NPM1 status, age, and cytogenetic risk group were respectively HR 1.07 (95%CI 1.01-1.13), p=0.02; HR 1.10 (95% CI 1.03-1.17), p=0.005; and HR 1.17 (95% CI 1.05-1.30), p=0.005.
High expression of a leukemic stem cell gene expression signature is independently associated with adverse outcomes in AML.
PMCID: PMC4089862  PMID: 21177505
9.  Characterization of Pancreatic Ductal Cell in Human Islet Preparations 
Substantial amounts of non-endocrine cells are implanted as part of human islet grafts, and possible influence of non-endocrine cells on clinical islet transplantation outcome has been postulated. There are currently no product release criteria specific for non-endocrine cells due to lack of available methods. Aims of this study were to develop a method for the evaluation of pancreatic ductal cells (PDC) for clinical islet transplantation, and to characterize them regarding phenotype, viability and function.
We assessed 161 human islet preparations using laser scanning cytometer (LSC/iCys) for phenotypic analysis of non-endocrine cells and flow cytometer (FACS) for PDC viability. PDC and β-cells obtained from different density fractions during the islet cell purification were compared in terms of viability. Furthermore, we examined PDC ability to produce pro-inflammatory cytokines/chemokines, vascular endothelial growth factor (VEGF) and tissue factor (TF), relevant to islet graft outcome.
Phenotypic analysis by LSC/iCys indicated that single staining for CK19 or CA19-9 was not enough for identifying PDC, and that double staining for amylase and CK19 or CA19-9 allowed for quantitative evaluation of acinar cells and PDC content in human islet preparation. PDC showed a significantly higher viability than β-cells (PDC vs. β-cell: 75.5±13.9 and 62.7±18.7 %; p<0.0001). Although β-cells viability was independent from the density, that of PDC was higher as the density from which they were recovered increased. There was no correlation between PDC and β-cells viability (R2=0.0078). PDC sorted from high-density fractions produced significantly higher amount of pro-inflammatory mediators and VEGF, but not TF.
PDC isolated from different fractions had different viability and function. The precise characterization and assessment of these cells in addition to β-cells in human islet cell products may be of assistance in understanding their contribution to islet engraftment and in developing strategies to enhance islet graft function.
PMCID: PMC3793849  PMID: 18779781
Human pancreatic ductal cells; Islet transplantation; Assessment; Cytokines; Laser Scanning Cytometer; VEGF; IL-8; CA19-9
10.  Analysis of Cell Cycle and Replication of Mouse Macrophages after In Vivo and In Vitro Cryptococcus neoformans Infection Using Laser Scanning Cytometry 
Infection and Immunity  2012;80(4):1467-1478.
We investigated the outcome of the interaction of Cryptococcus neoformans with murine macrophages using laser scanning cytometry (LSC). Previous results in our lab had shown that phagocytosis of C. neoformans promoted cell cycle progression. LSC allowed us to simultaneously measure the phagocytic index, macrophage DNA content, and 5-ethynyl-2′-deoxyuridine (EdU) incorporation such that it was possible to study host cell division as a function of phagocytosis. LSC proved to be a robust, reliable, and high-throughput method for quantifying phagocytosis. Phagocytosis of C. neoformans promoted cell cycle progression, but infected macrophages were significantly less likely to complete mitosis. Hence, we report a new cytotoxic effect associated with intracellular C. neoformans residence that manifested itself in impaired cell cycle completion as a consequence of a block in the G2/M stage of the mitotic cell cycle. Cell cycle arrest was not due to increased cell membrane permeability or DNA damage. We investigated alveolar macrophage replication in vivo and demonstrated that these cells are capable of low levels of cell division in the presence or absence of C. neoformans infection. In summary, we simultaneously studied phagocytosis, the cell cycle state of the host cell and pathogen-mediated cytotoxicity, and our results demonstrate a new cytotoxic effect of C. neoformans infection on murine macrophages: fungus-induced cell cycle arrest. Finally, we provide evidence for alveolar macrophage proliferation in vivo.
PMCID: PMC3318400  PMID: 22252872
11.  Fast Image Analysis for the Micronucleus Assay in a Fully Automated High-Throughput Biodosimetry System 
Radiation research  2014;181(2):146-161.
The development of, and results from an image analysis system are presented for automated detection and scoring of micronuclei in human peripheral blood lymphocytes. The system is part of the Rapid Automated Biodosimetry Tool, which was developed at the Center for High-Throughput Minimally Invasive Radiation Biodosimetry for rapid radiation dose assessment of many individuals based on single fingerstick samples of blood. Blood lymphocytes were subjected to the cytokinesis-block micronucleus assay and the images of cell cytoplasm and nuclei are analyzed to estimate the frequency of micronuclei in binucleated cells. We describe an algorithm that is based on dual fluorescent labeling of lymphocytes with separate analysis of images of cytoplasm and nuclei. To evaluate the performance of the system, blood samples of seven healthy donors were irradiated in vitro with doses from 0–10 Gy and dose-response curves of micronuclei frequencies were generated. To establish the applicability of the system to the detection of high doses, the ratios of mononucleated cells to binucleated cells were determined for three of the donors. All of the dose-response curves generated automatically showed clear dose dependence and good correlation (R2 from 0.914–0.998) with the results of manual scoring.
PMCID: PMC4011502  PMID: 24502354
12.  Objective quantitative analysis of eosinophils and bronchial epithelial cells in induced sputum by laser scanning cytometry 
Thorax  1999;54(2):124-130.
BACKGROUND—Sputum induction is an important non-invasive technique for measuring airway inflammation in asthma. Cell numbers are often too low for flow cytometric analysis. Laser scanning cytometry (LSC) is a novel technique that allows objective multicolour fluorescence analysis of cells on a microscope slide.
METHODS—LSC was used to determine sputum eosinophil and bronchial epithelial cell counts. We first confirmed that we could measure eosinophil counts accurately in peripheral blood using α-major basic protein (MBP) immunofluorescent staining. Sputum induction was performed according to standard protocols. Sputum samples from eight normal controls and 12 asthmatic patients were analysed by LSC and manual counting by two independent observers. Octospot cytospins were fixed and stained with mouse-α-human-MBP monoclonal antibody or mouse-α-human-cytokeratin antibody and goat-α-mouse Oregon Green conjugated second antibody.
RESULTS—Sputum induction provided a mean (SE) of 0.99 (0.2) × 106 cells per donor. More than 3000 cells on three cytospins per slide were analysed per cell type. The intraclass correlation coefficient (R) and standard deviation (SD) of differences in eosinophils determined by manual counting and LSC were 0.9 and 2.1, respectively, and for bronchial epithelial cell counts they were 0.7 and 2.0.Selective detection of labelled cells was confirmed visually after relocation.
CONCLUSION—Eosinophils and bronchial epithelial cells can be accurately and reproducibly counted in an objective manner. LSC is therefore a potentially powerful new method for immunophenotyping leucocytes and epithelial cells objectively in induced sputum in patients with asthma.

PMCID: PMC1745427  PMID: 10325916
13.  Cytokinesis-Blocked Micronucleus Cytome Assay Biomarkers Identify Lung Cancer Cases Amongst Smokers 
The multi-endpoint cytokinesis-blocked micronucleus assay is used for assessing chromosome aberrations. We have recently reported that this assay is extremely sensitive to genetic damage caused by the tobacco-specific nitrosamine 4-(methylnitrosamino)-1-(3-pyr-idyl)-1-butanone (NNK) and that the binucleated cells with micronuclei, nucleoplasmic bridges, and nuclear buds in lymphocytes (chromosome damage endpoints measured by the assay) are strong predictors of lung cancer risk. In the current study, we refined our analysis to include toxicity endpoints (micronuclei in mononucleated cells, apoptosis, necrosis, and nuclear division index) to investigate the benefit of including these variables on improving the predictive value of the assay. Baseline and NNK-induced micronuclei in mononucleated cells were significantly higher in patients (n = 139) than controls (n = 130; P < 0.001). Baseline apoptosis was higher among cases; however, the controls showed a significant higher fold increase in NNK-induced apoptosis compared with baseline (P < 0.001). Principal components analysis was used to derive a summary measure for all endpoints and calculate the positive predictive value (PPV) and negative predictive value (NPV) for disease status. First principal component for NNK-induced chromosome damage endpoints (binucleated cells with micronuclei, nucleoplasmic bridges, and nuclear buds) had an area under the curve = 97.9 (95% confidence interval, 95.9-99.0), PPV = 94.8, and NPV = 92.6. The discriminatory power improved when micronuclei in mononucleated cells were included: area under the curve = 99.1 (95% confidence interval, 97.9- 100.0), PPV = 98.7 and NPV = 95.6. The simplicity, rapidity, and sensitivity of the assay together with potential for automation make it a valuable tool for screening and prioritizing potential cases for intensive screening.
PMCID: PMC2854407  PMID: 18483333
14.  Identification and evaluation of novel synovial tissue biomarkers in rheumatoid arthritis by laser scanning cytometry 
Suitable biomarkers are essential for therapeutic strategies in personalized medicine in terms of diagnosis as well as of prognosis. With highly specific biomarkers, it is possible, for example, to identify patients with poor prognosis, which enables early intervention and intensive treatment. The aim of this study was to identify and validate biomarkers and possible combinations for a prospective use in immunoscintigraphy, which may improve diagnosis of rheumatoid arthritis (RA) patients with consideration of inflammatory activity in the affected joints. Therefore, we tested several monoclonal antibodies (mAbs) directed against cellular-surface molecules on cells likely to be involved in the pathogenesis of RA.
Synovial tissue from patients with long-standing RA (accompanied by synovitis with varying states of current activity) and patients with acute non-RA arthritis were stained for surface molecules on different cell types by using fluorochrome-labeled antibodies. Tissue analysis was done by laser scanning cytometry (LSC), and statistical evaluation, by discriminant analysis and ROC analysis.
CD11b, HLA-DR, CD90, and CD64 revealed significant differences between tissues from patients with RA and acute non-RA arthritis. Especially with the expression of CD64, both patient cohorts could be discriminated with high sensitivity and specificity. RA classification was improved by simultaneously investigating the expression of two or three different surface proteins, such as HLA-DR, CD90, and CD29 in the tissue. The simultaneous analysis of CD64 together with CD304 or the combination of CD11b and CD38 was suitable for the identification of RA patients with high current activity in synovitis.
In this study, we showed that LSC is a novel reliable method in biomarker prevalidation in RA. Hence, identified mAbs in situ may allow their potential use in in vivo approaches. Moreover, we proved that biomarker-combination analysis resulted in better discrimination than did single-marker analysis. Combinations of these markers make a novel and reliable panel for the discrimination between RA and acute non-RA arthritis. In addition, further expedient combinations may be novel promising biomarker panels to identify current activity in synovitis in RA.
PMCID: PMC3392796  PMID: 22251373
15.  Cell Fixation in Zinc Salt Solution is Compatible with DNA Damage Response Detection by Phospho-Specific Antibodies 
By virtue of superior preservation of proteins and nucleic acids the zinc salt-based fixatives (ZBF) has been proposed as an alternative to precipitants and cross-linking fixatives in histopathology. It was recently reported that ZBF is compatible with analysis of cell surface immunophenotype and detection of intracellular epitopes by flow cytometry. The aim of this study was to explore whether ZBF is also compatible with the detection of DNA damage response assessed by phospho-specific antibodies (Abs) detecting phosphorylation of the key proteins of that pathway. DNA damage in human pulmonary adenocarcinoma A549 cells was induced by treatment with the DNA topoisomerase I inhibitor camptothecin and phosphorylation of histone H2AX on Ser139 (γH2AX) and of ATM on Ser1981 was detected with phospho-specific Abs; cellular fluorescence was measured by laser scanning cytometry (LSC). The sensitivity and accuracy of detection of H2AX and ATM phosphorylation concurrent with the detection of DNA replication by EdU incorporation and “click chemistry” was found in ZBF fixed cells to be comparable to that of cell fixed in formaldehyde. The accuracy of DNA content measurement as evident from the resolution of DNA content frequency histograms of cells stained with DAPI was somewhat better in ZBF- than in formaldehyde-fixed cells. The pattern of chromatin condensation revealed by the intensity of maximal pixel of DAPI that allows one to identify mitotic and immediately post-mitotic cells by LSC was preserved after ZBF fixation. ZBF fixation was also compatible with the detection of γH2AX foci considered to be the hallmarks of induction of DNA double-strand breaks. Analysis of cells by flow cytometry revealed that ZBF fixation of lymphoblastoid TK6 cells led to about 60 and 33% higher intensity of the side and forward light scatter, respectively, compared to formaldehyde fixed cells.
PMCID: PMC3238498  PMID: 21595014
gammaH2AX; ATM activation; click chemistry; EdU incorporation; cell cycle; DNA replication; S phase; confocal microscopy
16.  Quantitative In Situ Analysis of FoxP3+ T Regulatory Cells on Transplant Tissue Using Laser Scanning Cytometry 
Cell transplantation  2011;21(1):113-125.
There is abundant evidence that immune cells infiltrating into a transplanted organ play a critical role for destructive inflammatory or regulatory immune reactions. Quantitative in situ analysis (i.e. in tissue sections) of immune cells remains challenging due to a lack of objective methodology. Laser scanning cytometry (LSC/iCys) is a recently developed methodology that utilizes fluorescence-based quantitative measurements on tissue sections or other cellular preparations at a single-cell level. In this study, we have developed a novel objective method for analysis of immune cells, including Foxp3+ T regulatory cell (T reg), on formalin-fixed / paraffin embedded (FFPE) transplant biopsy sections using LSC/iCys.
The development of multiple immunofluorescent staining was established using FFPE human tonsil sample. The CD4/CD8 ratio and the population of T reg among CD4+ cells were analyzed using LSC/iCys and compared with the results from conventional flow cytometry analysis (FCM).
Our multiple immunofluorescent staining techniques allow obtaining clear staining on FFPE sections. The CD4/CD8 ratio analyzed by LSC/iCys was concordant with those obtained by FCM. This method was also applicable for liver, small intestine, kidney, pancreas and heart transplant biopsy sections and provide an objective quantification of T regs within the grafts.
PMCID: PMC3777543  PMID: 21929847
T regulatory cell; Foxp3; laser scanning cytometry; transplant biopsy; quantification
17.  Quantification of retinal pigment epithelial phenotypic variation using laser scanning cytometry 
Molecular Vision  2010;16:1108-1121.
Quantifying phenotypic variation at the level of protein expression (variegation) within populations of retinal pigment epithelium (RPE) cells may be important in the study of pathologies associated with this variation. The lack of quantitative methods for examining single cells, however, and the variable presence of pigment and/or lipofuscin complicate this experimental goal. We have applied the technique of laser scanning cytometry (LSC) to paraffin sections of mouse and human eyes to evaluate the utility of LSC for these measurements.
Mouse eyes were perfusion fixed in 4% paraformaldehyde and embedded in paraffin. Postmortem human eyes were fixed and dissected to obtain a 9-mm punch, which was then embedded in paraffin. A laser scanning cytometer equipped with violet, argon, and helium-neon lasers and the detectors for blue, green, and long red were used to record the fluorescence of each individual cell at all three wavelengths. Raw data were recorded and processed using the WinCyte software. Individual nuclei were identified by the fluorescence of the 4’,6-diamidino-2-phenylindole (DAPI) nuclear counterstain. Next, RPE cells were uniquely identified in the green channel using an anti-retinal pigment epithelium-specific protein 65 kDa (anti-RPE65) monoclonal antibody with an Alexa Fluor 488-labeled secondary antibody. Mn-superoxide dismutase (MnSOD) was quantified in the long-red channel using an anti-MnSOD antibody and an Alexa Fluor 647-labeled secondary antibody. MnSOD+ and RPE65+ cells exhibited peaks in the plot of fluorescence intensity versus cell number, which could be characterized by the mean fluorescence intensity (MFI), the coefficient of variation (CV), and the percentage of total RPE cells that were also labeled for MnSOD.
RPE cells can be uniquely identified in human and mouse paraffin sections by immunolabeling with anti-RPE65 antibody. A second antigen, such as MnSOD, can then be probed only within this set of RPE. Results are plotted primarily with the population frequency diagram, which can be subdivided into multiple regions. The data collected for each region include the MFI, the CV, and the number of cells that are immunolabeled in that region. Background interference from pigment or autofluorescent material can be successfully overcome by elevating the concentrations of fluorescent secondary antibodies. In the human and mouse eyes, age-related changes in MFI, CV, and percent RPE cells immunolabeled for MnSOD were observed.
The extent of the variability of gene expression in RPE cells at the protein level can be quantified by LSC. Relative changes in the MFI, the CV, and/or percentage of RPE cells double labeled for a second antigen quantify the changes observed. The analysis of these data also suggest whether the effects observed are related to local changes in transcription (alterations of CV) or major changes of protein expression (MFI), which are likely to be due to changes in the chromatin structure. The changes of these variables with age suggest that the observed age-related variegation is primarily due to changes in the chromatin structure in individual cells.
PMCID: PMC2893051  PMID: 20606706
18.  Translocation Biosensors – Cellular System Integrators to Dissect CRM1-Dependent Nuclear Export by Chemicogenomics 
Sensors (Basel, Switzerland)  2009;9(7):5423-5445.
Fluorescent protein biosensors are powerful cellular systems biology tools for dissecting the complexity of cellular processes with high spatial and temporal resolution. As regulated nucleo-cytoplasmic transport is crucial for the modulation of numerous (patho)physiological cellular responses, a detailed understanding of its molecular mechanism would open up novel options for a rational manipulation of the cell. In contrast to genetic approaches, we here established and employed high-content cellular translocation biosensors applicable for dissecting nuclear export by chemicogenomics. A431 cell lines, stably expressing a translocation biosensor composed of glutathione S-transferase, GFP and a rational combination of nuclear import and export signals, were engineered by antibiotic selection and flow cytometry sorting. Using an optimized nuclear translocation algorithm, the translocation response could be robustly quantified on the Cellomics Arrayscan® VTI platform. Subsequent to assay optimization, the assay was developed into a higher density 384-well format high-content assay and employed for the screening of the 17K ChemBioNet compound collection. This library was selected on the basis of a genetic algorithm used to identify maximum common chemical substructures in a database of annotated bioactive molecules and hence, is well-placed in the chemical space covered by bioactive compounds. Automated multiparameter data analysis combined with visual inspection allowed us to identify and to rationally discriminate true export inhibitors from false positives, which included fluorescent compounds or cytotoxic substances that dramatically affected the cellular morphology. A total of 120 potential hit compounds were selected for Cellomics Arrayscan® VTI based rescreening. The export inhibitory activity of 20 compounds effective at concentrations < 25 μM were confirmed by fluorescence microscopy in several cell lines. Interestingly, kinetic analysis allowed the identification of inhibitors capable to interfere with the export receptor CRM1-mediated nuclear export not only in an irreversible, but also in a reversible fashion. In sum, exploitation of biosensor based screening allows the identification of chemicogenomic tools applicable for dissecting nucleo-cytoplasmic transport in living cells.
PMCID: PMC3274152  PMID: 22346706
chemical biology; cancer; Exportin 1/CRM1; HIV-1 Rev; import; LMB; nucleocytoplasmic transport; nucleoporin
19.  The use of HaloTag-based technology in flow and laser scanning cytometry analysis of live and fixed cells 
BMC Research Notes  2011;4:340.
Combining the technologies of protein tag labeling and optical microscopy allows sensitive analysis of protein function in cells.
Here, we describe development of applications using protein tag technology (HaloTag (HT)-based) for flow and laser scanning cytometry (LSC). Cell lines, expressing recombinant surface β1-integrin-HT and HT-p65 fusion protein, and a CD4 T cell line (Jurkat) infected with human immunodeficiency virus type 1 (HIV-1) reporter virus expressing the unfused HT (HIV-1Lai-Halo), were stained with different HT ligands and successfully detected by flow cytometers equipped with 488 and 561 nm lasers as well as a laser scanning cytometer (equipped with 488 and 405 nm lasers) alone or combined with cell cycle and viability markers.
Use of HT technology for cytometric applications has advantages over its use in microscopy as it allows for the statistical measurement of protein expression levels in individual cells within a heterogeneous cell population in combination with cell cycle analysis. Another advantage is the ability of the HaloTag to withstand long fixation and high concentration of fixative, which can be useful in research of infectious agents like HIV and/or mycobacteria.
PMCID: PMC3189897  PMID: 21906296
20.  High Telomerase Activity Correlates with the Stabilities of Genome and DNA Ploidy in Renal Cell Carcinoma1 
Neoplasia (New York, N.Y.)  2002;4(2):103-111.
Malignant tumors have telomerase activity, which is thought to play a critical role in tumor growth. However, the relation between telomerase activity and genomic DNA status in tumor cells is poorly understood. In the present study, we examined telomerase activity in 13 clear cell type renal cell carcinomas (CRCCs) with similar clinicopathologic features by telomeric repeat amplification protocol assay (TRAP). Based on TRAP assay results, we divided the CRCCs into two groups: a high telomerase activity group and a low/no telomerase activity group. We then analyzed genomic aberration, DNA ploidy, and telomere status in these two groups by comparative genomic hybridization (CGH), laser scanning cytometry (LSC), and telomere-specific fluorescence in situ hybridization (T-FISH), respectively. CGH showed the high telomerase activity group to have fewer genomic changes than the low/no telomerase activity group, which had many genomic aberrations. Moreover, with LSC, DNA diploid cells were found more frequently in the high telomerase activity group than in the low/no telomerase activity group. In addition, T-FISH revealed strong telomere signal intensity in the high telomerase activity group compared with that of the low/no telomerase activity group. These results suggest that telomerase activity is linked to genomic DNA status and that high telomerase activity is associated with genomic stability, DNA ploidy, and telomere length in CRCC.
PMCID: PMC1550322  PMID: 11896565
Telomerase; CGH; DNA ploidy; cancer; genomic stability
21.  Acute vascular disruption and Aquaporin 4 loss after stroke 
Background and Purpose
Ischemic protection has been demonstrated by a decrease in stroke-infarct size in transgenic mice with deficient Aquaporin 4 (AQP4) expression. However, it is not known if AQP4 is rapidly reduced during acute stroke in animals with normal AQP4 phenotype, which may provide a potential self-protective mechanism.
Adult male rats underwent transient occlusion of the middle cerebral artery (tMCAo) for 1 to 8 hours and reperfusion for 30 minutes. Protein and mRNA expression of AQP4 and glial fibrillary acidic protein (GFAP) were determined by Western blot and rtPCR. Fluorescence quantitation was obtained with laser scanning cytometery (LSC) for Cy5-tagged immunoreactivity along with fluorescein signals from pathological uptake of plasma-borne high molecular weight fluorescein-dextran. Cell death was assessed with in vivo Propidium Iodide (PI) nucleus labeling.
In the ischemic hemisphere in tissue sections, patches of fluorescein-dextran uptake were overlapped with sites of focal loss of AQP4 immunoreactivity after tMCAo of 1 to 8 hours duration. However, the average levels of AQP4 protein and mRNA, in striatal homogenates, were not significantly reduced after 8 hours of tMCAo. Tissue section cytometry (LSC) of immunoreactivity in scan areas with high densities of fluorescein-dextran uptake, demonstrated reductions in AQP4, but not in IgG or GFAP, after tMCAo of 2 hours or longer. Scan areas with low densities of fluorescein-dextran did not lose AQP4. There was sparse astrocyte cell death as only 1.7 +/− 0.85 % (mean, sd) of DAPI labeled cells were PI and GFAP labeled after 8 hours of tMCAo.
During acute tMCAo, a rapid loss of AQP4 immunoreactivity from viable astrocytes can occur. However, AQP4 loss is spatially selective and occurs primarily in regions of vascular damage.
PMCID: PMC2753985  PMID: 19372455
Aquaporin 4; Blood Brain Barrier Breakdown; Stroke
22.  Low-dose triptolide in combination with idarubicin induces apoptosis in AML leukemic stem-like KG1a cell line by modulation of the intrinsic and extrinsic factors 
Liu, Y | Chen, F | Wang, S | Guo, X | Shi, P | Wang, W | Xu, B
Cell Death & Disease  2013;4(12):e948-.
Leukemia stem cells (LSCs) are considered to be the main reason for relapse and are also regarded as a major hurdle for the success of acute myeloid leukemia chemotherapy. Thus, new drugs targeting LSCs are urgently needed. Triptolide (TPL) is cytotoxic to LSCs. Low dose of TPL enhances the cytotoxicity of idarubicin (IDA) in LSCs. In this study, the ability of TPL to induce apoptosis in leukemic stem cell (LSC)-like cells derived from acute myeloid leukemia cell line KG1a was investigated. LSC-like cells sorted from KG1a were subjected to cell cycle analysis and different treatments, and then followed by in vitro methyl thiazole tetrazolium bromide cytotoxicity assay. The effects of different drug combinations on cell viability, intracellular reactive-oxygen species (ROS) activity, colony-forming ability and apoptotic status were also examined. Combination index-isobologram analysis indicates a synergistic effect between TPL and IDA, which inhibits the colony-forming ability of LSC-like cells and induces their apoptosis. We further investigated the expression of Nrf2, HIF-1α and their downstream target genes. LSC-like cells treated with both TPL and IDA have increased levels of ROS, decreased expression of Nrf2 and HIF-1α pathways. Our findings indicate that the synergistic cytotoxicity of TPL and IDA in LSCs-like cells may attribute to both induction of ROS and inhibition of the Nrf2 and HIF-1α pathways.
PMCID: PMC3877540  PMID: 24309935
triptolide; idarubicin; reactive-oxygen species; Nrf2; HIF-1α
23.  Nuclear anomalies in the buccal cells of calcite factory workers 
Genetics and Molecular Biology  2010;33(2):374-378.
The micronucleus (MN) assay on exfoliated buccal cells is a useful and minimally invasive method for monitoring genetic damage in humans. To determine the genotoxic effects of calcite dust that forms during processing, MN assay was carried out in exfoliated buccal cells of 50 (25 smokers and 25 non-smokers) calcite factory workers and 50 (25 smokers and 25 non-smokers) age- and sex-matched control subjects. Frequencies of nuclear abnormalities (NA) other than micronuclei, such as binucleates, karyorrhexis, karyolysis and ‘broken eggs', were also evaluated. Micronuclei and the other aforementioned anomalies were analysed by two way analysis of covariance. The linear correlations between the types of micronucleus and nuclear abnormalities were determined by Spearman's Rho. There was a positive correlation between micronuclei and other types of nuclear abnormalities in accordance with the Spearman's Rho test. Results showed statistically significant difference between calcite fabric workers and control groups. MN and NA frequencies in calcite fabric workers were significantly higher than those in control groups (p < 0.05). The results of this study indicate that calcite fabric workers are under risk of significant cytogenetic damage.
PMCID: PMC3036877  PMID: 21637497
calcite; exfoliated buccal cells; micronucleus (MN); genotoxicity
24.  Normal Hematopoietic Stem Cells within the AML Bone Marrow Have a Distinct and Higher ALDH Activity Level than Co-Existing Leukemic Stem Cells 
PLoS ONE  2013;8(11):e78897.
Persistence of leukemic stem cells (LSC) after chemotherapy is thought to be responsible for relapse and prevents the curative treatment of acute myeloid leukemia (AML) patients. LSC and normal hematopoietic stem cells (HSC) share many characteristics and co-exist in the bone marrow of AML patients. For the development of successful LSC-targeted therapy, enabling eradication of LSC while sparing HSC, the identification of differences between LSC and HSC residing within the AML bone marrow is crucial. For identification of these LSC targets, as well as for AML LSC characterization, discrimination between LSC and HSC within the AML bone marrow is imperative. Here we show that normal CD34+CD38– HSC present in AML bone marrow, identified by their lack of aberrant immunophenotypic and molecular marker expression and low scatter properties, are a distinct sub-population of cells with high ALDH activity (ALDHbright). The ALDHbright compartment contains, besides normal HSC, more differentiated, normal CD34+CD38+ progenitors. Furthermore, we show that in CD34-negative AML, containing solely normal CD34+ cells, LSC are CD34– and ALDHlow. In CD34-positive AML, LSC are also ALDHlow but can be either CD34+ or CD34–. In conclusion, although malignant AML blasts have varying ALDH activity, a common feature of all AML cases is that LSC have lower ALDH activity than the CD34+CD38– HSC that co-exist with these LSC in the AML bone marrow. Our findings form the basis for combined functionally and immunophenotypically based identification and purification of LSC and HSC within the AML bone marrow, aiming at development of highly specific anti-LSC therapy.
PMCID: PMC3823975  PMID: 24244383
Transplantation  2010;90(8):836-842.
Assays for assessing human islet cell quality which provide results prior to transplantation would be very beneficial to improving outcomes for islet transplantation therapy. Parameters such as percent beta cell apoptosis and cell composition are found to vary markedly between different islet preparations, and may serve as markers of islet quality. We have developed fluorescence-based assays using laser scanning cytometry (LSC) for assessing beta cell apoptosis and islet cell composition on serial sections of intact isolated islets.
Isolated human islets were fixed in formalin and embedded in paraffin. Serial sections were immunostained for the pancreatic hormones, acinar and ductal cell markers. DNA fragmentation was used to label apoptotic cells. Stained cells were quantified using an iCys laser scanning cytometer.
Islet preparations from 102 human pancreatic islet isolations were analyzed. For the whole set of islet preparations we found a mean islet cell composition of 54.5±1.2% insulin positive; 33.9±1.2% glucagon; 12.1±0.7% somatostatin and 1.5±0.2% pancreatic polypeptide positive cells. The apoptotic beta cells were 2.85±0.4% with a range of 0.27% to 18.3%. The percentage of apoptotic beta cells correlated well (p<0.0001, n=59) with results obtained in vivo by transplantation of the corresponding islets in diabetic NODscid mice.
The analysis of whole, non-dissociated islets for cell composition and beta cell apoptosis using LSC is giving reliable and reproducible results and could be done both before islet transplantation, as well as on preserved cell blocks at any future time. Thus, they can be a powerful tool for islet quality assessment.
PMCID: PMC2959131  PMID: 20697327
Laser scanning cytometry; human pancreatic islets; islet cell composition; β cell apoptosis

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