Earth Mover's Distance (EMD): A True Metric for Comparing Biomarker Expression Levels in Cell Populations.
2016; 11 (3)
Dynamic quantification of antigen molecules with flow cytometry
JOURNAL OF IMMUNOLOGICAL METHODS
2015; 418: 66-74
Changes in the frequencies of cell subsets that (co)express characteristic biomarkers, or levels of the biomarkers on the subsets, are widely used as indices of drug response, disease prognosis, stem cell reconstitution, etc. However, although the currently available computational "gating" tools accurately reveal subset frequencies and marker expression levels, they fail to enable statistically reliable judgements as to whether these frequencies and expression levels differ significantly between/among subject groups. Here we introduce flow cytometry data analysis pipeline which includes the Earth Mover's Distance (EMD) metric as solution to this problem. Well known as an informative quantitative measure of differences between distributions, we present three exemplary studies showing that EMD 1) reveals clinically-relevant shifts in two markers on blood basophils responding to an offending allergen; 2) shows that ablative tumor radiation induces significant changes in the murine colon cancer tumor microenvironment; and, 3) ranks immunological differences in mouse peritoneal cavity cells harvested from three genetically distinct mouse strains.
View details for DOI 10.1371/journal.pone.0151859
View details for PubMedID 27008164
Light scattering by neutrophils: model, simulation, and experiment.
Journal of biomedical optics
; 13 (5): 054057
Traditional methods for estimating the number of expressed molecules, based on the detection of target antigens bound with fluorescently labeled antibodies, assume that the antigen-antibody reaction reaches equilibrium. A calibration procedure is used to convert the intensity of the fluorescence signal to the number of target molecules. Along with the different limitations of every calibration system, this substantially limits the applicability of the traditional approaches especially in the case of low affinity antibodies. We address this problem here with studies in which we demonstrate a new approach to the antigen molecule quantification problem. Instead of using a static calibration system, we analyzed mean fluorescence values over time by flow cytometry during antibody-antigen binding. Experimental data obtained with an LSRII cytometer were fitted by a diffusion-reaction mathematical model using the Levenberg-Marquardt nonlinear least squares curve-fitting algorithm in order to obtain the number of target antigen molecules per cell. Results were compared with the Quanti-BRITE calibration system. We conclude that, instead of using experiment-specific calibration, the value of the binding rate constant for each particular antibody-antigen reaction can be used to quantify antigen molecules with flow cytometry. The radius of CD8 antibody molecule binding site was found, that allows recalculating the binding rate constant for other conditions (different sizes of reagent molecules, fluorescent label, medium viscosity and temperature). This approach is independent of specially prepared calibration beads, antibody reagents and the specific dye and can be applied to both low and high affinity antibodies, under both saturating and non-saturating binding conditions. The method was demonstrated on a human blood sample dataset investigating CD8α antigen on T cells in stable binding conditions.
View details for DOI 10.1016/j.jim.2015.02.001
View details for Web of Science ID 000352660400008
View details for PubMedID 25687877
AutoGate: automating analysis of flow cytometry data
2014; 58 (2-3): 218-223
We studied the elastic light-scattering properties of human blood neutrophils, both experimentally and theoretically. The experimental study was performed with a scanning flow cytometer measuring the light-scattering patterns (LSPs) of individual cells over an angular range of 5-60 deg. We determined the absolute differential light-scattering cross sections of neutrophils. We also proposed an optical model for a neutrophil as a sphere filled by small spheres and prolate spheroids that correspond to granules and segmented nucleus, respectively. This model was used in simulations of LSPs using the discrete dipole approximation and different compositions of internal organelles. A comparison of experimentally measured and simulated LSPs gives a good qualitative agreement in LSP shape and quantitative agreement in overall magnitude of the differential light-scattering cross section.
View details for DOI 10.1117/1.2992140
View details for PubMedID 19021436
Arrangement of nuclear structures is not transmitted through mitosis but is identical in sister cells
JOURNAL OF CELLULAR BIOCHEMISTRY
2012; 113 (11): 3313-3329
Nowadays, one can hardly imagine biology and medicine without flow cytometry to measure CD4 T cell counts in HIV, follow bone marrow transplant patients, characterize leukemias, etc. Similarly, without flow cytometry, there would be a bleak future for stem cell deployment, HIV drug development and full characterization of the cells and cell interactions in the immune system. But while flow instruments have improved markedly, the development of automated tools for processing and analyzing flow data has lagged sorely behind. To address this deficit, we have developed automated flow analysis software technology, provisionally named AutoComp and AutoGate. AutoComp acquires sample and reagent labels from users or flow data files, and uses this information to complete the flow data compensation task. AutoGate replaces the manual subsetting capabilities provided by current analysis packages with newly defined statistical algorithms that automatically and accurately detect, display and delineate subsets in well-labeled and well-recognized formats (histograms, contour and dot plots). Users guide analyses by successively specifying axes (flow parameters) for data subset displays and selecting statistically defined subsets to be used for the next analysis round. Ultimately, this process generates analysis "trees" that can be applied to automatically guide analyses for similar samples. The first AutoComp/AutoGate version is currently in the hands of a small group of users at Stanford, Emory and NIH. When this "early adopter" phase is complete, the authors expect to distribute the software free of charge to .edu, .org and .gov users.
View details for DOI 10.1007/s12026-014-8519-y
View details for Web of Science ID 000336333700007
View details for PubMedID 24825775
Acetylation-dependent nuclear arrangement and recruitment of BMI1 protein to UV-damaged chromatin.
Journal of cellular physiology
2012; 227 (5): 1838-50
Although it is well known that chromosomes are non-randomly organized during interphase, it is not completely clear whether higher-order chromatin structure is transmitted from mother to daughter cells. Therefore, we addressed the question of how chromatin is rearranged during interphase and whether heterochromatin pattern is transmitted after mitosis. We additionally tested the similarity of chromatin arrangement in sister interphase nuclei. We noticed a very active cell rotation during interphase, especially when histone hyperacetylation was induced or transcription was inhibited. This natural phenomenon can influence the analysis of nuclear arrangement. Using photoconversion of Dendra2-tagged core histone H4 we showed that the distribution of chromatin in daughter interphase nuclei differed from that in mother cells. Similarly, the nuclear distribution of heterochromatin protein 1? (HP1?) was not completely identical in mother and daughter cells. However, identity between mother and daughter cells was in many cases evidenced by nucleolar composition. Moreover, morphology of nucleoli, HP1? protein, Cajal bodies, chromosome territories, and gene transcripts were identical in sister cell nuclei. We conclude that the arrangement of interphase chromatin is not transmitted through mitosis, but the nuclear pattern is identical in naturally synchronized sister cells. It is also necessary to take into account the possibility that cell rotation and the degree of chromatin condensation during functionally specific cell cycle phases might influence our view of nuclear architecture.
View details for DOI 10.1002/jcb.24208
View details for Web of Science ID 000308927200002
View details for PubMedID 22644811
Distribution function approach to the study of the kinetics of IgM antibody binding to FcγRIIIb (CD16b) receptors on neutrophils by flow cytometry.
Journal of theoretical biology
2011; 290: 1-6
Polycomb group (PcG) proteins, organized into Polycomb bodies, are important regulatory components of epigenetic processes involved in the heritable transcriptional repression of target genes. Here, we asked whether acetylation can influence the nuclear arrangement and function of the BMI1 protein, a core component of the Polycomb group complex, PRC1. We used time-lapse confocal microscopy, micro-irradiation by UV laser (355 nm) and GFP technology to study the dynamics and function of the BMI1 protein. We observed that BMI1 was recruited to UV-damaged chromatin simultaneously with decreased lysine acetylation, followed by the recruitment of heterochromatin protein HP1β to micro-irradiated regions. Pronounced recruitment of BMI1 was rapid, with half-time τ = 15 sec; thus, BMI1 is likely involved in the initiation step leading to the recognition of UV-damaged sites. Histone hyperacetylation, stimulated by HDAC inhibitor TSA, suppression of transcription by actinomycin D, and ATP-depletion prevented increased accumulation of BMI1 to γH2AX-positive irradiated chromatin. Moreover, BMI1 had slight ability to recognize spontaneously occurring DNA breaks caused by other pathophysiological processes. Taken together, our data indicate that the dynamics of recognition of UV-damaged chromatin, and the nuclear arrangement of BMI1 protein can be influenced by acetylation and occur as an early event prior to the recruitment of HPβ to UV-irradiated chromatin.
View details for DOI 10.1002/jcp.22912
View details for PubMedID 21732356
A nonfitting method using a spatial sine window transform for inhomogeneous effective-diffusion measurements by FRAP.
2011; 100 (2): 507-16
Though flow cytometry provides the entire distribution of cellular fluorescence (i.e., "fluorescence profile"), only mean fluorescence data are usually considered in studies of ligand-receptor binding. In this study, we presented a method of the treatment of the temporal evolution of the whole fluorescence profile with a comprehensive statistical approach extended to the reversible binding case. The method was demonstrated in the study of the 1D3 IgM monoclonal antibodies binding to FcγRIIIb receptors (CD16b) on neutrophils. Kinetic experiments were carried out using a FACSCalibur (Becton Dickinson, USA) flow cytometer. For each of four donors, we obtained the distribution of the number of FcγRIIIb surface receptors for neutrophils and the rate constants per receptor: the association rate constant of (2.7±0.4)×10(7) M(-1) min(-1), and the dissociation rate constant of (1.3±0.4)×10(-1) min(-1). Based on the obtained values, the size of the receptor reaction site was estimated at approximately 1 nm. It was found, that cell receptors distributions differed sufficiently between donors in mean and the skewness values, whereas the coefficient of variation (i.e., the ratio of the standard deviation to the mean) did not vary significantly.
View details for DOI 10.1016/j.jtbi.2011.08.026
View details for PubMedID 21920371
Structure and epigenetics of nucleoli in comparison with non-nucleolar compartments.
The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society
2010; 58 (5): 391-403
Determining averaged effective diffusion constants from experimental measurements of fluorescent proteins in an inhomogeneous medium in the presence of ligand-receptor interactions poses problems of analytical tractability. Here, we introduced a nonfitting method to evaluate the averaged effective diffusion coefficient of a region of interest (which may include a whole nucleus) by mathematical processing of the entire cellular two-dimensional spatial pattern of recovered fluorescence. Spatially and temporally resolved measurements of protein transport inside cells were obtained using the fluorescence recovery after photobleaching technique. Two-dimensional images of fluorescence patterns were collected by laser-scanning confocal microscopy. The method was demonstrated by applying it to an estimation of the mobility of green fluorescent protein-tagged heterochromatin protein 1 in the nuclei of living mouse embryonic fibroblasts. This approach does not require the mathematical solution of a corresponding system of diffusion-reaction equations that is typical of conventional fluorescence recovery after photobleaching data processing, and is most useful for investigating highly inhomogeneous areas, such as cell nuclei, which contain many protein foci and chromatin domains.
View details for DOI 10.1016/j.bpj.2010.11.080
View details for PubMedID 21244847
The nucleolus is a nuclear compartment that plays an important role in ribosome biogenesis. Some structural features and epigenetic patterns are shared between nucleolar and non-nucleolar compartments. For example, the location of transcriptionally active mRNA on extended chromatin loop species is similar to that observed for transcriptionally active ribosomal DNA (rDNA) genes on so-called Christmas tree branches. Similarly, nucleolus organizer region-bearing chromosomes located a distance from the nucleolus extend chromatin fibers into the nucleolar compartment. Specific epigenetic events, such as histone acetylation and methylation and DNA methylation, also regulate transcription of both rRNA- and mRNA-encoding loci. Here, we review the epigenetic mechanisms and structural features that regulate transcription of ribosomal and mRNA genes. We focus on similarities in epigenetic and structural regulation of chromatin in nucleoli and the surrounding non-nucleolar region and discuss the role of proteins, such as heterochromatin protein 1, fibrillarin, nucleolin, and upstream binding factor, in rRNA synthesis and processing.
View details for DOI 10.1369/jhc.2009.955435
View details for PubMedID 20026667