The authors thank Robert Giulitto (Hoxworth blood center) for human blood samples and Dr. Liang Niu for the normalization of gene expression reads. We also thank grant support from the National Institute of Environmental Health Sciences (ES006096), Center for Environmental Genetics (CEG) pilot project (S.H.), National Institute of Allergy and Infectious Diseases (AI115358) (S.H.), University of Cincinnati University Research Council award (S.H.), and University of Cincinnati College of Medicine Core Enhancement Funding (X. Z.).

Human protocols in this study were approved by the Institutional Review Board of the University of Cincinnati and all methods were performed in accordance with the relevant guidelines and regulations. Blood samples from healthy donors were obtained from the Hoxworth Blood Center at the University of Cincinnati Medical Center.
1. Transcriptomic Profiling of Pollutant-exposed Human Monocyte-derived DCs
<ol>
	<li>Total RNA extraction of BaP-exposed DCs
	<ol>
		<li>Differentiate human DCs using ...

<ol>
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Functional confirmation of an altered gene pathway is challenging, because of widely impacted gene expression involving multiple pathways and the difficulty to&#160;integrate individual and populational cellular activities. We employed imaging flow cytometry to specifically test CD1d trafficking in endocytic compartments. Imaging flow cytometry integrates the populational measurement of cells and the individual demonstration of subcellular colocalization of multiple proteins. Confocal microscopy has previously provided h...

Antigen presentation typically involves intracellular protein trafficking, which has been often investigated using morphological characterization and phenotypic profiling of antigen presenting cells1,2,3. To integrate the advantages of imaging and phenotyping methods, we describe an imaging analysis platform at both single cell and population levels to demonstrate an altered protein colocalization in human dendritic cells (DCs). In peptide antigen presentation, major histocompatibility complex (MHC) class I molecules bind a short peptide (8-10 residues) in the endoplasmic reticulum to activate conventional CD8+ T cells, while MHC class II molecules bind a relatively longer peptide (~20 residues) in endocytic compartments to activate conventional CD4+ T cells1,4. In contrast, lipid-specific T cells are activated by CD1 proteins with lipid antigens loaded mainly in endocytic compartments5,6. Lipid antigen presentation requires the supply of lipid metabolites produced in lipid metabolism7,8,9,10 and the loading of functional lipid metabolites to CD1 proteins in endocytic compartments5,6. In this context, various cellular factors modulating lipid antigen presentation, especially in environmental exposure of lipophilic pollutants and immune disorders, are critical to be defined. In this study, we used transcriptomic analysis, image profiling, and cellular and populational imaging analysis of human monocyte-derived DCs to determine the endocytic protein trafficking contributing to lipid antigen presentation in pollutant exposure. Certainly, this combined platform can be applied to studying subcellular protein trafficking and colocalization in different biological processes.
Technically, subcellular protein localization was usually demonstrated using confocal microscopy and statistically analyzed in a limited number of detected cells1,2,3,11. Moreover, flow cytometry has been broadly applied to gate cell populations with co-stained signals of multiple proteins at a cellular level12; however, this lacks a detailed visualization of subcellular protein colocalization. To achieve comprehensive and statistical analyses of percentage protein colocalization at both cellular and population levels, we incorporate imaging profiling and analysis approaches to determine the features of protein colocalization with biological relevance. Specifically, we use imaging flow cytometry to detect the colocalization of CD1d and lysosomal-associated membrane protein 1 (Lamp1) proteins in this study. Quantitative analysis of colocalized molecules was previously difficult to be performed at a populational scale. In this study, we adapted the ImageJ-Fiji program to examine the percentage of protein colocalization with a large number of co-stained cells at both populational and individual cellular levels. Specifically, we measured co-localized areas, intensity, and populational size to support the conclusion that the CD1d protein was largely retained in late endocytic compartments of human DCs in exposure to a lipophilic pollutant benzo[a]pyrene (BaP)13. This combined cellular and population imaging analysis provided highly reproducible, comprehensive, and statistically significant results of CD1d-Lamp1 colocalization relevant to inhibited lipid antigen presentation.
The transcriptome of BaP-exposed human DCs strongly supported the hypothesis that endocytic lipid metabolism and CD1d endocytic trafficking were impaired in BaP exposure. To test this hypothesis, we applied imaging flow cytometry to profile the images of DC population that were co-stained with multiple proteins including CD1d, endocytic markers, and DC markers. Finally, co-stained cells were statistically analyzed to demonstrate the percentage of intensity and areas of CD1d and Lamp1 colocalization.

<table border="0" cellpadding="0" cellspacing="0" style="width:1340px;" width="1340">
	<tbody>
		<tr height="19">
			<td height="19" style="height:19px;width:284px;">Transcriptomics</td>
			<td style="width:448px;">Illumina</td>
			<td style="width:417px;">HiSeq 2500 v4</td>
			<td style="width:191px;">Illumina HiSeq system</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;width:284px;">ImagingStream X</td>
			<td style="width:448px;">Millipore</td>
			<td>100220</td>
			<td>Imaging flow cytometry</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">mirVana miRNA Isolation Kit</td>
			<td style="width:448px;">Thermo Fisher</td>
			<td></td>
			<td>Total RNA extraction</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Agilent RNA 6000 Pico Kit</td>
			<td style="width:448px;">Agilent</td>
			<td></td>
			<td>Total RNA QC analysis</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Veriti 96-Well Fast Thermal Cycler</td>
			<td style="width:448px;">Thermo Fisher</td>
			<td></td>
			<td>PCR, enzyme reaction</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">NEBNext Poly(A) mRNA Magnetic Isolation Module&#160;</td>
			<td style="width:448px;">New England Biolab</td>
			<td></td>
			<td>PolyA RNA purification</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Automated SMARTer Apollo system</td>
			<td style="width:448px;">Takara</td>
			<td></td>
			<td>PolyA RNA purification</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">NEBNext Ultra RNA Library Prep Kit for Illumina</td>
			<td style="width:448px;">New England Biolab</td>
			<td></td>
			<td>Library preparation</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Agencourt AMPure XP magnetic beads</td>
			<td style="width:448px;">Beckman Coulter</td>
			<td></td>
			<td>DNA purification&#160;</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">2100 Bioanalyzer</td>
			<td style="width:448px;">Agilent</td>
			<td></td>
			<td>Library QC, size distribution analysis</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Agilent High Sensitivity DNA Kit</td>
			<td style="width:448px;">Agilent</td>
			<td></td>
			<td>Library QC, size distribution analysis</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">QuantStudio 5 Real-Time PCR System (Thermo Fisher)</td>
			<td style="width:448px;">Thermo Fisher</td>
			<td></td>
			<td>Library quantification</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">NEBNext Library Quant Kit</td>
			<td style="width:448px;">New England Biolab</td>
			<td></td>
			<td>Library quantification</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">cBot</td>
			<td style="width:448px;">Illumina</td>
			<td></td>
			<td>Library cluster generation</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">TruSeq SR Cluster Kit v3 - cBot &#8211; HS</td>
			<td style="width:448px;">Illumina</td>
			<td></td>
			<td>Library cluster generation</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">HiSeq 1000</td>
			<td style="width:448px;">Illumina</td>
			<td></td>
			<td>Sequencing</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">TruSeq SBS Kit v3 - HS (50-cycles)</td>
			<td style="width:448px;">Illumina</td>
			<td></td>
			<td>Sequencing</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;width:284px;">Phycoerythrin/Cyanine 7 (PE/Cy7)</td>
			<td style="width:448px;">Bio Legend</td>
			<td style="width:417px;">L243</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;width:284px;">Phycoerythrin/Cyanine 5 (PE/Cy5)</td>
			<td style="width:448px;">Bio Legend</td>
			<td align="right" style="width:417px;">3.9</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;width:284px;">Brilliant violet 421</td>
			<td style="width:448px;">Bio Legend</td>
			<td style="width:417px;">L161</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;width:284px;">PE-anti-mouse IgG2b</td>
			<td style="width:448px;">Bio Legend</td>
			<td align="right" style="width:417px;">51.1</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;width:284px;">Alexa Fluor 647 (AF647)</td>
			<td style="width:448px;">Bio Legend</td>
			<td style="width:417px;">CD107a(H4A3)</td>
			<td></td>
		</tr>
	</tbody>
</table>

integrate imaging flow cytometry and transcriptomic profiling to evaluate altered endocytic cd1d trafficking

Populational analyses of the morphological and functional alteration of endocytic proteins are challenging due to the demand of image capture at a single cell level and statistical image analysis at a populational level. To overcome this difficulty, we used imaging flow cytometry and transcriptomic profiling (RNA-seq) to determine altered subcellular localization of the cluster of differentiation 1d protein (CD1d) associated with impaired endocytic gene expression in human dendritic cells (DCs), which were exposed to the common lipophilic air pollutant benzo[a]pyrene. The colocalization of CD1d and endocytic marker Lamp1 proteins from thousands of cell images captured with imaging flow cytometry was analyzed using IDEAS and ImageJ-Fiji programs. Numerous cellular images with co-stained CD1d and Lamp1 proteins were visualized after gating on CD1d+Lamp1+ DCs using IDEAS. The enhanced CD1d and Lamp1 colocalization upon BaP exposure was further demonstrated using thresholded scatterplots, tested with Mander&#39;s coefficients for co-localized intensity, and plotted based on the percentage of co-localized areas using ImageJ-Fiji. Our data provide an advantageous instrumental and bioinformatic approach to measure protein colocalization at both single and populational cellular levels, supporting an impaired functional outcome of transcriptomic alteration in pollutant-exposed human DCs.

The lipophilic pollutant BaP alters endocytic gene clusters in human DCs. Human monocyte-derived DCs from each donor (n=3) were incubated with BaP and sorted for&#160;conventional DCs, which were further used for RNA extraction and transcriptomic analysis as described. Upon the normalization of gene expression, altered genes between BaP-exposed and non-exposed groups were clustered according to the functional correlation of differentially expressed genes. We input the altered gene list to...

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Integrate Imaging Flow Cytometry and Transcriptomic Profiling to Evaluate Altered Endocytic CD1d Trafficking

Imaging flow cytometry provides an ideal approach to detect the morphological and functional alteration of cells at individual and populational levels. Disrupted endocytic function for lipid antigen presentation in pollutant-exposed human dendritic cells was demonstrated with a combined transcriptomic profiling of gene expression and morphological demonstration of protein trafficking.

Populational analyses of the morphological and functional alteration of endocytic proteins are challenging due to the demand of image capture at a single ...

These methods integrate next generation sequencing and flow cytometry imaging analysis. It can help answer interesting questions, like whether some phenotypic alterations are implicate, instead of the transcriptome, especially in the pollutant exposure environment. The main advantage of this simple method for us is that we can use it to measure the colocalization of biologically important protein, to interpret the outcomes of key differential gene expression at a functional level.The implications of this technique extend toward the diagnosis of pathological and toxicological outcomes. As a normal imager approach, forsee has the ability to connect gene expression to protein function. Generally, individuals new to this method will struggle because of the high technical demands of the imaging and transcriptomic analysis.To sequence the the human monocyte derived dendritic cell library, first load the sequencing and indexing reagents onto the sequencing biosynthesis and indexing reagent racks, respectively, and place the racks in a laboratory grade water bath for one hour, until all of the ice has melted, and the reagents are mixed thoroughly. While the reagents are thawing, power on the sequencer, connecting the computer to a network drive when the Do Not Eject drive appears, and launch the sequencer control software. Next, add about 100 milliliters of maintenance wash solution to each of the bottles in the sequencing biosynthesis reagent rack, and screw a funnel cap onto each bottle.Add approximately 12 milliliters of maintenance wash solution to each 15 milliliter conical tube in the indexing reagent rack, and discard the caps. Then load both the racks onto the sequencer. Select Maintenance Wash within the sequencer control software, and follow the instructions for cleaning the sequencer fluid system.Use a flashlight to visually inspect the flow cell for bubbles passing through the lanes, to make sure there is no leakage. When the wash sequence is finished, open the Sequence tab, and start a new run, directing the output data to a network drive. Upload a sample sheet for demultiplexing, and enter the appropriate reagent information.Use a used flow cell to prime the system, with the sequencing reagents. Once the cluster generation is complete, remove the flow cell. And lightly spray the cell with water.Wipe the flow cell dry with lens paper, followed by a light spray with 95%ethanol. After wiping the flow cell dry again, check the flow cell's surface against the light to make sure that it is clean, without debris or salt residue. When the prime step is finished, load the clustered flow cell, and begin the sequencing.The sequence analysis viewer software will automatically be started. About 26 hours later, monitor the sequencing data quality via the high sequence control software, and sequencing analysis view software to assess the data quality, and for any troubleshooting. Then, when the sequence is finished, change the flow cell gasket, and perform a maintenance wash before beginning the next run.After flow cytometric imaging of the pollutant-exposed dendritic cells, open ImageJ Fiji, and merge the 100 saved cell images for the non-exposed and pollutant-exposed human dendritic cell sample groups into individual files according to the treatment group. To analyze CD1d, and Lamp1 colocalization within the two populations, open the pollutant-exposed 100 merged cell image, and select Image, Color, and Split Channels to split the image into two individual images with a single fluorophore per channel. To create a scatter plot of the colocalized pixels, select Analyze, Colocalization, and Colocalization Threshold, and press Print Screen to save the scatter plot.To calculate the Mander's colocalization coefficient for each single-cellular image, use the oval selection tool to select a single-cell image on the image file with the split channels, and select Analyze, Colocalization, and Colocalization Threshold again. Then select Channel 1 from the dialogue box for the region of interest, and click OK.When the coefficient has been calculated for all 100 cell images, import the results into an appropriate spreadsheet, and repeat the analysis for the control non-exposed cell sample. Using RNA sequencing and transcriptomic data analyses, several major altered gene clusters, including lipid metabolism and endocytic functions were identified in the pollutant-exposed DCs.At the individual cell image level, HLADR positive CD11c positive dendritic cells can be gated, according to their CD1d and Lamp1 coexpression. Control non-exposed dendritic cells demonstrate minimal CD1d and Lamp1 protein colocalization, indicating a basal level of CD1d endocytic trafficking, and a high level of surface expression under physiological conditions. Whereas CD1d is retained in the late endocytic compartments of pollutant-exposed dendritic cells, confirming altered endocytic gene profiles in this experimental cell population.After merging the individual cellular images into a single image file, the individual images can be split according to their fluorophore expression, and the colocalization of the pixel intensity between the two channels can be visualized in a scatter plot. The degree of colocalization between the CD1d and Lamp1 proteins in the two treatment groups can then be quantified using Mander's coefficients. If the protein intensity is hetergeneous between the colocalized and non-colocalized areas, the colocalized intensity will not be parallel to the colocalized areas, therefore it is also important to further assess the colocalization of the two proteins, based on the pixel intensity.Once mastered, the image analysis can be completed in two hours, and the RNA sequencing setup can be completed in three hours, if each technique is performed properly. While attempting this procedure, it is important to remember to make sure that all the reagents are properly loaded in the correct positions, and that there's no leakage in the sequencer. Following this procedure, other methods, like micro RNA, exome, or mast cell sequencing can be performed to answer additional questions about global micro RNA expression, gene mutation, or DNA methylation, respectively.So after it's development, this technique will help researchers in the field of cellular imaging analysis, and next generation sequencing to explore the effect of the environmental pollutant on gene expression and protein function. After watching this video, you should have a good understanding of how to set up the next generation sequencing, and the imager analysis of protein colocalization. Don't forget that working with a toxic pollutant chemicals in human blood samples can be extremely hazardous.Precautions such as using a chemical fume hood, and personal protective equipment, should always be taken when performing these procedures.

integrate-imaging-flow-cytometry-transcriptomic-profiling-to-evaluate

Research

JoVE Journal

Immunology and Infection

6.6K 次观看.  University of Cincinnati College of Medicine. 这些方法集成了下一代测序和流式细胞学成像分析。它可以帮助回答有趣的问题，如一些表型的改变是否涉及，而不是转录组，特别是在污染物暴露环境中。对于我们来说，这种简单方法的主要优点是，我们可以用它来测量具有生物重要作用的蛋白质的结肠化，在功能层面上解释关键微分基因表达的结果。该技术的含义延伸到病理和毒理学结果的诊断。作为一种正常的?...

视频: Integrate Imaging Flow Cytometry and Transcriptomic Profiling to Evaluate Altered Endocytic CD1d Trafficking

Imaging flow cytometry provides an ideal approach to detect the morphological and functional alteration of cells at individual and populational levels. Disrupted endocytic function for lipid antigen presentation in pollutant-exposed human dendritic cells was demonstrated with a combined transcriptomic profiling of gene expression and morphological demonstration of protein...

using flow cytometry to detect and quantitate altered blood formation in the developing zebrafish

Using Flow Cytometry to Detect and Quantitate Altered Blood Formation in the Developing Zebrafish

This assay is a simple method to quantitate hematopoietic cells in developing embryonic zebrafish. Blood cells from dissociated zebrafish are subjected to flow cytometry analysis. This allows the detection of blood defects in mutant animals and after genetic...

imaging flow cytometry to study microbial autoaggregation

Author Spotlight: Advancing Research in Microbial Autoaggregation Using Imaging Flow Cytometry

This protocol describes a quantitative approach to measure microbial autoaggregation using imaging flow...

Imaging Flow Cytometry to Study Microbial Autoaggregation

image-based flow cytometry technique to evaluate changes in granulocyte function in vitro

Image-based Flow Cytometry Technique to Evaluate Changes in Granulocyte Function In Vitro

This method demonstrates a technique for assessing granulocyte function by simultaneously measuring phagocytosis of bacteria and oxidative burst. Image-based flow cytometry allowed for the identification of three distinct subsets of activated granulocytes that all differed in their relative functional...

Image-based Flow Cytometry Technique to Evaluate Changes in Granulocyte Function In Vitro

measurement of t cell alloreactivity using imaging flow cytometry

Measurement of T Cell Alloreactivity Using Imaging Flow Cytometry

This paper describes a method for measuring alloreactivity in a mixed population of T cells using imaging flow...

automation of the micronucleus assay using imaging flow cytometry and artificial intelligence

Automation of the Micronucleus Assay Using Imaging Flow Cytometry and Artificial Intelligence

The micronucleus (MN) assay is a well-established test for quantifying DNA damage. However, scoring the assay using conventional techniques such as manual microscopy or feature-based image analysis is laborious and challenging. This paper describes the methodology to develop an artificial intelligence model to score the MN assay using imaging flow cytometry...

analyzing cellular internalization of nanoparticles and bacteria by multi-spectral imaging flow cytometry

Analyzing Cellular Internalization of Nanoparticles and Bacteria by Multi-spectral Imaging Flow Cytometry

In this article, we describe a method utilizing multi-spectral imaging flow cytometry to quantify the internalization of polyanhydride nanoparticles or bacteria by RAW 264.7...

wide-field fluorescent microscopy and fluorescent imaging flow cytometry on a cell-phone

Wide-field Fluorescent Microscopy and Fluorescent Imaging Flow Cytometry on a Cell-phone

We review our recent results on the integration of fluorescent microscopy and imaging flow cytometry tools on a cell-phone using compact and cost-effective opto-fluidic attachments. These cell-phone based micro-analysis devices might be useful for cytometric analysis, such as performing various cell counting tasks as well as for high-throughput screening of e.g., water samples in resource limited...

flow cytometry and confocal imaging analysis of low wnt expression in axin2-mturquoise2 reporter thymocytes

Flow Cytometry and Confocal Imaging Analysis of Low Wnt Expression in Axin2-mTurquoise2 Reporter Thymocytes

Signaling levels are known to regulate cell fate, indicating that regulation of Wnt signaling constitutes an interesting therapeutic target. Here, we describe flow cytometry and confocal microscopy analysis methods for a robust murine canonical Wnt signaling reporter model that measures distinct Wnt signaling levels.

localization and relative quantification of carbon nanotubes in cells with multispectral imaging flow cytometry

Localization and Relative Quantification of Carbon Nanotubes in Cells with Multispectral Imaging Flow Cytometry

In this study, the main purpose was to monitor the cellular uptake and eventual exocytosis of carbon nanotubes (CNTs). From this perspective, we proposed here a unique method using multispectral imaging flow cytometry allowing a quantification and localization of CNTs in a statistically relevant number of...

characterization of human monocyte subsets by whole blood flow cytometry analysis

Characterization of Human Monocyte Subsets by Whole Blood Flow Cytometry Analysis

Here we present a protocol for characterizing monocyte subsets by whole blood flow cytometry. This includes outlining how to gate the subsets and assess their expression of surface markers and giving an example of the assessment of the expression of M1 (inflammatory) and M2 markers...

an automated method to perform the in vitro micronucleus assay using multispectral imaging flow cytometry

An Automated Method to Perform The In Vitro Micronucleus Assay using Multispectral Imaging Flow Cytometry

The in vitro micronucleus assay is a well-established method for evaluating genotoxicity and cytotoxicity but scoring the assay using manual microscopy is laborious and suffers from subjectivity and inter-scorer variability. This paper describes the protocol developed to perform a fully automated version of the assay using multispectral imaging flow...

parallel-plate flow chamber and continuous flow circuit to evaluate endothelial progenitor cells under laminar flow shear stress

Parallel-plate Flow Chamber and Continuous Flow Circuit to Evaluate Endothelial Progenitor Cells under Laminar Flow Shear Stress

We are describing a method to subject adherent cells to laminar flow shear stress in a sterile continuous flow circuit.  The cells' adhesion, morphology can be studied through the transparent chamber, samples obtained from the circuit for metabolite analysis and cells harvested after shear exposure for future experiments or...

autofluorescence imaging to evaluate cellular metabolism

Autofluorescence Imaging to Evaluate Cellular Metabolism

This protocol describes fluorescence imaging and analysis of the endogenous metabolic coenzymes, reduced nicotinamide adenine (phosphate) dinucleotide (NAD(P)H), and oxidized flavin adenine dinucleotide (FAD). Autofluorescence imaging of NAD(P)H and FAD provides a label-free, nondestructive method to assess cellular...

qualitative and quantitative analysis of the immune synapse in the human system using imaging flow cytometry

Qualitative and Quantitative Analysis of the Immune Synapse in the Human System Using Imaging Flow Cytometry

Here, we describe a complete workflow for the qualitative and quantitative analysis of immune synapses between primary human T cells and antigen-presenting cells. The method is based on imaging flow cytometry, which allows the acquisition and evaluation of several thousand cell images within a relatively short period of...

isolating human peripheral blood mononuclear cells and cd4+ t cells from s&#233;zary syndrome patients for transcriptomic profiling

Isolating Human Peripheral Blood Mononuclear Cells and CD4+ T cells from S&amp;#233;zary Syndrome Patients for Transcriptomic Profiling

We present a simple protocol for the isolation of peripheral blood mononuclear cells from whole blood obtained from patients diagnosed with S&#233;zary Syndrome, followed by selection of CD4+ T cells, their stimulation with phorbol12-myristate13-acetate and A23187 ionophore, and preparation of RNA for transcriptomic...

Isolating Human Peripheral Blood Mononuclear Cells and CD4+ T cells from S&#233;zary Syndrome Patients for Transcriptomic Profiling

led thermo flow &#8212; combining optogenetics with flow cytometry

LED Thermo Flow &amp;#8212; Combining Optogenetics with Flow Cytometry

Optically controlled substances are powerful tools to study signaling pathways. To expand the spectrum of possible experiments, we developed a device for studying optically controlled substances in real time using flow cytometry: the LED Thermo...

LED Thermo Flow &#8212; Combining Optogenetics with Flow Cytometry

microfluidic imaging flow cytometry by asymmetric-detection time-stretch optical microscopy (atom)

Microfluidic Imaging Flow Cytometry by Asymmetric-detection Time-stretch Optical Microscopy ATOM

This protocol describes the implementation of an asymmetric-detection time-stretch optical microscopy system for single-cell imaging in ultrafast microfluidic flow and its applications in imaging flow cytometry.

Microfluidic Imaging Flow Cytometry by Asymmetric-detection Time-stretch Optical Microscopy (ATOM)

utilizing phluorin-tagged receptors to monitor subcellular localization and trafficking

Utilizing pHluorin-tagged Receptors to Monitor Subcellular Localization and Trafficking

Labeling the extracellular domain of a membrane protein with a pH sensitive fluorophore, superecliptic pHluorin (SEP), allows subcellular localization, expression, and trafficking to be determined. Imaging SEP-labeled proteins with total internal reflection fluorescence microscopy (TIRFM) enables the quantification of protein levels in the peripheral ER and plasma...

flow cytometry approach to characterize phagocytic properties of acutely-isolated adult microglia and brain macrophages in vitro

Flow Cytometry Approach to Characterize Phagocytic Properties of Acutely-Isolated Adult Microglia and Brain Macrophages In Vitro

Assessment of phagocytic properties of microglia and brain macrophages can provide a valuable functional dimension to molecular profiling studies. We describe a validated protocol that uses flow cytometry to rapidly and reliably quantify phagocytosis of fluorescent microspheres and amyloid beta fibrils by acutely-isolated microglia and brain macrophages from mouse...

Human In Vitro Suppression as Screening Tool for the Recognition of an Early State of Immune Imbalance

Regulatory T cells (Tregs) are critical mediators of immune tolerance to self-antigens. In addition, they are crucial regulators of the immune response following an infection. Despite efforts to identify unique surface marker on Tregs, the only unique feature is their ability to suppress the proliferation and function of effector T cells. While it is clear that only in vitro assays can be used in assessing human Treg function, this becomes problematic when assessing the results from cross-sectional studies where healthy cells and cells isolated from subjects with autoimmune diseases (like Type 1 Diabetes-T1D) need to be compared. There is a great variability among laboratories in the number and type of responder T cells, nature and strength of stimulation, Treg:responder ratios and the number and type of antigen-presenting cells (APC) used in human in vitro suppression assays. This variability makes comparison between studies measuring Treg function difficult. The Treg field needs a standardized suppression assay that will work well with both healthy subjects and those with autoimmune diseases. We have developed an in vitro suppression assay that shows very little intra-assay variability in the stimulation of T cells isolated from healthy volunteers compared to subjects with underlying autoimmune destruction of pancreatic &beta;-cells. The main goal of this piece is to describe an in vitro human suppression assay that allows comparison between different subject groups. Additionally, this assay has the potential to delineate a small loss in nTreg function and anticipate further loss in the future, thus identifying subjects who could benefit from preventive immunomodulatory therapy1. Below, we provide thorough description of the steps involved in this procedure. We hope to contribute to the standardization of the in vitro suppression assay used to measure Treg function. In addition, we offer this assay as a tool to recognize an early state of immune imbalance and a potential functional biomarker for T1D.

Human In Vitro Suppression as Screening Tool for the Recognition of an Early State of Immune Imbalance

Tregs are potent suppressors of the immune system. There is a lack of unique surface markers to define them, hence, definitions of Tregs are primarily functional. Here we describe an optimized in vitro assay capable of identifying immune imbalance in subjects at risk to develop T1D.

Regulatory T cells (Tregs) are critical mediators of immune tolerance to self-antigens. In addition, they are crucial regulators of the immune response ...

Cell-based Flow Cytometry Assay to Measure Cytotoxic Activity

Cytolytic activity of CD8+ T cells is rarely evaluated. We describe here a new cell-based assay to measure the capacity of antigen-specific CD8+ T cells to kill CD4+ T cells loaded with their cognate peptide. Target CD4+ T cells are divided into two populations, labeled with two different concentrations of CFSE. One population is pulsed with the peptide of interest (CFSE-low) while the other remains un-pulsed (CFSE-high). Pulsed and un-pulsed CD4+ T cells are mixed at an equal ratio and incubated with an increasing number of purified CD8+ T cells. The specific killing of autologous target CD4+ T cells is analyzed by flow cytometry after coculture with CD8+ T cells containing the antigen-specific effector CD8+ T cells detected by peptide/MHCI tetramer staining. The specific lysis of target CD4+ T cells measured at different effector versus target ratios, allows for the calculation of lytic units, LU30/106 cells. This simple and straightforward assay allows for the accurate measurement of the intrinsic capacity of CD8+ T cells to kill target CD4+ T cells.

This protocol describes a sensitive, cell-based cytotoxicity assay. By enumerating the decrease in frequency of live target CD4+ T cells in the presence of an increasing number of effector CD8+ T cells, this assay allows for the direct assessment of cytolytic activity of antigen-specific CD8+ T cells.

Cytolytic activity of CD8+ T cells is rarely evaluated. We describe here a new cell-based assay to measure the capacity of antigen-specific CD8+ T cells ...

Granulocytes play a key role in the body&#8217;s innate immune response to bacterial and viral infections. While methods exist to measure granulocyte function, in general these are limited in terms of the information they can provide. For example, most existing assays merely provide a percentage of how many granulocytes are activated following a single, fixed length incubation. Complicating matters, most assays focus on only one aspect of function due to limitations in detection technology. This report demonstrates a technique for simultaneous measurement of granulocyte phagocytosis of bacteria and oxidative burst. By measuring both of these functions at the same time, three unique phenotypes of activated granulocytes were identified: 1) Low Activation (minimal phagocytosis, no oxidative burst), 2) Moderate Activation (moderate phagocytosis, some oxidative burst, but no co-localization of the two functional events), and 3) High Activation (high phagocytosis, high oxidative burst, co-localization of phagocytosis and oxidative burst). A fourth population that consisted of inactivated granulocytes was also identified. Using assay incubations of 10, 20, and 40-min the effect of assay incubation duration on the redistribution of activated granulocyte phenotypes was assessed. A fourth incubation was completed on ice as a control. By using serial time incubations, the assay may be able to able to detect how a treatment spatially affects granulocyte function. All samples were measured using an image-based flow cytometer equipped with a quantitative imaging (QI) option, autosampler, and multiple lasers (488, 642, and 785 nm).

This method demonstrates a technique for assessing granulocyte function by simultaneously measuring phagocytosis of bacteria and oxidative burst. Image-based flow cytometry allowed for the identification of three distinct subsets of activated granulocytes that all differed in their relative functional capacity.

Granulocytes play a key role in the body&#8217;s innate immune response to bacterial and viral infections. While methods exist to measure granulocyte ...

A Simple and Rapid Protocol to Non-enzymatically Dissociate Fresh Human Tissues for the Analysis of Infiltrating Lymphocytes

The ability of malignant cells to evade the immune system, characterized by tumor escape from both innate and adaptive immune responses, is now accepted as an important hallmark of cancer. Our research on breast cancer focuses on the active role that tumor infiltrating lymphocytes play in tumor progression and patient outcome. Toward this goal, we developed a methodology for the rapid isolation of intact lymphoid cells from normal and abnormal tissues in an effort to evaluate them proximate to their native state. Homogenates prepared using a mechanical dissociator show both increased viability and cell recovery while preserving surface receptor expression compared to enzyme-digested tissues. Furthermore, enzymatic digestion of the remaining insoluble material did not recover additional CD45+ cells indicating that quantitative and qualitative measurements in the primary homogenate likely genuinely reflect infiltrating subpopulations in the tissue fragment. The lymphoid cells in these homogenates can be easily characterized using immunological (phenotype, proliferation, etc.) or molecular (DNA, RNA and/or protein) approaches. CD45+ cells can also be used for subpopulation purification, in vitro expansion or cryopreservation. An additional benefit of this approach is that the primary tissue supernatant from the homogenates can be used to characterize and compare cytokines, chemokines, immunoglobulins and antigens present in normal and malignant tissues. This protocol functions extremely well for human breast tissues and should be applicable to a wide variety of normal and abnormal tissues.

This protocol describes the rapid non-enzymatic dissociation of fresh human tissue fragments for qualitative and quantitative assessment of CD45+ cells (lymphocytes/leukocytes) present in various normal and malignant human tissues. Additionally, the supernatant obtained from the primary tissue homogenate can be collected and stored for further analysis or experimentation.

The ability of malignant cells to evade the immune system, characterized by tumor escape from both innate and adaptive immune responses, is now accepted ...

Fluorescence-activated Cell Sorting for Purification of Plasmacytoid Dendritic Cells from the Mouse Bone Marrow

Fluorescence-activated cell sorting (FACS) is a technique to purify specific cell populations based on phenotypes detected by flow cytometry. This method enables researchers to better understand the characteristics of a single cell population without the influence of other cells. Compared to other methods of cell enrichment, such as magnetic-activated cell sorting (MCS), FACS is more flexible and accurate for cell separation due to the ability of phenotype detection by flow cytometry. In addition, FACS is usually capable of separating multiple cell populations simultaneously, which improves the efficiency and diversity of experiments. Although FACS has some limitations, it has been broadly used to purify cells for functional studies in both in vitro and in vivo settings. Here we report a protocol using fluorescence-activated cell sorting to isolate a very rare population of immune cells, plasmacytoid dendritic cells (pDC), with high purity from the bone marrow of lupus-prone mice for in vitro functional studies of pDC.

We report a protocol using fluorescence-activated cell sorting to isolate plasmacytoid dendritic cells (pDC) with high purity from the bone marrow of lupus-prone mice for functional studies of pDC.

Fluorescence-activated cell sorting (FACS) is a technique to purify specific cell populations based on phenotypes detected by flow cytometry. This method ...

Murine Lymphocyte Labeling by 64Cu-Antibody Receptor Targeting for In Vivo Cell Trafficking by PET/CT

This protocol illustrates the production of 64Cu and the chelator conjugation/radiolabeling of a monoclonal antibody (mAb) followed by murine lymphocyte cell culture and 64Cu-antibody receptor targeting of the cells. In vitro evaluation of the radiolabel and non-invasive in vivo cell tracking in an animal model of an airway delayed-type hypersensitivity reaction (DTHR) by PET/CT are described.
In detail, the conjugation of a mAb with the chelator 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) is shown. Following the production of radioactive 64Cu, radiolabeling of the DOTA-conjugated mAb is described. Next, the expansion of chicken ovalbumin (cOVA)-specific CD4+ interferon (IFN)-&#947;-producing T helper cells (cOVA-TH1) and the subsequent radiolabeling of the cOVA-TH1 cells are depicted. Various in vitro techniques are presented to evaluate the effects of 64Cu-radiolabeling on the cells, such as the determination of cell viability by trypan blue exclusion, the staining for apoptosis with Annexin V for flow cytometry, and the assessment of functionality by IFN-&#947; enzyme-linked immunosorbent assay (ELISA). Furthermore, the determination of the radioactive uptake into the cells and the labeling stability are described in detail. This protocol further describes how to perform cell tracking studies in an animal model for an airway DTHR and, therefore, the induction of cOVA-induced acute airway DHTR in BALB/c mice is included. Finally, a robust PET/CT workflow including image acquisition, reconstruction, and analysis is presented.
The 64Cu-antibody receptor targeting approach with subsequent receptor internalization provides high specificity and stability, reduced cellular toxicity, and low efflux rates compared to common PET-tracers for cell labeling, e.g.64Cu-pyruvaldehyde bis(N4-methylthiosemicarbazone) (64Cu-PTSM). Finally, our approach enables non-invasive in vivo cell tracking by PET/CT with an optimal signal-to-background ratio for 48 h. This experimental approach can be transferred to different animal models and cell types with membrane-bound receptors that are internalized.

Murine Lymphocyte Labeling by 64Cu-Antibody Receptor Targeting for In Vivo  Cell Trafficking by PET/CT

Following the preparation of a 64Cu-modified monoclonal antibody binding to a transgenic murine T cell receptor, T cells are radiolabeled in vivo, analyzed for viability, functionality, labeling stability and apoptosis, and adoptively transferred into mice with an airway delayed-type hypersensitivity reaction for non-invasive imaging by positron emission tomography/computed tomography (PET/CT).

This protocol illustrates the production of 64Cu and the chelator conjugation/radiolabeling of a monoclonal antibody (mAb) followed by murine lymphocyte ...

The measurement of immunological reactivity to donor antigens in transplant recipients is likely to be crucial for the successful reduction or withdrawal of immunosuppression. The mixed leukocyte reaction (MLR), limiting dilution assays, and trans-vivo delayed-type hypersensitivity (DTH) assay have all been applied to this question, but these methods have limited predictive ability and/or significant practical limitations that reduce their usefulness. Imaging flow cytometry is a technique that combines the multiparametric quantitative powers of flow cytometry with the imaging capabilities of fluorescent microscopy. We recently made use of an imaging flow cytometry approach to define the proportion of recipient T cells capable of forming mature immune synapses with donor antigen-presenting cells (APCs). Using a well-characterized mouse heart transplant model, we have shown that the frequency of in vitro immune synapses among T-APC membrane contact events strongly predicted allograft outcome in rejection, tolerance, and a situation where transplant survival depends on induced regulatory T cells. The frequency of T-APC contacts increased with T cells from mice during acute rejection and decreased with T cells from mice rendered unresponsive to alloantigen. The addition of regulatory T cells to the in vitro system reduced prolonged T-APC contacts. Critically, this effect was also seen with human polyclonally expanded, naturally occurring regulatory T cells, which are known to control the rejection of human tissues in humanized mouse models. Further development of this approach may allow for a deeper characterization of the alloreactive T-cell compartment in transplant recipients. In the future, further development and evaluation of this method using human cells may form the basis for assays used to select patients for immunosuppression minimization, and it can be used to measure the impact of tolerogenic therapies in the clinic.

This paper describes a method for measuring alloreactivity in a mixed population of T cells using imaging flow cytometry.

The measurement of immunological reactivity to donor antigens in transplant recipients is likely to be crucial for the successful reduction or withdrawal ...

The immune synapse is the area of communication between T cells and antigen-presenting cells (APCs). T cells polarize surface receptors and proteins towards the immune synapse to assure a stable binding and signal exchange. Classical confocal, TIRF, or super-resolution microscopy have been used to study the immune synapse. Since these methods require manual image acquisition and time-consuming quantification, the imaging of rare events is challenging. Here, we describe a workflow that enables the morphological analysis of tens of thousands of cells. Immune synapses are induced between primary human T cells in pan-leukocyte preparations and Staphylococcus aureus enterotoxin B (SEB)-loaded Raji cells as APCs. Image acquisition is performed with imaging flow cytometry, also called In-Flow microscopy, which combines features of a flow cytometer and a fluorescence microscope. A complete gating strategy for identifying T cell/APC couples and analyzing the immune synapses is provided. As this workflow allows the analysis of immune synapses in unpurified pan-leukocyte preparations and hence requires only a small volume of blood (i.e., 1 mL), it can be applied to samples from patients. Importantly, several samples can be prepared, measured, and analyzed in parallel.

Here, we describe a complete workflow for the qualitative and quantitative analysis of immune synapses between primary human T cells and antigen-presenting cells. The method is based on imaging flow cytometry, which allows the acquisition and evaluation of several thousand cell images within a relatively short period of time.

The immune synapse is the area of communication between T cells and antigen-presenting cells (APCs). T cells polarize surface receptors and proteins ...

Visualizing Intracellular SNARE Trafficking by Fluorescence Lifetime Imaging Microscopy

Soluble N-ethylmaleimide sensitive fusion protein (NSF) attachment protein receptor (SNARE) proteins are key for membrane trafficking, as they catalyze membrane fusion within eukaryotic cells. The SNARE protein family consists of about 36 different members. Specific intracellular transport routes are catalyzed by specific sets of 3 or 4 SNARE proteins that thereby contribute to the specificity and fidelity of membrane trafficking. However, studying the precise function of SNARE proteins is technically challenging, because SNAREs are highly abundant and functionally redundant, with most SNAREs having multiple and overlapping functions. In this protocol, a new method for the visualization of SNARE complex formation in live cells is described. This method is based on expressing SNARE proteins C-terminally fused to fluorescent proteins and measuring their interaction by F&#246;rster resonance energy transfer (FRET) employing fluorescence lifetime imaging microscopy (FLIM). By fitting the fluorescence lifetime histograms with a multicomponent decay model, FRET-FLIM allows (semi-)quantitative estimation of the fraction of the SNARE complex formation at different vesicles. This protocol has been successfully applied to visualize SNARE complex formation at the plasma membrane and at endosomal compartments in mammalian cell lines and primary immune cells, and can be readily extended to study SNARE functions at other organelles in animal, plant, and fungal cells.

This protocol describes a new method allowing for the quantitative visualization of complex formation of SNARE proteins, based on F&#246;rster resonance energy transfer, and fluorescence lifetime imaging microscopy.

Soluble N-ethylmaleimide sensitive fusion protein (NSF) attachment protein receptor (SNARE) proteins are key for membrane trafficking, as they catalyze ...

Isolation and In Vitro Culture of Murine and Human Alveolar Macrophages

Alveolar macrophages are terminally differentiated, lung-resident macrophages of prenatal origin. Alveolar macrophages are unique in their long life and their important role in lung development and function, as well as their lung-localized responses to infection and inflammation. To date, no unified method for identification, isolation, and handling of alveolar macrophages from humans and mice exists. Such a method is needed for studies on these important innate immune cells in various experimental settings. The method described here, which can be easily adopted by any laboratory, is a simplified approach to harvesting alveolar macrophages from bronchoalveolar lavage fluid or from lung tissue and maintaining them in vitro. Because alveolar macrophages primarily occur as adherent cells in the alveoli, the focus of this method is on dislodging them prior to harvest and identification. The lung is a highly vascularized organ, and various cell types of myeloid and lymphoid origin inhabit, interact, and are influenced by the lung microenvironment. By using the set of surface markers described here, researchers can easily and unambiguously distinguish alveolar macrophages from other leukocytes, and purify them for downstream applications. The culture method developed herein supports both human and mouse alveolar macrophages for in vitro growth, and is compatible with cellular and molecular studies.

Isolation and In Vitro Culture of Murine and Human Alveolar Macrophages

This communication describes methodologies for isolation and culture of alveolar macrophages from humans and murine models for experimental purposes.

Alveolar macrophages are terminally differentiated, lung-resident macrophages of prenatal origin. Alveolar macrophages are unique in their long life and ...