Name: phospho flow cytometry with fluorescent cell barcoding for single cell signaling analysis and biomarker discovery
Uploaded: 2018-10-04T14:45:00
Description: Watch this Scientific Journal Video about Phospho Flow Cytometry with Fluorescent Cell Barcoding for Single Cell Signaling Analysis and Biomarker Discovery at JoVE.com

This work was conducted in the lab of Professor Kjetil Task&#233;n, and was supported by the Norwegian Cancer Society and Stiftelsen Kristian Gerhard Jebsen. Johannes Landskron and Marianne Enger are acknowledged for critical reading of the manuscript.

Blood samples were received following written informed consent from all donors. The study was approved by the Regional Committee for Medical and Health Research Ethics of South-East Norway and the research on human blood was carried out in accordance with the Declaration of Helsinki8.
NOTE: Steps 1-3 should be performed under sterile conditions in a tissue culture hood.
1. Isolation of Peripheral Blood Mononuclear Cells (PBMCs)...

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Phospho flow cytometry is a powerful technique to measure protein phosphorylation levels in single cells. Since the method relies on staining with antibodies, phospho flow cytometry is limited by antibody availability. Furthermore, in order to obtain reliable results, all antibodies should be titrated and verified before use. A detailed protocol for titration of phospho-specific antibodies has been described elsewhere12. During panel design, consideration of the signal-to-noise ratio is critical. ...

Phospho flow cytometry is used to analyze protein phosphorylation levels at single-cell resolution. The overall goal of the method is to map cellular signaling patterns under specified conditions. By exploiting the multiparameter capacity of flow cytometry, several signaling pathways can be analyzed simultaneously in different subsets of a heterogeneous cell population such as peripheral blood. These traits offer advantages over other antibody-based technologies such as immunohistochemistry, enzyme-linked immunosorbent assay (ELISA), protein array, and reverse phase protein array (RPPA)1. Phospho flow cytometry can be combined with fluorescent cell barcoding (FCB), which means that individual cell samples are labeled with unique signatures of fluorescent dyes so that they can be mixed together, stained and analyzed as a single sample2. This reduces the antibody consumption, increases the data robustness through the combination of control and treated samples, and enhances the speed of acquisition. The combined FCB population can then be divided into smaller samples and stained with up to 35 distinct phospho-specific antibodies, depending on the amount of starting material. Large profiling experiments can, thereby, be run with standard cytometer hardware. Phospho flow cytometry has been applied to profile signaling pathways in patient samples from several hematological cancers including chronic lymphocytic leukemia (CLL)3,4,5, acute myeloid leukemia (AML)6 and non-Hodgkin lymphomas7. Phospho flow cytometry is thus a powerful approach to characterize signaling aberrations, identify and validate biomarkers, and assess pharmacodynamics.
Here, the optimized protocol for analysis of CLL patient samples by phospho flow cytometry is provided (Figure 1A). Examples of basal signaling characterization, anti-IgM/B cell receptor stimulation and drug perturbation are shown. A detailed description of an FCB matrix is provided. The protocol can easily be adapted to other suspension cell types.

<table>
	<tbody>
		<tr>
			<td>RPMI 1640 GlutaMAX</td>
			<td>ThermoFisher Scientific</td>
			<td>61870-010</td>
			<td>Cell culture medium</td>
		</tr>
		<tr>
			<td>Fetal bovine serum</td>
			<td>ThermoFisher Scientific</td>
			<td>10270169</td>
			<td>Additive to cell culture medium</td>
		</tr>
		<tr>
			<td>Sodium pyruvate</td>
			<td>ThermoFisher Scientific</td>
			<td>11360-039</td>
			<td>Additive to cell culture medium</td>
		</tr>
		<tr>
			<td>MEM non-essential amino acids</td>
			<td>ThermoFisher Scientific</td>
			<td>11140-035</td>
			<td>Additive to cell culture medium</td>
		</tr>
		<tr>
			<td>Lymphoprep</td>
			<td>Alere Technologies AS</td>
			<td>1114547</td>
			<td>Density gradient medium</td>
		</tr>
		<tr>
			<td>Anti-IgM</td>
			<td>Southern Biotech</td>
			<td>2022-01</td>
			<td>For stimulation of the B cell receptor</td>
		</tr>
		<tr>
			<td>BD Phosflow Fix Buffer I</td>
			<td>BD</td>
			<td>557870</td>
			<td>Fixation buffer</td>
		</tr>
		<tr>
			<td>BD Phosflow Perm Buffer III</td>
			<td>BD</td>
			<td>558050</td>
			<td>Permeabilization buffer</td>
		</tr>
		<tr>
			<td>Alexa Fluor 488 5-TFP</td>
			<td>ThermoFisher Scientific</td>
			<td>A30005</td>
			<td>Barcoding reagent</td>
		</tr>
		<tr>
			<td>Pacific Blue Succinimidyl Ester</td>
			<td>ThermoFisher Scientific</td>
			<td>P10163</td>
			<td>Barcoding reagent</td>
		</tr>
		<tr>
			<td>Pacific Orange Succinimidyl Ester, Triethylammonium Salt</td>
			<td>ThermoFisher Scientific</td>
			<td>P30253</td>
			<td>Barcoding reagent</td>
		</tr>
		<tr>
			<td>Compensation beads</td>
			<td>Defined by user</td>
			<td></td>
			<td>Correct species reactivity</td>
		</tr>
		<tr>
			<td>Falcon tubes</td>
			<td>Defined by user</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Eppendorf tubes</td>
			<td>Defined by user</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>96 well V-bottom plates</td>
			<td>Defined by user</td>
			<td></td>
			<td>Compatible with the flow cytometer</td>
		</tr>
		<tr>
			<td>Centrifuges</td>
			<td>Defined by user</td>
			<td></td>
			<td>For Eppendorf tubes, Falcon tubes and plates</td>
		</tr>
		<tr>
			<td>Water bath</td>
			<td>Defined by user</td>
			<td></td>
			<td>Temperature regulated</td>
		</tr>
		<tr>
			<td>Flow cytometer</td>
			<td>Defined by user</td>
			<td></td>
			<td>With High Throughput Sampler (HTS)</td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Antigen</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>AKT (pS473)</td>
			<td>Cell Signaling Technologies</td>
			<td>4075</td>
			<td>Clone: D9E 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284 
			Parente-Ribes et al., 2016, Spleen tyrosine kinase inhibitors reduce&#8230;, Haematologica, 101(2):e59-62 
			Sk&#229;nland et al., 2014, T-cell co-stimulation through the CD2 and CD28&#8230;, Biochem J, 460(3):399-410 
			Kalland et al., 2012, Modulation of proximal signaling in normal and transformed&#8230;, Exp Cell Res, 318(14):1611-9</td>
		</tr>
		<tr>
			<td>ATF-2 (pT71)</td>
			<td>Santa Cruz Biotechnology</td>
			<td>sc-8398</td>
			<td>Clone: F-1 
			Reference: Sk&#229;nland et al., 2014, T-cell co-stimulation through the CD2 and CD28&#8230;, Biochem J, 460(3):399-410 
			Pollheimer et al., 2013, Interleukin-33 drives a proinflammatory endothelial&#8230;, Arterioscler Thromb Vasc Biol, 33(2):e47-55</td>
		</tr>
		<tr>
			<td>BLNK (pY84)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>558443</td>
			<td>Clone: J117-1278 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284 
			Parente-Ribes et al., 2016, Spleen tyrosine kinase inhibitors reduce&#8230;, Haematologica, 101(2):e59-62 
			Kalland et al., 2012, Modulation of proximal signaling in normal and transformed&#8230;, Exp Cell Res, 318(14):1611-9 
			Myklebust et al., 2017, Distinct patterns of B-cell receptor signaling in&#8230;, Blood, 129(6): 759-770</td>
		</tr>
		<tr>
			<td>Btk (pY223)/Itk (pY180)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>564846</td>
			<td>Clone: N35-86 
			Reference: Myklebust et al., 2017, Distinct patterns of B-cell receptor signaling in&#8230;, Blood, 129(6): 759-770</td>
		</tr>
		<tr>
			<td>Btk (pY551)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>558129</td>
			<td>Clone: 24a/BTK (Y551)&#160; 
			Reference: Kalland et al., 2012, Modulation of proximal signaling in normal and transformed&#8230;, Exp Cell Res, 318(14):1611-9</td>
		</tr>
		<tr>
			<td>Btk (pY551)/Itk (pY511)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>558134</td>
			<td>Clone: 24a/BTK (Y551)&#160; 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284 
			Parente-Ribes et al., 2016, Spleen tyrosine kinase inhibitors reduce&#8230;, Haematologica, 101(2):e59-62</td>
		</tr>
		<tr>
			<td>CD3&#950; (pY142)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>558489</td>
			<td>Clone: K25-407.69 
			Reference: Sk&#229;nland et al., 2014, T-cell co-stimulation through the CD2 and CD28&#8230;, Biochem J, 460(3):399-410</td>
		</tr>
		<tr>
			<td>Histone H3 (pS10)</td>
			<td>Cell Signaling Technologies</td>
			<td>9716</td>
			<td>Clone: D2C8 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284</td>
		</tr>
		<tr>
			<td>I&#954;B&#945;</td>
			<td>Cell Signaling Technologies</td>
			<td>5743</td>
			<td>Clone: L35A5 
			Reference: Myklebust et al., 2017, Distinct patterns of B-cell receptor signaling in&#8230;, Blood, 129(6): 759-770</td>
		</tr>
		<tr>
			<td>LAT (pY171)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>558518</td>
			<td>Clone: I58-1169 
			Reference: Sk&#229;nland et al., 2014, T-cell co-stimulation through the CD2 and CD28&#8230;, Biochem J, 460(3):399-410</td>
		</tr>
		<tr>
			<td>Lck (pY505)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>558577</td>
			<td>Clone: 4/LCK-Y505&#160; 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284</td>
		</tr>
		<tr>
			<td>MEK1 (pS298)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>560043</td>
			<td>Clone: J114-64 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284 
			Sk&#229;nland et al., 2014, T-cell co-stimulation through the CD2 and CD28&#8230;, Biochem J, 460(3):399-410</td>
		</tr>
		<tr>
			<td>NF-&#954;B p65 (pS529)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>558422</td>
			<td>Clone: K10-895.12.50 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284 
			Sk&#229;nland et al., 2014, T-cell co-stimulation through the CD2 and CD28&#8230;, Biochem J, 460(3):399-410 
			Kalland et al., 2012, Modulation of proximal signaling in normal and transformed&#8230;, Exp Cell Res, 318(14):1611-9 
			Pollheimer et al., 2013, Interleukin-33 drives a proinflammatory endothelial&#8230;, Arterioscler Thromb Vasc Biol, 33(2):e47-55</td>
		</tr>
		<tr>
			<td>NF-&#954;B p65 (pS536)</td>
			<td>Cell Signaling Technologies</td>
			<td>4887</td>
			<td>Clone: 93H1 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284 
			Sk&#229;nland et al., 2014, T-cell co-stimulation through the CD2 and CD28&#8230;, Biochem J, 460(3):399-410 
			Kalland et al., 2012, Modulation of proximal signaling in normal and transformed&#8230;, Exp Cell Res, 318(14):1611-9</td>
		</tr>
		<tr>
			<td>p38 MAPK (pT180/Y182)</td>
			<td>Cell Signaling Technologies</td>
			<td>4552</td>
			<td>Clone: 28B10 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284 
			Sk&#229;nland et al., 2014, T-cell co-stimulation through the CD2 and CD28&#8230;, Biochem J, 460(3):399-410 
			Pollheimer et al., 2013, Interleukin-33 drives a proinflammatory endothelial&#8230;, Arterioscler Thromb Vasc Biol, 33(2):e47-55</td>
		</tr>
		<tr>
			<td>p44/42 MAPK (pT202/Y204)</td>
			<td>Cell Signaling Technologies</td>
			<td>4375</td>
			<td>Clone: E10 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284 
			Parente-Ribes et al., 2016, Spleen tyrosine kinase inhibitors reduce&#8230;, Haematologica, 101(2):e59-62 
			Sk&#229;nland et al., 2014, T-cell co-stimulation through the CD2 and CD28&#8230;, Biochem J, 460(3):399-410 
			Kalland et al., 2012, Modulation of proximal signaling in normal and transformed&#8230;, Exp Cell Res, 318(14):1611-9 
			Pollheimer et al., 2013, Interleukin-33 drives a proinflammatory endothelial&#8230;, Arterioscler Thromb Vasc Biol, 33(2):e47-55</td>
		</tr>
		<tr>
			<td>p53 (pS15)</td>
			<td>Cell Signaling Technologies</td>
			<td>NN</td>
			<td>Clone: 16G8 
			Reference: Irish et al., 2007, Flt3 Y591 duplication and Bcl-2 overexpression&#8230;, Blood, 109(6):2589-96</td>
		</tr>
		<tr>
			<td>p53 (pS20)</td>
			<td>Cell Signaling Technologies</td>
			<td>NN</td>
			<td>Clone: Polyclonal 
			Reference: Irish et al., 2007, Flt3 Y591 duplication and Bcl-2 overexpression&#8230;, Blood, 109(6):2589-96</td>
		</tr>
		<tr>
			<td>p53 (pS37)</td>
			<td>Cell Signaling Technologies</td>
			<td>NN</td>
			<td>Clone: Polyclonal 
			Reference: Irish et al., 2007, Flt3 Y591 duplication and Bcl-2 overexpression&#8230;, Blood, 109(6):2589-96</td>
		</tr>
		<tr>
			<td>p53 (pS46)</td>
			<td>Cell Signaling Technologies</td>
			<td>NN</td>
			<td>Clone: Polyclonal 
			Reference: Irish et al., 2007, Flt3 Y591 duplication and Bcl-2 overexpression&#8230;, Blood, 109(6):2589-96</td>
		</tr>
		<tr>
			<td>p53 (pS392)</td>
			<td>Cell Signaling Technologies</td>
			<td>NN</td>
			<td>Clone: Polyclonal 
			Reference: Irish et al., 2007, Flt3 Y591 duplication and Bcl-2 overexpression&#8230;, Blood, 109(6):2589-96</td>
		</tr>
		<tr>
			<td>PLC&#947;2 (pY759)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>558498</td>
			<td>Clone: K86-689.37 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284 
			Myklebust et al., 2017, Distinct patterns of B-cell receptor signaling in&#8230;, Blood, 129(6): 759-770</td>
		</tr>
		<tr>
			<td>Rb (pS807/pS811)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>558590</td>
			<td>Clone: J112-906 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284 
			Pollheimer et al., 2013, Interleukin-33 drives a proinflammatory endothelial&#8230;, Arterioscler Thromb Vasc Biol, 33(2):e47-55</td>
		</tr>
		<tr>
			<td>S6-Ribos. Prot. (pS235/236)</td>
			<td>Cell Signaling Technologies</td>
			<td>4851</td>
			<td>Clone: D57.2.2E 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284</td>
		</tr>
		<tr>
			<td>SAPK/JNK (pT183/Y185)</td>
			<td>Cell Signaling Technologies</td>
			<td>9257</td>
			<td>Clone: G9 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284 
			Pollheimer et al., 2013, Interleukin-33 drives a proinflammatory endothelial&#8230;, Arterioscler Thromb Vasc Biol, 33(2):e47-55</td>
		</tr>
		<tr>
			<td>SLP76 (pY128)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>558438</td>
			<td>Clone: J141-668.36.58&#160; 
			Reference: Sk&#229;nland et al., 2014, T-cell co-stimulation through the CD2 and CD28&#8230;, Biochem J, 460(3):399-410</td>
		</tr>
		<tr>
			<td>STAT1 (pY701)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>612597</td>
			<td>Clone: 4a&#160; 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284 
			Myklebust et al., 2017, Distinct patterns of B-cell receptor signaling in&#8230;, Blood, 129(6): 759-770</td>
		</tr>
		<tr>
			<td>STAT3 (pY705)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>557815</td>
			<td>Clone: 4/P-STAT3 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284</td>
		</tr>
		<tr>
			<td>STAT4 (pY693)</td>
			<td>Zymed/ThermoFisher Scientific</td>
			<td>71-7900</td>
			<td>Clone: Polyclonal 
			Reference: Uzel et al., 2001, Detection of intracellular phosphorylated STAT-4 by flow cytometry, Clin Immunol, 100(3): 270-6</td>
		</tr>
		<tr>
			<td>STAT5 (pY694)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>612599</td>
			<td>Clone: 47/Stat5(pY694) 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284 
			Sk&#229;nland et al., 2014, T-cell co-stimulation through the CD2 and CD28&#8230;, Biochem J, 460(3):399-410 
			Myklebust et al., 2017, Distinct patterns of B-cell receptor signaling in&#8230;, Blood, 129(6): 759-770</td>
		</tr>
		<tr>
			<td>STAT6 (pY641)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>612601</td>
			<td>Clone: 18/P-Stat6 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284</td>
		</tr>
		<tr>
			<td>SYK (pY525/Y526)</td>
			<td>Cell Signaling Technologies</td>
			<td>12081</td>
			<td>Clone: C87C1 
			Reference: Myhrvold et al., 2018, Single cell profiling of phospho-protein levels in.., Oncotarget, 9(10):9273-9284 
			Parente-Ribes et al., 2016, Spleen tyrosine kinase inhibitors reduce&#8230;, Haematologica, 101(2):e59-62</td>
		</tr>
		<tr>
			<td>ZAP70/SYK (pY319/Y352)</td>
			<td>Beckton Dickinson Pharmingen</td>
			<td>557817</td>
			<td>Clone: 17A/P-ZAP70 
			Reference: Sk&#229;nland et al., 2014, T-cell co-stimulation through the CD2 and CD28&#8230;, Biochem J, 460(3):399-410 
			Kalland et al., 2012, Modulation of proximal signaling in normal and transformed&#8230;, Exp Cell Res, 318(14):1611-9 
			Myklebust et al., 2017, Distinct patterns of B-cell receptor signaling in&#8230;, Blood, 129(6): 759-770</td>
		</tr>
	</tbody>
</table>

phospho flow cytometry with fluorescent cell barcoding for single cell signaling analysis and biomarker discovery

Aberrant cell signaling plays a central role in cancer development and progression. Most novel targeted therapies are indeed directed at proteins and protein functions, and cell signaling aberrations may therefore serve as biomarkers to indicate personalized treatment options. As opposed to DNA and RNA analyses, changes in protein activity can more efficiently evaluate the mechanisms underlying drug sensitivity and resistance. Phospho flow cytometry is a powerful technique that measures protein phosphorylation events at the cellular level, an important feature that distinguishes this method from other antibody-based approaches. The method allows for simultaneous analysis of multiple signaling proteins. In combination with fluorescent cell barcoding, larger medium- to high-throughput data-sets can be acquired by standard cytometer hardware in short time. Phospho flow cytometry has applications both in studies of basic biology and in clinical research, including signaling analysis, biomarker discovery and assessment of pharmacodynamics. Here, a detailed experimental protocol is provided for phospho flow analysis of purified peripheral blood mononuclear cells, using chronic lymphocytic leukemia cells as an example.

The main steps of the phospho flow cytometry protocol are illustrated in Figure 1A. In the presented example, CLL cells were stained with the barcoding reagent Pacific Blue at four dilutions. Three-dimensional barcoding can be performed by combining three barcoding dyes, as illustrated in Figure 1B. The individual samples are then deconvoluted by subsequent gating on each barcoding reagent versus SSC-A (<strong class="xf...

Watch this Scientific Journal Video about Phospho Flow Cytometry with Fluorescent Cell Barcoding for Single Cell Signaling Analysis and Biomarker Discovery at JoVE.com

Phospho Flow Cytometry with Fluorescent Cell Barcoding for Single Cell Signaling Analysis and Biomarker Discovery

Here, a protocol for medium- to high-throughput analysis of protein phosphorylation events at the cellular level is presented. Phospho flow cytometry is a powerful approach to characterize signaling aberrations, identify and validate biomarkers, and assess pharmacodynamics.

Aberrant cell signaling plays a central role in cancer development and progression. Most novel targeted therapies are indeed directed at proteins and ...

This method can help answer key questions in the fields of cell biology and immunology such as how are signaling pathways affected by different stimuli or drugs? The main advantage of this technique is that it allows you to perform single cell signaling analysis in the medium to high throughput fashion. After re-suspending the cells in supplemented RPMI 16/40 medium, transfer the required amount of cell suspension to the wells of a 96 well V-bottom plate.Transfer the plate to a preheated 37 degree Celsius water bath and allow it to rest there for 10 minutes. Then add 60 microliters of fixed buffer one to each well of a new 96 well plate to set up the fix plate. Place this plate in the 37 degree Celsius water bath.Transfer a 50 microliter control sample to the plate and mix by pipetting up and down. Optionally, add 10 microliters per milliliter anti-IgM to the cells to start the simulation time course and mix by pipetting up and down. Transfer a 50 microliter sample to the fix plate at each time point, mixing each sample as it is added.After the last sample is added, leave the fix plate in the water bath for 10 minutes. First, wash the cells three times with PBS. Centrifuge the plate at 500 times G for five minutes and discard the supernatant.Next, prepare a fresh 96 well V-bottom plate with barcoding reagents, by pipetting five microliters of each barcoding reagent into each well filling the number of wells required to stain each of the samples. In the fixed cell plate, resuspend the cells in each well with 190 microliters of PBS. Then, transfer each well of cells to the corresponding well in the barcoding plate, mixing each well thoroughly.Let the plate rest at room temperature for 20 minutes in the dark. Centrifuge the plate at 500 times G for five minutes and discard the supernatant. After this, wash the cells in each well twice with the flow wash.Then add 190 microliters of flow wash to each well of cells. Combine all of the barcoded samples into one 15 milliliter tube and transfer each compensation control to a separate 1.7 milliliter tube. Centrifuge at 500 times G for five minutes and discard the supernatant.To begin, transfer two milliliters of perm buffer three to a 15 milliliter tube. Store at minus 20 degrees Celsius so it will be ice cold when used. When ready, add 1.5 milliliters of ice cold perm buffer to the 15 milliliter tube containing the barcoded cell population dropwise while vortexing to avoid cell clumping.Add 100 microliters of ice cold perm buffer to each of the compensation controls in the same manner. Immediately transfer the cells to a freezer at minus 80 degrees Celsius for a minimum of 30 minutes. When ready to begin antigen staining, remove the cells from the freezer and transfer them to a box of ice.Wash the cells three times with an excess of flow wash. Centrifuge the cells at 500 times G and four degrees Celsius for five minutes. Discard the supernatant and re-suspend the barcoded cell population in a volume of flow wash, such is that there is 25 microliters of cell suspension per phospho-antibody stain.Re-suspend the compensation controls in 200 microliters of flow wash. To begin preparing antibodies for staining, add 10 microliters of phospho-specific antibody, diluted in flow wash, to each well of a fresh 96 well V-bottom plate. Add 15 microliters of surface marker, diluted in flow wash and 25 microliters of cell suspension to each well for a final volume of 50 microliters per well.Let the cells rest for 30 minutes at room temperature in the dark. After this, wash the stained cells twice with flow wash. Centrifuge at 500 times G for five minutes.Discard the supernatant and re-suspend the cells in 150 microliters of flow wash. Then perform flow cytometry analysis as outlined in the text protocol. In the presented protocol, three dimensional barcoding is performed by combining three barcoding dyes.Individual samples are then de-convoluted by subsequent gating on each barcoding reagent versus side scatter area. The basal and stimulation induced phosphorylation levels of 20 signaling molecules downstream of the B cell receptor are then characterized in B cells from CLL patients and normal controls under various conditions. The stat3 phospho tyrosine 705 is seen to be significantly up regulated.Cells are stimulated with anti-IgM for up to 30 minutes in order to identify signaling aberrations induced through the B cell receptor pathway. While CLL cells from patients with unmutated IGVH display increased sensitivity towards anti-IgM stimulation, it is only statistically significant for AKT phosphor serine 473. Cells are then exposed to the PI 3-kinase delta inhibitor idelalisib to test if the aberrant AKT pS473 signal can be reversed.As shown here, the aberrant levels are significantly reduced upon treatment in a concentration dependent manner demonstrating that kinase inhibitors can be applied to normalize aberrant signaling in CLL cells. Before attempting this procedure it's important to remember to titrate barcoding reagents and antibodies, and to verify that selected surface markers are compatible with fixation and permeabilization reagents. The cells need to be in suspension for phosphor analysis, still the protocol can be adapted to aberrant cells or tissue following procedures to obtain single cell suspension, such as whole trypzination.

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Unit 1

Principles of Cell Signaling

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Target Cell Pre-enrichment and Whole Genome Amplification for Single Cell Downstream Characterization

Rare target cells can be isolated from a high background of non-target cells using antibodies specific for surface proteins of target cells. A recently ...

Flow Cytometric Analysis of Mitochondrial Reactive Oxygen Species in Murine Hematopoietic Stem and Progenitor Cells and MLL-AF9 Driven Leukemia

We present a flow cytometric approach for analyzing mitochondrial ROS in various live bone marrow (BM)-derived stem and progenitor cell populations from ...

Characterize Disease-related Mutants of RAF Family Kinases by Using a Set of Practical and Feasible Methods

The rapidly accelerated fibrosarcoma (RAF) family kinases play a central role in cell biology and their dysfunction leads to cancers and developmental ...

Cell Cycle-specific Measurement of &#947;H2AX and Apoptosis After Genotoxic Stress by Flow Cytometry

The presented method or slightly modified versions have been devised to study specific treatment responses and side effects of various anti-cancer ...

Evaluating Cell Death Using Cell-Free Supernatant of Probiotics in Three-Dimensional Spheroid Cultures of Colorectal Cancer Cells

This manuscript describes a protocol to evaluate cancer cell deaths in three dimensional (3D) spheroids of multicellular types of cancer cells using ...

Exploring the Arginine Methylome by Nuclear Magnetic Resonance Spectroscopy

Protein-bound arginine is commonly methylated in many proteins and regulates their function by altering the physicochemical properties, their interaction ...

Simultaneous Imaging and Flow-Cytometry-based Detection of Multiple Fluorescent Senescence Markers in Therapy-Induced Senescent Cancer Cells

Chemotherapeutic drugs can induce irreparable DNA damage in cancer cells, leading to apoptosis or premature senescence. Unlike apoptotic cell death, ...

Far-Red Fluorescent Senescence-Associated &#946;-Galactosidase Probe for Identification and Enrichment of Senescent Tumor Cells by Flow Cytometry

Cellular senescence is a state of proliferative arrest induced by biological damage that normally accrues over years in aging cells but may also emerge ...

A Flow Cytometry-Based Cell Surface Protein Binding Assay for Assessing Selectivity and Specificity of an Anticancer Aptamer

A key challenge in developing an anticancer aptamer is to efficiently determine the selectivity and specificity of the developed aptamer to the target ...

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

Multiplexed imaging technology using antibody barcoding with oligonucleotides, which sequentially detects multiple epitopes in the same tissue section, is ...