Name: multiplexed fluorescent immunohistochemical staining of four endometrial immune cell types in recurrent miscarriage
Uploaded: 2021-08-04T15:00:00
Description: Watch this Scientific Journal Video about Multiplexed Fluorescent Immunohistochemical Staining of Four Endometrial Immune Cell Types in Recurrent Miscarriage at JoVE.com

This study was supported by Hong Kong Obstetrical and Gynecological Trust Fund in 2018 and Hong Kong Health and Medical Research Fund (06170186, 07180226).

The study was approved by the Joint Chinese University of Hong Kong-New Territories East Cluster Clinical Research Ethics Committee. Informed consent was obtained from the participants before collecting the endometrial biopsies. Refer to the introduction section for inclusion criteria of the control and RM groups.
1. Sample preparation
<ol>
	<li>Ensure that all the women in this study undergo a daily urine dipstick test from day 9 of the menstrual cycle onwards to identify the luteinizing ho...

<ol>
	<li>ESHRE Guideline Group on RPL et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ESHRE+guideline:+recurrent+pregnancy+loss.">ESHRE guideline: recurrent pregnancy loss.</a> Human Reproduction Open. 2018 (2), 004 (2018).</li><li>Stirrat, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recurrent+miscarriage.">Recurrent miscarriage.</a> Lancet. 336 (8716), 673-675 (1990).</li><li>Rai, R., Regan, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recurrent+miscarriage.">Recurrent miscarriage.</a> Lancet. 368 (9535), 601-611 (2006).</li><li>Royal College of Obstetricians &amp; Gynaecologists. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+investigation+and+treatment+of+couples+with+recurrent+first-trimester+and+second-trimester+miscarriage.+Green-top+Guideline+No.+17.">The investigation and treatment of couples with recurrent first-trimester and second-trimester miscarriage. Green-top Guideline No. 17.</a> Royal College of Obstetricians &amp; Gynaecologists. , (2011).</li><li>King, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Uterine+leukocytes+and+decidualization.">Uterine leukocytes and decidualization.</a> Human Reproduction Update. 6 (1), 28-36 (2000).</li><li>Le Bouteiller, P., Piccinni, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+NK+cells+in+pregnant+uterus:+why+there.">Human NK cells in pregnant uterus: why there.</a> American Journal of Reproductive Immunology. 59 (5), 401-406 (2008).</li><li>Lash, G. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Standardisation+of+uterine+natural+killer+(uNK)+cell+measurements+in+the+endometrium+of+women+with+recurrent+reproductive+failure.">Standardisation of uterine natural killer (uNK) cell measurements in the endometrium of women with recurrent reproductive failure.</a> Journal of Reproductive Immunology. 116, 50-59 (2016).</li><li>Yang, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HOXA-10+and+E-cadherin+expression+in+the+endometrium+of+women+with+recurrent+implantation+failure+and+recurrent+miscarriage.">HOXA-10 and E-cadherin expression in the endometrium of women with recurrent implantation failure and recurrent miscarriage.</a> Fertility and Sterility. 107 (1), 136-143 (2017).</li><li>Tuckerman, E., Laird, S. M., Prakash, A., Li, T. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Prognostic+value+of+the+measurement+of+uterine+natural+killer+cells+in+the+endometrium+of+women+with+recurrent+miscarriage.">Prognostic value of the measurement of uterine natural killer cells in the endometrium of women with recurrent miscarriage.</a> Human Reproduction. 22 (8), 2208-2213 (2007).</li><li>Jasper, M. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Macrophage-derived+LIF+and+IL1B+regulate+alpha(1,2)fucosyltransferase+2+(Fut2)+expression+in+mouse+uterine+epithelial+cells+during+early+pregnancy.">Macrophage-derived LIF and IL1B regulate alpha(1,2)fucosyltransferase 2 (Fut2) expression in mouse uterine epithelial cells during early pregnancy.</a> Biology of Reproduction. 84 (1), 179-188 (2011).</li><li>Kopcow, H. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=T+cell+apoptosis+at+the+maternal-fetal+interface+in+early+human+pregnancy,+involvement+of+galectin-1.">T cell apoptosis at the maternal-fetal interface in early human pregnancy, involvement of galectin-1.</a> Proceedings of the National Academy of Sciences of the United States of America. 105 (47), 18472-18477 (2008).</li><li>Johnson, P. M., Christmas, S. E., Vince, G. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Immunological+aspects+of+implantation+and+implantation+failure.">Immunological aspects of implantation and implantation failure.</a> Human Reproduction. 14, 26-36 (1999).</li><li>Hong, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiplexed+fluorescent+immunohistochemical+staining,+imaging,+and+analysis+in+histological+samples+of+lymphoma.">Multiplexed fluorescent immunohistochemical staining, imaging, and analysis in histological samples of lymphoma.</a> Journal of Visualized Experiments: JoVE. (143), e58711 (2019).</li><li>Carstens, J. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spatial+computation+of+intratumoral+T+cells+correlates+with+survival+of+patients+with+pancreatic+cancer.">Spatial computation of intratumoral T cells correlates with survival of patients with pancreatic cancer.</a> Nature Communications. 8, 15095 (2017).</li><li>Zhao, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+use+of+multiplex+staining+to+measure+the+density+and+clustering+of+four+endometrial+immune+cells+around+the+implantation+period+in+women+with+recurrent+miscarriage:+comparison+with+fertile+controls.">The use of multiplex staining to measure the density and clustering of four endometrial immune cells around the implantation period in women with recurrent miscarriage: comparison with fertile controls.</a> Journal of Molecular Histology. 51 (5), 593-603 (2020).</li></ol>

Critical steps within the protocol 
It is important to note that multiplex staining requires diligent optimization. Antigen retrieval, using citrate buffer and microwave technology, requires optimization to ensure complete antibody stripping and maintain tissue viability. As TSA reagents covalently bind to sites surrounding the antigen, they can potentially inhibit the binding of a subsequent primary antibody through steric hindrance (also known as the &#34;umbrella effect&#34;). This tends to occur...

Recurrent miscarriage (RM) can be defined as the loss of two or more pregnancies before 24 weeks of gestation1. This frequent reproductive condition affects up to 1% of couples worldwide2,3. The pathophysiology is multifactorial and can be divided into embryologically driven causes (mainly due to an abnormal embryonic karyotype) and maternally driven causes that affect the endometrium and/or placental development. This manifestation can result from parental genetic abnormalities, uterine anomalies, prothrombotic conditions, endocrinology factors, and immunological disorders4.
In recent years, immune effector cell dysfunction has been implicated in the pathogenesis of early pregnancy loss5. This has inspired many investigations into elucidating the specific populations of immune cells in the endometrium during the menstrual cycle, implantation, and early pregnancy, with specific roles in early pregnancy. Among these immune cells, uterine natural killer (uNK) cells play a critical role during embryo implantation and pregnancy, particularly in the processes of trophoblastic invasion and angiogenesis6. Studies have shown an increased uNK cell density in the endometrium of women with RM7,8, although this finding was not associated with an increased risk of miscarriage9. However, this stimulated research evaluating the density of other immune cell types (such as macrophages, uterine dendritic cells) in the endometrium in women with RM10, 11. Nevertheless, it remains uncertain whether there is a significant alteration in the immune cell density in the peri-implantation endometrium in women with RM.
One possible explanation for the uncertainty is that evaluation of the endometrial immune cell density might be difficult due to the rapid changes in the endometrium during the window of implantation. During the 24 h timeframe, significant changes in the endometrium alter immune cell density and cytokine secretion, introducing a source of variation in these results12. In addition, most reports mainly rely on the use of single-cell staining (e.g., traditional IHC methods) that could not examine multiple markers on the same tissue section. Although flow cytometry can be used for detecting multiple cell populations in a single sample, the large amounts of cells required and the time-consuming optimization hinder the popularity and efficiency of this method. Hence, the recent advancement in multiplex IHC staining could solve this problem by immunostaining multiple markers on the same slide to evaluate multiple parameters, including cell lineage and histological localization of individual immune subpopulations. Further, this technology can maximize the information obtained in case of limited tissue availability. Ultimately, this technique can help elucidate the differences in immune cell interactions in the endometrium between fertile women and women with RM.
Two groups of women were recruited from the Prince of Wales Hospital, including fertile control women (FC) and women with unexplained recurrent miscarriage (RM). Fertile control was defined as women who had at least one live birth without any history of spontaneous miscarriage, and RM women were defined as those who had a history of &#8805;2 consecutive miscarriages before 20 weeks gestation. The subjects from the two groups met the following inclusion criteria: (a) age between 20 to 42 years old, (b) non-smoker, (c) regular menstrual cycle (25-35 days) and normal uterine structure, (d) no use of any hormonal regimen for at least 3 months before the endometrial biopsy, (e) no hydrosalpinx by hystero-salpingogram. In addition, all the subjects recruited had normal karyotyping, normal 3-dimensional ultrasonography hysterosalpingogram, day 2 follicle-stimulating hormone &#60; 10 IU/L, mid-luteal progesterone &#62; 30 nmol/L, normal thyroid function, and tested negative for lupus anticoagulant and anticardiolipin IgG and IgM antibodies.
To better understand the immunological basis of RM, it would be most desirable to simultaneously quantify and localize the major immune cell types present in the endometrium at the time of implantation. This paper describes the entire protocol from sample preparation, the multiplex optimization with markers for immune cell subtypes, and the scanning of the slides, followed by data analysis with specific reference to detecting endometrial immune cells. Moreover, this paper describes how to determine the density and clustering of the immune cell types simultaneously in the endometrium.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Amplification Diluent</td>
			<td>Perkin Elmer</td>
			<td>FP1498</td>
			<td>Fluorophore diluent buffer</td>
		</tr>
		<tr>
			<td>Antibody diluent</td>
			<td>Perkin Elmer</td>
			<td>ARD1001EA</td>
			<td>Diluting the antibody</td>
		</tr>
		<tr>
			<td>CD3</td>
			<td>Spring Bioscience</td>
			<td>M3072</td>
			<td>Primary antibody</td>
		</tr>
		<tr>
			<td>CD20</td>
			<td>Biocare Medical</td>
			<td>CM004B</td>
			<td>Primary antibody</td>
		</tr>
		<tr>
			<td>CD56</td>
			<td>Leica</td>
			<td>NCL-CD56-504</td>
			<td>Primary antibody</td>
		</tr>
		<tr>
			<td>CD68</td>
			<td>Spring Bioscience</td>
			<td>M5510</td>
			<td>Primary antibody</td>
		</tr>
		<tr>
			<td>Citrate Buffer Solution, pH 6.0 (10x)</td>
			<td>Abcam</td>
			<td>AB64214</td>
			<td>Antigen retrieval solution</td>
		</tr>
		<tr>
			<td>EMSURE Xylene (isomeric mixture)</td>
			<td>Merck</td>
			<td>108297</td>
			<td>Dewaxing</td>
		</tr>
		<tr>
			<td>Ethanol absolute</td>
			<td>Merck</td>
			<td>107017</td>
			<td>Ethyl alcohol for rehydration</td>
		</tr>
		<tr>
			<td>HistoCore BIOCUT Manual Rotary Leica Microtome</td>
			<td>Leica</td>
			<td>RM2125RTS</td>
			<td>Sectioning of paraffin-embedded tissue</td>
		</tr>
		<tr>
			<td>inForm Advanced Image Analysis Software</td>
			<td>Perkin Elmer</td>
			<td>inForm&#174; Tissue Finder Software 2.2.1 (version 14.0)</td>
			<td>Data Analysis software</td>
		</tr>
		<tr>
			<td>Mantra&#174; Workstation</td>
			<td>Akoya Biosciences</td>
			<td>CLS140089</td>
			<td>Spectral imaging</td>
		</tr>
		<tr>
			<td>Microwave</td>
			<td>Panasonic</td>
			<td>Inverter</td>
			<td>Microwave stripping</td>
		</tr>
		<tr>
			<td>Opal 520</td>
			<td>Perkin Elmer</td>
			<td>FP1487A</td>
			<td>Appropriate tyramide based fluorescent reagent</td>
		</tr>
		<tr>
			<td>Opal 620</td>
			<td>Perkin Elmer</td>
			<td>FP1495A</td>
			<td>Appropriate tyramide based fluorescent reagent</td>
		</tr>
		<tr>
			<td>Opal 650</td>
			<td>Perkin Elmer</td>
			<td>FP1496A</td>
			<td>Appropriate tyramide based fluorescent reagent</td>
		</tr>
		<tr>
			<td>Opal 690</td>
			<td>Perkin Elmer</td>
			<td>FP1497A</td>
			<td>Appropriate tyramide based fluorescent reagent</td>
		</tr>
		<tr>
			<td>Oven</td>
			<td>Memmert</td>
			<td>U10</td>
			<td>Dewaxing</td>
		</tr>
		<tr>
			<td>Peroxidase Blocking Solution</td>
			<td>DAKO</td>
			<td>S2023</td>
			<td>Removal of tissue peroxidase activities</td>
		</tr>
		<tr>
			<td>Poly-L-lysine coated slide</td>
			<td>FISHER SCIENTIFIC</td>
			<td>120-550-15</td>
			<td>Slide for routine histological use</td>
		</tr>
		<tr>
			<td>PolyHRP Broad Spectrum</td>
			<td>Perkin Elmer</td>
			<td>ARH1001EA</td>
			<td>Secondary antibody</td>
		</tr>
		<tr>
			<td>ProLong&#8482; Gold Antifade Mountant</td>
			<td>ThemoFisher Scientific</td>
			<td>P36930</td>
			<td>Mounting</td>
		</tr>
		<tr>
			<td>Spatstat</td>
			<td>/</td>
			<td>Version 2.1-0</td>
			<td>Spatial point pattern analysis</td>
		</tr>
		<tr>
			<td>Spectral DAPI</td>
			<td>Perkin Elmer</td>
			<td>FP1490A</td>
			<td>Nucleic acid staining</td>
		</tr>
		<tr>
			<td>Tissue Processor</td>
			<td>Thermo Fischer</td>
			<td>Excelsior ES</td>
			<td>Tissue processing for dehydration and paraffination</td>
		</tr>
		<tr>
			<td>Tris Buffer Saline (TBS), 10x</td>
			<td>Cell Signaling Technology</td>
			<td>12498S</td>
			<td>Washing solution</td>
		</tr>
		<tr>
			<td>Tween 20</td>
			<td>Sigma-Aldrich</td>
			<td>P1370-1L</td>
			<td>Nonionic detergent</td>
		</tr>
	</tbody>
</table>

multiplexed fluorescent immunohistochemical staining of four endometrial immune cell types in recurrent miscarriage

Immunohistochemistry is the most commonly used method for the identification and visualization of tissue antigens in biological research and clinical diagnostics. It can be used to characterize various biological processes or pathologies, such as wound-healing, immune response, tissue rejection, and tissue-biomaterial interactions. However, the visualization and quantification of multiple antigens (especially for immune cells) in a single tissue section using conventional immunohistochemical (IHC) staining remains unsatisfactory. Hence, multiplexed technologies were introduced in recent years to identify multiple biological markers in a single tissue sample or an ensemble of different tissue samples. 
These technologies can be especially useful in differentiating the changes in immune cell-to-cell interactions within the endometrium between fertile women and women with recurrent miscarriages during implantation. This paper describes a detailed protocol for multiplexed fluorescence IHC staining to investigate the density and clustering of four major immune cell types simultaneously in precisely timed endometrial specimens during embryo implantation. The method includes sample preparation, multiplex optimization with markers for immune cell subtypes, and the scanning of the slides, followed by data analysis, with specific reference to detecting endometrial immune cells. 
Using this method, the density and clustering of four major immune cell types in the endometrium can be simultaneously analyzed in a single tissue section. In addition, this paper will discuss the critical factors and troubleshooting to overcome possible fluorophore interference between the fluorescent probes being applied. Importantly, the results from this multiplex staining technique can help provide an in-depth understanding of the immunologic interaction and regulation during embryo implantation.

The overall schematic process of performing a 4-color multiplex assay for the detection of 4 endometrial immune cell types is shown in Figure 1. In brief, the protocol for this multiplex immunofluorescence staining required 8 key steps: 1. Slide preparation, 2. Epitope retrieval, 3. Blocking, 4. Primary antibody application, 5. Secondary antibody application, 6. Signal amplification, 7. Removal of antibody, and 8. Counterstain and mount. Image rendering and analysis were then conducted using...

Watch this Scientific Journal Video about Multiplexed Fluorescent Immunohistochemical Staining of Four Endometrial Immune Cell Types in Recurrent Miscarriage at JoVE.com

Multiplexed Fluorescent Immunohistochemical Staining of Four Endometrial Immune Cell Types in Recurrent Miscarriage

Despite the advancements in multiplex immunohistochemistry and multispectral imaging, characterizing the density and clustering of major immune cells simultaneously in the endometrium remains a challenge. This paper describes a detailed multiplex staining protocol and imaging for the simultaneous localization of four immune cell types in the endometrium.

Immunohistochemistry is the most commonly used method for the identification and visualization of tissue antigens in biological research and clinical ...

The present technology allows the use of antibody raised in the same species for detecting up to seven markers. Demonstrating the procedure will be Loucia Chan, a technician from the laboratory. Begin by preparing the formalin fixed paraffin embedded glass slides mounted with the tissue sample, by placing the slides flat in an oven, to bake at 60 degrees celsius with the tissue facing upwards.After one hour, de-wax and rehydrate the slides per 10 minutes each with the series of chemicals, as described in the manuscript. Submerge the slides in tris-buffered saline, and then in a plastic slide box filled with a mixture of formaldehyde diluted in methanol, to fix the samples. Next, wash the slides twice in deionized water for two minutes.Proceed to epitope retrieval, by placing the rack of slides in a heat resistance box filled with citric acid buffer at pH 6.0. And then placing the box in the microwave, to heat the slides first at 100%power for 50 seconds, followed by 20 minutes at 20%power, to maintain the same temperature. After rinsing the slides in distilled water, and washing with TBST, immerse the slide into a jar containing a peroxidation blocking solution for 10 minutes.After the incubation, rinse the slides in distilled water and wash with TBST, then use a hydrophobic barrier pen to mark a boundary around the tissue section on the slide. Then rinse the slide in TBST, cover the tissue sections with the blocking buffer and incubate the slides in a humidified chamber for 15 minutes. To remove the blocking reagents, first incubate the slides with the primary antibody of interest, and then remove the primary antibody by washing the slides thrice with TBST, before incubation with the polymer horseradish peroxidase labeled, secondary antibody.Following the incubation, wash the slides before applying the Opal flora for TSA working solution, and then rinse the slide with the antigen retrieval buffer. Perform the microwave-based stripping by heating the slides in antigen retrieval buffer in a microwave at 100%power, for 50 seconds, followed by 20%power for 20 minutes in the microwave safe containers. After cooling the samples at room temperature for 15 minutes, rinse the slides in distilled water and TBST and later incubate with dappy solution for five minutes.Then air dry the slide before mounting with the appropriate mounting medium. Before imaging of the slides preset the appropriate filters in the workstation. Capture a minimum of 10 fields for analysis under 200 times magnification.To count the cells, click on the count objects button in the step bar, to display the object counting settings panel. If the tissue has been segmented, select the tissue category in which the objects are to be found. Then select the desired signal scaling from auto-scale or fixed scale.For object segmentation, select the primary component from the drop-down list. To detect objects touching other objects as individual and not combined objects, check the maximum size and pixels box and then opt for the refined splitting. Next, count all stromal cells in the immune cells separately, to express the data as the percentages of the immune cells relative to the total number of stromal cells for each captured image.Later, report the final cell count as an average of all fields. Using the view editor, examine the resulting data tables post-processing and then export the count data table. In the representative analysis, four immune cell types in the endometrium sample we're differentiated.The processed image shows tissue segmentation as epithelial, and stromal compartments. The multiplex immunostaining was performed on the endometrial biopsies from a fertile control woman and a woman with unexplained recurrent miscarriage, single floor for us representing CD3, CD56, CD68, and CD20 were revealed in the immunostaining. Once the immune sound has been identified, further staining under the cytokine can help to address their interaction and mechanism for implantation success.

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Preparation of 2-dGuo-Treated Thymus Organ Cultures

In the thymus, interactions between developing T-cell precursors and stromal cells that include cortical and medullary epithelial cells are known to play a key role in the development of a functionally competent T-cell pool. However, the complexity of T-cell development in the thymus in vivo can limit analysis of individual cellular components and particular stages of development. In vitro culture systems provide a readily accessible means to study multiple complex cellular processes. Thymus organ culture systems represent a widely used approach to study intrathymic development of T-cells under defined conditions in vitro. Here we describe a system in which mouse embryonic thymus lobes can be depleted of endogenous haemopoeitic elements by prior organ culture in 2-deoxyguanosine, a compound that is selectively toxic to haemopoeitic cells. As well as providing a readily accessible source of thymic stromal cells to investigate the role of thymic microenvironments in the development and selection of T-cells, this technique also underpins further experimental approaches that include the reconstitution of alymphoid thymus lobes in vitro with defined haemopoietic elements, the transplantation of alymphoid thymuses into recipient mice, and the formation of reaggregate thymus organ cultures. (This article is based on work first reported Methods in Molecular Biology 2007, Vol. 380 pages 185-196).

This video demonstrates the dissection and removal of the fetal thymus as well the preparation of ex vivo cultures of 2-dGuo-treated thymus.

In the thymus, interactions between developing T-cell precursors and stromal cells that include cortical and medullary epithelial cells are known to play ...

Live Cell Imaging of F-actin Dynamics via Fluorescent Speckle Microscopy (FSM)

In this protocol we describe the use of Fluorescent Speckle Microscopy (FSM) to capture high-resolution images of actin dynamics in PtK1 cells. A unique advantage of FSM is its ability to capture the movement and turnover kinetics (assembly/disassembly) of the F-actin network within living cells. This technique is particularly useful in deriving quantitative measurements of F-actin dynamics when paired with computer vision software (qFSM).  We describe  the selection, microinjection and visualization of fluorescent actin probes in living cells. Importantly, similar procedures are applicable to visualizing other macomolecular assemblies. FSM has been demonstrated for microtubules, intermediate filaments, and adhesion complexes.  

Live Cell Imaging of F-actin Dynamics via Fluorescent Speckle Microscopy FSM

Selection, microinjection, and imaging of fluorescently-labeled F-actin via fluorescent speckle microscopy (FSM).

In this protocol we describe the use of Fluorescent Speckle Microscopy (FSM) to capture high-resolution images of actin dynamics in PtK1 cells. A unique ...

Whole-mount Immunohistochemical Analysis for Embryonic Limb Skin Vasculature: a Model System to Study Vascular Branching Morphogenesis in Embryo

Whole-mount immunohistochemical analysis for imaging the entire vasculature is pivotal for understanding the cellular mechanisms of branching morphogenesis. We have developed the limb skin vasculature model to study vascular development in which a pre-existing primitive capillary plexus is reorganized into a hierarchically branched vascular network. Whole-mount confocal microscopy with multiple labelling allows for robust imaging of intact blood vessels as well as their cellular components including endothelial cells, pericytes and smooth muscle cells, using specific fluorescent markers. Advances in this limb skin vasculature model with genetic studies have improved understanding molecular mechanisms of vascular development and patterning. The limb skin vasculature model has been used to study how peripheral nerves provide a spatial template for the differentiation and patterning of arteries. This video article describes a simple and robust protocol to stain intact blood vessels with vascular specific antibodies and fluorescent secondary antibodies, which is applicable for vascularized embryonic organs where we are able to follow the process of vascular development.

We introduce a whole-mount immunohistochemistry and laser scanning confocal microscopy with multiple labelling for analyzing intricate vascular network formation in mouse embryonic limb skin.

Whole-mount immunohistochemical analysis for imaging the entire vasculature is pivotal for understanding the cellular mechanisms of branching ...

Analysis of Single-cell Gene Transcription by RNA Fluorescent In Situ Hybridization (FISH)

Adhesion of Plasmodium falciparum infected erythrocytes (IE) to human endothelial receptors during malaria infections is mediated by expression of PfEMP1 protein variants encoded by the var genes.
The haploid P. falciparum genome harbors approximately 60 different var genes of which only one has been believed to be transcribed per cell at a time during the blood stage of the infection. How such mutually exclusive regulation of var gene transcription is achieved is unclear, as is the identification of individual var genes or sub-groups of var genes associated with different receptors and the consequence of differential binding on the clinical outcome of P. falciparum infections. Recently, the mutually exclusive transcription paradigm has been called into doubt by transcription assays based on individual P. falciparum transcript identification in single infected erythrocytic cells using RNA fluorescent in situ hybridization (FISH) analysis of var gene transcription by the parasite in individual nuclei of P. falciparum IE1.
Here, we present a detailed protocol for carrying out the RNA-FISH methodology for analysis of var gene transcription in single-nuclei of P. falciparum infected human erythrocytes. The method is based on the use of digoxigenin- and biotin- labeled antisense RNA probes using the TSA Plus Fluorescence Palette System2 (Perkin Elmer), microscopic analyses and freshly selected P. falciparum IE. The in situ hybridization method can be used to monitor transcription and regulation of a variety of genes expressed during the different stages of the P. falciparum life cycle and is adaptable to other malaria parasite species and other organisms and cell types.

Analysis of Single-cell Gene Transcription by RNA Fluorescent In Situ Hybridization FISH

Fluorescent in situ hybridization (FISH) to identify mRNA transcripts in individual cells allows analysis of polygenic activity such as the simultaneous transcription of more than one member of the var multigene family in Plasmodium falciparum infected erythrocytes 1. The technique is adaptable and can be used on different types of genes, cells and organisms.

Adhesion of Plasmodium falciparum infected erythrocytes (IE) to human endothelial receptors during malaria infections is mediated by expression of PfEMP1 ...

Separation of Spermatogenic Cell Types Using STA-PUT Velocity Sedimentation

Mammalian spermatogenesis is a complex differentiation process that occurs in several stages in the seminiferous tubules of the testes. Currently, there is no reliable cell culture system allowing for spermatogenic differentiation in vitro, and most biological studies of spermatogenic cells require tissue harvest from animal models like the mouse and rat. Because the testis contains numerous cell types - both non-spermatogenic (Leydig, Sertoli, myeloid, and epithelial cells) and spermatogenic (spermatogonia, spermatocytes, round spermatids, condensing spermatids and spermatozoa) - studies of the biological mechanisms involved in spermatogenesis require the isolation and enrichment of these different cell types. The STA-PUT method allows for the separation of a heterogeneous population of cells - in this case, from the testes - through a linear BSA gradient. Individual cell types sediment with different sedimentation velocity according to cell size, and fractions enriched for different cell types can be collected and utilized in further analyses. While the STA-PUT method does not result in highly pure fractions of cell types, e.g. as can be obtained with certain cell sorting methods, it does provide a much higher yield of total cells in each fraction (~1 x 108 cells/spermatogenic cell type from a starting population of 7-8 x 108 cells). This high yield method requires only specialized glassware and can be performed in any cold room or large refrigerator, making it an ideal method for labs that have limited access to specialized equipment like a fluorescence activated cell sorter (FACS) or elutriator.

The STA-PUT method allows for the separation of different populations of spermatogenic cells based on size and density.

Mammalian spermatogenesis is a complex  differentiation process that occurs in several stages in the seminiferous  tubules of the testes. Currently, there ...

Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications

Fluorescent proteins, fluorescent dyes and fluorophores in general have revolutionized the field of molecular cell biology. In particular, the discovery of fluorescent proteins and their genes have enabled the engineering of protein fusions for localization, the analysis of transcriptional activation and translation of proteins of interest, or the general tracking of individual cells and cell populations. The use of fluorescent protein genes in combination with retroviral technology has further allowed the expression of these proteins in mammalian cells in a stable and reliable manner. Shown here is how one can utilize these genes to give cells within a population of cells their own biosignature. As the biosignature is achieved with retroviral technology, cells are barcoded &#180;indefinitely&#180;. As such, they can be individually tracked within a mixture of barcoded cells and utilized in more complex biological applications. The tracking of distinct populations in a mixture of cells is ideal for multiplexed applications such as discovery of drugs against a multitude of targets or the activation profile of different promoters. The protocol describes how to elegantly develop and amplify barcoded mammalian cells with distinct genetic fluorescent markers, and how to use several markers at once or one marker at different intensities. Finally, the protocol describes how the cells can be further utilized in combination with cell-based assays to increase the power of analysis through multiplexing.

Since the discovery of the green fluorescent protein gene, fluorescent proteins have impacted molecular cell biology. This protocol describes how expression of distinct fluorescent proteins through genetic engineering is used for barcoding individual cells. The procedure enables tracking distinct populations in a cell mixture, which is ideal for multiplexed applications.

Fluorescent proteins, fluorescent dyes and fluorophores in general have revolutionized the field of molecular cell biology. In particular, the discovery ...

Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging

Immunohistochemistry is a commonly used clinical and research lab detection technique for investigating protein expression and localization within tissues. Many semi-quantitative systems have been developed for scoring expression using immunohistochemistry, but inherent subjectivity limits reproducibility and accuracy of results. Furthermore, the investigation of spatially overlapping biomarkers such as nuclear transcription factors is difficult with current immunohistochemistry techniques. We have developed and optimized a system for simultaneous investigation of multiple proteins using high throughput methods of multiplexed immunohistochemistry and multispectral imaging. Multiplexed immunohistochemistry is performed by sequential application of primary antibodies with secondary antibodies conjugated to horseradish peroxidase or alkaline phosphatase. Different chromogens are used to detect each protein of interest. Stained slides are loaded into an automated slide scanner and a protocol is created for automated image acquisition. A spectral library is created by staining a set of slides with a single chromogen on each. A subset of representative stained images are imported into multispectral imaging software and an algorithm for distinguishing tissue type is created by defining tissue compartments on images. Subcellular compartments are segmented by using hematoxylin counterstain and adjusting the intrinsic algorithm. Thresholding is applied to determine positivity and protein co-localization. The final algorithm is then applied to the entire set of tissues. Resulting data allows the user to evaluate protein expression based on tissue type (ex. epithelia vs. stroma) and subcellular compartment (nucleus vs. cytoplasm vs. plasma membrane). Co-localization analysis allows for investigation of double-positive, double-negative, and single-positive cell types. Combining multispectral imaging with multiplexed immunohistochemistry and automated image acquisition is an objective, high-throughput method for investigation of biomarkers within tissues.

Immunohistochemistry is a powerful lab technique for evaluating protein localization and expression within tissues. Current semi-automated methods for quantitation introduce subjectivity and often create irreproducible results. Herein, we describe methods for multiplexed immunohistochemistry and objective quantitation of protein expression and co-localization using multispectral imaging.

Immunohistochemistry is a commonly used clinical and research lab detection technique for investigating protein expression and localization within ...

Development of an Insert Co-culture System of Two Cellular Types in the Absence of Cell-Cell Contact

The role of secreted soluble factors in the modification of cellular responses is a recurrent theme in the study of all tissues and systems. In an attempt to make straightforward the very complex relationships between the several cellular subtypes that compose multicellular organisms, in vitro techniques have been developed to help researchers acquire a detailed understanding of single cell populations. One of these techniques uses inserts with a permeable membrane allowing secreted soluble factors to diffuse. Thus, a population of cells grown in inserts can be co-cultured in a well or dish containing a different cell type for evaluating cellular changes following paracrine signaling in the absence of cell-cell contact. Such insert co-culture systems offer various advantages over other co-culture techniques, namely bidirectional signaling, conserved cell polarity and population-specific detection of cellular changes. In addition to being utilized in the field of inflammation, cancer, angiogenesis and differentiation, these co-culture systems are of prime importance in the study of the intricate relationships that exist between the different cellular subtypes present in the central nervous system, particularly in the context of neuroinflammation. This article offers general methodological guidelines in order to set up an experiment in order to evaluating cellular changes mediated by secreted soluble factors using an insert co-culture system. Moreover, a specific protocol to measure the neuroinflammatory effects of cytokines secreted by lipopolysaccharide-activated N9 microglia on neuronal PC12 cells will be detailed, offering a concrete understanding of insert co-culture methodology.

In multicellular organisms, secreted soluble factors elicit responses from different cell types as a result of paracrine signaling. Insert co-culture systems offer a simple way to assess the changes mediated by secreted soluble factors in the absence of cell-cell contact.

The role of secreted soluble factors in the modification of cellular responses is a recurrent theme in the study of all tissues and systems. In an attempt ...

Effect of Fluorescent Proteins on Fusion Partners Using Polyglutamine Toxicity Assays in Yeast

For the investigation of protein localization and trafficking using live cell imaging, researchers often rely on fusing their protein of interest to a fluorescent reporter. The constantly evolving list of genetically encoded fluorescent proteins (FPs) presents users with several alternatives when it comes to fluorescent fusion design. Each FP has specific optical and biophysical properties that can affect the biochemical, cellular, and functional properties of the resulting fluorescent fusions. For instance, several FPs tend to form nonspecific oligomers that are susceptible to impede on the function of the fusion partner. Unfortunately, only a few methods exist to test the impact of FPs on the behavior of the fluorescent reporter. Here, we describe a simple method that enables the rapid assessment of the impact of FPs using polyglutamine (polyQ) toxicity assays in the budding yeast Saccharomyces cerevisiae. PolyQ-expanded huntingtin proteins are associated with the onset of Huntington&#39;s disease (HD), where the expanded huntingtin aggregates into toxic oligomers and inclusion bodies. The aggregation and toxicity of polyQ expansions in yeast are highly dependent on the sequences flanking the polyQ region, including the presence of fluorescent tags, thus providing an ideal experimental platform to study the impact of FPs on the behavior of their fusion partner.

This article describes protocols to assess the effect of fluorescent proteins on the aggregation and toxicity of misfolded polyglutamine expansion for the rapid evaluation of a newly uncharacterized fluorescent protein in the context of fluorescent reporters.

For the investigation of protein localization and trafficking using live cell imaging, researchers often rely on fusing their protein of interest to a ...

Isolation and Transcriptome Analysis of Plant Cell Types

In multicellular organisms, developmental programming and environmental responses can be highly divergent in different cell types or even within cells, which is known as cellular heterogeneity. In recent years, single-cell and cell-type isolation combined with next-generation sequencing (NGS) techniques have become important tools for studying biological processes at single-cell resolution. However, isolating plant cells is relatively more difficult due to the presence of plant cell walls, which limits the application of single-cell approaches in plants. This protocol describes a robust procedure for fluorescence-activated cell sorting (FACS)-based single-cell and cell-type isolation with plant cells, which is suitable for downstream multi-omics analysis and other studies. Using Arabidopsis root fluorescent marker lines, we demonstrate how particular cell types, such as xylem-pole pericycle cells, lateral root initial cells, lateral root cap cells, cortex cells, and endodermal cells, are isolated. Furthermore, an effective downstream transcriptome analysis method using Smart-seq2 is also provided. The cell isolation method and transcriptome analysis techniques can be adapted to other cell types and plant species and have broad application potential in plant science.

The feasibility and effectiveness of high-throughput scRNA-seq methods herald a single-cell era in plant research. Presented here is a robust and complete procedure for isolating specific Arabidopsis thaliana root cell types and subsequent transcriptome library construction and analysis.

In multicellular organisms, developmental programming and environmental responses can be highly divergent in different cell types or even within cells, ...