Name: a fluorescence-based lymphocyte assay suitable for high-throughput screening of small molecules
Uploaded: 2017-03-10T14:00:00
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This work was supported by the Merck Frosst Start-up funds provided by Universit&#233; de Montr&#233;al. We would like to thank Drs Jean Duchaine and Dominic Salois from the High-throughput platform at the Institute for Research in Immunology and Cancer for their discussion, comments and feedbacks. Moutih Rafei holds a Fonds de la Recherche en Sant&#233; du Qu&#233;bec Junior 1 Award.

All animal protocols were approved by the Animal Care Committee of Universit&#233; de Montr&#233;al. Mice were euthanized by gradual inhalation of CO2 until no vital signs were observed followed by cervical dislocation. The procedure was carried out by a certified person to ensure that animals were euthanized in a humane manner and according to the recommendations of the Canadian Council on Animal Care.
1. Preparation of Splenocyte Medium and Flow-cytometry Buffer
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	<li>Perfor...

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Several read-out methods have been exploited for the development of sensitive and reliable HTS assays. These include colorimetric, luminescent or fluorescent methods. Although colorimetric methods are simple to set-up, they require multiple additions of chemicals, which may interfere or disrupt the cells being tested.23 In addition, they do not permit dynamic assessment of a biological response as the pharmacological effect is assessed at a specific endpoint. Furthermore, this method may require e...

High throughput screening (HTS) is a proven strategy widely adopted for the identification of new therapeutic molecules or for the repositioning of FDA-approved drugs in new medical indications.1 So far, the achieved HTS success can be measured by the plethora of previously discovered drugs. For instance, the tyrosine kinase inhibitor lapatinib used for the treatment of breast cancer, sitagliptin; a dipeptidyl peptidase-4 (DPP-4) inhibitor used as an anti-hyperglycemic drug, and the oral Bcr-Abl tyrosine kinase inhibitor dasatinib used for the treatment of chronic myelogenous leukemia represent few examples of a long list of approved drugs originally discovered by HTS.2 Although the productivity of the pharmaceutical industry has lately suffered from a lack in the discovery of new chemical entities, the likelihood of successful drug discovery can be improved through an increase in the number of pre-clinical candidates displaying modulatory biological/biochemical properties. Accordingly, the development of new HTS assays adapted for phenotypic screening could offer the potential to provide important pharmacological tools for the discovery of new drug hits.3,4,5,6 Furthermore, HTS can now be performed at a faster pace due to significant technological transformations in recent years including custom-designed flexible robotic installations, novel read-out technologies and extensive miniaturization.2,7 Among the factors contributing to the growing interest in the use of phenotypic screening (aka forward pharmacology) is the perception that focusing on functional effects rather than oversimplified reductionist assumptions regarding molecular targets (target-based screening/biochemical reactions) is more likely to show clinical efficacy. Thus, phenotypic screening holds the promise to uncover new potentially therapeutic compounds and molecular pathways of currently untreatable diseases.2
To properly identify inhibitors or activators for a given molecular target or cellular function, a highly sensitive and reliable assay is required in order to differentiate between bona fide hits and false positives. So, what makes a good assay? The quality of a given assay must be first judged by the signal-to-noise ratio (reflected through a Z factor).8 Second, the targeted effect or the goal of the screen should be clearly established. For example, functional cell-based approaches can offer significant advantages for receptor screening as opposed to an assay specifically designed to assess ligand-receptor binding. The reason for this is that the latter approach cannot differentiate between agonist and antagonist ligands.9 In contrast, a cell-based approach is likely to be more effective as receptor function can be directly assessed in a biological phenotype (proliferation, cell cycle arrest, apoptosis, and/or differentiation). However, it must be noted that biochemical assays can provide significant advantages over phenotypic assays as they infringe on a specific intracellular target. A well-optimized biochemical assay will generally have less data scatter than a phenotypic screening while simplifying afterwards investigations related to the drug molecular mechanism of action. However, the major drawback of target-based or biochemical assays is the chance of amplifying the rate of false positive hits that may affect non-specific targets when tested in a biological system (loss of the specificity originally studied in the biochemical assay).10 Although a well-established cut-off point between negative and positive hits can minimize the number of false positives in the primary screening, the use of a physiologically relevant system mimicking the native cellular environment such as intact cells, whole tissue or whole animal remains the core of the assay design pendulum. Therefore, phenotypic screening enables lead discovery with desirable biological/phenotypic effects for diseases with no identified drug targets without having prior knowledge of the compound&#39;s activity or mode of action.11
The herein study concerns the development and testing of an optimized and reproducible phenotypic screening based on two important components: a commercially available mouse model and a clustered sub-family of chemical compounds. With respect to the animal model, the assay relies on the use of lymphocytes derived from a mouse strain (Nur77GFP) harboring a bacterial artificial chromosome containing a cassette in which the expression of the green fluorescent protein (GFP) is driven by the Nur77 promoter.12 The hallmark of this stimulation is based on the fact that Nur77 is an immediate early gene up-regulated following T-cell receptor (TCR) or B-cell receptor (BCR) stimulation.12 As for the screening method itself, an approach was used to help avoiding the screening of trivial analogues while minimizing the time needed to assess a large chemical library (&#62;105 compounds). To do so, a database of chemical compounds selected by medicinal chemists using virtual screening tools was exploited to identify topologically similar compounds using known active seed structures as references. This approach allowed us to screen 4,398 compounds representing an overall library of over 136,000 chemical entities.

<table border="0" cellpadding="0" cellspacing="0" width="725">
	<tbody>
		<tr height="64">
			<td height="64" style="height:64px;width:211px;">Nur77GFP mice</td>
			<td style="width:157px;">The Jackson Laboratory</td>
			<td style="width:135px;">Mouse strain No. 016617</td>
			<td style="width:224px;">An in house colony was established at our animal facility&#160;</td>
		</tr>
		<tr height="57">
			<td height="57" style="height:57px;width:211px;">96 wells-U culture plates, sterile</td>
			<td style="width:157px;">VWR International</td>
			<td style="width:135px;">10062-902</td>
			<td style="width:224px;">T-cell activation using the magnetic beads</td>
		</tr>
		<tr height="50">
			<td height="50" style="height:50px;width:211px;">70&#181;m cell strainer, sterile</td>
			<td style="width:157px;">Corning Inc.</td>
			<td style="width:135px;">352350</td>
			<td style="width:224px;">Generation of splenocytes cell suspension</td>
		</tr>
		<tr height="61">
			<td height="61" style="height:61px;width:211px;">5 ml polystyrene round bottom tubes, sterile</td>
			<td style="width:157px;">Corning Inc.</td>
			<td style="width:135px;">352058</td>
			<td style="width:224px;">Generation of splenocytes cell suspension</td>
		</tr>
		<tr height="70">
			<td height="70" style="height:70px;width:211px;">50 ml polypropylene conical bottom tubes, sterile</td>
			<td style="width:157px;">VWR International</td>
			<td style="width:135px;">89039-656&#160;</td>
			<td style="width:224px;">Generation of splenocytes cell suspension</td>
		</tr>
		<tr height="52">
			<td height="52" style="height:52px;width:211px;">10 ml syringe without needle, sterile</td>
			<td style="width:157px;">Becton, Dickinson and Company</td>
			<td style="width:135px;">305482</td>
			<td style="width:224px;">To mash the spleen</td>
		</tr>
		<tr height="52">
			<td height="52" style="height:52px;">T-25 culture flask</td>
			<td style="width:157px;">Greiner Bio-One</td>
			<td style="width:135px;">690 175</td>
			<td style="width:224px;">To incudabte B cells during activation</td>
		</tr>
		<tr height="52">
			<td height="52" style="height:52px;width:211px;">5 ml cell culture dish, sterile</td>
			<td style="width:157px;">Greiner Bio-One</td>
			<td style="width:135px;">627 160</td>
			<td style="width:224px;">To mash the spleen</td>
		</tr>
		<tr height="57">
			<td height="57" style="height:57px;width:211px;">Penicillin- Streptomycin (10,000 U/mL)</td>
			<td style="width:157px;">WISENT Inc.</td>
			<td style="width:135px;">450-200-EL&#160;&#160;</td>
			<td style="width:224px;">Component of the splenocyte media</td>
		</tr>
		<tr height="68">
			<td height="68" style="height:68px;width:211px;">RPMI 1600 with sodium bicarbonate and L- glutamine</td>
			<td style="width:157px;">WISENT Inc.</td>
			<td style="width:135px;">350-002-CL&#160;</td>
			<td style="width:224px;">Component of the splenocyte media</td>
		</tr>
		<tr height="49">
			<td height="49" style="height:49px;width:211px;">MEM non-essential amino acids</td>
			<td style="width:157px;">WISENT Inc.</td>
			<td style="width:135px;">321-010-EL&#160;</td>
			<td style="width:224px;">Component of the splenocyte media</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:211px;">HEPES free acid 1 M</td>
			<td style="width:157px;">WISENT Inc.</td>
			<td style="width:135px;">330-050-EL&#160;</td>
			<td style="width:224px;">Component of the splenocyte media</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:211px;">Sodium pyruvate solution (100mM)</td>
			<td style="width:157px;">WISENT Inc.</td>
			<td style="width:135px;">600-110-EL&#160;</td>
			<td style="width:224px;">Component of the splenocyte media</td>
		</tr>
		<tr height="72">
			<td height="72" style="height:72px;width:211px;">Fetal Bovine Serum (FBS)&#160;</td>
			<td style="width:157px;">WISENT Inc.</td>
			<td style="width:135px;">080-910&#160;</td>
			<td style="width:224px;">Component of the splenocyte media and flow-cytometry buffer</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:211px;">Phosphate buffered saline (PBS)</td>
			<td style="width:157px;">WISENT Inc.</td>
			<td style="width:135px;">311-010-CL</td>
			<td style="width:224px;">Component of flow-cytometry buffer</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:211px;">2-Mercaptoethanol (55mM)</td>
			<td style="width:157px;">Thermo Fisher Scientific</td>
			<td style="width:135px;">21985-023</td>
			<td style="width:224px;">Component of the splenocyte media</td>
		</tr>
		<tr height="44">
			<td height="44" style="height:44px;width:211px;">T- Cells isolation kit</td>
			<td style="width:157px;">Stemcell Technologies</td>
			<td style="width:135px;">19851</td>
			<td style="width:224px;">To isolate T cells</td>
		</tr>
		<tr height="36">
			<td height="36" style="height:36px;width:211px;">B- Cells isolation kit</td>
			<td style="width:157px;">Stemcell Technologies</td>
			<td style="width:135px;">19854</td>
			<td style="width:224px;">To isolate B cells</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:211px;">Mouse T-Activator CD3/CD28 superparamagnetic beads</td>
			<td style="width:157px;">Thermo Fisher Scientific</td>
			<td style="width:135px;">11452D</td>
			<td style="width:224px;">To activate T cells&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:211px;">Cell isolation magnet</td>
			<td style="width:157px;">Stemcell Technologies</td>
			<td style="width:135px;">18000</td>
			<td style="width:224px;">To isolate T cells and remove the magnetic beads&#160;</td>
		</tr>
		<tr height="76">
			<td height="76" style="height:76px;width:211px;">AffiniPure F(ab&#39;)2 Fragment Goat Anti-Mouse IgG + IgM (H+L)</td>
			<td style="width:157px;">Jackson ImmunoResearch Laboratories, Inc.</td>
			<td style="width:135px;">115-006-068</td>
			<td style="width:224px;">To stimulate B cells</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:211px;">Recombinant Murine IL-7</td>
			<td style="width:157px;">Peprotech</td>
			<td style="width:135px;">217-17&#160;</td>
			<td style="width:224px;">To support T-cell survival during activation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:211px;">Recombinant CD40L</td>
			<td style="width:157px;">R&#38;D Systems</td>
			<td style="width:135px;">8230-CL/CF</td>
			<td style="width:224px;">To stimulate B cells</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:211px;">Anti-mouse CD3 antibody</td>
			<td style="width:157px;">BD Pharmingen</td>
			<td style="width:135px;">561799</td>
			<td style="width:224px;">To stain T cells for flow-cytometry</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:211px;">Anti-mouse CD19 antibody</td>
			<td style="width:157px;">BD Pharmingen</td>
			<td style="width:135px;">553786</td>
			<td style="width:224px;">To stain B cells for flow-cytometry</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:211px;">Biomed FXp</td>
			<td style="width:157px;">PerkinElmer Inc.</td>
			<td style="width:135px;">A31842</td>
			<td style="width:224px;">To re-suspend cells after 24 hours incubation</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:211px;">Opera Phenix High Content Screening System</td>
			<td style="width:157px;">PerkinElmer Inc.</td>
			<td style="width:135px;">HH14000000</td>
			<td style="width:224px;">To analyze GFP/Hoechst signal</td>
		</tr>
	</tbody>
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a fluorescence-based lymphocyte assay suitable for high-throughput screening of small molecules

High-throughput screening (HTS) is currently the mainstay for the identification of chemical entities capable of modulating biochemical reactions or cellular processes. With the advancement of biotechnologies and the high translational potential of small molecules, a number of innovative approaches in drug discovery have evolved, which explains the resurgent interest in the use of HTS. The oncology field is currently the most active research area for drug screening, with no major breakthrough made for the identification of new immunomodulatory compounds targeting transplantation-related complications or autoimmune ailments. Here, we present a novel in vitro murine fluorescent-based lymphocyte assay easily adapted for the identification of new immunomodulatory compounds. This assay uses T or B cells derived from a transgenic mouse, in which the Nur77 promoter drives GFP expression upon T- or B-cell receptor stimulation. As the GFP intensity reflects the activation/transcriptional activity of the target cell, our assay defines a novel tool to study the effect of given compound(s) on cellular/biological responses. For instance, a primary screening was performed using 4,398 compounds in the absence of a &#34;target hypothesis&#34;, which led to the identification of 160 potential hits displaying immunomodulatory activities. Thus, the use of this assay is suitable for drug discovery programs exploring large chemical libraries prior to further in vitro/in vivo validation studies.

Design of the HTS assay
Two important factors were taken into consideration when designing the herein fluorescent assay. First, we needed to replicate a physiological condition in which T- or B cell activation would represent an ailment (e.g. graft-versus-host disease). Second, the assessment of cellular activation should be performed using a sensitive and quantitative method. Fluorescence is nowadays one of the primary ch...

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A Fluorescence-based Lymphocyte Assay Suitable for High-throughput Screening of Small Molecules

We present in the current study a novel fluorescence-based assay using lymphocytes derived from a transgenic mouse. This assay is suitable for high-throughput screening (HTS) of small molecules endowed with the capacity of either inhibiting or promoting lymphocyte activation.

High-throughput screening (HTS) is currently the mainstay for the identification of chemical entities capable of modulating biochemical reactions or ...

The overall goal of this florescence-based lymphocyte assay is to identify new small molecule immunomodulators. This method can help answer key questions in the field of immunology about the mechanism of lymphocyte activation and inhibition. The main advantage of this phenotypic function and assay, that it can be adapted for drug discovery.Demonstrating the procedure will be Ahmed Fouda, a graduate student from our laboratory. Under a sterile work hood, disinfect the fur of a six to eight week old female Nurr77 GFP mouse with 70%ethanol, and place the animal on its right side. Next, make an incision in the skin and muscles of the upper left abdominal quadrant, and locate and remove the spleen, placing the tissue into splenocyte medium on ice.When all of the spleens have been collected, transfer the tissues to a 10 centimeter squared cell culture dish containing five milliliters of prewarmed splenocyte medium, and use a sterile syringe plunger to mash the tissues until the solution is turbid. Following extensive mashing in splenocyte medium, filter the cell suspension through a 70 micron cell strainer into a 50 milliliter tube to remove any debris, and centrifuge the resulting single cell suspension. Resuspend the pellet in two to three milliliters of red blood cell lysis buffer, sopping the reaction with five milliliters of RPMI, or another suitable buffer, after 20 to 30 seconds.Then collect the cells with another centrifugation, and resuspend the pellet in twp milliliters of splenocyte medium for cell counting. To isolate the T cells, centrifuge the cells again, and resuspend the pellet in serum free RPMI medium at a one times 10 to the seven cells per milliliter concentration. Transfer the cells to a five milliliter polystyrene tube, and set aside a 100 microliter aliquot of splenocytes to be used later for purity assessment.Next, add 50 microliters per milliliter of normal rat serum to the cells, followed by the addition of 50 microliters per milliliter of T cell isolation antibody cocktail with gentle mixing. After 10 minutes, incubate the cells with streptavidin conjugated magnetic beads for two and a half minutes. Then, add serum free medium to the cells for a final volume of two and a half milliliters, and place the tube in a cell isolation magnet for three minutes.At the end of the incubation, holding the tube in the magnet, pour the supernatant into a new polystyrene tube in one move. The T cells can then be counted. Seed T cells into a round bottom 96-well plate at a concentration of 2.5 times 10 to the fifth cells per well containing 200 microliters of fresh splenocyte medium per well.Add recombinant interleukin 7 and CD3/CD28 magnetic beads to the appropriate wells, and place the plate in a cell culture incubator. 12 hours later, gently triturate the cell suspension in each well to break up any bead cell aggregates. Then transfer the cell suspensions from each well into individual five milliliter polystyrene tubes.When all of the cells have been collected, place each tube of cells into the separation magnet for five minutes at a time, and decant the supernatants when the tube still inside the magnet, into new polystyrene tubes at the end up each incubation. Then collect the cells by centrifugation, and resuspend the pellets in fresh splenocyte medium at two times 10 to the sixth cells per milliliter concentrations. For small molecule high-throughput screening, plate 40 microliters of cells per well in a 384-well plate, and treat the appropriate wells with the drug or vehicle of choice for the desired treatment period in the cell culture incubator.30 minutes before the GFP analysis, stain the cells with the appropriate concentration of Hoechst solution, thoroughly distributing the stain with gentle pipetting. When all of the wells have been dyed, centrifuge the plates to collect the cells at the bottom of the wells, and allow the cells to rest for 15 minutes at room temperature. Load the plate according to the manufacturer's instructions.Then, set the objective at 40X or higher. Set camera number four for the UV lamp, and then set camera number one for laser 488. Load the plate to the high content screening system.Next, set the automated confocal high content screening system to read six to 10 fields per well with two sequential readings per field, at 488 nanometers and UV light. CD3 positive T cells represent approximately 30%of a given mouse spleen, demonstrating a 10%basal GFP expression. Following CD3/CD28 T cell receptor bead stimulation, a five to six fold increase in the percentage of GFP expression is observed.Likewise, CD19 positive B cells represent 50 to 55%of the total splenocytes with the basal GFP expression similar to that of non activated T cells. Interestingly, B cell receptor stimulation using anti-mouse IgG, IgM, and recombinant CD40L, triggers only a trivial increase in GFP expression. After magnetic bead isolation as just demonstrated, the isolated CD3 positive T cells still display a 10%basal GFP expression.CD3/CD28 bead stimulation however, induces a significant upregulation of the GFP response. Similarly, after B cell magnetic bead isolation, the purified activated B cells exhibit a higher expression of GFP compared to activated B cells in splenocytes. In this representative experiment, primary high-throughput screening of 4398 compounds revealed several activators and inhibitors of T cell activation.But the observed GFP expression of the stimulated T cells, 20 times higher than that measured for the unstimulated T cells. Allowing the generation of a window of action zone where the GFP inhibitory compounds could easily be detected. Once mastered, this technique can be completed in 36 to 48 hours if it is performed properly.While attempting this procedure, it is important to remember to count the cells after each step. Following this procedure, other methods like ELISA or western blotting can be performed to answer any other additional questions. This technique will pave the way for drug discovery immunomodulation in rodents.After watching this video, you should have a good understanding of how to isolate and activate T or B cells derived from the Nurr77 GFP mouse plates.

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Research

JoVE Journal

Immunology and Infection

Quantitative High-throughput Single-cell Cytotoxicity Assay For T Cells

Cancer immunotherapy can harness the specificity of immune response to target and eliminate tumors. Adoptive cell therapy (ACT) based on the adoptive transfer of T cells genetically modified to express a chimeric antigen receptor (CAR) has shown considerable promise in clinical trials1-4. There are several advantages to using CAR+ T cells for the treatment of cancers including the ability to target non-MHC restricted antigens and to functionalize the T cells for optimal survival, homing and persistence within the host; and finally to induce apoptosis of CAR+ T cells in the event of host toxicity5.
Delineating the optimal functions of CAR+ T cells associated with clinical benefit is essential for designing the next generation of clinical trials. Recent advances in live animal imaging like multiphoton microscopy have revolutionized the study of immune cell function in vivo6,7. While these studies have advanced our understanding of T-cell functions in vivo, T-cell based ACT in clinical trials requires the need to link molecular and functional features of T-cell preparations pre-infusion with clinical efficacy post-infusion, by utilizing in vitro assays monitoring T-cell functions like, cytotoxicity and cytokine secretion. Standard flow-cytometry based assays have been developed that determine the overall functioning of populations of T cells at the single-cell level but these are not suitable for monitoring conjugate formation and lifetimes or the ability of the same cell to kill multiple targets8.
Microfabricated arrays designed in biocompatible polymers like polydimethylsiloxane (PDMS) are a particularly attractive method to spatially confine effectors and targets in small volumes9. In combination with automated time-lapse fluorescence microscopy, thousands of effector-target interactions can be monitored simultaneously by imaging individual wells of a nanowell array. We present here a high-throughput methodology for monitoring T-cell mediated cytotoxicity at the single-cell level that can be broadly applied to studying the cytolytic functionality of T cells.

We describe a single-cell high-throughput assay to measure cytotoxicity of T cells when incubated with tumor target cells. This method employs a dense, elastomeric array of sub-nanoliter wells (~100,000 wells/array) to spatially confine the T cells and target cells at defined ratios and is coupled to fluorescence microscopy to monitor effector-target conjugation and subsequent apoptosis.

Cancer immunotherapy can harness the specificity of  immune response to target and eliminate tumors. Adoptive cell therapy (ACT)  based on the adoptive ...

A Microscopic Phenotypic Assay for the Quantification of Intracellular Mycobacteria Adapted for High-throughput/High-content Screening

Despite the availability of therapy and vaccine, tuberculosis (TB) remains one of the most deadly and widespread bacterial infections in the world. Since several decades, the sudden burst of multi- and extensively-drug resistant strains is a serious threat for the control of tuberculosis. Therefore, it is essential to identify new targets and pathways critical for the causative agent of the tuberculosis, Mycobacterium tuberculosis (Mtb) and to search for novel chemicals that could become TB drugs. One approach is to set&#160;up methods suitable for the genetic and chemical screens of large scale libraries enabling the search of a needle in a haystack. To this end, we developed a phenotypic assay relying on the detection of fluorescently labeled Mtb within fluorescently labeled host&#160;cells using automated confocal microscopy. This in vitro assay allows an image based quantification of the colonization process of Mtb&#160;into the host and was optimized for the 384-well microplate format, which is proper for screens of siRNA-, chemical compound- or Mtb mutant-libraries. The images are then processed for multiparametric analysis, which provides read&#160;out inferring on the pathogenesis of Mtb&#160;within host cells.

Here, we describe a phenotypic assay applicable to the High-throughput/High-content screens of small-interfering synthetic RNA (siRNA), chemical compound, and Mycobacterium tuberculosis mutant libraries. This method relies on the detection of fluorescently labeled Mycobacterium tuberculosis within fluorescently labeled host&#160;cell using automated confocal microscopy.

Despite the availability of therapy and vaccine, tuberculosis (TB) remains one of the most deadly and widespread bacterial infections in the world. Since ...

High-throughput Screening for Broad-spectrum Chemical Inhibitors of RNA Viruses

RNA viruses are responsible for major human diseases such as flu, bronchitis, dengue, Hepatitis C or measles. They also represent an emerging threat because of increased worldwide exchanges and human populations penetrating more and more natural ecosystems. A good example of such an emerging situation is chikungunya virus epidemics of 2005-2006 in the Indian Ocean. Recent progresses in our understanding of cellular pathways controlling viral replication suggest that compounds targeting host cell functions, rather than the virus itself, could inhibit a large panel of RNA viruses. Some broad-spectrum antiviral compounds have been identified with host target-oriented assays. However, measuring the inhibition of viral replication in cell cultures using reduction of cytopathic effects as a readout still represents a paramount screening strategy. Such functional screens have been greatly improved by the development of recombinant viruses expressing reporter enzymes capable of bioluminescence such as luciferase. In the present report, we detail a high-throughput screening pipeline, which combines recombinant measles and chikungunya viruses with cellular viability assays, to identify compounds with a broad-spectrum antiviral profile.

In vitro assays to measure virus replication have been greatly improved by the development of recombinant RNA viruses expressing luciferase or other enzymes capable of bioluminescence. Here we detail a high-throughput screening pipeline that combines such recombinant strains of measles and chikungunya viruses to isolate broad-spectrum antivirals from chemical libraries.

RNA viruses are responsible for major human diseases such as flu, bronchitis, dengue, Hepatitis C or measles. They also represent an emerging threat ...

High-throughput Quantitative Real-time RT-PCR Assay for Determining Expression Profiles of Types I and III Interferon Subtypes

Described in this report is a qRT-PCR assay for the analysis of seventeen human IFN subtypes in a 384-well plate format that incorporates highly specific locked nucleic acid (LNA) and molecular beacon (MB) probes, transcript standards, automated multichannel pipetting, and plate drying. Determining expression among the type I interferons (IFN), especially the twelve IFN-&#945; subtypes, is limited by their shared sequence identity; likewise, the sequences of the type III IFN, especially IFN-&#955;2 and -&#955;3, are highly similar. This assay provides a reliable, reproducible, and relatively inexpensive means to analyze the expression of the seventeen interferon subtype transcripts.

This protocol describes a high-throughput qRT-PCR assay for the analysis of type I and III IFN expression signatures. The assay discriminates single base pair differences between the highly similar transcripts of these genes. Through batch assembly and robotic pipetting, the assays are consistent and reproducible.

Described in this report is a qRT-PCR assay for the analysis of seventeen human IFN subtypes in a 384-well plate format that incorporates highly specific ...

Establishment of a High-throughput Setup for Screening Small Molecules That Modulate c-di-GMP Signaling in Pseudomonas aeruginosa

Bacterial resistance to traditional antibiotics has driven research attempts to identify new drug targets in recently discovered regulatory pathways. Regulatory systems that utilize intracellular cyclic di-GMP (c-di-GMP) as a second messenger are one such class of target. c-di-GMP is a signaling molecule found in almost all bacteria that acts to regulate an extensive range of processes including antibiotic resistance, biofilm formation and virulence. The understanding of how c-di-GMP signaling controls aspects of antibiotic resistant biofilm development has suggested approaches whereby alteration of the cellular concentrations of the nucleotide or disruption of these signaling pathways may lead to reduced biofilm formation or increased susceptibility of the biofilms to antibiotics. We describe a simple high-throughput bioreporter protocol, based on green fluorescent protein (GFP), whose expression is under the control of the c-di-GMP responsive promoter cdrA, to rapidly screen for small molecules with the potential to modulate c-di-GMP cellular levels in Pseudomonas aeruginosa (P. aeruginosa). This simple protocol can screen upwards of 3,500 compounds within 48 hours and has the ability to be adapted to multiple microorganisms.

Establishment of a High-throughput Setup for Screening Small Molecules That Modulate c-di-GMP Signaling in Pseudomonas aeruginosa

This article describes the high-throughput assay that has been successfully established to screen large libraries of small molecules for their potential ability to manipulate cellular levels of cyclic di-GMP in Pseudomonas aeruginosa, providing a new powerful tool for antibacterial drug discovery and compound testing.

Bacterial resistance to traditional antibiotics has driven research attempts to identify new drug targets in recently discovered regulatory pathways. ...

Cell-free Biochemical Fluorometric Enzymatic Assay for High-throughput Measurement of Lipid Peroxidation in High Density Lipoprotein

Low high-density lipoprotein cholesterol (HDL-C) levels are one of the most powerful independent negative predictors of atherosclerotic cardiovascular disease (CVD). The structure and function of HDL rather than HDL-C may more accurately predict atherosclerosis. Several HDL protein and lipid compositional changes that impair HDL function occur in inflammatory states such as atherosclerosis. HDL function is usually determined by cell based assays such as cholesterol efflux assay but these assays have numerous drawbacks lack of standardization. Cell-free assays may give more robust measures of HDL function compared to cell-based assays. HDL oxidation impairs HDL function. HDL has a major role in lipid peroxide transport and high amount of lipid peroxides is related to abnormal HDL function. Lipid-probe interactions should be considered when interpreting the results of non-enzymatic fluorescence assays for measuring the lipid oxidative state. This motivated us to develop a cell-free biochemical enzymatic method to assess HDL lipid peroxide content (HDLox) that contributes to HDL dysfunction. This method is based on the enzyme horseradish peroxidase (HRP) and the fluorochrome Amplex Red that can quantify (without cholesterol oxidase) the lipid peroxide content per mg of HDL-C. Here a protocol is describedfor determination of HDL-lipid peroxidation using the fluorochrome reagent. Assay variability can be reduced by strict standardization of experimental conditions. Higher HDLox values are associated with reduced HDL antioxidant function. The readout of this assay is associated with readouts of validated cell-based assays, surrogate measures of cardiovascular disease, systemic inflammation, immune dysfunction, and associated cardiovascular and metabolic risk phenotypes. This technical approach is a robust method to assess HDL function in human disease where systemic inflammation, oxidative stress and oxidized lipids have a key role (such as atherosclerosis).

We describe here a fluorometric cell-free biochemical assay for determination of HDL-lipid peroxidation. This rapid and reproducible assay can be used to determine HDL function in large scale studies and can contribute to our understanding of HDL function in human disease.

Low high-density lipoprotein cholesterol (HDL-C) levels are one of the most powerful independent negative predictors of atherosclerotic cardiovascular ...

A High-throughput Platform for the Screening of Salmonella spp./Shigella spp.

Fecal-oral transmission of acute gastroenteritis occurs from time to time, especially when people who handled food and water are infected by Salmonella spp./Shigella spp. The gold standard method for the detection of Salmonella spp./Shigella spp. is direct culture but this is labor-intensive and time-consuming. Here, we describe a high-throughput platform for Salmonella spp./Shigella spp. screening, using real-time polymerase chain reaction (PCR) combined with guided culture. There are two major stages: real-time PCR and the guided culture. For the first stage (real-time PCR), we explain each step of the method: sample collection, pre-enrichment, DNA extraction and real-time PCR. If the real-time PCR result is positive, then the second stage (guided culture) is performed: selective culture, biochemical identification and serological characterization. We also illustrate representative results generated from it. The protocol described here would be a valuable platform for the rapid, specific, sensitive and high-throughput screening of Salmonella spp./Shigella spp.

A High-throughput Platform for the Screening of Salmonella spp./Shigella spp.

Salmonella spp./Shigella spp. are common pathogens attributed to diarrhea. Here, we describe a high-throughput platform for the screening of Salmonella spp./Shigella spp. using real-time PCR combined with guided culture.

Fecal-oral transmission of acute gastroenteritis occurs from time to time, especially when people who handled food and water are infected by Salmonella ...

A High-throughput Assay to Assess and Quantify Neutrophil Extracellular Trap Formation

Neutrophil extracellular traps (NETs) are immunogenic extracellular DNA structures that can be released by neutrophils upon a wide variety of triggers. NETs have been demonstrated to serve as an important host defense mechanism that traps and kills microorganisms. On the other hand, they have been implicated in diverse systemic autoimmune diseases. NETs are immunogenic and toxic structures that contain a pool of relevant autoantigens including anti-neutrophil cytoplasmic antibodies (ANCA)-associated vasculitis (AAV) and systemic lupus erythematosus (SLE). Different forms of NETs can be induced depending on the stimulus. The amount of NETs can be quantified using different techniques including measuring DNA release in supernatants, measuring DNA-complexed with NET-molecules like myeloperoxidase (MPO) or neutrophil elastase (NE), measuring the presence of citrullinated histones by fluorescence microscopy, or flow cytometric detection of NET-components which all have different features regarding their specificity, sensitivity, objectivity, and quantity. Here is a protocol to quantify ex vivo NET formation in a highly-sensitive, high-throughput manner by using three-dimensional immunofluorescence confocal microscopy. This protocol can be applied to address various research questions about NET formation and degradation in health and disease.

This protocol describes a highly sensitive and high throughput neutrophil extracellular trap (NET) assay for the semi-automated quantification of ex vivo NET formation by immunofluorescence three-dimensional confocal microscopy. This protocol can be used to evaluate NET formation and degradation after different stimuli and can be used to study potential NET-targeted therapies.

Neutrophil extracellular traps (NETs) are immunogenic extracellular DNA structures that can be released by neutrophils upon a wide variety of triggers. ...

A High-throughput Shigella-specific Bactericidal Assay

Serum bactericidal assays (SBAs) measure the functional activity of antibodies and have been used for many decades. SBAs directly measure antibody killing activity by assessing the ability of antibodies in serum to bind to bacteria and activate complement. This complement activation results in the lysis and killing of the target bacteria. These assays are valuable because they go beyond quantifying antibody production to elucidate the biological functions that these antibodies have, allowing researchers to study the role that antibodies may play in preventing infection. SBAs have been used to study immune responses for many human pathogens, but there is no widely accepted methodology for Shigella at present. Historically, SBAs have been very labor-intensive, requiring many time-consuming steps to accurately quantify surviving bacteria. This protocol describes a simple, robust, and high-throughput assay that measures functional antibodies specific for Shigella in serum in vitro. The method described here offers many advantages over traditional SBAs, including the use of frozen bacterial stocks, 96 well assay plates, a micro-culture system, and automated colony-counting. All of these modifications make this assay less labor-intensive and more high-throughput. This protocol is simpler and faster to perform than traditional SBAs while still using simple technologies and readily available reagents. The protocol has been successfully applied in multiple independent laboratories and the assay is robust and reproducible. The assay can be used to assess immune responses in pre-clinical as well as clinical studies. Quantifying shigellacidal antibody titers both before and after antigen exposure (either by immunization or infection) allows for a broader understanding of how functional antibody responses are generated and their contribution to protective immunity. The development of this standardized, well-characterized assay may greatly facilitate Shigella vaccine design.

A High-throughput Shigella-specific Bactericidal Assay

Here we present a protocol to measure Shigellacidal activity of antibodies in serum. Serum is mixed with bacteria and exogenous complement, incubated, and the reaction mixture is plated on agar plates. Viable bacteria form colonies which are counted, using an automated colony enumerator, and used to determine the bactericidal titer.

Serum bactericidal assays (SBAs) measure the functional activity of antibodies and have been used for many decades. SBAs directly measure antibody killing ...

High-throughput Screening of Chemical Compounds to Elucidate Their Effects on Bacterial Persistence

Bacterial persisters are defined as a small subpopulation of phenotypic variants with the capability of tolerating high concentrations of antibiotics. They are an important health concern as they have been associated with recurrent chronic infections. Although stochastic and deterministic dynamics of stress-related mechanisms are known to play a significant role in persistence, mechanisms underlying the phenotypic switch to/from the persistence state are not completely understood. While persistence factors triggered by environmental signals (e.g., depletion of carbon, nitrogen and oxygen sources) have been extensively studied, the impacts of osmolytes on persistence are yet to be determined. Using microarrays (i.e., 96 well plates containing various chemicals), we have designed an approach to elucidate the effects of various osmolytes on Escherichia coli persistence in a high throughput manner. This approach is transformative as it can be readily adapted for other screening arrays, such as drug panels and gene knockout libraries.

In this method paper, we present a high-throughput screening strategy to identify chemical compounds, such as osmolytes, that have a significant impact on bacterial persistence.

Bacterial persisters are defined as a small subpopulation of phenotypic variants with the capability of tolerating high concentrations of antibiotics. ...