High Throughput, em tempo real, Teste Dual-leitura dos intracelular Actividade Antimicrobiana e citotoxicidade celular eucariótica

Summary

A high throughput, real-time assay was developed to simultaneously identify (1) eukaryotic cell-penetrant antimicrobials targeting an intracellular bacterial pathogen, and (2) assess eukaryotic cell cytotoxicity. A variation on the same technology was thereafter combined with digital dispensing technology to enable facile, high-resolution, dose-response, and two- and three-dimensional synergy studies.

Abstract

as medidas tradicionais de atividade antimicrobiana intracelular e citotoxicidade de célula eucariótica contar com ensaios de ponto de extremidade. Tais ensaios de ponto final requerem vários passos experimentais adicionais antes da leitura, tais como lise celular, a determinação da unidade de formação de colónias, ou adição de reagentes. Ao realizar milhares de ensaios, por exemplo, durante a triagem de alto rendimento, a jusante do esforço necessário para estes tipos de ensaios é considerável. Portanto, para facilitar a descoberta de alto rendimento antimicrobianos, foi desenvolvido um ensaio em tempo real simultaneamente para identificar inibidores de crescimento bacteriano intracelular e avaliar a citotoxicidade de células eucarióticas. Especificamente, a detecção de crescimento bacteriano intracelular em tempo real foi habilitado pela marcação estirpes bacterianas de triagem, quer com um operon bacteriano lux (1 ensaio de geração de ^st) ou repórteres de proteínas fluorescentes (de ^2ª geração, ensaio ortogonal). Um não-tóxico, célula de membrana-impermeabilizante, corante de ligação de ácido nucleicoTambém foi adicionado durante a infecção inicial de macrófagos. Estes corantes são excluídos a partir de células viáveis. No entanto, as células hospedeiras não viáveis ​​perder a integridade da membrana permitindo a entrada e marcação fluorescente de DNA nuclear (ácido desoxirribonucléico). Notavelmente, ADN de ligação está associado a um grande aumento no rendimento quântico fluorescente que fornece uma leitura à base de solução de morte da célula hospedeira. Temos utilizado este ensaio combinado para executar uma tela de alto rendimento em formato de microplacas, e para avaliar o crescimento intracelular e citotoxicidade por microscopia. Notavelmente, os agentes antimicrobianos podem demonstrar sinergia em que o efeito combinado de dois ou mais agentes antimicrobianos, quando aplicados em conjunto seja maior do que quando aplicados separadamente. Teste para sinergia in vitro contra patógenos intracelulares é normalmente uma tarefa prodigiosa como permutações combinatórias de antibióticos em diferentes concentrações, devem ser avaliados. No entanto, descobrimos que nosso ensaio em tempo real combinada com automatizada, dispensando tecnologia digital permitted testes sinergia fácil. Usando estas abordagens, que foram capazes de levantamento sistematicamente acção de um grande número de agentes antimicrobianos sozinho e em combinação contra o patogénio intracelular, Legionella pneumophila.

Introduction

Pathogens that grow or reside temporarily in intracellular compartments are difficult to therapeutically eradicate. Obligate or relatively obligate intracellular pathogens such as Legionella pneumophila, Coxiella burnetii, Brucella spp., Francisella tularensis, and Mycobacterium spp. often require prolonged courses of antimicrobial therapy for cure that may range from months to even years. Furthermore, extracellular pathogens may transiently occupy intracellular niches and in this way escape clearance by normal courses of antimicrobial therapy and later emerge to start new rounds of virulent infection. Staphylococcus aureus¹ and uropathogenic Enterobacteriaceae^2,3 infections are two increasingly recognized examples. Therefore, a fundamental drug discovery goal is to identify novel antimicrobials that penetrate into intracellular compartments. Optimal therapy to quickly eradicate intracellular organisms and prevent development of resistance through sub-inhibitory antimicrobial exposure is especially desirable.

To this end, we developed a high-throughput screening technology to identify intracellular-penetrant antimicrobials targeting the intracellular growth of the model pathogen, Legionella pneumophila.⁴ Previous clinical observations indicate that standard antimicrobial susceptibility testing did not accurately predict in vivo therapeutic efficacy against this organism.⁵ Specifically, this was because major classes of antimicrobials such as β-lactams and aminoglycosides, although highly effective against axenically grown Legionella, do not sufficiently penetrate into the intracellular compartments where Legionella resides.^5,6 Later evidence suggested that technically more complex intracellular growth assays effectively predicted clinical efficacy.⁷ Unfortunately, these assays were extremely laborious endpoints assays, requiring infected macrophages, treated with antimicrobials, to be lysed at different times points for colony forming unit enumeration. Such assays are impractical to do on a large scale and are unsuitable for high-throughput drug discovery.

Therefore, we developed technology for real-time determination of intracellular bacterial growth.⁶ This was accomplished through use of a bacterial strain modified through integration of either a bacterial luciferase operon⁸ (first generation assay, described previously)⁴ or fluorescent protein⁹ reporters (second generation, orthogonal assay, described here) into the bacterial chromosome. In this way, luminescent or fluorescent signal provides a surrogate, real-time readout of bacterial number.

However, these attributes do not address a major confounder in intracellular infection assays, off-target effects on host cells. In particular, the death of the host cell inherently limits intracellular growth and leads to false positive identification of antimicrobial effect. As many compounds in screening libraries are eukaryotic cell toxic, such false positives would overwhelm true antimicrobials, necessitating a large number of follow-up, endpoint cytotoxicity assays for resolution.

Thus, it was of great interest to be able to assess eukaryotic cell viability and intracellular growth simultaneously. Notably, a characteristic of non-viable eukaryotic cells is loss of cell membrane integrity. Probes that test the permeability of the cell membrane may therefore be used to assess cell viability. We previously characterized the ability of a series of putatively cell membrane-impermeant, fluorescent, DNA-binding dyes to access and stain nuclear DNA of dead cells.⁴ On binding nuclear DNA, these dyes display a large increase in quantum fluorescent yield resulting in increased signal over background solution fluorescence. As such, these dyes provided a quantitative readout of eukaryotic cell death.⁴ Notably, we found that several were non-toxic themselves during prolonged co-incubation with J774 macrophages. When added during initial infection, they provided a real-time, fluorescent readout of eukaryotic cell death that can be measured by a microplate fluorimeter or observed microscopically.

Therefore, by combining use of a bacterial reporter and non-toxic, membrane-impermeant, DNA-binding dyes, we were able to develop a simple, non-destructive, real-time assay to measure both bacterial load and eukaryotic cell cytotoxicity simultaneously. This assay has allowed us to screen in 384-well plate format ~10,000 known bioactives including ~250 antimicrobials and >240,000 small molecules with functionally uncharacterized activity for the ability to inhibit intracellular growth of Legionella pneumophila, while at the same time generating eukaryotic cell cytotoxicity data for each compound.⁶ Our analysis of known antimicrobials against intracellular growth of Legionella was the most comprehensive exploration of this type to date.⁶

Based on the efficiency of our assay format, we also subsequently explored the potentially synergistic effects of known antimicrobials when used in combination. One of the most common synergy tests, the so-called checkerboard assay, is standardly performed by assessing combinatorial effects of two-fold serial dilutions of two or more antimicrobials.¹⁰ In these assays, synergy is defined by the observation of greater effect when two or more antimicrobials are applied together than the sum of the effects of each applied separately. Of note, heretofore, only focused and selective synergy testing was performed against intracellular Legionella pneumophila because of the great effort involved in traditional endpoint assays multiplied by the combinatorial permutations required.

To facilitate synergy testing, we made use of our real-time intracellular growth/eukaryotic cytotoxicity assay in combination with automated digital dispensing technology⁶. This automation permitted us to dispense serial dilutions of compounds dissolved in DMSO or aqueous solution alone or in combination in 384-well format.¹¹ Furthermore, such robust liquid handling technology permitted us to easily perform higher resolution, square-root-of-two (rather than the standard, lower resolution, doubling) dilution combinations to achieve higher levels of specificity in our two-dimensional, checkerboard synergy analysis. This resolution was especially valuable in addressing concerns in the synergy field about reproducibility when using two-fold dilution series¹². Lastly, our assay was quantitative and also therefore measured gradations of inhibition. As a result, the assay captured the entirety of inhibitory information, expressible in isocontour isobolograms in which isocontours connect combinatorial concentrations with similar levels of growth inhibition.⁶ This plotting strategy allowed visualization of combinatorial dose-response curves. To illustrate our methodology, we describe our protocol for performing these assays and show representative results.

Protocol

1. Real Time Intracellular Growth and Eukaryotic Cell Cytotoxicity Assay Preparing Host Cells (J774A.1 Cells) Culture J774A.1 Mus musculus macrophage-like cells in suspension in RPMI 1640 with 9% iron-supplemented calf serum. Initially passage in tissue culture flasks. After cells have become confluent in a 75 cm2 tissue culture flask in 15 ml of medium, split by scraping and dilution to 65 ml with the same type of medium, of which 15 ml is returned to the tissue culture flask…

Representative Results

Microplate intracellular growth assay Figure 1 diagrams the assay steps. The automated steps shown can be performed manually. However, throughput is greatly facilitated using liquid handling systems. Figure 2 shows representative results from a 384-well microplate, dual-readout, real-time intracellular growth and eukaryotic cell cytoto…

Discussion

We describe real-time assays for simultaneous detection of intracellular bacterial growth and host cell cytotoxicity. There are several critical steps in the protocol. First, for robust assay performance, there must be sufficient spectral separation between bacterial and cytotoxicity readouts. Such separation is intrinsic for combinations of luciferase operon reporters and fluorescent DNA-binding dyes. However, based on our experience (Table 1-3, Figure 2), use of dual, fluorescent reado…

Materials

J774A.1 cells	American Type Culture Collection	TIB-67	Host cell
ACES	Sigma-Aldrich	A9758	For making buffered charcoal yeast extract agar and buffered yeast extract medium
Yeast extract, ultrafiltered	Becton-Dickinson/Difco	210929	For making buffered charcoal yeast extract agar and buffered yeast extract medium; lower grades may cause impaired growth and/or alter sensitivity of Legionella to growth inhibitors
Alpha-ketoglutaric acid, monopotassium salt	Sigma-Aldrich	K2000	For making buffered charcoal yeast extract agar and buffered yeast extract medium
Sodium pyruvate	Sigma-Aldrich	P5280	For making buffered charcoal yeast extract agar and buffered yeast extract medium
Potassium phosphate, dibasic	Thermo Fisher Scientific	P288-500	For making buffered charcoal yeast extract agar and buffered yeast extract medium
L-cysteine	Sigma-Aldrich	C-7755	For making buffered charcoal yeast extract agar and buffered yeast extract medium
Ammonium iron(III) citrate	Sigma-Aldrich	F5879	For making buffered charcoal yeast extract agar and buffered yeast extract medium; ferric pyrophosphate may be used instead but is more difficult to weigh accurately
Potassium hydroxide solution, concentrated	Thermo Fisher Scientific	SP236-500	For making buffered charcoal yeast extract agar and buffered yeast extract medium
Deonized water	N/A	N/A	For making buffered charcoal yeast extract agar and buffered yeast extract medium
Thymidine (tissue culture grade)	Sigma-Aldrich	T1895	For supplementing both RPMI 1640 and buffered yeast extract agar/medium — lower grade thymidine may be used for the latter, but may cause impaired cell growth and/or cell death in RPMI 1640
RPMI 1640, standard formulation	Corning via Thermo Fisher Scientific	10-040-CV	For growing J774A.1 cells prior to plating; includes 2 mM L-glutamine
RPMI 1640 lacking phenol red	Corning via Thermo Fisher Scientific	17-105-CV	For plating J774A.1 cells in 384 well dishes (not suitable for growth prior to plating); also lacks L-glutamine — supplement to 2 mM before use
L-glutamine, 200 mM in 0.85% NaCl (tissue culture grade)	HyClone via Thermo Fisher Scientific	SH30034.02	For supplementing RPMI 1640 lacking L-glutamine, to 2 mM final concentration
Iron-supplemented calf serum	Gemini Bioproducts	100-510	For supplementing RPMI 1640, to 9.1% final concentration
Trypan Blue solution	Sigma-Aldrich	T8154	For staining for J774A.1 cell death determination while counting cell density
SYTOX Green, 5 mM solution in DMSO	Thermo Fisher Scientific	S7020	For staining for J774A.1 cell death determination by fluorescence reading or epifluorescence microscopy (in conjunction with orange-red or far red fluorescent bacteria). Use at 125 nM final concentration.
GelRed, 10000X solution in water	Biotium	41003	For staining for J774A.1 cell death determination by epifluorescence microscopy (in conjunction with green fluorescent bacteria). Use Gel Red  at 1X final concentration.
Cell culture incubator	Thermo Fisher Scientific	13-255-26	For incubation of J774A.1 cells (both before and after infection); can also be used for incubation of bacteria, or a standard atmosphere incubator can be used instead)
Orbital shaker	BellCo Glass	7744-01010	For shaking incubation of J774A.1 cells before infection; fits inside cell culture incubator; includes shaker base 7744-01000 and tray 7740-01010 (these are also available separately)
Shaker flasks (250 ml)	ChemGlass Life Sciences	CLS-2038-04	For shaking incubation of J774A.1 cells before infection
Shaker clamps for flasks (250 ml)	BellCo Glass	7744-16250	For shaking incubation of J774A.1 cells before infection
Shaker flasks (1000 ml)	ChemGlass Life Sciences	CLS-2038-07	For shaking incubation of J774A.1 cells before infection
Shaker clamps for flasks (1000 ml)	BellCo Glass	7744-16100	For shaking incubation of J774A.1 cells before infection
Sponge foam caps for flasks (250 ml – 1000 ml)	ChemGlass Life Sciences	CLS-1490-038	For shaking incubation of J774A.1 cells before infection; reduces risk of contamination relative to standard metal caps
MultiDrop Combi programmable multichannel peristaltic pump	Thermo Fisher Scientific	5840300	For dispensing J774A.1 cells, medium, and bacterial suspension containing fluorophores to large numbers of 384 well dishes
Combi standard bore manifold	Thermo Fisher Scientific	24072670	Default predispense volume of 20 ml is insufficient to compensate for settling — increase to 80 ml
White 384 well dishes treated for tissue culture	Corning	3570	For reading luminescence and fluorescence; Greiner catalog # 781080 also tested successfully
DMSO (tissue culture grade, in sealed ampoules)	Sigma-Aldrich	D2650	For dissolving positive control and test compounds
Azithromycin	Sigma-Aldrich	PHR1088	Antibiotic positive control
Saponin (from Quillaja bark)	Sigma-Aldrich	S-4521	Cytoxicity positive control
Multichannel pipettor	Thermo Fisher Scientific	Finnpipette	For transfer of fixed amounts of positive control compounds; pipettor must have digital dispensing with detents to enable repetitive fixed volume dispensing
Epson pin transfer robot	Epson/ICCB-L	(Custom equipment)	For transfer of fixed amounts of test compounds from library arrays
D300 digital dispensing system	Hewlett-Packard via Tecan	D300	For transfer of variable amounts of test compounds ranging from 11 picoliters to 10 microliters
T8+ cartridges for D300 digital dispensing system	Hewlett-Packard via Tecan	T8+	For dispensing test compounds
EnVision multi-mode plate reader	Perkin-Elmer	(Contact manufacturer)	For optimal detection of SYTOX Green fluorescence, use excitation filter 485/14, emission filter 535/25, and dichroic mirror 505 nm, with selection of minimum gain and transmittance, and “high concentration mode. For luminescence detection, use the "USLUM" protocol for high-sensitivity detection. For mNeptune2 detection, use excitation filter 600/8, emission filter 665/7.5, and dichroic mirror 658 nm, with selection of gain and transmittance to achieve the highest maximum signal possible without saturating the photomultiplier.
Epifluorescence microscope with computer-connected digital camera	Nikon	Ti	For live cell imaging; any standard fluorescent microscope can substitute, with phase contrast or DIC optics, capable of imaging green (fluorescein), orange-red to red (Texas Red), and far-red (Cy5) fluorescence, with 100X oil objective for highest resolution
Glass-bottom tissue culture dishes	MatTek Corporation	P35G-1.5-20-C	For live cell imaging. Dishes such as the MatTek allow microscopic visualization at 600X or 1000X magnification through use of an inverted epifluorescent or confocal microscope.  These specific dishes are 3.5 cm nominal diameter, 3.3 cm inside diameter, with 20 mm diameter #1.5 thickness cover slips inserted into the bottoms.
Photoshop CS6	Adobe		Adobe photoshop or similar programs can be used to pseudocolor and merge light microscopic and fluorescent images.
Mathematica 10	Wolfam		For generation of two-dimensioonal isocontour isobolograms and three-dimensional surface isobolograms.