Multiparametric cell cycle analysis by automated microscopy

Cell cycle analysis using flow cytometry (FC) to measure cellular DNA content is a common procedure in drug mechanism of action studies. Although this technique lends itself readily to cell lines that grow in suspension, adherent cell cultures must be resuspended in a cumbersome and potentially invasive procedure that normally involves trypsinization and mechanical agitation of monolayer cultures. High-content analysis (HCA), an automated microscopy-based technology, is well suited to analysis of monolayer cell cultures but provides intrinsically less accurate determination of cellular DNA content than does FC and thus is not the method of choice for cell cycle analysis. Using Cellomics's ArrayScan reader, the authors have developed a 4-color multiparametric HCA approach for cell cycle analysis of adherent cells based on detection of DNA content (4,6-diamidino-2-phenylindole [DAPI] fluorescence), together with the known cell cycle markers bromo-2-deoxyuridine (BrdU) incorporation, cyclin B1 expression, and histone H3 (Ser28) phosphorylation within a single cell population. Considering all 4 markers together, a reliable and accurate quantification of cell cycle phases was possible, as compared with flow cytometric analysis. Using this assay, specific cell cycle blocks induced by treatment with thymidine, paclitaxel, or nocodazole as test drugs were easily monitored in adherent cultures of U-2 OS osteosarcoma cells.     

High-content analysis of proapoptotic EphA4 dependence receptor functions using small-molecule libraries

Small-molecule compounds (SMCs) can provide an inexpensive and selective approach to modifying biological responses. High-content analysis (HCA) of SMC libraries can help identify candidate molecules that inhibit or activate cellular responses. In particular, regulation of cell death has important implications for many pathological conditions. Dependence receptors are a new classification of proapoptotic membrane receptors that, unlike classic death receptors, initiate apoptotic signals in the absence of their ligands. EphA4 has recently been identified as a dependence receptor that may have important functions in conditions as disparate as cancer biology and CNS injury and disease. To screen potential candidate SMCs that inhibit or activate EphA4-induced cell death, HCA of an SMC library was performed using stable EphA4-expressing NIH 3T3 cells. Our results describe a high-content method for screening dependence receptor-signaling pathways and demonstrate that several candidate SMCs can inhibit EphA4-mediated cell death.     

High-content screening in infectious diseases

The last decade has seen the development of automated microscopy and its adaptation for various areas of research, particularly infectious disease. Most of the high-content screening (HCS) platforms now integrate all of the following necessary steps: automated pipettes for assay miniaturization in 384-well plates, automated image acquisition and data storage and analysis. HCS was initially associated with RNA interference genetic screens for identifying host factors involved in host-pathogen interactions. More recently, both in academia and in industry, HCS has been adapted for drug discovery purposes. High-content analysis enables intracellular tracking of viral particles to profile the antiviral mechanisms of each compound. Adaptation to high-throughput screening in bacteriology and parasitology has already led to the discovery of new types of host-specific inhibitors that differ from those inhibitors that act directly on microbes.     

High content analysis to determine cytotoxicity of the antimicrobial peptide, melittin and selected structural analogs

Antimicrobial peptides (AMPs) are naturally occurring entities with potential as pharmaceutical candidates and/or food additives. They are present in many organisms including bacteria, insects, fish and mammals. While their antimicrobial activity is equipotent with many commercial antibiotics, current limitations are poor pharmacokinetics, stability and potential toxicology issues. Most elicit antimicrobial action via perturbation of bacterial membranes. Consequently, associated cytotoxicity in human cells is reflected by their capacity to lyse erythrocytes. However, more rigorous toxicological assessment of AMPs is required in order to predict potential failure at a later stage of development. We describe a high-content analysis (HCA) screening protocol recently established for determination and prediction of safety in pharmaceutical drug discovery. HCA is a powerful, multi-parameter bioanalytical tool that amalgamates the actions of fluorescence microscopy with automated cell analysis software in order to understand multiple changes in cellular health. We describe the application of HCA in assessing cytotoxicity of the cytolytic α-helical peptide, melittin, and selected structural analogs. The data shows that structural modification of melittin reduces its cytotoxic action and that HCA is suitable for rapidly identifying cytotoxicity.     

Quantitative analysis of cellular senescence phenotypes using an imaging cytometer

Until now, various stimuli as well as serial passaging have been known to induce cellular senescence in normal human diploid fibroblasts. However, in many cases, we have encountered difficulty in quantitatively analyzing the cellular senescence phenotypes of senescent cells in a physiological condition. High-content screening (HCS)-based image analysis is becoming an important and powerful research tool. In the present study, an automated and quantitative cellular image-analysis system was employed to quantify the cellular senescence phenotypes induced in normal human diploid fibroblasts, TIG-1 cells, and found to be a powerful tool in the cellular senescence study.     

PCaAnalyser: A 2D-Image Analysis Based Module for Effective Determination of Prostate Cancer Progression in 3D Culture

Three-dimensional (3D) in vitro cell based assays for Prostate Cancer (PCa) research are rapidly becoming the preferred alternative to that of conventional 2D monolayer cultures. 3D assays more precisely mimic the microenvironment found in vivo, and thus are ideally suited to evaluate compounds and their suitability for progression in the drug discovery pipeline. To achieve the desired high throughput needed for most screening programs, automated quantification of 3D cultures is required. Towards this end, this paper reports on the development of a prototype analysis module for an automated high-content-analysis (HCA) system, which allows for accurate and fast investigation of in vitro 3D cell culture models for PCa. The Java based program, which we have named PCaAnalyser, uses novel algorithms that allow accurate and rapid quantitation of protein expression in 3D cell culture. As currently configured, the PCaAnalyser can quantify a range of biological parameters including: nuclei-count, nuclei-spheroid membership prediction, various function based classification of peripheral and non-peripheral areas to measure expression of biomarkers and protein constituents known to be associated with PCa progression, as well as defining segregate cellular-objects effectively for a range of signal-to-noise ratios. In addition, PCaAnalyser architecture is highly flexible, operating as a single independent analysis, as well as in batch mode; essential for High-Throughput-Screening (HTS). Utilising the PCaAnalyser, accurate and rapid analysis in an automated high throughput manner is provided, and reproducible analysis of the distribution and intensity of well-established markers associated with PCa progression in a range of metastatic PCa cell-lines (DU145 and PC3) in a 3D model demonstrated.     

Effect of Fenton reagent shock and recovery periods on anaerobic microbial community structure and degradation of chlorinated aliphatics

This study investigates the effect of Fenton reagent on the structure and function of a microbial consortium during the anaerobic degradation of hexachloroethane (HCA) and tetrachloroethene (PCE). Anaerobic biodegradation tests of HCA and PCE were performed in batch reactors using an anaerobic microbial consortium that had been exposed to Fenton reagent for durations of 0, 0.04, and 2 days and then allowed to recover for periods of 0, 3, and 7 days. The bacterial community structure was determined using culture-independent methods of 16S rRNA gene sequencing and automated ribosomal intergenic spacer analysis. Larger recovery periods partially restored the microbial community structure; however, the recovery periods did not restore the loss of ability to degrade HCA and PCE in cultures shocked for 0.04 days, and PCE in cultures shocked for 2 days. Overall the exposure to Fenton reagent had an impact on bacterial community structure with downstream effects on HCA and PCE degradation. This study highlights that the impacts of short- and long-term shocks on microbial community structure and function can be correlated using a combination of biodegradation tests and community structure analysis tools.     

High-content imaging of human hepatic spheroids for researching the mechanism of duloxetine-induced hepatotoxicity

Duloxetine (DLX) has been approved for the successful treatment of psychiatric diseases, including major depressive disorder, diabetic neuropathy, fibromyalgia and generalized anxiety disorder. However, since the usage of DLX carries a manufacturer warning of hepatotoxicity given its implication in numerous cases of drug-induced liver injuries (DILI), it is not recommended for patients with chronic liver diseases. In our previous study, we developed an enhanced human-simulated hepatic spheroid (EHS) imaging model system for performing drug hepatotoxicity evaluation using the human hepatoma cell line HepaRG and the support of a pulverized liver biomatrix scaffold, which demonstrated much improved hepatic-specific functions. In the current study, we were able to use this robust model to demonstrate that the DLX-DILI is a human CYP450 specific, metabolism-dependent, oxidative stress triggered complex hepatic injury. High-content imaging analysis (HCA) of organoids exposed to DLX showed that the potential toxicophore, naphthyl ring in DLX initiated oxidative stress which ultimately led to mitochondrial dysfunction in the hepatic organoids, and vice versa. Furthermore, DLX-induced hepatic steatosis and cholestasis was also detected in the exposed EHSs. We also discovered that a novel compound S-071031B, which replaced DLX’s naphthyl ring with benzodioxole, showed dramatically lower hepatotoxicities through reducing oxidative stress. Thus, we conclusively present the human-relevant EHS model as an ideal, highly competent system for evaluating DLX induced hepatotoxicity and exploring related mechanisms in vitro. Moreover, HCA use on functional hepatic organoids has promising application prospects for guiding compound structural modifications and optimization in order to improve drug development by reducing hepatotoxicity.Subject terms: Drug safety, Translational research, Toxicology     

High curvature and jerk analyses of arm ataxia

We investigated high curvature analysis (HCA) and integrated absolute jerk (IAJ) for differentiating healthy and cerebellopathy (CB) patients performing pointing tasks. Seventeen CB patients and seventeen healthy controls were required to move a pointer at their preferred pace between two 50.8 cm laterally spaced targets while standing with their arm extended in front of their body. HCA was used to quantify the frequency of sharp turns in the horizontal-plane (anterior-posterior and medio-lateral) velocity trajectory of the hand-held pointer. IAJ was assessed by integration of absolute jerk (second time derivative of velocity) time histories in the anterior-posterior and medio-lateral directions. HCA scores and IAJ scores were then compared between CB patients and healthy controls; for both analyses, higher scores indicate less smooth movements. We hypothesized that CB patients would have less smooth movement trajectories than healthy controls due to upper extremity ataxia associated with cerebellar disease and degeneration. We found that CB patients had higher HCA scores than healthy controls (P = 0.014). Although CB patients had higher IAJ scores in both anterior-posterior (P = 0.060) and medio-lateral (P = 0.231) directions compared to the healthy controls, the differences were not significant. The difference in sensitivity between the HCA and the IAJ analysis might be explained by primitive neural activation commands, ubiquitous though only evident with some cerebellar dysfunctions, which produce sub-movements which are themselves minimal jerk curves. We conclude that HCA may be a useful tool for quantifying upper extremity ataxia in CB patients performing a repeated pointing task. Received: 17 December 1999 / Accepted in revised form: 7 July 2000     

Induction of aquaporin-1 mRNA following cardiopulmonary bypass and reperfusion.

BACKGROUND: Cardiopulmonary bypass (CPB) and hypothermic circulatory arrest (HCA) are important components of congenital cardiac surgery. Ischemia/reperfusion injury and inflammatory cascade activation result in endothelial damage and vascular leak which are clinically manifested as pulmonary edema and low cardiac output postoperatively. Newborns are particularly susceptible. Subtraction cloning is a useful method of isolating induced genes and can be applied to CPB/HCA. MATERIALS AND METHODS: We used a newborn lamb model replicating infant CPB with HCA to obtain tissues during various periods of reperfusion. We utilized subtraction cloning to identify mRNA induced in lung following CPB/HCA and reperfusion. Ribonuclease protection was used to quantify mRNA levels. RESULTS: We isolated a cDNA encoding ovine aquaporin-1 in a subtracted cDNA screen comparing control lung with lung exposed to CPB/HCA and reperfusion. Aquaporin-1 mRNA levels increased 3-fold in lung (p = .006) exposed to CPB/HCA and 6 hr of reperfusion. No induction was observed immediately following bypass or after 3 hr of reperfusion. We found no significant induction of aquaporin-1 mRNA following bypass, arrest, and reperfusion in other tissues surveyed, including ventricle, atrium, skeletal muscle, kidney, brain, and liver. CONCLUSIONS: Our finding that aquaporin-1 mRNA is reproducibly induced in lung following CPB/HCA with 6 hr of reperfusion suggests an important role for the water channel in the setting of pulmonary edema. Induction of Aquaporin-1 is late compared with other inflammatory mediators (ICAM-1, E-selectin, IL-8). Further studies are needed to determine if aquaporin-1 contributes to the disease process or if it is part of the recovery phase.     

A support vector machine classifier for recognizing mitotic subphases using high-content screening data

High-content screening studies of mitotic checkpoints are important for identifying cancer targets and developing novel cancer-specific therapies. A crucial step in such a study is to determine the stage of cell cycle. Due to the overwhelming number of cells assayed in a high-content screening experiment and the multiple factors that need to be taken into consideration for accurate determination of mitotic subphases, an automated classifier is necessary. In this article, the authors describe in detail a support vector machine (SVM) classifier that they have implemented to recognize various mitotic subphases. In contrast to previous studies to recognize subcellular patterns, they used only low-resolution cell images and a few parameters that can be calculated inexpensively with off-the-shelf image-processing software. The performance of the SVM was evaluated with a cross-validation method and was shown to be comparable to that of a human expert.     

Automated fluorescence lifetime imaging plate reader and its application to Förster resonant energy transfer readout of Gag protein aggregation

Fluorescence lifetime measurements can provide quantitative readouts of local fluorophore environment and can be applied to biomolecular interactions via Förster resonant energy transfer (FRET). Fluorescence lifetime imaging (FLIM) can therefore provide a high content analysis (HCA) modality to map protein‐protein interactions (PPIs) with applications in drug discovery, systems biology and basic research. We present here an automated multiwell plate reader able to perform rapid unsupervised optically sectioned FLIM of fixed and live biological samples and illustrate its potential to assay PPIs through application to Gag protein aggregation during the HIV life cycle. We demonstrate both hetero‐FRET and homo‐FRET readouts of protein aggregation and report the first quantitative evaluation of a FLIM HCA assay by generating dose response curves through addition of an inhibitor of Gag myristoylation. Z ′ factors exceeding 0.6 are realised for this FLIM FRET assay. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Hydrophobic cluster analysis: procedures to derive structural and functional information from 2-D-representation of protein sequences

Hydrophobic cluster analysis (HCA) [15] is a very efficient method to analyse and compare protein sequences. Despite its effectiveness, this method is not widely used because it relies in part on the experience and training of the user. In this article, detailed guidelines as to the use of HCA are presented and include discussions on: the definition of the hydrophobic clusters and their relationships with secondary and tertiary structures; the length of the clusters; the amino acid classification used for HCA; the HCA plot programs; and the working strategies. Various procedures for the analysis of a single sequence are presented: structural segmentation, structural domains and secondary structure evaluation. Like most sequence analysis methods, HCA is more efficient when several homologous sequences are compared. Procedures for the detection and alignment of distantly related proteins by HCA are described through several published examples along with 2 previously unreported cases: the beta-glucosidase from Ruminococcus albus is clearly related to the beta-glucosidases from Clostridum thermocellum and Hansenula anomala although they display a reverse organization of their constitutive domains; the alignment of the sequence of human GTPase activating protein with that of the Crk oncogene is presented. Finally, the pertinence of HCA in the identification of important residues for structure/function as well as in the preparation of homology modelling is discussed.     

Improved Visualization and Quantitative Analysis of Drug Effects Using Micropatterned Cells

To date, most HCA (High Content Analysis) studies are carried out with adherent cell lines grown on a homogenous substrate in tissue-culture treated micro-plates. Under these conditions, cells spread and divide in all directions resulting in an inherent variability in cell shape, morphology and behavior. The high cell-to-cell variance of the overall population impedes the success of HCA, especially for drug development. The ability of micropatterns to normalize the shape and internal polarity of every individual cell provides a tremendous opportunity for solving this critical bottleneck ^1-2.To facilitate access and use of the micropatterning technology, CYTOO has developed a range of ready to use micropatterns, available in coverslip and microwell formats. In this video article, we provide detailed protocols of all the procedures from cell seeding on CYTOOchip micropatterns, drug treatment, fixation and staining to automated acquisition, automated image processing and final data analysis. With this example, we illustrate how micropatterns can facilitate cell-based assays. Alterations of the cell cytoskeleton are difficult to quantify in cells cultured on homogenous substrates, but culturing cells on micropatterns results in a reproducible organization of the actin meshwork due to systematic positioning of the cell adhesion contacts in every cell. Such normalization of the intracellular architecture allows quantification of even small effects on the actin cytoskeleton as demonstrated in these set of protocols using blebbistatin, an inhibitor of the actin-myosin interaction.Download video file.^{(98M, mov)}     

Production of hydroxycitric acid by microorganisms

Hydroxycitric acid (HCA) is a major acid component of the tropical plants Garcinia cambogia and Hibiscus subdariffa. (2S,3S)-HCA from G. cambogia was shown to be a potent inhibitor of ATP citrate lyase (EC4.1.3.8), which catalyzes the extramitochondrial cleavage of citrate to oxaloacetate and acetyl-CoA. (2S,3R)-HCA from H. subdariffa inhibits alpha-amylase and alpha-glucosidase, leading to reduction of carbohydrate metabolism. The availability of HCA is limited by the restricted habitat of the plants as well as the difficulty of stereoselective organic synthesis. Hence, we screened microorganisms producing HCA to find an alternative source of optically pure bulk HCA. Two strains, Streptomyces sp. U121 and Bacillus megaterium G45C, were screened by HPLC analysis. Particular metabolites were purified from their culture broths and compared with authentic HCA from plants. NMR studies indicated that the products are identical to Hibiscus-type HCA. This is the first report showing isolation of microorganisms producing HCA.     

GroEL-induced topological dislocation of a substrate protein β-sheet core: a solution EPR spin–spin distance study

The Hsp60-type chaperonin GroEL assists in the folding of the enzyme human carbonic anhydrase II (HCA II) and protects it from aggregation. This study was aimed to monitor conformational rearrangement of the substrate protein during the initial GroEL capture (in the absence of ATP) of the thermally unfolded HCA II molten-globule. Single- and double-cysteine mutants were specifically spin-labeled at a topological breakpoint in the β-sheet rich core of HCA II, where the dominating antiparallel β-sheet is broken and β-strands 6 and 7 are parallel. Electron paramagnetic resonance (EPR) was used to monitor the GroEL-induced structural changes in this region of HCA II during thermal denaturation. Both qualitative analysis of the EPR spectra and refined inter-residue distance calculations based on magnetic dipolar interaction show that the spin-labeled positions F147C and K213C are in proximity in the native state of HCA II at 20 °C (as close as ～8 Å), and that this local structure is virtually intact in the thermally induced molten-globule state that binds to GroEL. In the absence of GroEL, the molten globule of HCA II irreversibly aggregates. In contrast, a substantial increase in spin–spin distance (up to >20 Å) was observed within minutes, upon interaction with GroEL (at 50 and 60 °C), which demonstrates a GroEL-induced conformational change in HCA II. The GroEL binding-induced disentanglement of the substrate protein core at the topological break-point is likely a key event for rearrangement of this potent aggregation initiation site, and hence, this conformational change averts HCA II misfolding.     

Pharmacological profiling of chemokine receptor-directed compounds using high-content screening

High-content screening, typically defined as automated fluorescence microscopy combined with image analysis, is now well established as a means to study test compound effects in cellular disease-modeling systems. In this work, the authors establish several high-content screening assays in the 384-well format to measure the activation of the CC-type chemokine receptors 2B and 3 (CCR2B, CCR3). As a cellular model system, the authors use Chinese hamster ovary cells, stably transfected with 1 of the respective receptors. They characterize receptor stimulation by human monocyte chemoattractant protein-1 for CCR2B and by human eotaxin-1 for CCR3: Receptor internalization and receptor-induced phosphorylation of ERK1/2 (pERK) were quantified using fluorescence imaging and image analysis. The 4 assay formats were robust, displayed little day-to-day variability, and delivered good Z' statistics for both CCRs. For each of the 2 receptors, the authors evaluated the potency of inhibitory compounds in the internalization format and the pERK assay and compared the results with those from other assays (ligand displacement binding, Ca(2+) mobilization, guanosine triphosphate exchange, chemotaxis). Both physiological agonists and test compounds differed significantly with respect to potencies and efficacies in the various profiling assays. The diverse assay formats delivered partially overlapping and partially complementary information, enabling the authors to reduce the probability of test compound-related technology artifacts and to specify the mode of action for individual test compounds. Transfer of the high-content screening format to a fully automated medium-throughput screening platform for CCR3 enabled the profiling of large compound numbers with respect to G protein signaling and possible tolerance-inducing liabilities.     

新型肝癌相关性抗原HCA519及其变异体HCA90的基因克隆和表达

通过利用肝癌病人体内血清中所含的对肿瘤抗原产生的特异性抗体筛选肝癌组织cDNA表达文库的方法 (SEREX) ,筛选得到了可以诱导肝癌病人抗体免疫应答的两个新抗原HCA5 19基因(GenBankAF14 6 731)及其变异体HCA90基因 (GenBankAF 2 872 6 5 ) .它们定位于染色体 2 0q11 2 ,HCA5 19含 18个外显子 ,HCA90含 19个外显子 .其中HCA90所特有的外显子序列长 10 8bp ,属Alu重复序列片段 ,插入于HCA5 19外显子 10和 11之间 ,原为HCA5 19内含子序列 .该插入片段位于HCA5 19开放阅读框架之内 ,不改变HCA5 19的读码框 ,使HCA5 19编码的 74 7个氨基酸增长至HCA90的 783个氨基酸 .通过Northern杂交和RT PCR分析发现 ,HCA5 19和HCA90基因分别在 9 9例和 6 9例肝癌组织中高表达 ,RT PCR显示 ,它们在正常肝组织和其它正常组织中有极低水平转录本表达 .而这种低表达转录本在Northern杂交中不能被检测到 .HCA5 19蛋白被首次发现在肿瘤病人中能够诱导机体的抗体免疫应答 ,为一个新的肿瘤相关性抗原分子 .其变异体HCA90抗原基因为首次发现的新基因 .其功能可能与细胞的恶性增殖相关 ,并可进一步研究其作为临床肿瘤治疗和诊断的靶分子的可行性