Automated Flow Cytometry Research Articles

BayesFlow: latent modeling of flow cytometry cell populations.

BackgroundFlow cytometry is a widespread single-cell measurement technology with a multitude of clinical and research applications. Interpretation of flow cytometry data is hard; the instrumentation is delicate and can not render absolute measurements, hence samples can only be interpreted in relation to each other while at the same time comparisons are confounded by inter-sample variation. Despite this, most automated flow cytometry data analysis methods either treat samples individually or ignore the variation by for example pooling the data. A key requirement for models that include multiple samples is the ability to visualize and assess inferred variation, since what could be technical variation in one setting would be different phenotypes in another.ResultsWe introduce BayesFlow, a pipeline for latent modeling of flow cytometry cell populations built upon a Bayesian hierarchical model. The model systematizes variation in location as well as shape. Expert knowledge can be incorporated through informative priors and the results can be supervised through compact and comprehensive visualizations.BayesFlow is applied to two synthetic and two real flow cytometry data sets. For the first real data set, taken from the FlowCAP I challenge, BayesFlow does not only give a gating which would place it among the top performers in FlowCAP I for this dataset, it also gives a more consistent treatment of different samples than either manual gating or other automated gating methods. The second real data set contains replicated flow cytometry measurements of samples from healthy individuals. BayesFlow gives here cell populations with clear expression patterns and small technical intra-donor variation as compared to biological inter-donor variation.ConclusionsModeling latent relations between samples through BayesFlow enables a systematic analysis of inter-sample variation. As opposed to other joint gating methods, effort is put at ensuring that the obtained partition of the data corresponds to actual cell populations, and the result is therefore directly biologically interpretable. BayesFlow is freely available at GitHub.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0862-z) contains supplementary material, which is available to authorized users.

Condition-specific genetic interaction maps reveal crosstalk between the cAMP/PKA and the HOG MAPK pathways in the activation of the general stress response.

Cells must quickly respond and efficiently adapt to environmental changes. The yeast Saccharomyces cerevisiae has multiple pathways that respond to specific environmental insults, as well as a generic stress response program. The later is regulated by two transcription factors, Msn2 and Msn4, that integrate information from upstream pathways to produce fast, tunable, and robust response to different environmental changes. To understand this integration, we employed a systematic approach to genetically dissect the contribution of various cellular pathways to Msn2/4 regulation under a range of stress and growth conditions. We established a high-throughput liquid handling and automated flow cytometry system and measured GFP levels in 68 single-knockout and 1,566 double-knockout strains that carry an HSP12-GFP allele as a reporter for Msn2/4 activity. Based on the expression of this Msn2/4 reporter in five different conditions, we identified numerous genetic and epistatic interactions between different components in the network upstream to Msn2/4. Our analysis gains new insights into the functional specialization of the RAS paralogs in the repression of stress response and identifies a three-way crosstalk between the Mediator complex, the HOG MAPK pathway, and the cAMP/PKA pathway.

Rapid and automated flow cytometry crossmatch for optimizing inter-assay and inter-operator consistency

Background Flow cytometry crossmatch (FCXM) is a high sensitive tool to identify donor cell specific antibodies in recipient’s serum. However, the procedure is time consuming and fraught with inter-assay and inter-operator variabilities. Aim To optimize instrumentation for automated tagging (AT) in FCXM that will both quicken the procedure and exclude inter-operator variability. Methods Serum, spleen, or peripheral blood mononuclear cells were isolated from human subjects. AT was performed using a combination of Precision-XS and EL406 instruments (BioTek Instruments, Inc.) and compared to manual tagging (MT) (both in 96 well plates). FITC-goat α-human IgG channel shift (CS) of >40 for T cells and >50 for B cells was considered positive. Results AT of two cell specimens took 90 min vs. 100 min by MT. AT did not cause cell loss. Automated Tagging vs. Manual Tagging: AT and MT of specimens (N = 6) provided similar CS results (T cell-(P = 0.8) and B cell-FCXM (P = 0.9); (Fig 1A)) and median channel intensity results for T cell FCXM (%CV: negative control (NC) = 8 vs. 11; positive control (PC) = 10 vs. 14) and B cell FCXM (%CV: NC = 6 vs. 17; PC = 10 vs. 9). Intra-assay variability: When AT was performed in duplicates in a plate (N = 3), no intra-assay variability was noted in CS results (T cell FCXM: P = 0.1; B cell FCXM: P = 0.1 (Fig 1B)) or in median channel intensity results [T cell FCXM (%CV: NC = 1 vs. 5; PC = 4 vs. 2) and B cell FCXM (%CV: NC = 2 vs. 1; PC = 5 vs. 4).] Inter-assay variability: When AT was performed in two different plates (N = 3), no inter-assay variability was noted in CS results (T cell FCXM: P = 0.8; B cell FCXM: P = 0.9 (Fig 1C)) or in median channel intensity results [T cell FCXM (%CV: NC = 8; and PC = 6) and B cell FCXM (%CV: NC = 11; PC = 5)]. Inter-operator variability: Inter-operator variability was not noted when FCXM were performed by AT (Fig 1D). Conclusions Combination of Precision-XS- and EL406-instruments helps making a FCXM faster and automatous, and provides reliable results with inter-assay and inter-operator consistency. Download : Download full-size image

An Introduction to Automated Flow Cytometry Gating Tools and Their Implementation.

Current flow cytometry (FCM) reagents and instrumentation allow for the measurement of an unprecedented number of parameters for any given cell within a homogenous or heterogeneous population. While this provides a great deal of power for hypothesis testing, it also generates a vast amount of data, which is typically analyzed manually through a processing called “gating.” For large experiments, such as high-content screens, in which many parameters are measured, the time required for manual analysis as well as the technical variability inherent to manual gating can increase dramatically, even becoming prohibitive depending on the clinical or research goal. In the following article, we aim to provide the reader an overview of automated FCM analysis as well as an example of the implementation of FLOw Clustering without K, a tool that we consider accessible to researchers of all levels of computational expertise. In most cases, computational assistance methods are more reproducible and much faster than manual gating, and for some, also allow for the discovery of cellular populations that might not be expected or evident to the researcher. We urge any researcher who is planning or has previously performed large FCM experiments to consider implementing computational assistance into their analysis pipeline.

High-resolution analysis of a North Sea phytoplankton community structure based on in situ flow cytometry observations and potential implication for remote sensing

Abstract. Phytoplankton observation in the ocean can be a challenge in oceanography. Accurate estimations of its biomass and dynamics will help to understand ocean ecosystems and refine global climate models. Relevant data sets of phytoplankton defined at a functional level and on a sub-meso- and daily scale are thus required. In order to achieve this, an automated, high-frequency, dedicated scanning flow cytometer (SFC, Cytobuoy b.v., the Netherlands) has been developed to cover the entire size range of phytoplankton cells whilst simultaneously taking pictures of the largest of them. This cytometer was directly connected to the water inlet of a PocketFerryBox during a cruise in the North Sea, 08–12 May 2011 (DYMAPHY project, INTERREG IV A "2 Seas"), in order to identify the phytoplankton community structure of near surface waters (6 m) with a high spatial resolution basis (2.2 ± 1.8 km). Ten groups of cells, distinguished on the basis of their optical pulse shapes, were described (abundance, size estimate, red fluorescence per unit volume). Abundances varied depending on the hydrological status of the traversed waters, reflecting different stages of the North Sea blooming period. Comparisons between several techniques analysing chlorophyll a and the scanning flow cytometer, using the integrated red fluorescence emitted by each counted cell, showed significant correlations. For the first time, the community structure observed from the automated flow cytometry data set was compared with PHYSAT reflectance anomalies over a daily scale. The number of matchups observed between the SFC automated high-frequency in situ sampling and remote sensing was found to be more than 2 times better than when using traditional water sampling strategies. Significant differences in the phytoplankton community structure within the 2 days for which matchups were available suggest that it is possible to label PHYSAT anomalies using automated flow cytometry to resolve not only dominant groups but also community structure.

Brain-derived circulating endothelial cells in peripheral blood of newborn infants with seizures: a potential biomarker for cerebrovascular injury.

Neonatal seizures have been associated with cerebrovascular endothelial injury and neurological disabilities. In a piglet model, the long-term loss of endothelial regulation of cerebral blood flow coincides with the surge of brain-derived circulating endothelial cells (BCECs) in blood. We hypothesized that BCECs could serve as a noninvasive biomarker of cerebrovascular injury in neonates with seizures. In a prospective pilot feasibility study, we enrolled newborn infants with confirmed diagnoses of perinatal asphyxia and intraventricular hemorrhage (IVH); both are commonly associated with seizures. Infants without clinical evidence of cerebrovascular injuries were representative of the control group. BCECs were detected in the CD45-negative fraction of peripheral blood mononuclear cells by coexpression of CD31 (common endothelial antigen) and GLUT1 (blood-brain barrier antigen) via automated flow cytometry method. In Infants with asphyxia (n = 12) and those with IVH grade III/IV (n = 5), the BCEC levels were 9.9 ± 0.9% and 19.0 ± 2.0%, respectively. These levels were significantly higher than the control group (n = 27), 0.9 ± 0.2%, P < 0.001. BCECs in infants with cerebrovascular insults with documented clinical seizures (n = 10; 16.8 ± 1.3%) were significantly higher than infants with cerebrovascular insults with subclinical or no seizures (n = 7; 9.5 ± 1.2%); P < 0.001. BCEC levels decreased with seizure control. BCECs levels were elevated in infants with seizures caused by severe IVH and perinatal asphyxia. We suggest that monitoring BCEC levels in peripheral blood can potentially offer a biological marker that reflects cerebrovascular insult and recovery. Further studies with a larger number of patients are required to support these findings.

Novel Assay for Ex Vivo Evaluation of Antiproliferative Effect of Hypomethylating Agents 5-Azacytidine and Decitabine in AML Patient Samples

Introduction: Acute myeloid leukemia (AML) is characterized by dysregulated gene expression and aberrant DNA methylation status. One alternative treatment for AML is hypomethylating agents such as 5-Azacytidine (AZA) and Decitabine (DAC), but just around 30% of the patients obtain a clinical response. These agents are slow acting requiring 3-4 cycles to demonstrate some efficacy, for both reasons looking for biomarkers to identify sensitive patients before treatment could be very beneficial to the patients.Objective: Design an ex-vivo model using the automated flow cytometry ExviTech® platform to identify the antiproliferative effect of hypomethylating agents such as 5-Azacytidine and Decitabine in leukemic cells from AML whole bone marrow patient samples. This assay may capture changes of hypomethylating agents effect that may potentially predict ex vivo the patient clinical outcome.Methods: Bone-marrow samples from 10 patients diagnosed of AML were sent to Vivia from 24 hospitals across Spain within 24h. Whole sample were incubated for 72h in in well plates containing 8 concentrations of AZA and DAC. To induce blast proliferation, AML cells were resuspended in RPMI medium and human cytokines including GM-DSF, IL3, SCF, G-CSF, EPO and transferrin. The number of proliferative and no proliferative live leukemic cells was determined using the CFDA dye. Blast population and viability was determined labeling with monoclonal antibodies and Annexin V. Dose-response curves of AZA and DEC were measured in these 10 patient samples.Results: To corroborate the hypothesis that AZA or DAC induce cell cycle arrest and this effect is different from cytotoxicity, we evaluated the effect of DAC in an AML cell line (KG-1) that grow spontaneously with medium and serum. As shown in figure 1, a decrease in the number of cells is observed when the AML cell line (KG-1) is incubated with DAC (blue line). Interestingly, an exactly proportional increase in the Mean Fluorescent Intensity (MFI) of CFDA is observed (red line), the symmetry between these curves indicate they measure the same effect; the drug-concentration dependent decrease in proliferating cells. Green line represents the percentage of apoptosis, as a measurement of the cytotoxic activity, clearly different that the other 2 measurements and only relevant at much higher doses, indicating that DAC has an essentially antiproliferative effect in the cell line. Once tested the hypothesis, we translate the idea to fresh AML samples inducing the blast proliferation with a very complete cytokine medium. In all patients included in this study, an average population of 47.2%±16.9% proliferating cells was identified. A clear difference in the sensitivity of no proliferative vs proliferative cell subset was observed, while DAC had no activity on the no proliferating cells (flat dose response in Figure 2), it was potently (1 uM) inhibiting almost completely proliferation in the proliferating cell subset.Conclusion: Although the mechanism of action of hypomethylating agents is not still entirely clear, we hypothesize that is associated with antiproliferative effects. In this study, using our Exvitech platform we have developed an ex-vivo model to measure the antiproliferative effect of hypomethylating agents, using whole stimulated bone marrow samples from AML patients. If this new assay would correlate with patient treatment response, it could become a valuable tool to personalize hypomethylating treatments for AML patients. [Display omitted] [Display omitted] Figure 1Figure 2 DisclosuresHernandez:Vivia Biotech: Employment. Gomez:Vivia Biotech: Employment. Robles:Vivia Biotech: Employment. Gorrochategui:Vivia Biotech: Employment. Sanchez:Vivia Biotech: Employment. Ballesteros:Vivia Biotech: Employment. Martinez:Vivia Biotech: Membership on an entity’s Board of Directors or advisory committees.

Development of a High-Throughput Screening Assay with Nurse-like Cell-Based Microenviroment in Chronic Lymphoid Leukemia Cells.

Background and Objectives: B-cell chronic lymphoid leukemia (CLL) is a lymphoproliferative disorder where specific microenvironment between B-cells and nurse-like Cells (NLC) seem to be involved in disease progression providing cell survival, proliferation and drug resistance. Consequently, functional screening platforms that can assess drug candidates within this microenvironment are needed. Our aim is to show the ability of the Exvitech® automated flow cytometry platform to screen agents that interfere with the microenvironmentxs protective scenario such as ibrutinib or idelalisib or standard CLL drugs such as fludarabine or prednisolone. This approach will allow us to select candidates in an in vitro assay and could personalize the treatment according the response to the drugs.Patients and methods: We have adapted Jan Burger’s published assay1. Peripheral blood mononuclear cells (PBMCs) from not previously treated CLL patients were isolated by density gradient centrifugation over Ficoll-Pacque and were used fresh (N=14) or cryopreserved (N=6). B-cells were assessed to be >90% viable by flow cytometry. NLC co-cultures were stablished by suspending PBMCs from CLL patients in complete RPMI medium with 10% FBS to a concentration of 2x107/ml. Cells were incubated for 14 days in 96-well plates and presence of NLC was confirmed by microscopy. After that, viability was investigated in B-cells treated with 8 concentrations of ibrutinib, idelalisib, fludarabine and prednisolone after 72h of incubation with annexin-V and the appropriate CLL flow cytometry markers. Drug response was evaluated as a depletion survival index of the B-cell population relative to the average of the control wells with NLC but without drug.Results: As expected, depletion of B-cells cultured without NLCs were significant greater than with NLC after the 72h incubation supporting the assay where NLCs protect B-CLL cells from in vitro spontaneous apoptosis. In a similar way, viability of fresh samples with NLC was higher than the corresponding frozen samples (84% vs 25%), though both could be used. Our results show a lower pharmacological median potency, measured as a higher EC50, when we work with NLC versus without NLC for ibrutinib (10µM vs 4µM), idelalisib (17µM vs 0.4µM) and prednisolone (3.5µM vs 1.5µM). However, the effect of fludarabine seems to be independent of the presence of the NLC in the cell culture (7µM vs 6µM). This is consistent with the protective role of microenvironment; more pronounced for ibrutinib and idelalisib. Interestingly with NLC, for each drug there is a significant interpatient variability (Figure 1); each line correspond to a different patient, reflecting the possibility that patients might be more sensitive or resistant to a certain drug in this particular scenario. There is a higher degree of patient sample stratification for idelalisib, fludarabine or prednisolone, where there are still an important % of B-cells alive for some patients after drug exposure at high concentration, supporting the notion of drug resistance. Synergism between some of these drugs was evaluated in 3 samples, with some samples being more synergistic than other, requiring a larger number of samples.Conclusions: Cellular and molecular interactions between B-cells and the microenvironment represented here with the NLC, have become an attractive target for CLL therapy. Because novel drugs such as ibrutinib or idelalisib are transforming CLL therapy targeting the microenvironment, novel technologies that could predict its effect are necessary. Here we have adapted a Nurse-Like Cell assay mimicking the microenvironment published by Burger1 to our ExviTech platform. The automated platform enables scaling of the data points acquired with this assay supporting characterization of drug activity by pharmacological dose response curves, as well as exploring synergistic interactions. As showed in the results and illustrated in Figure 1, there is a interpatient variability of the pharmacological profile for the studied drugs, if clinically validated, could help guiding a personalized treatment selection; measuring the drug activity inside this particular microenvironment responsible of drug resistance.1.- Burger JA et al. Blood. 2000 Oct 15;96(8):2655-63. [Display omitted] DisclosuresPrimo:Vivia Biotech: Employment. Martinez:Vivia Biotech: Membership on an entity’s Board of Directors or advisory committees. Gorrochategui:Vivia Biotech: Employment. Espinosa:Vivia Biotech: Employment. Arroyo:Vivia Biotech: Employment. Ballesteros:Vivia Biotech: Employment. Hernandez:Vivia Biotech: Employment.

An Automated High-Throughput Cell-Based Multiplexed Flow Cytometry Assay to Identify Novel Compounds to Target Candida albicans Virulence-Related Proteins

Although three major classes of systemic antifungal agents are clinically available, each is characterized by important limitations. Thus, there has been considerable ongoing effort to develop novel and repurposed agents for the therapy of invasive fungal infections. In an effort to address these needs, we developed a novel high-throughput, multiplexed screening method that utilizes small molecules to probe candidate drug targets in the opportunistic fungal pathogen Candida albicans. This method is amenable to high-throughput automated screening and is based upon detection of changes in GFP levels of individually tagged target proteins. We first selected four GFP-tagged membrane-bound proteins associated with virulence or antifungal drug resistance in C. albicans. We demonstrated proof-of-principle that modulation of fluorescence intensity can be used to assay the expression of specific GFP-tagged target proteins to inhibitors (and inducers), and this change is measurable within the HyperCyt automated flow cytometry sampling system. Next, we generated a multiplex of differentially color-coded C. albicans strains bearing C-terminal GFP-tags of each gene encoding candidate drug targets incubated in the presence of small molecules from the Prestwick Chemical Library in 384-well microtiter plate format. Following incubation, cells were sampled through the HyperCyt system and modulation of protein levels, as indicated by changes in GFP-levels of each strain, was used to identify compounds of interest. The hit rate for both inducers and inhibitors identified in the primary screen did not exceed 1% of the total number of compounds in the small-molecule library that was probed, as would be expected from a robust target-specific, high-throughput screening campaign. Secondary assays for virulence characteristics based on null mutant strains were then used to further validate specificity. In all, this study presents a method for the identification and verification of new antifungal drugs targeted to fungal virulence proteins using C. albicans as a model fungal pathogen.

Identification of Bacteria in Water by a Fluorescent Array

AbstractWe report a method for the rapid and efficient identification of bacteria making use of five probes having fluorescent characteristics (F‐array) and subsequent statistical analysis. Eight kinds of bacteria, including normal and multidrug‐resistant bacteria, are differentiated successfully. Our easy‐to‐perform and time‐saving method consists of mixing bacteria and probes, recording fluorescent intensity data by automated flow cytometry, and statistical analysis. No washing steps are required in order to identify the different bacteria simultaneously.

Diagnostic Performance of Automated Urinalysis and Urine Dipstick for UTIs in Young Children

In a prospective observational study, investigators determined performance characteristics of urine automated flow cytometry and point-of care dipstick testing for diagnosing urinary tract infections (UTIs) in children <48 months of age presenting with fever (≥38°C) to a single pediatric emergency department over one year. Urine was collected by sterile catheterization technique at the discretion of the treating …

Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry

Cells adjust to changes in environmental conditions using complex regulatory programs. These cellular programs are the result of an intricate interplay between gene expression, cellular growth rate, and protein degradation fluxes. New technologies that enable simultaneous and time-resolved measurements of these variables are necessary to dissect cellular homeostatic strategies. Here, we report the development of a novel automated flow-cytometry robotic setup that enables real-time measurement of precise and simultaneous relative growth and protein synthesis rates of multiplexed microbial populations across many conditions. These measurements generate quantitative profiles of dynamically-evolving protein synthesis and degradation rates. We demonstrate this setup in the context of gene regulation of the unfolded protein response (UPR) and uncover a dynamic and complex landscape of gene expression, growth dynamics, and proteolysis following perturbations.

Platelet Turnover in Stable Coronary Artery Disease – Influence of Thrombopoietin and Low-Grade Inflammation

BackgroundNewly formed platelets are associated with increased aggregation and adverse outcomes in patients with coronary artery disease (CAD). The mechanisms involved in the regulation of platelet turnover in patients with CAD are largely unknown.AimTo investigate associations between platelet turnover parameters, thrombopoietin and markers of low-grade inflammation in patients with stable CAD. Furthermore, to explore the relationship between platelet turnover parameters and type 2 diabetes, prior myocardial infarction, smoking, age, gender and renal insufficiency.MethodsWe studied 581 stable CAD patients. Platelet turnover parameters (immature platelet fraction, immature platelet count, mean platelet volume, platelet distribution width and platelet large cell-ratio) were determined using automated flow cytometry (Sysmex XE-2100). Furthermore, we measured thrombopoietin and evaluated low-grade inflammation by measurement of high-sensitive CRP and interleukin-6.ResultsWe found strong associations between the immature platelet fraction, immature platelet count, mean platelet volume, platelet distribution width and platelet large cell ratio (r = 0.61–0.99, p<0.0001). Thrombopoietin levels were inversely related to all of the platelet turnover parameters (r = −0.17–−0.25, p<0.0001). Moreover, thrombopoietin levels were significantly increased in patients with diabetes (p = 0.03) and in smokers (p = 0.003). Low-grade inflammation evaluated by high-sensitive CRP correlated significantly, yet weakly, with immature platelet count (r = 0.10, p = 0.03) and thrombopoietin (r = 0.16, p<0.001). Also interleukin-6 correlated with thrombopoietin (r = 0.10, p = 0.02).ConclusionIn stable CAD patients, thrombopoietin was inversely associated with platelet turnover parameters. Furthermore, thrombopoietin levels were increased in patients with diabetes and in smokers. However, low-grade inflammation did not seem to have a substantial impact on platelet turnover parameters.

Teriparatide (PTH 1-34) Treatment Increases Peripheral Hematopoietic Stem Cells in Postmenopausal Women

Cells of the osteoblast lineage play an important role in regulating the hematopoietic stem cell (HSC) niche and early B-cell development in animal models, perhaps via parathyroid hormone (PTH)-dependent mechanisms. There are few human clinical studies investigating this phenomenon. We studied the impact of long-term daily teriparatide (PTH 1-34) treatment on cells of the hematopoietic lineage in postmenopausal women. Twenty-three postmenopausal women at high risk of fracture received teriparatide 20 mcg sc daily for 24 months as part of a prospective longitudinal trial. Whole blood measurements were obtained at baseline, 3, 6, 12, and 18 months. Flow cytometry was performed to identify hematopoietic subpopulations, including HSCs (CD34+/CD45(moderate); ISHAGE protocol) and early transitional B cells (CD19+, CD27-, IgD+, CD24[hi], CD38[hi]). Serial measurements of spine and hip bone mineral density (BMD) as well as serum P1NP, osteocalcin, and CTX were also performed. The average age of study subjects was 64 ± 5 years. We found that teriparatide treatment led to an early increase in circulating HSC number of 40% ± 14% (p = 0.004) by month 3, which persisted to month 18 before returning to near baseline by 24 months. There were no significant changes in transitional B cells or total B cells over the course of the study period. In addition, there were no differences in complete blood count profiles as quantified by standard automated flow cytometry. Interestingly, the peak increase in HSC number was inversely associated with increases in bone markers and spine BMD. Daily teriparatide treatment for osteoporosis increases circulating HSCs by 3 to 6 months in postmenopausal women. This may represent a proliferation of marrow HSCs or increased peripheral HSC mobilization. This clinical study establishes the importance of PTH in the regulation of the HSC niche within humans. © 2014 American Society for Bone and Mineral Research.

Pharmacological Profiles of Acute Myeloid Leukemia Treatments in Patient Samples by Automated Flow Cytometry: A Bridge to Individualized Medicine

We have evaluated the ex vivo pharmacology of single drugs and drug combinations in malignant cells of bone marrow samples from 125 patients with acute myeloid leukemia using a novel automated flow cytometry-based platform (ExviTech). We have improved previous ex vivo drug testing with 4 innovations: identifying individual leukemic cells, using intact whole blood during the incubation, using an automated platform that escalates reliably data, and performing analyses pharmacodynamic population models. Samples were sent from 24 hospitals to a central laboratory and incubated for 48 hours in whole blood, after which drug activity was measured in terms of depletion of leukemic cells. The sensitivity of single drugs is assessed for standard efficacy (EMAX) and potency (EC50) variables, ranked as percentiles within the population. The sensitivity of drug-combination treatments is assessed for the synergism achieved in each patient sample. We found a large variability among patient samples in the dose-response curves to a single drug or combination treatment. We hypothesize that the use of the individual patient ex vivo pharmacological profiles may help to guide a personalized treatment selection.

Population Pharmacological Profiles Of AML Treatments In Patient Samples By Automated Flow Cytometry; A Bridge To Individualized Medicine

BackgroundTo aid in the identification of effective treatments for individual patients, ex vivo assays for detecting cell death inducible by drugs for hematological malignancies have been in development for over 20 years. We have developed a novel approach incorporating 4 key innovations; incubating drugs in whole bone marrow sample without isolating leukocytes, using flow cytometry enables identification of the malignant cells selectively, an automated flow cytometry-based platform (ExviTech) decreases errors and enables full pharmacological characterization, and analyzing the data using pharmacodynamic population models. AimThe purpose of this study is to derive the ex vivo pharmacological profiles across the AML patient population of single drugs and combination treatments as a tool for individualized treatment selection. Patients and MethodsBone-marrow samples from 160 patients diagnosed with AML were sent to Vivia from 24 hospitals across Spain within 24 hrs. The plates were incubated for 48-hours prior to analysis with ExviTech, The percentage of leukemic cell death was determined via labeling with monoclonal antibodies and AnnexinV-FITC. A survival index is computed for each drug, the lower the survival index, the more effective the drug. Dose-response curves of cytarabine, idarubicin, daunorubicine, etoposide, mitoxantrone, fludarabine, clofarabine, and 6-thioguanine were measured in 160 patient samples. The added benefit of combining these drugs into 12 combination treatments was assessed by measuring their synergy in each individual patient. In 39 patients treated with CYT IDA we had clinical data of response, and then we performed a blinded interpretation of this in vitro test by an expert hematologist, to predict the clinical response based in this test result. ResultsThere was a large range of interpatient variability in the response to a single drug and even larger in the synergism between drugs. The Population Pharmacological Profiles for an individual patient is shown on the figure below. The relative drug potency in terms of their percentile ranking within the population is shown in the left panel from 0 (weakest) to 100 (most potent). Green lines represent the individual patient potency relative to the population ranking, with confidence intervals. Third column lists when a drug leaves a significant % of leukemic cells alive, potential resistant clones. The panel on the right side shows the synergism of the drug combinations treatments shown as box-plots at 10-25-75-90% to highlight their distribution. The synergism value for an individual patient in each combination is shown in green, with confidence interval as parallel dotted green lines. This representation of the Pharmacological Profile of an individual patient sample quickly identifies extreme values, when a drug or combination is very sensitive (rightward shift green lines, green boxes) or very resistant (leftward shift green lines, red boxes). This patient showed average sensitivities for most drugs though highly resistant to Clofarabine (red box) that leaves 45% alive. However this patient showed lack of synergism in multiple treatments (right, red boxes). CYT and IDA show average potencies but lack of synergism, suggesting CYT-DAU might be a more efficient treatment. These representations lead to clear guidelines in >90% samples, and based on hematologist's interpretation of these guidelines show a clinical correlation with clinical responses to CYT-IDA of 84%. ConclusionWe have developed an improved a methodology to measure the pharmacological activity of drugs and drug combinations in AML patient samples as well as modeling their pharmacological behavior. This information may be useful in selecting the optimal treatment for the individual patient, especially relapse/refractory patients in need of therapeutic alternatives. By testing the drugs used in the treatment protocols for AML directly on patient samples, a pharmacological based model has been developed to infer drug resistance or sensitivity, patient by patient.▪ Disclosures:Ballesteros:Vivia Biotech: Equity Ownership. Primo:Vivia Biotech: Employment. Hernandez-Campo:Vivia Biotech: Employment. Rojas:Vivia Biotech: Employment. Liebana:Vivia Biotech: Employment. Lopez:Vivia Biotech: Employment. Iñaki:Vivia Biotech: Consultancy. Bennett:Vivia Biotech: Employment.

Personalizing Therapies With Ex Vivo Pharmacological Responses May Uncover The Differences Between IDA-DNR-MIT Among European AML Protocols

Background and objectivesProtocols for acute myeloid leukemia (AML) 1st line patients are centered on the combination of Cytarabine and an anthracycline; Idarubicin (IDA), Daunorubicin (DNR), or Mitoxantrone (MIT). Patients may be treated with IDA, DNR, or MIT depending on the country of residence, because multiple clinical trials have not found significant differences among them. A new Personalized Medicine (PM) test developed by Vivia Biotech based on pharmacological responses in patient samples (ex vivo) is uncovering individual responses to these treatments. Our objective is to explore whether a significant % of individual patients may respond differently to IDA vs DNR vs MIT treatments, in spite that of their “on average” similar response shown by clinical trials. Patients and MethodsMulticenter, prospective, non-interventional study of the PETHEMA group for treatment of AML. Bone Marrow (BM) samples were collected at diagnosis for 160 AML patients. Samples were incubated for 48 hours in 96-well plates, each well containing different drugs or drug combinations, each at 8 different concentrations, enabling calculation of dose response curves for each single drug (CYT, IDA, DNR, MIT) and combination used in treatments (CYT-IDA, CYT-DNR, CYT-MIT). Drug response was evaluated as depletion of AML malignant cells in each well after 48 hours incubations. Annexin V-FITC was used to quantify the ability of the drugs to induce apoptosis. Malignant cells were identified with monoclonal antibodies and light scatter properties. 1) We use the whole bone marrow sample, retaining the erythrocyte population and serum proteins, during the entire incubation period; and after 48 h leukocytes are isolated prior to evaluation by flow cytometry. 2) We have pioneered development of a proprietary automated flow cytometry platform called ExviTech. 3) Pharmacological responses are calculated using pharmacokinetic population models. ResultsFigure left panel shows dose responses for both IDA (red) and DNR (blue) in 125 AML patient samples. Although their average curves (thick red & blue) are similar, the interpatient variability of either drug is quite large. We hypothesized that some patients could show very differential sensitivities to both drugs, as illustrated by the green arrow where a patient sample is resistant to DNR (right shifted dose response curve) but sensitive to IDA (left shifted dose response curve). To identify these cases Figure right panel shows a comparison of the potency IDA vs DNR. Potency is represented by their EC50 (concentration that kills 50% of the cells). Most dots tend to line up, but red dots represent patient samples with a difference in potency between these drugs >30%. Repeating this exercise for IDA-MIT and DNR-MIT to cover all alternatives among the 3 anthracyclines identifies 40% of patients samples with >30% different potency among IDA-DNR-MIT. Repeating this exercise with the combination treatments CYT-IDA, CYT-DNR, CYT-MIT increases to 58% the population of patients whose samples have a differential sensitivity to these anthracyclines. A fraction of this 57% of patients may benefit in if treatment selection among these 3 treatments were to be aided by this ex vivo testing sensitivities. To identify which fraction would benefit we would need a trial specifically designed. ConclusionsThis preliminary results show that Vivia's PM test seems able to identify a subset of AML patients who's ex vivo pharmacological response to anthracycline drugs is significantly different. Because this ex vivo test accurately predicts the clinical response to CYT-IDA, if these selective anthracycline ex vivo responses translate to clinical responses, a fraction of this 57% subpopulation could benefit significantly from receiving 1st or 2nd line treatments based on either IDA, DNR, MIT, and their combinations. Hence this approach stands for European integration of treatment protocols, based on ex vivo individual responses data rather than nationality. [Display omitted] Disclosures:Primo:Vivia Biotech: Employment. Hernandez-Campo:Vivia Biotech: Employment. Rojas:Vivia Biotech: Employment. Bennett:Vivia Biotech: Employment. Liebana:Vivia Biotech: Employment. Lopez:Vivia Biotech: Employment. Ballesteros:Vivia Biotech: Equity Ownership.

A low-cost, multiplexable, automated flow cytometry procedure for the characterization of microbial stress dynamics in bioreactors

BackgroundMicrobial cell population heterogeneity is now recognized as a major source of issues in the development and optimization of bioprocesses. Even if single cell technologies are available for the study of microbial population heterogeneity, only a few of these methods are available in order to study the dynamics of segregation directly in bioreactors. In this context, specific interfaces have been developed in order to connect a flow cytometer directly to a bioreactor for automated analyses. In this work, we propose a simplified version of such an interface and demonstrate its usefulness for multiplexed experiments.ResultsA low-cost automated flow cytometer has been used in order to monitor the synthesis of a destabilized Green Fluorescent Protein (GFP) under the regulation of the fis promoter and propidium iodide (PI) uptake. The results obtained showed that the dynamics of GFP synthesis are complex and can be attributed to a complex set of biological parameters, i.e. on the one hand the release of protein into the extracellular medium and its uptake modifying the activity of the fis promoter, and on the other hand the stability of the GFP molecule itself, which can be attributed to the protease content and energy status of the cells. In this respect, multiplexed experiments have shown a correlation between heat shock and ATP content and the stability of the reporter molecule.ConclusionThis work demonstrates that a simplified version of on-line FC can be used at the process level or in a multiplexed version to investigate the dynamics of complex physiological mechanisms. In this respect, the determination of new on-line parameters derived from automated FC is of primary importance in order to fully integrate the power of FC in dedicated feedback control loops.

Microbial heterogeneity affects bioprocess robustness: Dynamic single‐cell analysis contributes to understanding of microbial populations

Heterogeneity or segregation of microbial populations has been the subject of much research, but the real impact of this phenomenon on bioprocesses remains poorly understood. The main reason for this lack of knowledge is the difficulty in monitoring microbial population heterogeneity under dynamic process conditions. The main concepts resulting in microbial population heterogeneity in the context of bioprocesses have been summarized by two distinct hypotheses. The first involves the individual history of microbial cells or the "path" followed during their residence time inside the process equipment. The second hypothesis involves a coordinated response by the microbial population as a bet-hedging strategy, in order to cope with process-related stresses. The respective contribution of each hypothesis to microbial heterogeneity in bioprocesses is still unclear. This illustrates the fact that, although microbial phenotypic heterogeneity has been thoroughly investigated at a fundamental level, the implications of this phenomenon in the context of microbial bioprocesses are still subject to debate. At this time, automated flow cytometry is the best technique for investigating microbial heterogeneity under process conditions. However, dedicated software and relevant biomarkers are needed for the proper integration of flow cytometry as a bioprocess control tool.

Pediatric reference values for urine particle quantification by using automated flow cytometer: Results of a multicenter study of Italian urinalysis group

ObjectivesThe purpose of this Italian multicenter study was to define pediatric upper reference values for urine particle quantification by using automated flow cytometry. Design and methodsFour hospital-based clinical laboratories participated in this multicenter investigation, which included a total study population of 161 Italian children aged from 1 to 12years. Two laboratories used Sysmex UF-100 and analyzed 86 children, whereas the other two used Sysmex UF-1000i and analyzed 75 subjects. Particle quantification included the analysis of white blood cells (WBC), red blood cells (RBC), squamous epithelial cells (EC), transitional epithelial cells (TC), casts (CAST) and bacteria (BACT). ResultsThe upper reference values in subjects tested with the Sysmex UF-100 were 9.7WBC/μL, 10.1RBC/μL, 7.5EC/μL, 2.5TC/μL, 0.7CAST/μL and 3090BACT/μL, whereas the upper reference values in subjects tested with the Sysmex UF-1000i were 10.5WBC/μL, 8.3RBC/μL, 7.2EC/μL, 2.9TC/μL, 0.7CAST/μL and 48BACT/μL. No statistically significant differences between genders were found in the value distribution of any of the parameters tested. Similarly, no statistically significant differences were observed between the two urine analyzers, except for BACT. ConclusionsAutomated analysis of urine particles appears a suitable means to optimize the workflow of routine urinalysis of children specimens. The upper reference limits for pediatric subjects obtained in this study were comparable to those previously reported in the literature, with no significant differences between genders and analyzers.