Image-based Assay Research Articles

Label-free prediction of cell painting from brightfield images

Cell Painting is a high-content image-based assay applied in drug discovery to predict bioactivity, assess toxicity and understand mechanisms of action of chemical and genetic perturbations. We investigate label-free Cell Painting by predicting the five fluorescent Cell Painting channels from brightfield input. We train and validate two deep learning models with a dataset representing 17 batches, and we evaluate on batches treated with compounds from a phenotypic set. The mean Pearson correlation coefficient of the predicted images across all channels is 0.84. Without incorporating features into the model training, we achieved a mean correlation of 0.45 with ground truth features extracted using a segmentation-based feature extraction pipeline. Additionally, we identified 30 features which correlated greater than 0.8 to the ground truth. Toxicity analysis on the label-free Cell Painting resulted a sensitivity of 62.5% and specificity of 99.3% on images from unseen batches. We provide a breakdown of the feature profiles by channel and feature type to understand the potential and limitations of label-free morphological profiling. We demonstrate that label-free Cell Painting has the potential to be used for downstream analyses and could allow for repurposing imaging channels for other non-generic fluorescent stains of more targeted biological interest.

Live imaging-based assay for visualising species-specific interactions in gamete adhesion molecules

Successful gamete fusion requires species-specific membrane adhesion. However, the interaction of adhesion molecules in gametes is difficult to study in real time through low-throughput microscopic observation. Therefore, we developed a live imaging-based adhesion molecule (LIAM) assay to study gamete adhesion molecule interactions in cultured cells. First, we modified a fusion assay previously established for fusogens introduced into cultured cells, and confirmed that our live imaging technique could visualise cell–cell fusion in the modified fusion assay. Next, instead of fusogen, we introduced adhesion molecules including a mammalian gamete adhesion molecule pair, IZUMO1 and JUNO, and detected their temporal accumulation at the contact interfaces of adjacent cells. Accumulated IZUMO1 or JUNO was partly translocated to the opposite cells as discrete spots; the mutation in amino acids required for their interaction impaired accumulation and translocation. By using the LIAM assay, we investigated the species specificity of IZUMO1 and JUNO of mouse, human, hamster, and pig in all combinations. IZUMO1 and JUNO accumulation and translocation were observed in conspecific, and some interspecific, combinations, suggesting potentially interchangeable combinations of IZUMO1 and JUNO from different species.

Image-based cell profiling enhancement via data cleaning methods.

With the advent of high-throughput assays, a large number of biological experiments can be carried out. Image-based assays are among the most accessible and inexpensive technologies for this purpose. Indeed, these assays have proved to be effective in characterizing unknown functions of genes and small molecules. Image analysis pipelines have a pivotal role in translating raw images that are captured in such assays into useful and compact representation, also known as measurements. CellProfiler is a popular and commonly used tool for this purpose through providing readily available modules for the cell/nuclei segmentation, and making various measurements, or features, for each cell/nuclei. Single cell features are then aggregated for each treatment replica to form treatment "profiles". However, there may be several sources of error in the CellProfiler quantification pipeline that affects the downstream analysis that is performed on the profiles. In this work, we examined various preprocessing approaches to improve the profiles. We consider the identification of drug mechanisms of action as the downstream task to evaluate such preprocessing approaches. Our enhancement steps mainly consist of data cleaning, cell level outlier detection, toxic drug detection, and regressing out the cell area from all other features, as many of them are widely affected by the cell area. Our experiments indicate that by performing these time-efficient preprocessing steps, image-based profiles can preserve more meaningful information compared to raw profiles. In the end, we also suggest possible avenues for future research.

Macrophage Clearance of Neutrophil Extracellular Traps (NETs)

Abstract Neutrophil Extracellular Traps (NETs) are formed from dying neutrophils expelling their contents to capture pathogens and limit the spread of infection. While they are beneficial during infection, overproduction of NETs or the inability to degrade them can be pathogenic. Different inflammatory disorders and autoimmune diseases have been shown to be associated with an increase in NET production. Therefore, it is important to understand the method in which NETs are removed or broken down. Cayman Chemical has developed an imaging-based assay to sensitively assay NET uptake by phagocytic cells. Imaging was found to be an ideal method to monitor NET clearance in vitro, in part due to the ability to monitor the uptake of NETs kinetically. Both primary monocyte-derived macrophages and differentiated THP-1 cells, which are frequently used as phagocytic cell models, were shown to take up NETs. Putative modulators of NET uptake were tested in the assay. We aimed to develop a method in which the process of NET uptake can be monitored and quantified. Modulators of NET uptake can be tested in this assay, allowing for further studies toward treating autoimmune disorders that are driven by aberrant NETs.

PAR4 Primarily Mediates Thrombin‐induced Morphological Changes in MEG‐01 Cells through PI3K/Akt and RhoA/ROCK Signaling Pathways

Platelet activation is critical in hemostasis and thrombosis. Thrombin most potently activates platelets via two protease‐activated receptors (PARs): PAR1 and PAR4. While PAR1 activation results in a rapid and transient signal required for the initiation phase of platelet aggregation, PAR4 activation induces a sustained signal associated with later phases responsible for stable thrombus formation. The present study focused on the differential signaling pathways by PAR1 and PAR4 involved in thrombin‐induced intracellular events in human megakaryoblastic leukemia cell line, MEG‐01. Interestingly, we found that thrombin triggers not only Gq/PLC‐mediated calcium signaling, but also G12/13/RhoA/ROCK‐mediated morphological changes in MEG‐01 cells via PAR1 and PAR4, which showed close similarity to those observed in platelets. We developed a new image‐based assay to quantify the morphological changes in living cells and extensively investigated on the underlying mechanism for thrombin‐induced morphological changes in MEG‐01 cells. Selective blockade of PAR1 and PAR4 by vorapaxar and BMS‐986120, respectively, indicated that PAR4 activation primarily mediates thrombin‐induced morphological changes in MEG‐01 cells. Moreover, treatment of a set of kinase inhibitors showed that the PAR4‐mediated morphological changes were predominantly mediated via PI3K/Akt and RhoA/ROCK signaling pathways. As in the platelets, PAR4‐mediated signaling pathways are significant in thrombin‐induced morphological changes in MEG‐01 cells. Based on the close similarity to thrombin‐induced signaling in platelets, MEG‐01 cell line is a useful complementary in vitro model that can be used in research on platelets and thrombosis.

Climate Change Impact on Wheat Performance-Effects on Vigour, Plant Traits and Yield from Early and Late Drought Stress in Diverse Lines.

Global climate change is threatening wheat productivity; improved yield under drought conditions is urgent. Here, diverse spring-wheat lines (modern, old and wheat-rye introgressions) were examined in an image-based early-vigour assay and a controlled-conditions (Biotron) trial that evaluated 13 traits until maturity. Early root vigour was significantly higher in the old Swedish lines (root length 8.50 cm) and introgressed lines with 1R (11.78 cm) and 1RS (9.91 cm) than in the modern (4.20 cm) and 2R (4.67 cm) lines. No significant correlation was noted between early root and shoot vigour. A higher yield was obtained under early drought stress in the 3R genotypes than in the other genotype groups, while no clear patterns were noted under late drought. Evaluating the top 10% of genotypes in terms of the stress-tolerance index for yield showed that root biomass, grains and spikes per plant were accountable for tolerance to early drought, while 1000-grain weight and flag-leaf area were accountable for tolerance to late drought. Early root vigour was determined as an important focus trait of wheat breeding for tolerance to climate-change-induced drought. The responsible genes for the trait should be searched for in these diverse lines. Additional drought-tolerance traits determined here need further elaboration to identify the responsible genes.

Niclosamide induces miR-148a to inhibit PXR and sensitize colon cancer stem cells to chemotherapy.

SummaryTumor recurrence is often attributed to cancer stem cells (CSCs). We previously demonstrated that down-regulation of Pregnane X Receptor (PXR) decreases the chemoresistance of CSCs and prevents colorectal cancer recurrence. Currently, no PXR inhibitor is usable in clinic. Here, we identify miR-148a as a targetable element upstream of PXR signaling in CSCs, which when over-expressed decreases PXR expression and impairs tumor relapse after chemotherapy in mouse tumor xenografts. We then develop a fluorescent reporter screen for miR-148a activators and identify the anti-helminthic drug niclosamide as an inducer of miR-148a expression. Consequently, niclosamide decreased PXR expression and CSC numbers in colorectal cancer patient-derived cell lines and synergized with chemotherapeutic agents to prevent CSC chemoresistance and tumor recurrence in vivo. Our study suggests that endogenous miRNA inducers is a viable strategy to down-regulate PXR and illuminates niclosamide as a neoadjuvant repurposing strategy to prevent tumor relapse in colon cancer.

Collection of Data Variation Using a High-Throughput Image-Based Assay Platform Facilitates Data-Driven Understanding of TRPA1 Agonist Diversity

Because transient receptor potential ankyrin 1 (TRPA1) is involved in various physiological functions, TRPA1-targeting drugs have been energetically developed. Although TRPA1 is considered a multimodal receptor, the structural diversity of TRPA1 agonists is not fully elucidated. We hypothesized that collecting a wider variation of TRPA1–compound interaction data would aid the understanding of its complex mechanism and aimed to challenge such data collection using an “image-based TRPA1 assay system combined with an in silico chemical space clustering concept.” Our library was clustered with 27 physicochemical molecular descriptors in silico, and structurally diverse compounds from each cluster were selected for a detailed kinetic assay to investigate variations of agonist structural rules. Through two sets of assays evaluating various compounds in parallel with validating effects of the previously established structural rules, we discovered that different chemical groups contribute to agonist activity, indicating that there are multiple agonist design concepts. A novel core structure for a TRPA1 agonist has been also proposed. Our new approach, “collection of TRPA1 activity data on compounds with physicochemical diversity,” will not only facilitate the understanding of the structural diversity of TRPA1 agonists but also contribute to the development of a new type of TRPA1-targeting drug.

Quantitative Dissection of the Proximal Ciona brachyury Enhancer.

A major goal in biology is to understand the rules by which cis-regulatory sequences control spatially and temporally precise expression patterns. Here we present a systematic dissection of the proximal enhancer for the notochord-specific transcription factor brachyury in the ascidian chordate Ciona. The study uses a quantitative image-based reporter assay that incorporates a dual-reporter strategy to control for variable electroporation efficiency. We identified and mutated multiple predicted transcription factor binding sites of interest based on statistical matches to the JASPAR binding motif database. Most sites (Zic, Ets, FoxA, RBPJ) were selected based on prior knowledge of cell fate specification in both the primary and secondary notochord. We also mutated predicted Brachyury sites to investigate potential autoregulation as well as Fos/Jun (AP1) sites that had very strong matches to JASPAR. Our goal was to quantitatively define the relative importance of these different sites, to explore the importance of predicted high-affinity versus low-affinity motifs, and to attempt to design mutant enhancers that were specifically expressed in only the primary or secondary notochord lineages. We found that the mutation of all predicted high-affinity sites for Zic, FoxA or Ets led to quantifiably distinct effects. The FoxA construct caused a severe loss of reporter expression whereas the Ets construct had little effect. A strong Ets phenotype was only seen when much lower-scoring binding sites were also mutated. This supports the enhancer suboptimization hypothesis proposed by Farley and Levine but suggests that it may only apply to some but not all transcription factor families. We quantified reporter expression separately in the two notochord lineages with the expectation that Ets mutations and RBPJ mutations would have distinct effects given that primary notochord is induced by Ets-mediated FGF signaling whereas secondary notochord is induced by RBPJ/Su(H)-mediated Notch/Delta signaling. We found, however, that ETS mutations affected primary and secondary notochord expression relatively equally and that RBPJ mutations were only moderately more severe in their effect on secondary versus primary notochord. Our results point to the promise of quantitative reporter assays for understanding cis-regulatory logic but also highlight the challenge of arbitrary statistical thresholds for predicting potentially important sites.

Can two wrongs make a right? F508del-CFTR ion channel rescue by second-site mutations in its transmembrane domains

Deletion of phenylalanine 508 (F508del) in the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel is the most common cause of cystic fibrosis. The F508 residue is located on nucleotide-binding domain 1 (NBD1) in contact with the cytosolic extensions of the transmembrane helices, in particular intracellular loop 4 (ICL4). To investigate how absence of F508 at this interface impacts the CFTR protein, we carried out a mutagenesis scan of ICL4 by introducing second-site mutations at 11 positions in cis with F508del. Using an image-based fluorescence assay, we measured how each mutation affected membrane proximity and ion-channel function. The scan strongly validated the effectiveness of R1070W at rescuing F508del defects. Molecular dynamics simulations highlighted two features characterizing the ICL4/NBD1 interface of F508del/R1070W-CFTR: flexibility, with frequent transient formation of interdomain hydrogen bonds, and loosely stacked aromatic sidechains (F1068, R1070W, and F1074, mimicking F1068, F508, and F1074 in WT CFTR). F508del-CFTR displayed a distorted aromatic stack, with F1068 displaced toward the space vacated by F508, while in F508del/R1070F-CFTR, which largely retained F508del defects, R1070F could not form hydrogen bonds and the interface was less flexible. Other ICL4 second-site mutations which partially rescued F508del-CFTR included F1068M and F1074M. Methionine side chains allow hydrophobic interactions without the steric rigidity of aromatic rings, possibly conferring flexibility to accommodate the absence of F508 and retain a dynamic interface. These studies highlight how both hydrophobic interactions and conformational flexibility might be important at the ICL4/NBD1 interface, suggesting possible structural underpinnings of F508del-induced dysfunction.

PAR4-Mediated PI3K/Akt and RhoA/ROCK Signaling Pathways Are Essential for Thrombin-Induced Morphological Changes in MEG-01 Cells.

Thrombin stimulates platelets via a dual receptor system of protease-activated receptors (PARs): PAR1 and PAR4. PAR1 activation induces a rapid and transient signal associated with the initiation of platelet aggregation, whereas PAR4 activation results in a prolonged signal, required for later phases, that regulates the stable formation of thrombus. In this study, we observed differential signaling pathways for thrombin-induced PAR1 and PAR4 activation in a human megakaryoblastic leukemia cell line, MEG-01. Interestingly, thrombin induced both calcium signaling and morphological changes in MEG-01 cells via the activation of PAR1 and PAR4, and these intracellular events were very similar to those observed in platelets shown in previous studies. We developed a novel image-based assay to quantitatively measure the morphological changes in living cells, and observed the underlying mechanism for PAR1- and PAR4-mediated morphological changes in MEG-01 cells. Selective inhibition of PAR1 and PAR4 by vorapaxar and BMS-986120, respectively, showed that thrombin-induced morphological changes were primarily mediated by PAR4 activation. Treatment of a set of kinase inhibitors and 2-aminoethoxydiphenyl borate (2-APB) revealed that thrombin-mediated morphological changes were primarily regulated by calcium-independent pathways and PAR4 activation-induced PI3K/Akt and RhoA/ROCK signaling pathways in MEG-01 cells. These results indicate the importance of PAR4-mediated signaling pathways in thrombin-induced morphological changes in MEG-01 cells and provide a useful in vitro cellular model for platelet research.

Optimizing the Pharmacological and Optical Dosimetry for Photodynamic Therapy with Methylene Blue and Nanoliposomal Benzoporphyrin on Pancreatic Cancer Spheroids

Photodynamic therapy (PDT) is a cancer treatment that relies on the remote-controlled activation of photocatalytic dyes (photosensitizers) in cancer tissues. To effectively treat cancer, a variety of pharmacological and optical parameters require optimization, which are dependent on the photosensitizer type. As most photosensitizers are hydrophobic molecules, nanoliposomes are frequently used to increase the biocompatibility of these therapeutics. However, as nanoliposomes can influence the therapeutic performance of photosensitizers, the most suitable treatment parameters need to be elucidated. Here, we evaluate the efficacy of PDT on spheroid cultures of PANC-1 and MIA PaCa-2 pancreatic cancer cells. Two strategies to photosensitize the pancreatic microtumors were selected, based on either nanoliposomal benzoporphyrin derivative (BPD), or non-liposomal methylene blue (MB). Using a comprehensive image-based assay, our findings show that the PDT efficacy manifests in distinct manners for each photosensitizer. Moreover, the efficacy of each photosensitizer is differentially influenced by the photosensitizer dose, the light dose (radiant exposure or fluence in J/cm2), and the dose rate (fluence rate in mW/cm2). Taken together, our findings illustrate that the most suitable light dosimetry for PDT strongly depends on the selected photosensitization strategy. The PDT dose parameters should therefore always be carefully optimized for different models of cancer.

Image-based Quantification of Macropinocytosis Using Dextran Uptake into Cultured Cells.

Macropinocytosis is an evolutionarily conserved process, which is characterized by the formation of membrane ruffles and the uptake of extracellular fluid. We recently demonstrated a role for CYFIP-related Rac1 Interactor (CYRI) proteins in macropinocytosis. High-molecular weight dextran (70kDa or higher) has generally been used as a marker for macropinocytosis because it is too large to fit in smaller endocytic vesicles, such as those of clathrin or caveolin-mediated endocytosis. Through the use of an image-based dextran uptake assay, we showed that cells lacking CYRI proteins internalise less dextran compared to their wild-type counterparts. Here, we will describe a step-by-step experimentation procedure to detect internalised dextran in cultured cells, and an image pipeline to analyse the acquired images, using the open-access software ImageJ/Fiji. This protocol is detailed yet simple and easily adaptable to different treatment conditions, and the analysis can also be automated for improved processing speed.

Generating Large Numbers of Pancreatic Microtumors on Alginate-Gelatin Hydrogels for Quantitative Imaging of Tumor Growth and Photodynamic Therapy Optimization.

The emerging use of 3D culture models of cancer has provided novel insights into the therapeutic mechanisms of photodynamic therapy on a mesoscopic scale. Especially microscale tumors grown on scaffolds of extracellular matrix can provide statistically robust data on the effects of photosensitizers and photodynamic therapy by leveraging high-throughput imaging-based assays. Although highly informative, the use of such 3D cultures can be impractical due to the high costs and inter-batch variability of the extracellular matrix scaffolds that are necessary to establish such cultures. In this study, we therefore provide a protocol to generate inexpensive and defined hydrogels composed of sodium alginate and gelatin that can be used for culturing 3D microtumors in a manner that is compatible with state-of-the-art imaging assays. Our results reveal that the alginate-gelatin hydrogels can perform similarly to a commercially available ECM scaffold in terms of facilitating microtumor growth. We then applied these microtumor models to quantify the uptake and dark toxicity of benzoporphyrin derivative encapsulated in liposomes with either an anionic or a cationic surface charge. The results indicate that cationic liposomes achieve the highest level of uptake in the microtumors, yet also exert minor toxicity. Moreover, we reveal that there is typically a significant positive correlation between microtumor size and liposome uptake. In conclusion, alginate-based hydrogels are inexpensive and effective scaffolds for 3D culture models of cancer, with versatile applications in research toward photodynamic therapy.

Novel reverse genetics of genotype I and III Japanese encephalitis viruses assembled through transformation associated recombination in yeast: The reporter viruses expressing a green fluorescent protein for the antiviral screening assay

Japanese encephalitis virus (JEV) belongs to a zoonotic flavivirus and is the main cause of viral encephalitis in humans throughout Asia. During the past two decades, both genotypes I (G) and III (GIII) JEVs co-existed in many Asian countries, and the prevalent strains have shifted from GIII to GI. Since all licensed JE vaccines are derived from GIII strains and no specific treatment is available, the development of novel vaccines and specific antiviral drugs against both genotypes is urgently required. To solve the unstable issue of the JEV infectious cDNA clone and establish a reliable antiviral screening assay, we established the yeast artificial chromosome (YAC)-based reverse genetics systems for GI and GIII JEV strains through transformation-associated recombination (TAR) technology in yeast. The YAC-based infectious clones of GI and GIII JEV exhibited high genetic stability both in yeast and E. coli. Using these reverse genetics systems, recombinant EGFP-reporter viruses were generated and remained stable for at least 10 passages in vitro. An image-based antiviral assay for JEV was developed with the EGFP-reporter viruses, and two drugs were identified to have a broad-spectrum inhibitory effect on GI and GIII JEV replication, which provide potential new therapeutic for the treatment of multiple genotypes JEV infection.

Imaging-Based Machine Learning Analysis of Patient-Derived Tumor Organoid Drug Response

Three-quarters of compounds that enter clinical trials fail to make it to market due to safety or efficacy concerns. This statistic strongly suggests a need for better screening methods that result in improved translatability of compounds during the preclinical testing period. Patient-derived organoids have been touted as a promising 3D preclinical model system to impact the drug discovery pipeline, particularly in oncology. However, assessing drug efficacy in such models poses its own set of challenges, and traditional cell viability readouts fail to leverage some of the advantages that the organoid systems provide. Consequently, phenotypically evaluating complex 3D cell culture models remains difficult due to intra- and inter-patient organoid size differences, cellular heterogeneities, and temporal response dynamics. Here, we present an image-based high-content assay that provides object level information on 3D patient-derived tumor organoids without the need for vital dyes. Leveraging computer vision, we segment and define organoids as independent regions of interest and obtain morphometric and textural information per organoid. By acquiring brightfield images at different timepoints in a robust, non-destructive manner, we can track the dynamic response of individual organoids to various drugs. Furthermore, to simplify the analysis of the resulting large, complex data files, we developed a web-based data visualization tool, the Organoizer, that is available for public use. Our work demonstrates the feasibility and utility of using imaging, computer vision and machine learning to determine the vital status of individual patient-derived organoids without relying upon vital dyes, thus taking advantage of the characteristics offered by this preclinical model system.

Improving Generation of Cardiac Organoids from Human Pluripotent Stem Cells Using the Aurora Kinase Inhibitor ZM447439.

Drug-induced cardiotoxicity reduces the success rates of drug development. Thus, the limitations of current evaluation methods must be addressed. Human cardiac organoids (hCOs) derived from induced pluripotent stem cells (hiPSCs) are useful as an advanced drug-testing model; they demonstrate similar electrophysiological functionality and drug reactivity as the heart. How-ever, similar to other organoid models, they have immature characteristics compared to adult hearts, and exhibit batch-to-batch variation. As the cell cycle is important for the mesodermal differentiation of stem cells, we examined the effect of ZM447439, an aurora kinase inhibitor that regulates the cell cycle, on cardiogenic differentiation. We determined the optimal concentration and timing of ZM447439 for the differentiation of hCOs from hiPSCs and developed a novel protocol for efficiently and reproducibly generating beating hCOs with improved electrophysiological functionality, contractility, and yield. We validated their maturity through electro-physiological- and image-based functional assays and gene profiling with next-generation sequencing, and then applied these cells to multi-electrode array platforms to monitor the cardio-toxicity of drugs related to cardiac arrhythmia; the results confirmed the drug reactivity of hCOs. These findings may enable determination of the regulatory mechanism of cell cycles underlying the generation of iPSC-derived hCOs, providing a valuable drug testing platform.

Imaging-based evaluation of pathogenicity by novel DNM2 variants associated with centronuclear myopathy.

A centronuclear myopathy (CNM) is a group of inherited congenital diseases showing clinically progressive muscle weakness associated with the presence of centralized myonuclei, diagnosed by genetic testing and muscle biopsy. The gene encoding dynamin 2, DNM2, has been identified as a causative gene for an autosomal dominant form of CNM. However, the information of a DNM2 variant alone is not always sufficient to gain a definitive diagnosis as the pathogenicity of many gene variants is currently unknown. In this study, we identified five novel DNM2 variants in our cohort. To establish the pathogenicity of these variants without using clinicopathological information, we used a simple in cellulo imaging-based assay for T-tubule-like structures to provide quantitative data that enable objective determination of pathogenicity by novel DNM2 variants. With this assay, we demonstrated that the phenotypes induced by mutant dynamin 2 in cellulo are well correlated with biochemical gain-of-function features of mutant dynamin 2 as well as the clinicopathological phenotypes of each patient. Our approach of combining an in cellulo assay with clinical information of the patients also explains the course of a disease progression by the pathogenesis of each variant in DNM2-associated CNM.

Abstract P158: Phenotypic analysis of myeloid cells in a 3D image-based repolarization assay with tumor spheroids

Abstract Background The immunosuppressive tumor microenvironment (TME) involves multiple cell types and a better understanding of the interplay between these cells could potentially unleash the full potential of many different types of immunotherapies. Tumor infiltrating myeloid cells have both cancer-restraining and cancer-promoting functions. Therefore, to further increase the biological relevance of in vitro platform, we incorporated the myeloid cell compartment into 3D co-cultures of tumor cells and T cells to measure the effects of immune-modulators. Using our proprietary image analysis software and machine learning, a set of morphological features was identified that allowed discrimination between undifferentiated monocytes, M1 and M2 macrophages, and dendritic cells. In addition, the phenotypic profiles of the myeloid cells could be analyzed in the presence of the tumor supernatants or in co-cultures with tumor cells. This assay allows a better understanding of the suppressive tumor microenvironment including multiple cell types and is suitable to test different cancer immunotherapies. Materials and Methods Different myeloid cell populations were generated from healthy PBMCs. Polarized M1 and M2 macrophages, DCs, and undifferentiated monocytes were then co-cultured with tumor conditioned media, spheroids derived from different cancer cell lines, or colorectal cancer organoids (CRC), growing in protein hydrogel in 384 well-plates for 1-7 days. In addition, purified T cells were also incorporated in these cultures. The cellular interactions were visualized using high-content microscopy and OMiner® software, which was trained to identify phenotypic profiles of different myeloid cell populations in 3D, was used to quantify their similarity to the defined subsets upon treatment. Results Myeloid cell populations were classified according to their phenotypic features identified by 3D image analysis, which verified the repolarization of M2 macrophages by their shift into phenotypic space of the M1 type macrophages upon treatment with CSF1r inhibitor or STING agonist. Repolarization was confirmed with an increased similarity score towards M1 macrophages upon treatment. This approach was further used to reveal the different effects of tumor cells and their immunosuppressive TME on myeloid cell phenotypes, showing that each tumor differently influenced the repolarization of the myeloid cells. In addition, triple co-cultures with T cells revealed the suppressive effect of tumor associated myeloid cells on the proliferation and infiltration of T cells. Conclusions The phenotypic analysis of different myeloid cells in 3D co-cultures could be visualized and quantified elucidating the bi-directional interplay between tumor and immune cells, and the functional reprograming of the suppressive tumor associated population towards an M1 phenotype induced by drug candidates. This advanced platform for testing cancer immunotherapies combines the ability to examine the complexity of the TME with the robustness of a high-throughput screening platform. Citation Format: Gera Goverse, Nataliia Beztsinna, Benjamin Visser, Tomas Veenendaal, Marjan van de Merbel, Emma Spanjaard, Ashgard Weterings, Kuan Yan, Leo Price, Lidia Daszkiewicz. Phenotypic analysis of myeloid cells in a 3D image-based repolarization assay with tumor spheroids [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P158.

A Novel Dibenzoxazepine Attenuates Intracellular Salmonella Typhimurium Oxidative Stress Resistance.

ABSTRACTSalmonella enterica serovar Typhimurium is the leading cause of invasive nontyphoidal salmonellosis. Additionally, the emergence of multidrug-resistant S. Typhimurium has further increased the difficulty of controlling its infection. Previously, we showed that an antipsychotic drug, loxapine, suppressed intracellular Salmonella in macrophages. To exploit loxapine’s antibacterial activity, we simultaneously evaluated the anti-intracellular Salmonella activity and cytotoxicity of newly synthesized loxapine derivatives using an image-based high-content assay. We identified that SW14 exhibits potent suppressive effects on intramacrophagic S. Typhimurium with an 50% effective concentration (EC50) of 0.5 μM. SW14 also sensitized intracellular Salmonella to ciprofloxacin and cefixime and effectively controlled intracellular multidrug- and fluoroquinolone-resistant S. Typhimurium strains. However, SW14 did not affect bacterial growth in standard microbiological broth or minimal medium that mimics the phagosomal environment. Cellular autophagy blockade by 3-methyladenine (3-MA) or shATG7 elevated the susceptibility of intracellular Salmonella to SW14. Finally, reactive oxygen species (ROS) scavengers reduced the antibacterial efficacy of SW14, but the ROS levels in SW14-treated macrophages were not elevated. SW14 decreased the resistance of outer membrane-compromised S. Typhimurium to H2O2. Collectively, our data indicated that the structure of loxapine can be further optimized to develop new antibacterial agents by targeting bacterial resistance to host oxidative-stress defense.IMPORTANCE The incidence of diseases caused by pathogenic bacteria with resistance to common antibiotics is consistently increasing. In addition, Gram-negative bacteria are particularly difficult to treat with antibiotics, especially those that can invade and proliferate intracellularly. In order to find a new antibacterial compound against intracellular Salmonella, we established a cell-based high-content assay and identified SW14 from the derivatives of the antipsychotic drug loxapine. Our data indicate that SW14 has no effect on free bacteria in the medium but can suppress the intracellular proliferation of multidrug-resistant (MDR) S. Typhimurium in macrophages. We also found that SW14 can suppress the resistance of outer membrane compromised Salmonella to H2O2, and its anti-intracellular Salmonella activity can be reversed by reactive oxygen species (ROS) scavengers. Together, the findings suggest that SW14 might act via a virulence-targeted mechanism and that its structure has the potential to be further developed as a new therapeutic against MDR Salmonella.