3D Cell-Based High-Content Screening (HCS) Using a Micropillar and Microwell Chip Platform

Application and progress of highcontent imaging in molecular biology

Humans have adopted many different methods to explore matter imaging, among which high content imaging (HCI) could conduct automated imaging analysis of cells while maintaining its structural and functional integrity. Meanwhile, as one of the most important research tools for diagnosing human diseases, HCI is widely used in the frontier of medical research, and its future application has attracted researchers' great interests. Here, the meaning of HCI was briefly explained, the history of optical imaging and the birth of HCI were described, and the experimental methods of HCI were described. Furthermore, the directions of the application of HCI were highlighted in five aspects: protein localization changes, gene identification, chemical and genetic analysis, microbiology, and drug discovery. Most importantly, some challenges and future directions of HCI were discussed, and the application and optimization of HCI were expected to be further explored.

3D cell subculturing pillar dish for pharmacogenetic analysis and high-throughput screening

A pillar dishe for subculture of 3D cultured cells on hydrogel spots (Matrigel and alginate) have been developed. Cells cultured in 3D in an extracellular matrix (ECM) can retain their intrinsic properties, but cells cultured in 2D lose their intrinsic properties as the cells stick to the bottom of the well. Previously, cells and ECM spots were dispensed on a conventional culture dish for 3D cultivation. However, as the spot shape and location depended on user handling, pillars were added to the dish to realize uniform spot shape and stable subculture, supporting 3D cell culture-based high-throughput screening (HTS). Matrigel and alginate were used as ECMs during 6-passage subculture. The growth rate of lung cancer cell (A549) was higher on Matrigel than on alginate. Cancer cell was subcultured in three dimensions in the proposed pillar dish and used for drug screening and differential gene expression analysis. Interestingly, stemness markers, which are unique characteristics of lung cancer cells inducing drug resistance, were upregulated in 3D-subcultured cells compared with those in 2D-subcultured cells. Additionally, the PI3K/Akt/mTOR, VEGFR1/2, and Wnt pathways, which are promising therapeutic targets for lung cancer, were activated, showing high drug sensitivity under 3D-HTS using the 3D-subcultured cells.

In Vitro Three-dimensional (3D) Cell Culture Tools for Spheroid and Organoid Models

Three-dimensional (3D) cell culture technology has been steadily studied since the 1990's due to its superior biocompatibility compared to the conventional two-dimensional (2D) cell culture technology, and has recently developed into an organoid culture technology that further improved biocompatibility. Since the 3D culture of human cell lines in artificial scaffolds was demonstrated in the early 90's, 3D cell culture technology has been actively developed owing to various needs in the areas of disease research, precision medicine, new drug development, and some of these technologies have been commercialized. In particular, 3D cell culture technology is actively being applied and utilized in drug development and cancer-related precision medicine research. Drug development is a long and expensive process that involves multiple steps-from target identification to lead discovery and optimization, preclinical studies, and clinical trials for approval for clinical use. Cancer ranks first among life-threatening diseases owing to intra-tumoral heterogeneity associated with metastasis, recurrence, and treatment resistance, ultimately contributing to treatment failure and adverse prognoses. Therefore, there is an urgent need for the development of efficient drugs using 3D cell culture techniques that can closely mimic in vivo cellular environments and customized tumor models that faithfully represent the tumor heterogeneity of individual patients. This review discusses 3D cell culture technology focusing on research trends, commercialization status, and expected effects developed until recently. We aim to summarize the great potential of 3D cell culture technology and contribute to expanding the base of this technology.

Optimization of 3D-aggregated spheroid model (3D-ASM) for selecting high efficacy drugs

Various three-dimensional (3D) cell culture methods have been developed to implement tumor models similar to in vivo. However, the conventional 3D cell culture method has limitations such as difficulty in using an extracellular matrix (ECM), low experimental reproducibility, complex 3D cell culture protocol, and difficulty in applying to high array plates such as 96- or 384-plates. Therefore, detailed protocols related to robust 3D-aggregated spheroid model (3D-ASM) production were optimized and proposed. A specially designed wet chamber was used to implement 3D-ASM using the hepatocellular carcinoma (HCC) cell lines, and the conditions were established for the icing step to aggregate the cells in one place and optimized ECM gelation step. Immunofluorescence (IF) staining is mainly used to simultaneously analyze drug efficacy and changes in drug-target biomarkers. By applying the IF staining method to the 3D-ASM model, confocal microscopy imaging and 3D deconvolution image analysis were also successfully performed. Through a comparative study of drug response with conventional 2D-high throughput screening (HTS), the 3D-HTS showed a more comprehensive range of drug efficacy analyses for HCC cell lines and enabled selective drug efficacy analysis for the FDA-approved drug sorafenib. This suggests that increased drug resistance under 3D-HTS conditions does not reduce the analytical discrimination of drug efficacy, also drug efficacy can be analyzed more selectively compared to the conventional 2D-HTS assay. Therefore, the 3D-HTS-based drug efficacy analysis method using an automated 3D-cell spotter/scanner, 384-pillar plate/wet chamber, and the proposed 3D-ASM fabrication protocol is a very suitable platform for analyzing target drug efficacy in HCC cells.

High Throughput 3D Cell Migration Assay Using Micropillar/Microwell Chips

The 3D cell migration assay was developed for the evaluation of drugs that inhibit cell migration using high throughput methods. Wound-healing assays have commonly been used for cell migration assays. However, these assays have limitations in mimicking the in vivo microenvironment of the tumor and measuring cell viability for evaluation of cell migration inhibition without cell toxicity. As an attempt to manage these limitations, cells were encapsulated with Matrigel on the surface of the pillar, and an analysis of the morphology of cells attached to the pillar through Matrigel was performed for the measurement of cell migration. The micropillar/microwell chips contained 532 pillars and wells, which measure the migration and viability of cells by analyzing the roundness and size of the cells, respectively. Cells seeded in Matrigel have a spherical form. Over time, cells migrate through the Matrigel and attach to the surface of the pillar. Cells that have migrated and adhered have a diffused shape that is different from the initial spherical shape. Based on our analysis of the roundness of the cells, we were able to distinguish between the diffuse and spherical shapes. Cells in Matrigel on the pillar that were treated with migration-inhibiting drugs did not move to the surface of the pillar and remained in spherical forms. During the conduct of experiments, 70 drugs were tested in single chips and migration-inhibiting drugs without cell toxicity were identified. Conventional migration assays were performed using transwell for verification of the four main migration-inhibiting drugs found on the chip.

Cell Proliferation Receptor-Enhanced 3D High-Throughput Screening Model for Optimized Drug Efficacy Evaluation in Breast Cancer Cells

A higher correlation of epidermal growth factor receptor (EGFR)-targeting drugs has been reported with the use of the cell proliferation receptor-enhanced three-dimensional high-throughput screening model (CPRE 3D-HTS model) compared with two-dimensional (2D) cell-based HTS. A greater expression of differential human EGFR 2 (HER2) protein between HER2-positive and HER2-negative cell lines was observed in breast cancer (BC) cell lines cultured using the CPRE 3D-HTS model compared with 2D-cultured cells. When using 2D-cultured cells, properties such as the expression of the cell proliferation receptor are lost as the cells attach to the bottom of the well plate. In an effort to solve this problem, the CPRE 3D-HTS model expressing high cell proliferation receptors was optimized by the selection of alginate as the extracellular matrix. Results from the use of the CPRE 3D-HTS model showed higher drug resistance with increased expression of drug resistance-related proteins. Of particular interest, a higher correlation of HER2-targeted drugs was observed with the use of the CPRE 3D-HTS model. In order to validate this higher correlation of target drugs observed in the CPRE 3D-HTS model, the results of Western blot analysis and high content imaging analysis were analyzed, which confirmed that 3D-cultured BC cell lines showed a greater difference in the expression of HER2-positive and HER2-negative BC cell lines than 2D-cultured cells. Thus, the use of CPRE 3D-HTS using a 384-pillar plate resulted in increased accuracy when screening HER2-targeted drugs in BC, and it is a very useful platform for analyzing the efficacy of targeted drugs by enhancing the expression of HER2.

A novel 3D pillar/well array platform using patient-derived head and neck tumor to predict the individual radioresponse

•

Radiotherapy is a critical modality in head and neck cancer treatment.

•

A novel 3D pillar/well array platform provides the individual radioresponse biomarker, RT_auc.

•

Poor and good radioresponse group by RT_auc correlates with other clinical features.

•

RT_auc shows potential for radioresponse biomarker, useful in clinical decision-making.

Predicting individual radiotherapy (RT) response is valuable in managing head and neck squamous cell carcinoma (HNSCC). We assessed the feasibility of our novel 3D culture platform to measure radioresponse using patient-derived cells (PDCs) from HNSCC patients.

Cells from the FaDu line and tumor samples from 39 HNSCC patients were cultivated serially in Matrigel^TM on a 3D pillar/well array culture system. The 3D tumor models were exposed to 0 to 8 Gy of radiation dose, and the radioresponse index (RT_auc, area under the dose-response curve) was measured quantitatively with Calcein AM staining of live tumor cells. Calcein AM fluorescence showed reduced density and the number of FaDu colonies as radiation increased, implying a dose-dependent effect on cell viability in the 3D pillar/well culture system. 3D tumor models using PDCs were established successfully from 39 HNSCC patient tumor samples, maintaining original genomic and pathological characteristics. These 3D tumor models were exposed to ionizing radiation on a 3D pillar/well array, with a mean period of 12 days from tumor harvest to the measurement of RT_auc. The RT_auc of all PDCs varied from 3.5 to 9.4, and the lower 40th percentile (Z-score = -0.26) was considered a good radioresponse group with a threshold RT_auc of 4.6. The good radioresponse group showed fewer adverse features than others. As of the last follow-up, recurrence-free survival was better in the good radioresponse group (p = 0.037). 3D pillar/well array platforms using PDC could rapidly quantify radioresponse index in patients with HNSCC, showing potential as a novel prognosticator.

Patient-Derived Tumor Organoids for Guidance of Personalized Drug Therapies in Recurrent Glioblastoma

An obstacle to effective uniform treatment of glioblastoma, especially at recurrence, is genetic and cellular intertumoral heterogeneity. Hence, personalized strategies are necessary, as are means to stratify potential targeted therapies in a clinically relevant timeframe. Functional profiling of drug candidates against patient-derived glioblastoma organoids (PD-GBO) holds promise as an empirical method to preclinically discover potentially effective treatments of individual tumors. Here, we describe our establishment of a PD-GBO-based functional profiling platform and the results of its application to four patient tumors. We show that our PD-GBO model system preserves key features of individual patient glioblastomas in vivo. As proof of concept, we tested a panel of 41 FDA-approved drugs and were able to identify potential treatment options for three out of four patients; the turnaround from tumor resection to discovery of treatment option was 13, 14, and 15 days, respectively. These results demonstrate that this approach is a complement and, potentially, an alternative to current molecular profiling efforts in the pursuit of effective personalized treatment discovery in a clinically relevant time period. Furthermore, these results warrant the use of PD-GBO platforms for preclinical identification of new drugs against defined morphological glioblastoma features.

High-dose drug heat map analysis for drug safety and efficacy in multi-spheroid brain normal cells and GBM patient-derived cells

To test the safety and efficacy of drugs via a high does drug heat map, a multi-spheroids array chip was developed by adopting a micropillar and microwell structure. In the chip, patient-derived cells were encapsulated in alginate and grown to maturity for more than 7 days to form cancer multi-spheroids. Multi-spheroids grown in conventional well plates require many cells and are easily damaged as a result of multiple pipetting during maintenance culture or experimental procedures. To address these issues, we applied a micropillar and microwell structure to the multi-spheroids array. Patient-derived cells from patients with Glioblastoma (GBM), the most common and lethal form of central nervous system cancer, were used to validate the array chip performance. After forming multi-spheroids with a diameter greater than 100μm in a 12×36 pillar array chip (25mm × 75mm), we tested 70 drug compounds (6 replicates) using a high-dose to determine safety and efficacy for drug candidates. Comparing the drug response of multi-spheroids derived from normal cells and cancer cells, we found that four compounds (Dacomitinib, Cediranib, LY2835219, BGJ398) did not show toxicity to astrocyte cell and were efficacious to patient-derived GBM cells.

U-Net Deep-Learning-Based 3D Cell Counter for the Quality Control of 3D Cell-Based Assays through Seed Cell Measurement

Conventional cell-counting software uses contour or watershed segmentations and focuses on identifying two-dimensional (2D) cells attached on the bottom of plastic plates. Recently developed software has been useful tools for the quality control of 2D cell-based assays by measuring initial seed cell numbers. These algorithms do not, however, quantitatively test in three-dimensional (3D) cell-based assays using extracellular matrix (ECM), because cells are aggregated and overlapped in the 3D structure of the ECM such as Matrigel, collagen, and alginate. Such overlapped and aggregated cells make it difficult to segment cells and to count the number of cells accurately. It is important, however, to determine the number of cells to standardize experiments and ensure the reproducibility of 3D cell-based assays. In this study, we apply a 3D cell-counting method using U-net deep learning to high-density aggregated cells in ECM to identify initial seed cell numbers. The proposed method showed a 10% counting error in high-density aggregated cells, while the contour and watershed segmentations showed 30% and 40% counting errors, respectively. Thus, the proposed method can reduce the seed cell-counting error in 3D cell-based assays by providing the exact number of cells to researchers, thereby enabling the acquisition of quality control in 3D cell-based assays.

3D-printed microplate inserts for long term high-resolution imaging of live brain organoids

BACKGROUND

Organoids are a reliable model used in the study of human brain development and under pathological conditions. However, current methods for brain organoid culture generate tissues that range from 0.5 to 2 mm of size, which need to be constantly agitated to allow proper oxygenation. The culture conditions are, therefore, not suitable for whole-brain organoid live imaging, required to study developmental processes and disease progression within physiologically relevant time frames (i.e. days, weeks, months).

RESULTS

Here we designed 3D-printed microplate inserts adaptable to standard 24 multi-well plates, which allow the growth of multiple organoids in pre-defined and fixed XYZ coordinates. This innovation facilitates high-resolution imaging of whole-cerebral organoids, allowing precise assessment of organoid growth and morphology, as well as cell tracking within the organoids, over long periods. We applied this technology to track neocortex development through neuronal progenitors in brain organoids, as well as the movement of patient-derived glioblastoma stem cells within healthy brain organoids.

CONCLUSIONS

This new bioengineering platform constitutes a significant advance that permits long term detailed analysis of whole-brain organoids using multimodal inverted fluorescence microscopy.

Micropatterned Coculture Platform for Screening Nerve-Related Anticancer Drugs

Accumulating evidence suggests that the neural microenvironment plays a vital role in the development and metastasis of cancers. The development of drug candidates or drug combinations targeting the neural microenvironment is thus becoming increasingly urgent. However, the low content of conventional drug screening platforms is a bottleneck that limits the drug evaluation process. In this study, we present a micropatterned coculture-based high-content (μCHC) platform by integrating a micropatterned coculture chip with the high-content analysis (HCA) system, for studying the neuron-cancer cell interactions and drug screening (simultaneously detecting 96 kinds of post-drug-treated conditions). We investigate the contribution of neurons on the migration of cancer cells from different tissues and validate the capability of the μCHC system to study the interaction between neurons and cancer cells. Moreover, we test the effects of individual or combinatory agents targeting the neuron or cancer cell on the neuron-cancer cell interactions, which proposes an optimized therapy regime for targeting both nervous and cancerous factors. Our study suggests that the μCHC system is a facile platform for screening drug candidates or drug combinations for clinical cancer therapy with high efficiency and fidelity.

On-demand mixing and dispersion in mini-pillar based microdroplets

The analysis and detection of ultra-trace biomarkers are often carried out in microliter droplets. Common stirring approaches have some difficulties in precise and contactless mixing and dispersion in microdroplets. In this work, an open mini-pillar-based platform that integrates with ultrasound units is developed to achieve contactless mixing and dispersion in microliter samples. On such a platform, mini-pillars can anchor microdroplets as individual microreactors, and each ultrasound unit can be remotely controlled to achieve on-demand contactless micro-stirring, which is also confirmed by mixing and dispersing of Fe3O4 nanoparticles (1 μm) in microdroplets (10 μL). Such on-demand high-throughput mixing and dispersion that integrates ultrasound mixing with microdroplet technology provides a potential robot-based platform for achieving high-throughput and ultra-trace biosensing in microliter droplets.

Droplet array for open-channel high-throughput SERS biosensing

Open-channel and high throughput are two important aspects of clinical diagnosis, correlation biochemical analysis, cell culture techniques and food safety. Here, we propose the mini-pillar based array for open-channel and high-throughput SERS detection of miRNA. The polydimethylsiloxane (PDMS) mini-pillars are used as a high-throughput platform, which have good anchoring and aggregation effects on microdroplets, greatly reducing the amount of analytical solution and facilitate the homogeneous sample distribution after evaporation. The deposited gold nanorods (Au NRs) on the pillars with optimized diameter served as SERS-active substrate, can greatly improve the sensitivity of SERS signal compared to other planar substrates. On the open-channel biological chip, sensitive, simultaneous, and specific detection of breast cancer marker miRNA-1246 can be performed. In this mini-pillar array SERS system, the limit of detection (LOD) is 10^-12 M. The mini-pillar array shows enormous potential for open channel, high-throughput biomolecular detection, providing an opportunity for biomedical point-of-care testing (POCT) and drug screening.

A rapid quantification of invasive phenotype in head and neck squamous cell carcinoma: A novel 3D pillar array system

BACKGROUND

The widely used in vitro invasion assays for head and neck squamous cell carcinoma (HNSCC) are wound healing, transwell, and organotypic assays. However, these are still lab-intensive and time-consuming tasks. For the rapid detection and high throughput screening of invasiveness in 3D condition, we propose a novel spheroid invasion assay using commercially available pillar platform system.

MATERIALS AND METHODS

Using the pillar-based spheroid invasion assay, migration and invasion was evaluated in three patient-derived cells (PDCs) of HNSCC. Immunofluorescence of live cells was used for the quantitative measurement of migratory and invaded cells attached to the pillar. Expression of epithelial-mesenchymal transition (EMT)-related gene (snai1/2) was measured by qRT-PCR. We also tested the impact of drug treatments (cisplatin, docetaxel) on the changes in the invasive phenotype.

RESULTS

All PDCs successfully formed spheroid at 4 days and can be measured invasiveness within 7 days. Intriguingly, one PDC (#1) obtained from the advanced stage showed robust migration, invasion and higher transcription of snai1/2, compared with the other two PDCs. Furthermore, the invasion ratio of the control spheroids was about 70% while the invasion ratios of drug-treated spheroids were lower than 50%, and the difference showed statistical significance (p < 0.01).

CONCLUSION

The presented spheroid invasion assay using pillar array could be useful for the evaluation of cancer cell behavior and physiology in response to diverse therapeutic drugs.

Systematic Evaluation of Gastric Tumor Cell Index and Two-Drug Combination Therapy via 3-Dimensional High-Throughput Drug Screening

Tumor heterogeneity greatly limits personalized treatment of cancer. Patient-derived tumor cell (PDC) models precisely recapitulate the molecular properties and biology of the disease, making them effective preclinical tools for assessing anti-cancer drug activities. Accurate estimation of tumor purity is essential for performing high-throughput drug screening (HTS). In the present study, we measured and predicted the tumor population index in PDC models for two-drug combinational strategies using HTS system. Gastric cancer cell-lines and PDCs were subjected to multi-color immunofluorescence analysis against EpCAM and vimentin to evaluate the tumor cell index based on EpCAM expression levels. We generated a tumor purity prediction model using five different gastric cancer cell-lines (AGS, KATO-III, MKN-45, NCI-N87, SNU-216) with fluorescence intensity-based techniques. Afterwards, stage IV gastric cancer PDC models were evaluated using a micropillar/microwell chip-based HTS system. HER2/CCNE1-amplified PDCs were considerably resistant to an HER2 inhibitor, while combinational treatment consisting of an HER2 inhibitor with anti-WEE1 compound substantially suppressed tumor cellular growth. Moreover, PDCs with BRCA1/2 mutations were synergistically sensitive to HER2 and PARP inhibition therapy. Finally, somatic mutations in TP53 and CDKN2A with MYC amplification rendered PDCs susceptible to the drug combination of WEE1 and HER2. Collectively, our systematic method of high-throughput drug sensitivity screening is an integral pre-clinical platform for evaluating potential two-drug combinational approaches for personalized treatment of cancer.

A Cancer Spheroid Array Chip for Selecting Effective Drug

A cancer spheroid array chip was developed by modifying a micropillar and microwell structure to improve the evaluation of drugs targeting specific mutations such as phosphor-epidermal growth factor receptor (p-EGFR). The chip encapsulated cells in alginate and allowed cancer cells to grow for over seven days to form cancer spheroids. However, reagents or media used to screen drugs in a high-density spheroid array had to be replaced very carefully, and this was a tedious task. Particularly, the immunostaining of cancer spheroids required numerous steps to replace many of the reagents used for drug evaluation. To solve this problem, we adapted a micropillar and microwell structure to a spheroid array. Thus, culturing cancer spheroids in alginate spots attached to the micropillar allowed us to replace the reagents in the microwell chip with a single fill of fresh medium, without damaging the cancer spheroids. In this study, a cancer spheroid array was made from a p-EGFR-overexpressing cell line (A549 lung cancer cell line). In a 12 by 36 column array chip (25 mm by 75 mm), the spheroid over 100 µm in diameter started to form at day seven and p-EGFR was also considerably overexpressed. The array was used for p-EGFR inhibition and cell viability measurement against seventy drugs, including ten EGFR-targeting drugs. By comparing drug response in the spheroid array (spheroid model) with that in the single-cell model, we demonstrated that the two models showed different responses and that the spheroid model might be more resistant to some drugs, thus narrowing the choice of drug candidates.