High-Throughput Miniaturized Synthesis of PROTAC-Like Molecules.

The development of miniaturized high-throughput in situ screening platforms capable of handling the entire process of drug synthesis to final screening is essential for advancing drug discovery in the future. In this study, an approach based on combinatorial solid-phase synthesis, enabling the efficient synthesis of libraries of proteolysis targeting chimeras (PROTACs) in an array format is presented. This on-chip platform allows direct biological screening without the need for transfer steps.  UV-induced release of target molecules into individual droplets facilitates further on-chip experimentation. Utilizing a mitogen-activated protein kinase kinases (MEK1/2) degrader as a template, a series of 132 novel PROTAC-like molecules is synthesized using solid-phase Ugi reaction. These compounds are further characterized using various methods, including matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) imaging, while consuming only a few milligrams of starting materials in total. Furthermore, the feasibility of culturing cancer cells on the modified spots and quantifying the effect of MEK suppression is demonstrated. The miniaturized synthesis platform lays a foundation for high-throughput in situ biological screening of potent PROTACs for potential anticancer activity and offers the potential for accelerating the drug discovery process by integrating miniaturized synthesis and biological steps on the same array.

The genetic variant rs55986091 HLA-DQB1 is associated with a protective effect against cervical cancer.

Introduction: Cervical cancer (CC) is a prevalent malignancy affecting women globally. The primary causative factor of CC is the high-risk oncogenic human papillomavirus (HR-HPV). However, it is noteworthy that not all women infected with HR-HPV develop cancer, indicating the potential involvement of genetic predisposition in the development of CC. This study aims to identify genetic risks and their distribution in groups of women with different epidemiological features of HR-HPV. Materials and methods: A comparison was conducted among four groups of women, comprising 218 HPV-negative women, 120 HPV-positive women, 191 women diagnosed with cervical intraepithelial neoplasia (CIN) grade 2 or 3, and 124 women diagnosed with CC. The analysis focused on four single nucleotide polymorphisms (SNPs): rs55986091 in HLA-DQB1, rs138446575 in TTC34, rs1048943 in CYP1A1, and rs2910164 in miRNA-146a. Results: The rs55986091-A allele exhibited a protective effect within the "CC" group when compared to the "HPV-Negative" group (OR = 0.4, 95% CI= 0.25-0.65) using a log-additive model. Additionally, similar protective effects were observed in the "CIN 2/3" group compared to the "HPV-Negative" group (OR = 0.47, 95% CI = 0.28-0.79). Conclusion: The data obtained emphasize the importance of developing PCR-based diagnostic kits for the identification of SNP alleles, particularly for rs55986091, among HR-HPV-positive women within the Russian population.

Repurposing FDA-Approved Drugs for Temozolomide-Resistant IDH1 Mutant Glioma Using High-Throughput Miniaturized Screening on Droplet Microarray Chip.

To address the challenge of drug resistance and limited treatment options for recurrent gliomas with IDH1 mutations, a highly miniaturized screening of 2208 FDA-approved drugs is conducted using a high-throughput droplet microarray (DMA) platform. Two patient-derived temozolomide-resistant tumorspheres harboring endogenous IDH1 mutations (IDH1mut ) are utilized. Screening identifies over 20 drugs, including verteporfin (VP), that significantly affected tumorsphere formation and viability. Proteomics analysis reveals that nuclear pore complex may be a potential VP target, suggesting a new mechanism of action independent of its known effects on YAP1. Knockdown experiments exclude YAP1 as a drug target in tumorspheres. Pathway analysis shows that NUP107 is a potential upstream regulator associated with VP response. Analysis of publicly available genomic datasets shows a significant correlation between high NUP107 expression and decreased survival in IDH1mut astrocytoma, suggesting NUP107 may be a potential biomarker for VP response. This study demonstrates a miniaturized approach for cost-effective drug repurposing using 3D glioma models and identifies nuclear pore complex as a potential target for drug development. The findings provide preclinical evidence to support in vivo and clinical studies of VP and other identified compounds to treat IDH1mut gliomas, which may ultimately improve clinical outcomes for patients with this challenging disease.

Automated high-throughput image processing as part of the screening platform for personalized oncology.

Cancer is a devastating disease and the second leading cause of death worldwide. However, the development of resistance to current therapies is making cancer treatment more difficult. Combining the multi-omics data of individual tumors with information on their in-vitro Drug Sensitivity and Resistance Test (DSRT) can help to determine the appropriate therapy for each patient. Miniaturized high-throughput technologies, such as the droplet microarray, enable personalized oncology. We are developing a platform that incorporates DSRT profiling workflows from minute amounts of cellular material and reagents. Experimental results often rely on image-based readout techniques, where images are often constructed in grid-like structures with heterogeneous image processing targets. However, manual image analysis is time-consuming, not reproducible, and impossible for high-throughput experiments due to the amount of data generated. Therefore, automated image processing solutions are an essential component of a screening platform for personalized oncology. We present our comprehensive concept that considers assisted image annotation, algorithms for image processing of grid-like high-throughput experiments, and enhanced learning processes. In addition, the concept includes the deployment of processing pipelines. Details of the computation and implementation are presented. In particular, we outline solutions for linking automated image processing for personalized oncology with high-performance computing. Finally, we demonstrate the advantages of our proposal, using image data from heterogeneous practical experiments and challenges.

Relationship between Phenolic Compounds and Antioxidant Activity in Berries and Leaves of Raspberry Genotypes and Their Genotyping by SSR Markers.

The red raspberry is one of the world's most popular berries. The main direction of its breeding has switched to nutritional quality, and the evaluation of raspberry germplasm for antioxidant content and activity is very important. As berries, raspberry leaves contain valuable bioactive compounds, but the optimal time for their collection is unknown. We evaluated 25 new breeding lines and standard raspberry cultivars for their polyphenolic content and antioxidant capacity. The antioxidant activity of berries correlated better with the content of total phenolics (0.88 and 0.92) and flavonoids (0.76 and 0.88) than with anthocyanins (0.37 and 0.66). Two breeding lines were significantly superior to the standard cultivars and can be used in further breeding. Leaves collected in three phenological phases of the raspberry contained more phenolics (5.4-fold) and flavonoids (4.1-fold) and showed higher antioxidant activities (2.4-fold in FRAP assay, 2.2-fold in ABTS) than berries. The optimal time for harvesting raspberry leaves is the fruit ripening stage, with exceptions for some cultivars. Genetic diversity analysis using microsatellite (SSR) markers from flavonoid biosynthesis genes divided the genotypes into five clusters, generally in agreement with their kinships. The relationship between genetic data based on metabolism-specific SSR markers and the chemical diversity of cultivars was first assessed. The biochemical and genetic results show a strong correlation (0.78). This study is useful for further the improvement of raspberry and other berry crops.

Extracellular matrix remodeling in anthracycline-induced cardiotoxicity: What place on the pedestal?

OBJECTIVE: To evaluate the role of matrix metalloproteinases (MMP)-2 and 9 and the gene polymorphisms of MMP-2 (rs243865) and MMP-9 (rs3918242) in the course of anthracycline-induced cardiotoxicity (AIC) in women without previous cardiovascular diseases (CVD) during 24-months. METHODS: A total of 114 women (47.0 [44.0; 52.0] years old) with AIC of NYHA class I-III who received doxorubicin for breast cancer were enrolled. RESULTS: After 24 months patients had breast cancer remission and were divided into 2 groups: group 1 comprised women with adverse course of AIC (n = 54), group 2 comprised those without it (n = 60). Serum levels of MMP-2 were higher by 8% (p = 0.017) MMP9 by 18.4% (p < 0.001) in group 1 than in group 2. In group 1 the levels of MMP-2 increased (p < 0.001) from 376.8 (329.5; 426.7) to 481.4 (389.8; 518.7) pg/mL, and MMP-9 increased (p < 0.001) from 23.6 (21.4; 24.6) to 26.0 (23.3; 27.0) pg/mL at 24 months. In group 2 the both MMP-2 and MMP-9 level decreased at 24 months. Based on ROC-analysis, the levels of MMP2 ≥ 388.2 pg/mL (AUС = 0.64; р = 0.013) and MMP-9 ≥ 21.25 pg/mL (AUС = 0.9; р < 0.001) were identified as predictors for adverse course of AIHF. The presence of C/C genotype of MMP2 (OR = 4.76; p = 0.029) and C/C genotype of MMP-9 (OR = 15.2; p < 0.0001) were related with adverse course of AIHF and higher levels of MMP-2 and MMP-9. CONCLUSION: Gene polymorphisms of MMP-2 (rs243865) and MMP-9 (rs3918242) and serum levels of MMP-2 and MMP-9 levels in women without previous CVD were associated with adverse course of AIC during 24 months.

Anthracycline-induced cardiotoxicity in women without cardiovascular diseases: molecular and genetic predictors.

OBJECTIVE: To evaluate role of molecular (endothelin-1, soluble Fas-L, NT-proBNP, TNF-α, interleukin-1ß,) and genetic factors (NOS3 (rs1799983), EDNRA (C + 70G, rs5335), NADPH oxidase (C242T, rs4673), p53 protein (polymorphic marker-Arg72Pro exon 4, rs1042522), NOS3 (Glu298Asp, rs1799983), Caspase 8 (CASP8, rs3834129 and rs1045485), interleukin-1ß gene (Il-1ß, rs1143634), TNF-α gene (rs1800629), SOD2 (rs4880), GPX1 (rs1050450) in development of anthracycline-induced cardiotoxicity (AIC) in women without cardiovascular diseases. METHODS: A total of 176 women with breast cancer and without cardiovascular diseases who received anthracyclines were enrolled in the study. After the 12 months of chemotherapy (CT), all patients were divided into two groups: group 1 (n = 52) comprised patients with AIC, group 2 (n = 124) comprised those without it. RESULTS: Based on ROC-analysis, levels of endothelin-1 of ≥9.0 pg/mL (AUC of 0.699), sFas-L of ≥98.3 ng/mL (AUC of 0.990), and NT-proBNP of ≥71.5 pg/mL (AUC of 0.994;) were identified as a cut-off values predicting AIC during 12 months after CT. Whereas, NT-proBNP and sFas-L were more significant predictors than endothelin-1 (p < 0.001). The development of AIC was significantly related to Arg/Arg of p53 protein gene (OR = 2.972; p = 0.001), T/T of NOS3 gene (OR = 3.059, p = 0.018), T/T of NADPH oxidase gene (OR = 2.753, p = 0.008), and C/C of GPX1 (OR = 2.345; p = 0.007). CONCLUSION: Evaluation of polymorphisms genes of p53 (rs1042522), NOS3 (rs1799983), GPX1 (rs1050450), and NADPH oxidase (rs4673) can be recommended before CT for the risk assessment of AIC development. The serum levels of NT-proBNP and soluble Fas-L after CT may be considered as non-invasive biomarkers for prediction of AIC development during the 12 months.

Fast Nanoliter-Scale Cell Assays Using Droplet Microarray-Mass Spectrometry Imaging.

In pharmaceutical research and development, cell-based assays are primarily used with readout that rely on fluorescence-based and other label-dependent techniques for analysis of different cellular processes. Superhydrophobic-hydrophilic droplet microarrays (DMA) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) have recently emerged as key technologies for miniaturized high-throughput cell assays and for label-free molecular high-content drug profiling, respectively. Here, nanoliter-scale cell assays are integrated on DMAs with MALDI-MS imaging (MALDI-MSI) approaches to a droplet microarray-mass spectrometry imaging (DMA-MSI) platform. Using A549 lung cancer cells, concentration-response profiling of a pharmaceutical compound, the fatty acid synthase inhibitor GSK2194069, are demonstrated. Direct cell culture on DMAs enables combination of microscopy and high speed, high molecular content analysis using MALDI-MSI. Miniaturization of array spots down to 0.5 mm confining 40 nL droplets allows for MALDI imaging analysis of as few as ten cells per spot. Partial automation ensures a fast sample preparation workflow. Taken together, the integrated DMA-MSI platform that combines MALDI-MSI, as a label-free analytical readout, with the miniaturized droplet microarray platform is a valuable complement to high throughput cell-based assays technologies.

Anthracycline-Induced Cardiotoxicity: The Role of Endothelial Dysfunction.

Cardiovascular disease remains the leading cause of mortality accounting up to 40% of all deaths, but, currently, cancer is prominent cause of death globally. Anthracyclines are the cornerstone of chemotherapy in women with breast cancer. However, its clinical use is limited by their cardiotoxic effects that can trigger heart failure development. Vascular toxicity of chemotherapy may be linked with endothelial dysfunction because anthracycline damage of endothelial cells can lead to the development and progression of cardiomyopathy by decreasing the release and activity of endothelial factors and, ultimately, endothelial cell death. These processes suppress anti-inflammatory and vascular reparative functions and initiate the development of future cardiovascular events. Recent studies have shown that chemotherapy may induce toxicity in the vascular endothelium and is accompanied by systemic endothelial dysfunction in patients with diagnosed cardiovascular diseases. Because the initial endothelial cell insult is likely asymptomatic, there is often a long delay between the termination of doxorubicin therapy and the onset of vascular disorders. In this case, genetic susceptibility factor will help to identify susceptible patients in the future. The objectives of this study were to evaluate prognostic role of molecular (endothelin-1) and genetic factors (gene polymorphisms of endothelial nitric oxide (NO) synthase (NOS3, rs1799983), endothelin-1 receptor type A (EDNRA, C+70G, rs5335) and NADPH oxidase (C242T, rs4673) in development of endothelial dysfunction and anthracycline-induced cardiotoxicity in women without cardiovascular diseases.

Miniaturized Drug Sensitivity and Resistance Test on Patient-Derived Cells Using Droplet-Microarray.

Testing the sensitivity of patient-derived tumor cells ex vivo can potentially help determining the appropriate treatment for each patient and spot the development of resistance to a given therapy. The number of cells obtainable from a biopsy is, however, often insufficient for performing ex vivo tests in conventional microtiter plates. Here, we introduce a novel Droplet-Microarray platform based on a hydrophilic-superhydrophobic patterned surface that enables screenings using only 100 cells and 30 picomoles of a drug per individual nanoliter-sized droplet. We demonstrate that the dose-response of as few as 100 primary patient-derived chronic lymphocytic leukemia (CLL) cells to anticancer compounds on the Droplet-Microarray platform resembles the dose-response obtained in 384-well plates requiring 20,000 tumor cells per experiment. The extremely miniaturized Droplet-Microarray platform thus carries great potential for ex vivo drug sensitivity and resistance tests on patient-derived tumor cells and potentially for implementing such tests in medical practice of precision medicine.

Assembly of Multi-Spheroid Cellular Architectures by Programmable Droplet Merging.

Artificial multicellular systems are gaining importance in the field of tissue engineering and regenerative medicine. Reconstruction of complex tissue architectures in vitro is nevertheless challenging, and methods permitting controllable and high-throughput fabrication of complex multicellular architectures are needed. Here, a facile and high-throughput method is developed based on a tunable droplet-fusion technique, allowing programmed assembly of multiple cell spheroids into complex multicellular architectures. The droplet-fusion technique allows for construction of various multicellular architectures (double-spheroids, multi-spheroids, hetero-spheroids) in a miniaturized high-density array format. As an example of application, the propagation of Wnt signaling is investigated within hetero-spheroids formed from two fused Wnt-releasing and Wnt-reporter cell spheroids. The developed method provides an approach for miniaturized, high-throughput construction of complex 3D multicellular architectures and can be applied for studying various biological processes including cell signaling, cancer invasion, embryogenesis, and neural development.

Droplet Microarray Based on Nanosensing Probe Patterns for Simultaneous Detection of Multiple HIV Retroviral Nucleic Acids.

Multiplexed detection of viral nucleic acids is important for rapid screening of viral infection. In this study, we present a molybdenum disulfide (MoS2) nanosheet-modified dendrimer droplet microarray (DMA) for rapid and sensitive detection of retroviral nucleic acids of human immunodeficiency virus-1 (HIV-1) and human immunodeficiency virus-2 (HIV-2) simultaneously. The DMA platform was fabricated by omniphobic-omniphilic patterning on a surface-grafted dendrimer substrate. Functionalized MoS2 nanosheets modified with fluorescent dye-labeled oligomer probes were prepatterned on positively charged amino-modified omniphilic spots to form a fluorescence resonance energy transfer (FRET) sensing microarray. With the formation of separated microdroplets of sample on the hydrophobic-hydrophilic micropattern, prepatterned oligomer probes specifically hybridized with the target HIV genes and detached from the MoS2 nanosheet surface due to weakening of the adsorption force, leading to fluorescence signal recovery. As a proof of concept, we used this microarray with a small sample size (<150 nL) for simultaneous detection of HIV-1 and HIV-2 nucleic acids with a limit of detection (LOD) of 50 pM. The multiplex detection capability was further demonstrated for simultaneous detection of five viral genes (HIV-1, HIV-2, ORFlab, and N genes of SARS-COV-2 and M gene of Influenza A). This work demonstrated the potential of this novel MoS2-DMA FRET sensing platform for high-throughput multiplexed viral nucleic acid screening.

Facile One Step Formation and Screening of Tumor Spheroids Using Droplet-Microarray Platform.

Tumor spheroids or microtumors are important 3D in vitro tumor models that closely resemble a tumor's in vivo "microenvironment" compared to 2D cell culture. Microtumors are widely applied in the fields of fundamental cancer research, drug discovery, and precision medicine. In precision medicine tumor spheroids derived from patient tumor cells represent a promising system for drug sensitivity and resistance testing. Established and commonly used platforms for routine screenings of cell spheroids, based on microtiter plates of 96- and 384-well formats, require relatively large numbers of cells and compounds, and often lead to the formation of multiple spheroids per well. In this study, an application of the Droplet Microarray platform, based on hydrophilic-superhydrophobic patterning, in combination with the method of hanging droplet, is demonstrated for the formation of highly miniaturized single-spheroid-microarrays. Formation of spheroids from several commonly used cancer cell lines in 100 nL droplets starting with as few as 150 cells per spheroid within 24-48 h is demonstrated. Established methodology carries a potential to be adopted for routine workflows of high-throughput compound screening in 3D cancer spheroids or microtumors, which is crucial for the fields of fundamental cancer research, drug discovery, and precision medicine.

Evaluation of the Droplet-Microarray Platform for High-Throughput Screening of Suspension Cells.

Phenotypic cell-based high-throughput screenings play a central role in drug discovery and toxicology. The main tendency in cell screenings is the increase of the throughput and decrease of reaction volume in order to accelerate the experiments, reduce the costs, and enable screenings of rare cells. Conventionally, cell-based assays are performed in microtiter plates, which exist in 96- to 1536-wells formats and cannot be further miniaturized. In addition, performing screenings of suspension cells is associated with risk of losing cell content during the staining procedures and incompatibility with high-content microscopy. Here, we evaluate the Droplet-Microarray screening platform for culturing, screening, and imaging of suspension cells. We demonstrate pipetting-free cell seeding and proliferation of cells in individual droplets of 3-80 nL in volume. We developed a methodology to perform parallel treatment, staining, and fixation of suspension cells in individual droplets. Automated imaging of live suspension cells directly in the droplets combined with algorithms for pattern recognition for image analysis is demonstrated. We evaluated the developed methodology by performing a dose-response study with antineoplastic drugs. We believe that the DMA screening platform carries great potential to be adopted for broad spectrum of screenings of suspension cells.

Droplet Microarray Based on Superhydrophobic-Superhydrophilic Patterns for Single Cell Analysis.

Single-cell analysis provides fundamental information on individual cell response to different environmental cues and is a growing interest in cancer and stem cell research. However, current existing methods are still facing challenges in performing such analysis in a high-throughput manner whilst being cost-effective. Here we established the Droplet Microarray (DMA) as a miniaturized screening platform for high-throughput single-cell analysis. Using the method of limited dilution and varying cell density and seeding time, we optimized the distribution of single cells on the DMA. We established culturing conditions for single cells in individual droplets on DMA obtaining the survival of nearly 100% of single cells and doubling time of single cells comparable with that of cells cultured in bulk cell population using conventional methods. Our results demonstrate that the DMA is a suitable platform for single-cell analysis, which carries a number of advantages compared with existing technologies allowing for treatment, staining and spot-to-spot analysis of single cells over time using conventional analysis methods such as microscopy.