Discovery Of Pathways Research Articles

New small molecules in dermatology: for the autoimmunity, inflammation and beyond.

The discovery of new inflammatory pathways and the mechanism of action of inflammatory, autoimmune, genetic, and neoplastic diseases led to the development of immunologically driven drugs. We aimed to perform a narrative review regarding the rising of a new class of drugs capable of blocking important and specific intracellular signals in the maintenance of these pathologies: the small molecules. A total of 114 scientific papers were enrolled in this narrative review. We describe in detail the families of protein kinases-Janus Kinase (JAK), Src kinase, Syk tyrosine kinase, Mitogen-Activated Protein Kinase (MAPK), and Bruton Tyrosine Kinase (BTK)-their physiologic function and new drugs that block these pathways of intracellular signaling. We also detail the involved cytokines and the main metabolic and clinical implications of these new medications in the field of dermatology. Despite having lower specificity compared to specific immunobiological therapies, these new drugs are effective in a wide variety of dermatological diseases, especially diseases that had few therapeutic options, such as psoriasis, psoriatic arthritis, atopic dermatitis, alopecia areata, and vitiligo.

Exciting new discoveries in phytochrome-mediated light signaling pathways

Exciting new discoveries in phytochrome-mediated light signaling pathways

Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens.

Most variants associated with complex traits and diseases identified by genome-wide association studies (GWAS) map to noncoding regions of the genome with unknown effects. Using ancestrally diverse, biobank-scale GWAS data, massively parallel CRISPR screens, and single-cell transcriptomic and proteomic sequencing, we discovered 124 cis-target genes of 91 noncoding blood trait GWAS loci. Using precise variant insertion through base editing, we connected specific variants with gene expression changes. We also identified trans-effect networks of noncoding loci when cis target genes encoded transcription factors or microRNAs. Networks were themselves enriched for GWAS variants and demonstrated polygenic contributions to complex traits. This platform enables massively parallel characterization of the target genes and mechanisms of human noncoding variants in both cis and trans.

Statins and highly sensitive cardiac troponins: cardiotoxicity or cross-reactivity?

To date, hypolipidemic drugs of the statin group are among the most popular therapeutic agents used for the prevention and treatment of the most common worldwide atherosclerotic cardiovascular diseases (CVD). Therefore, considerable attention of researchers is focused on statins to study the additional effects of these drugs, which is accompanied by the discovery of new mechanisms of action and properties that should be taken into account to optimize the tactics of managing patients with CVD. In addition to the key lipid-lowering effect of statins associated with the inhibition of the ratelimiting enzyme (3-hydroxy-3-methylglutaryl-coenzyme A reductase), researchers report a variety of other properties of these drugs. Important circumstances contributing to the disclosure of new effects of statins are: improvement of research methods, and first of all, their sensitivity and specificity; the discovery of new molecules and molecular pathways that may be affected by statins. In general, the currently established numerous non-lipid effects of statin drugs can be divided into two groups: favorable and side effects, which must be taken into account when managing patients with CVD and comorbid diseases. Thanks to recent studies using modern clinical diagnostic cardiomarkers (highly sensitive cardiac troponins (CT)), molecular genetic and morphological methods, potential cardiotoxic properties of statin group drugs have been identified. Of particular concern are the data on a statininduced increase in the concentration of highly sensitive CT, which are a key and generally recognized criterion for myocardial damage. In this article we discuss possible mechanisms of increasing the concentration of CT and cardiotoxic effects when using statins.

Precision Medicine in Bladder Cancer: Present Challenges and Future Directions.

Bladder cancer (BC) is characterized by significant histopathologic and molecular heterogeneity. The discovery of molecular pathways and knowledge of cellular mechanisms have grown exponentially and may allow for better disease classification, prognostication, and development of novel and more efficacious noninvasive detection and surveillance strategies, as well as selection of therapeutic targets, which can be used in BC, particularly in a neoadjuvant or adjuvant setting. This article outlines recent advances in the molecular pathology of BC with a better understanding and deeper focus on the development and deployment of promising biomarkers and therapeutic avenues that may soon make a transition into the domain of precision medicine and clinical management for patients with BC.

Current progress on the endoscopic features of colorectal sessile serrated lesions.

Along with the discovery and refinement of serrated pathways, the World Health Organization amended the classification of digestive system tumors in 2019, recommending the renaming of sessile serrated adenomas/polyps to sessile serrated lesions (SSLs). Given the particularity of the endoscopic appearance of SSLs, it could easily be overlooked and missed in colonoscopy screening, which is crucial for the occurrence of interval colorectal cancer. Existing literature has found that adequate bowel preparation, reasonable withdrawal time, and awareness of colorectal SSLs have improved the quality and accuracy of detection. More particularly, with the continuous advancement and development of endoscopy technology, equipment, and accessories, a potent auxiliary tool is provided for accurate observation and immediate diagnosis of SSLs. High-definition white light endoscopy, chromoendoscopy, and magnifying endoscopy have distinct roles in the detection of colorectal SSLs and are valuable in identifying the size, shape, character, risk degree, and potential malignant tendency. This article delves into the relevant factors influencing the detection rate of colorectal SSLs, reviews its characteristics under various endoscopic techniques, and expects to attract the attention of colonoscopists.

Deciphering the Olefin Isomerization-Polymerization Paradox of Palladium(II) Diimine Catalysts: Discovery of Simultaneous and Independent Pathways of Olefin Isomerization and Living Polymerization

This work elucidates a long-standing unexplained paradox commonly observed within the polymerization of α-olefin using palladium (Pd)(II)-diimine catalysts, in which isomerization and living polymerization of α-olefins are both observed. With a classical mechanistic understanding of these complexes, this behavior is often dismissed and interpreted as experimental error. Herein, we present a comprehensive mechanistic investigation into this phenomenon that supports the existence of a novel mechanistic pathway for Pd(II)-diimine complexes. Part one of the mechanistic study lays the foundation of the proposed mechanism, in which neutral Pd(II)-diimine complexes were found to exhibit a moderate to good catalytic activity for olefin isomerization of α-olefins despite the established notion that catalyst activation is required. Extensive experimental and computational studies reveal the possibility of a partial dissociation of the diimine ligand, which frees up one coordination site and enables coordination-insertion. This finding is significant as the coexistence of two reactive coordination sites at the palladium center becomes a valid proposal for the activated cationic Pd(II)-diimine complexes. In part two, we examined and validated the simultaneously observed α-olefin isomerization and living polymerization using the cationic Pd(II)-diimine catalyst, which supports the presence of two independent reaction pathways of isomerization and polymerization, respectively. Moreover, the addition of a strong Lewis acid, such as AlCl3, accelerates the ligand dissociation and the consequential isomerization as it weakens the palladium-nitrogen bond through competitive binding. In part three, Lewis acid-triggered olefin isomerization-polymerization is employed to prepare living olefinic block copolymers and further synthesize novel polyolefin-polar block copolymers with unique architectures, distinct levels of branching, crystallinity, and polar functionality in a one-pot manner.

Asthma: The Use of Animal Models and Their Translational Utility

Asthma is characterized by chronic lower airway inflammation that results in airway remodeling, which can lead to a permanent decrease in lung function. The pathophysiology driving the development of asthma is complex and heterogenous. Animal models have been and continue to be essential for the discovery of molecular pathways driving the pathophysiology of asthma and novel therapeutic approaches. Animal models of asthma may be induced or naturally occurring. Species used to study asthma include mouse, rat, guinea pig, cat, dog, sheep, horse, and nonhuman primate. Some of the aspects to consider when evaluating any of these asthma models are cost, labor, reagent availability, regulatory burden, relevance to natural disease in humans, type of lower airway inflammation, biological samples available for testing, and ultimately whether the model can answer the research question(s). This review aims to discuss the animal models most available for asthma investigation, with an emphasis on describing the inciting antigen/allergen, inflammatory response induced, and its translation to human asthma.

Abstract 3177: Prediction of pathway-omics signature of histopathology images via attention-based deep learning in lung adenocarcinoma and squamous cell carcinoma

Abstract Introduction: Unraveling the underlying signaling pathways and multi-omics expression is vital for cancer research. We aim to construct an analytic deep learning (DL) pipeline toward the discovery of pathways and multi-omics signatures with high confidence from histopathological whole slide images (WSIs) for lung cancer. Methods: A total of 458 and 442 diagnostic WSIs from TCGA-LUAD and TCGA-LUSC cohorts, respectively, were preprocessed via steps including patch generation, color normalization, blurry removal, K-means clustering, and pre-trained Convolutional Neural Network (CNN) based feature extraction. The attention-based model was trained on the CNN-extracted features that provided the importance score for each cluster which was utilized for the final prediction of (1) pathway activities, (2) gene expression, and (3) protein expression. The model was first used to predict 1387 pathway activity scores using PARADIGM as the ground truth. The thresholds for Spearman’s correlation R >= 0.5 and R >= 0.45at p-value <0.05 were set for LUAD and LUSC, respectively, for selecting the well-predicted pathways. Later, multiple models were trained to predict the expression value of the genes and proteins involved in these well-predicted pathways. Moreover, leveraging the attention mechanism, heat maps were generated to visualize the high and low-activated areas on the WSIs thus providing a better interpretation of the predictions. Results: The models demonstrated good performance in predicting pathway scores, genes, and proteins’ expression using the hold-out testing sets. For LUAD, the model successfully predicted important pathways such as interleukin-, uPAR-, and Sema4D-related and PIP3-activated AKT signaling pathways, which have been proven to be associated with LUAD. At the gene- and protein expression level, the model predicted IRF4, EREG, CCNA2, IL2RB, GRB2, CCNB1, STAT5A genes, and AKT protein, respectively, with high and significant correlation. Similarly, for LUSC, the model predicted highly correlated pathways such as the regulation of telomerase and inflammasomes as well as important genes including AIM2, SIN3A, EGFR, and ATM with significant correlation. Furthermore, the highly activated hot spots from the heat map could assist in decoding the model prediction for crucial tissue locations, eventually contributing to a better interpretation of the final output. Conclusion: The proposed attention-based DL pipeline not only provides high-resolution results at the pathways, and multi-omics levels, but offers a cost-effective approach that enables high throughput screening for potential targets rapidly and robustly via a single WSI. Citation Format: Han-Ru Chen, Nam Nhut Phan, Tzu-Pin Lu, Liang-Chuan Lai, Mong-Hsun Tsai, Amrita Chattopadhyay, Eric Y. Chuang. Prediction of pathway-omics signature of histopathology images via attention-based deep learning in lung adenocarcinoma and squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3177.

Abstract 4956: Discovering novel targetable pathways by combining functional and multi-omic data from primary ovarian cancer samples

Abstract Background: There is a critical necessity to reveal novel and tractable targets for anti-cancer treatments in indications with high unmet medical need, such as high grade serous ovarian cancer (HGSOC). However, standard process for target discovery using models such as outgrown cell lines and well-averaged readouts has yielded a less than 5% approval rate for drugs entering trials (Thomas et al. 2016 Bio.org). Here, we describe patient-centric target discovery through the use of disease relevant primary OC samples and single cell functional characterization using a platform with proven hemonc translatability (Kornauth et al. 2021, Snijder et al. 2017). We integrate data from our functional drug testing platform under multiple drug perturbations with matching genomic and transcriptomic data to reveal associations with novel downstream regulators of sensitivity. Methods: Sensitivity of the cancer cell compartment in primary malignant ascites samples (n = 20; 75% HGSOC) to 85 small molecule drugs, was evaluated using a proprietary and translatable deep learning-driven single cell imaging platform (Vladimer et al. 2017). Cancer cell sensitivity from the drugs was combined with WES, bulk-RNAseq and drug induced changes in phosphoproteome, and single cell RNAseq transcriptome to identify perturbed targets and pathways. Results: Here we describe a family of TKIs including ALKi that induce cytotoxicity of cancer cells in primary samples, not previously captured in publicly available cell line drug sensitivity screening data (Iorio et al. 2016). We report novel sensitivity of OC driven by non-canonical targets of ceritinib such as FAK1 or IGF1R, mediated by the downstream signaling hub YBX1 (Kuenzi et al. 2017), involved in NFB pathway regulation (Motolani et al. 2021). Indeed, transcriptomic scRNA analysis upon ceritinib treatment of primary OC cells revealed rapid perturbation of numerous NFB pathway members, alongside YBX1 inactivation. Conclusions: Combining functional endpoints and single cell-based differential expression analysis of primary OC samples, we have identified the NFB pathway and the regulator YBX1 as a promising novel sensitivity for HGSOC treatment development. These and several other important targetable nodes identified, sit outside the recently suggested JAK/STAT pathway (Izar et al. 2020), thereby demonstrating a pipeline towards novel drug target and pathway discovery driven by patient-centric, disease relevant models of high-need indications. Citation Format: Irene Gutierrez-Perez, Bekir Ergüner, Pisanu Buphamalai, Joost Van Ham, Paul Heinz, Valentin Aranha, Rin Okumura, Elisabeth Waltenberger, Isabella Alt, Claudia Baumgaertler, Maja Stulic, Edgar Petru, Christoph Minichsdorfer, Judith Lafleur, Lukas Hefler, Laudia Hadjari, Lucia Dzurillova, Jozef Sufliarsky, Nikolaus Krall, Thorsten Füreder, Gregory Ian Vladimer, Bojan Vilagos, Robert Sehlke. Discovering novel targetable pathways by combining functional and multi-omic data from primary ovarian cancer samples. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4956.

Unraveling the Complex Interplay between Alpha-Synuclein and Epigenetic Modification

Alpha-synuclein (αS) is a small, presynaptic neuronal protein encoded by the SNCA gene. Point mutations and gene multiplication of SNCA cause rare familial forms of Parkinson's disease (PD). Misfolded αS is cytotoxic and is a component of Lewy bodies, which are a pathological hallmark of PD. Because SNCA multiplication is sufficient to cause full-blown PD, gene dosage likely has a strong impact on pathogenesis. In sporadic PD, increased SNCA expression resulting from a minor genetic background and various environmental factors may contribute to pathogenesis in a complementary manner. With respect to genetic background, several risk loci neighboring the SNCA gene have been identified, and epigenetic alterations, such as CpG methylation and regulatory histone marks, are considered important factors. These alterations synergistically upregulate αS expression and some post-translational modifications of αS facilitate its translocation to the nucleus. Nuclear αS interacts with DNA, histones, and their modifiers to alter epigenetic status; thereby, influencing the stability of neuronal function. Epigenetic changes do not affect the gene itself but can provide an appropriate transcriptional response for neuronal survival through DNA methylation or histone modifications. As a new approach, publicly available RNA sequencing datasets from human midbrain-like organoids may be used to compare transcriptional responses through epigenetic alterations. This informatic approach combined with the vast amount of transcriptomics data will lead to the discovery of novel pathways for the development of disease-modifying therapies for PD.

Cooperative driver pathways discovery by multiplex network embedding.

Cooperative driver pathways discovery helps researchers to study the pathogenesis of cancer. However, most discovery methods mainly focus on genomics data, and neglect the known pathway information and other related multi-omics data; thus they cannot faithfully decipher the carcinogenic process. We propose CDPMiner (Cooperative Driver Pathways Miner) to discover cooperative driver pathways by multiplex network embedding, which can jointly model relational and attribute information of multi-type molecules. CDPMiner first uses the pathway topology to quantify the weight of genes in different pathways, and optimizes the relations between genes and pathways. Then it constructs an attributed multiplex network consisting of micro RNAs, long noncoding RNAs, genes and pathways, embeds the network through deep joint matrix factorization to mine more essential information for pathway-level analysis and reconstructs the pathway interaction network. Finally, CDPMiner leverages the reconstructed network and mutation data to define the driver weight between pathways to discover cooperative driver pathways. Experimental results on Breast invasive carcinoma and Stomach adenocarcinoma datasets show that CDPMiner can effectively fuse multi-omics data to discover more driver pathways, which indeed cooperatively trigger cancers and are valuable for carcinogenesis analysis. Ablation study justifies CDPMiner for a more comprehensive analysis of cancer by fusing multi-omics data.

Development of pseudo-targeted profiling of isotopic metabolomics using combined platform of high resolution mass spectrometry and triple quadrupole mass spectrometry with application of 13C6-glucose tracing in HepG2 cells

Isotope tracing assisted metabolic analysis is becoming a unique tool to understand metabolic regulation in cell biology and biomedical research. Targeted mass spectrometry analysis based on selected reaction monitoring (SRM) has been widely applied in isotope tracing experiment with the advantages of high sensitivity and broad linearity. However, its application for new pathway discovery is largely restrained by molecular coverage. To overcome this limitation, we describe a strategy called pseudo-targeted profiling of isotopic metabolomics (PtPIM) to expand the analysis of isotope labeled metabolites beyond the limit of known pathways and chemical standards. Pseudo-targeted metabolomics was first established with ion transitions and retention times transformed from high resolution (orbitrap) mass spectrometry. Isotope labeled MRM transitions were then generated according to chemical formulas of fragments, which were derived from accurate ion masses acquired by HRMS. An in-house software “PseudoIsoMRM” was developed to simulate isotope labeled ion transitions in batch mode and correct the interference of natural isotopologues. This PtPIM strategy was successfully applied to study 13C6-glucose traced HepG2 cells. As 313 molecules determined as analysis targets, a total of 4104 ion transitions were simulated to monitor 13C labeled metabolites in positive-negative switching mode of QQQ mass spectrometer with minimum dwell time of 0.3 ms achieved. A total of 68 metabolites covering glycolysis, TCA cycle, nucleotide biosynthesis, one-carbon metabolism and related derivatives were found to be labeled (> 2%) in HepG2 cells. Active pentose phosphate pathway was observed with diverse labeling status of glycolysis intermediates. Meanwhile, our PtPIM strategy revealed that rotenone severely suppressed mitochondrial function e.g. oxidative phosphorylation and fatty acid beta-oxidation. In this case, anaerobic respiration became the major source of energy metabolism by producing abundant lactate. Conclusively, the simulation based PtPIM method demonstrates a strategy to broaden metabolite coverage in isotope tracing analysis independent of standard chemicals.

Unusual peptide-binding proteins guide pyrroloindoline alkaloid formation in crocagin biosynthesis

Ribosomally synthesized and post-translationally modified peptide natural products have provided many highly unusual scaffolds. This includes the intriguing alkaloids crocagins, which possess a tetracyclic core structure and whose biosynthesis has remained enigmatic. Here we use in vitro experiments to demonstrate that three proteins, CgnB, CgnC and CgnE, are sufficient for the production of the hallmark tetracyclic crocagin core from the precursor peptide CgnA. The crystal structures of the homologues CgnB and CgnE reveal them to be the founding members of a peptide-binding protein family and allow us to rationalize their distinct functions. We further show that the hydrolase CgnD liberates the crocagin core scaffold, which is subsequently N-methylated by CgnL. These insights allow us to propose a biosynthetic scheme for crocagins. Bioinformatic analyses based on these data led to the discovery of related biosynthetic pathways that may provide access to a structurally diverse family of peptide-derived pyrroloindoline alkaloids.

The Evolving Management and Treatment Options for Patients with Pulmonary Hypertension: Current Evidence and Challenges.

Pulmonary hypertension may develop as a disease process specific to pulmonary arteries with no identifiable cause or may occur in relation to other cardiopulmonary and systemic illnesses. The World Health Organization (WHO) classifies pulmonary hypertensive diseases on the basis of primary mechanisms causing increased pulmonary vascular resistance. Effective management of pulmonary hypertension begins with accurately diagnosing and classifying the disease in order to determine appropriate treatment. Pulmonary arterial hypertension (PAH) is a particularly challenging form of pulmonary hypertension as it involves a progressive, hyperproliferative arterial process that leads to right heart failure and death if untreated. Over the last two decades, our understanding of the pathobiology and genetics behind PAH has evolved and led to the development of several targeted disease modifiers that ameliorate hemodynamics and quality of life. Effective risk management strategies and more aggressive treatment protocols have also allowed better outcomes for patients with PAH. For those patients who experience progressive PAH with medical therapy, lung transplantation remains a life-saving option. More recent work has been directed at developing effective treatment strategies for other forms of pulmonary hypertension, such as chronic thromboembolic pulmonary hypertension (CTEPH) and pulmonary hypertension due to other lung or heart diseases. The discovery of new disease pathways and modifiers affecting the pulmonary circulation is an ongoing area of intense investigation.

Application of Transcriptomics and Proteomics in Pulmonary Arterial Hypertension

The onset and progression of pulmonary arterial hypertension (PAH), a malignant disease, are associated with environmental and epigenetic factors. Recent advancements in transcriptomics and proteomics technology have provided new insights into PAH and identified novel gene targets involved in the development of the disease. Transcriptomic analysis has led to the discovery of possible novel pathways, such as miR-483 targeting several PAH-related genes and a mechanistic link between the increase in HERV-K mRNA and protein. Proteomic analysis has revealed crucial details, including the loss of SIRT3 activity and the significance of the CLIC4/Arf6 pathway in PAH pathogenesis. Gene profiles and protein interaction networks of PAH have been analyzed, clarifying the roles of differentially expressed genes or proteins in the occurrence and development of PAH. This article discusses these recent advances.

Transcriptome studies of inherited dilated cardiomyopathies.

Dilated cardiomyopathy (DCM) is a group of heart muscle diseases that often lead to heart failure, with more than 50 causative genes have being linked to DCM. The heterogenous nature of the inherited DCMs suggest the need of precision medicine. Consistent with this emerging concept, transcriptome studies in human patients with DCM indicated distinct molecular signature for DCMs of different genetic etiology. To facilitate this line of research, we reviewed the status of transcriptome studies of inherited DCMs by focusing on three predominant DCM causative genes, TTN, LMNA, and BAG3. Besides studies in human patients, we summarized transcriptomic analysis of these inherited DCMs in a variety of model systems ranging from iPSCs to rodents and zebrafish. We concluded that the RNA-seq technology is a powerful genomic tool that has already led to the discovery of new modifying genes, signaling pathways, and related therapeutic avenues. We also pointed out that both temporal (different pathological stages) and spatial (different cell types) information need to be considered for future transcriptome studies. While an important bottle neck is the low throughput in experimentally testing differentially expressed genes, new technologies in efficient animal models such as zebrafish starts to be developed. It is anticipated that the RNA-seq technology will continue to uncover both unique and common pathological events, aiding the development of precision medicine for inherited DCMs.

Complement in the Brain: Contributions to Neuroprotection, Neuronal Plasticity, and Neuroinflammation.

The complement system is an ancient collection of proteolytic cascades with well-described roles in regulation of innate and adaptive immunity. With the convergence of a revolution in complement-directed clinical therapeutics, the discovery of specific complement-associated targetable pathways in the central nervous system, and the development of integrated multi-omic technologies that have all emerged over the last 15 years, precision therapeutic targeting in Alzheimer disease and other neurodegenerative diseases and processes appears to be within reach. As a sensor of tissue distress, the complement system protects the brain from microbial challenge as well as the accumulation of dead and/or damaged molecules and cells. Additional more recently discovered diverse functions of complement make it of paramount importance to design complement-directed neurotherapeutics such that the beneficial roles in neurodevelopment, adult neural plasticity, and neuroprotective functions of the complement system are retained.

Complex scaffold remodeling in plant triterpene biosynthesis.

Triterpenes with complex scaffold modifications are widespread in the plant kingdom. Limonoids are an exemplary family that are responsible for the bitter taste in citrus (e.g., limonin) and the active constituents of neem oil, a widely used bioinsecticide (e.g., azadirachtin). Despite the commercial value of limonoids, a complete biosynthetic route has not been described. We report the discovery of 22 enzymes, including a pair of neofunctionalized sterol isomerases, that catalyze 12 distinct reactions in the total biosynthesis of kihadalactone A and azadirone, products that bear the signature limonoid furan. These results enable access to valuable limonoids and provide a template for discovery and reconstitution of triterpene biosynthetic pathways in plants that require multiple skeletal rearrangements and oxidations.

An ex vivo ovulation system enables the discovery of novel ovulatory pathways and nonhormonal contraceptive candidates†.

Ovulation is an integral part of women's menstrual cycle and fertility. Understanding the mechanisms of ovulation has broad implications for the treatment of anovulatory diseases and the development of novel contraceptives. Now, few studies have developed effective models that both faithfully recapitulate the hallmarks of ovulation and possess scalability. We established a three-dimensional encapsulated in vitro follicle growth (eIVFG) system that recapitulates folliculogenesis and produces follicles that undergo ovulation in a controlled manner. Here, we determined whether ex vivo ovulation preserves molecular signatures of ovulation and demonstrated its use in discovering novel ovulatory pathways and nonhormonal contraceptive candidates through a high-throughput ovulation screening. Mature murine follicles from eIVFG were induced to ovulate ex vivo using human chorionic gonadotropin and collected at 0, 1, 4, and 8hours post-induction. Phenotypic analyses confirmed key ovulatory events, including cumulus expansion, oocyte maturation, follicle rupture, and luteinization. Single-follicle RNA-sequencing analysis revealed the preservation of ovulatory genes and dynamic transcriptomic profiles and signaling. Soft clustering identified distinct gene expression patterns and new pathways that may critically regulate ovulation. We further used this ex vivo ovulation system to screen 21 compounds targeting established and newly identified ovulatory pathways. We discovered that proprotein convertases activate gelatinases to sustain follicle rupture and do not regulate luteinization and progesterone secretion. Together, our ex vivo ovulation system preserves molecular signatures of ovulation, presenting a new powerful tool for studying ovulation and anovulatory diseases as well as for establishing a high-throughput ovulation screening to identify novel nonhormonal contraceptives for women.