3D Summit Cambridge Livestream

Postdoctoral Research Scholar, Memorial Sloan Kettering Cancer Center

Presentation: Physical Confinement Alters Cellular Dynamics from the Multi-Cellular to the Single-Cell Scale

Abstract: Physical confinement refers to the mechanical forces that constrain dynamic cellular processes. We propose that physical confinement is defined by the compressive stresses exerted on cells during processes like migration and growth. We focus on two distinct in vitro models where we study confinement 1) of multi-cellular pancreatic ductal organoids grown in 3D, engineered hydrogels and 2) of single macrophages migrating through ductal cell junctions. Recently, we identified the differential effects of confinement on healthy and tumor-derived ductal organoids. By challenging organoid growth with a confining, engineered 3D hydrogel and Corning® Matrigel® matrix composite, we discovered two emergent collective cell behaviors in murine pancreatic ductal organoid models.

Tumor-derived organoids exhibited a collective “pulsing” behavior that increased in frequency when confined and generated radially persistent forces that locally rearranged the microenvironment in the direction of organoid growth. In contrast, healthy organoids exhibit unidirectional rotation, generating more subtle rotational movements in the microenvironment orthogonal to the direction of growth. When confined, we found tumor-derived organoids grew at similar rates as in less confined conditions while normal organoid grew much more slowly and failed to establish proper apicobasal polarity.

Organoid Facility Manager, Cancer Center, Cold Spring Harbor Laboratory

Presentation: Optimizing Patient-derived Organoid Platforms for High-Throughput Pharmacotyping

Abstract: Patient-derived organoids (PDOs) are the avatars of cancer growing in the lab. PDOs can be used in clinical settings to establish personalized cancer treatments. However, the speed and success rate of validated PDO establishment are major limiting factors for pancreatic cancer. Performing pharmacotyping on PDO cultures within a clinically suitable timeframe is challenging. Miniaturization of pharmacotyping assays helps test multiple chemotherapeutic compounds using minimal cells from PDO culture. Using 1536-well plates enables a 16-fold miniaturization compared to traditional 96-well plates. This high-throughput miniaturization presents its own set of challenges, which can be overcome using various liquid handling technologies. Further validating PDO cultures using dd-PCR could prevent normal outgrowth. Also, in vitro modeling of stromal TME in pancreas cancer is possible with PDO-CAFs co-cultures. With these advances, pharmacotyping test on PDOs can be feasible within an appropriate clinical timeframe.

Researcher, Cold Spring Harbor Laboratory

Presentation: The Potential of Patient-derived Organoids in Pancreatic Cancer

Abstract: Our work uses patient-derived organoids (PDOs) to model pancreatic cancer tumors, as PDOs retain key genomic, molecular, and clonality characteristics of the patient. In our laboratory, their pharmacotyping and next-generation sequencing yield results on drug sensitivity and resistance that are applicable in clinical and academic research. This includes screening novel therapeutic compounds, such as RAS inhibitors. This presentation will discuss our standard workflow from organoid generation to pharmacotyping and highlight the various projects that implement these data, including the PASS-01 clinical trial and the New York Genome Center Polyethnic-1000 project. Furthermore, it will introduce data from our recent drug screens against our novel attempts at growing organoids from pre-cancerous lesions to understand disease progression and our new High Content Imaging pipeline for drug screening and co-culture assays with fibroblasts.

Professor, Associate Director, Center for Pathogen Research, University of Massachusetts-Lowell

Presentation: Organoid-Microbe Coculture Model to Develop Personalized Therapies in Chronic Diseases

Abstract: Gut microbes are linked to infections, gastro-intestinal diseases, and other chronic diseases. It is essential to develop a disease model that mimics physiological conditions and is closer to humans than the existing animal models. Utilizing the recent developments in stem-cell biology, we have developed a “gut-in-a-dish” model that utilizes patient-derived-organoids and microbes associated with the disease. Besides the influences of genetic factors and the changes in microbial populations, diet and environmental factors also impact the disease outcome; however, their roles are not completely known. To address this, we have predicted gene signatures using our computational disease model that are validated by experimental approaches with organoid-microbe coculture model. In inflammatory bowel disease and colorectal cancer, our gut-in-a-dish model is used in identifying key cellular pathways and in the development of new personalized therapies by screening drugs and gene editing.

Technical Director of the Organoid and Cell Culture Core, Columbia University

Presentation: Modeling Malignant Transformation of Aero-upper Digestive Epithelia in 3D Organoids and High-Throughput Drug Screening

Abstract: We model preneoplasia and cancer in murine- and patient-derived organoids grown in Corning® Matrigel® matrix, which recapitulate pathological epithelial changes of the aero-upper digestive tract. These organoids encapsulate progressive morphological and molecular changes of the original tissues during carcinogenesis as captured by growth kinetics, histopathology, gene expression and mutations. We have developed an unprecedented large scale drug screening protocol to screen over 10,000 bioactive compounds. By testing 7 independent PDO lines, we have identified 220 drugs that killed the majority and identified molecular targets and pathways (e.g., proteasome, epigenetics, cell cycle, BCL2, NF-kB, and various kinases) essential in the pathogenesis of these cancers. These high hitters included FDA-approved compounds that displayed IC₅₀ values lower than the Cmax, the highest concentration in the patients’ blood, thus deemed promising if used in patients. Additionally, we have identified drugs that specifically killed cancer but not normal cells in PDO, disclosing cancer cell-specific vulnerability. Amongst such drugs were those targeting DNA damage response (DDR), such as ATR inhibitors. Further studies have suggested that cancer cells show increasing dependence on ATR for survival during carcinogenesis. Finally, PDO-based drug screening revealed differential drug responses of individual PDO lines to various drugs, reinforcing the utility of PDO as a tool predict therapy response.

Professor of Medicine at Columbia University

Presentation: Modeling Eosinophilic Esophagitis in 3D Esophageal Organoids

Abstract: Reactive epithelial changes are linked to the pathogenesis of eosinophilic esophagitis (EoE), a Th2 cytokine-mediated chronic inflammatory disorder, affecting both adults and children. The reactive epithelial change, also known as basal cell hyperplasia (BCH), is characterized by disruption of the proliferation-differentiation gradient of the normal squamous epithelium in the esophagus. EoE-related BCH is linked to cytokine-induced oxidative stress and mitochondrial dysfunction. We have modeled EoE-related BCH in patient- and mouse-derived organoids (PDO and MDO) which recapitulate morphological and functional changes in the original tissues. Utilizing MDO grown in Matrigel matrix, coupled with genetically engineered mouse models of EoE, we identify a unique esophageal cell population that is responsible for BCH. Furthermore, CRISPR interference in MDO lines generated from dCas9 knock-in mice permitted genetic screening to identify PGC1A, the master regulator of mitochondrial biogenesis, as essential in the pathogenesis of EoE-related BCH and mitochondrial dysfunction. Finally, omeprazole, the first-line EoE treatment, alleviated mitochondrial damage and dysfunction in EoE-related BCH modeled in MDO and PDO. These organoids serve as a robust experimental platform to gain insights into the pathogenesis of benign esophageal diseases and explore novel therapies.

Population Geneticist, Molecular Devices

Presentation: Tackling Complexity in 3D Culture: How Automation Improves Efficiency and Consistency When Culturing Complex, 3D Models

Abstract: As the use of complex, 3D biological models become more widespread, the challenges associated with culturing and analyzing these systems are increasingly evident. These workflows are not only technically demanding—often requiring specialized labware and reagents—but also significantly more labor-intensive than traditional methods. Given the limitations in space and skilled personnel, relying solely on manual processes is no longer sustainable. In this talk, we will examine the unique demands of working with 3D models and demonstrate how purpose-built automation can enhance operational efficiency, improve reproducibility, and enable broader adoption of these advanced systems.

Senior Scientist, Corning Life Sciences

Presentation: Mastering the Third Dimension: Tools, Tips and Tricks for Optimizing 3D Cell Culture Models

Abstract: In the last several years, many research publications have shown increased value of using 3D cell models compared to traditional 2D systems. Although considered by many as a more representative model of in vivo biology, setup of 3D models can be more challenging, especially when the throughput is further increased. Furthermore, 3D cell culture models are varied and diverse, often making it difficult to choose the best technology for your application. The right tool often depends on the study goals and desired objective.

During this presentation, you’ll learn about the variety of tools available for working with 3D cultures and helpful tips and tricks for improving spheroid and organoid formation, handling, and processing.