OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics.

SUMMARY: Organoid model systems recapitulate key features of mammalian tissues and enable high throughput experiments. However, the impact of these experiments may be limited by manual, non-standardized, static or qualitative phenotypic analysis. OrgDyn is an open-source and modular pipeline to quantify organoid shape dynamics using a combination of feature- and model-based approaches on time series of 2D organoid contour images. Our pipeline consists of (i) geometrical and signal processing feature extraction, (ii) dimensionality reduction to differentiate dynamical paths, (iii) time series clustering to identify coherent groups of organoids and (iv) dynamical modeling using point distribution models to explain temporal shape variation. OrgDyn can characterize, cluster and model differences among unique dynamical paths that define diverse final shapes, thus enabling quantitative analysis of the molecular basis of tissue development and disease. AVAILABILITY AND IMPLEMENTATION: https://github.com/zakih/organoidDynamics (BSD 3-Clause License). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Organotypic culture assays for murine and human primary and metastatic-site tumors.

Cancer invasion and metastasis are challenging to study in vivo since they occur deep inside the body over extended time periods. Organotypic 3D culture of fresh tumor tissue enables convenient real-time imaging, genetic and microenvironmental manipulation and molecular analysis. Here, we provide detailed protocols to isolate and culture heterogenous organoids from murine and human primary and metastatic site tumors. The time required to isolate organoids can vary based on the tissue and organ type but typically takes <7 h. We describe a suite of assays that model specific aspects of metastasis, including proliferation, survival, invasion, dissemination and colony formation. We also specify comprehensive protocols for downstream applications of organotypic cultures that will allow users to (i) test the role of specific genes in regulating various cellular processes, (ii) distinguish the contributions of several microenvironmental factors and (iii) test the effects of novel therapeutics.

Microscale pressure measurements based on an immiscible fluid/fluid interface.

A method of microscale pressure measurement based on immiscible fluid/fluid interface is proposed. This method utilizes observed curvature changes in a fluid/fluid interface, and can accurately report hydraulic pressure in fluids at length scales of 10 microns. The method is especially suited for measuring fluid pressure in micro-scale biological samples. Using this method, we probe fluid pressure build up in epithelial domes, murine mammary gland organoids embedded in hydrogel, and lumen pressure in the developing mouse embryo. Results reveal that the pressure developed across epithelial barriers is on the order of 100~300 Pa, and is modulated by ion channel activity.

Engineering an Artificial T-Cell Stimulating Matrix for Immunotherapy.

T cell therapies require the removal and culture of T cells ex vivo to expand several thousand-fold. However, these cells often lose the phenotype and cytotoxic functionality for mediating effective therapeutic responses. The extracellular matrix (ECM) has been used to preserve and augment cell phenotype; however, it has not been applied to cellular immunotherapies. Here, a hyaluronic acid (HA)-based hydrogel is engineered to present the two stimulatory signals required for T-cell activation-termed an artificial T-cell stimulating matrix (aTM). It is found that biophysical properties of the aTM-stimulatory ligand density, stiffness, and ECM proteins-potentiate T cell signaling and skew phenotype of both murine and human T cells. Importantly, the combination of the ECM environment and mechanically sensitive TCR signaling from the aTM results in a rapid and robust expansion of rare, antigen-specific CD8+ T cells. Adoptive transfer of these tumor-specific cells significantly suppresses tumor growth and improves animal survival compared with T cells stimulated by traditional methods. Beyond immediate immunotherapeutic applications, demonstrating the environment influences the cellular therapeutic product delineates the importance of the ECM and provides a case study of how to engineer ECM-mimetic materials for therapeutic immune stimulation in the future.

Interfacial thiol-ene photoclick reactions for forming multilayer hydrogels.

Interfacial visible light-mediated thiol-ene photoclick reactions were developed for preparing step-growth hydrogels with multilayer structures. The effect of a noncleavage type photoinitiator eosin-Y on visible-light-mediated thiol-ene photopolymerization was first characterized using in situ photorheometry, gel fraction, and equilibrium swelling ratio. Next, spectrophotometric properties of eosin-Y in the presence of various relevant macromer species were evaluated using ultraviolet-visible light (UV-vis) spectrometry. It was determined that eosin-Y was able to reinitiate the thiol-ene photoclick reaction, even after light exposure. Because of its small molecular weight, most eosin-Y molecules readily leached out from the hydrogels. The diffusion of residual eosin-Y from preformed hydrogels was exploited for fabricating multilayer step-growth hydrogels. Interfacial hydrogel coating was formed via the same visible-light-mediated gelation mechanism without adding fresh initiator. The thickness of the thiol-ene gel coating could be easily controlled by adjusting visible light exposure time, eosin-Y concentration initially loaded in the core gel, or macromer concentration in the coating solution. The major benefits of this interfacial thiol-ene coating system include its simplicity and cytocompatibility. The formation of thiol-ene hydrogels and coatings neither requires nor generates any cytotoxic components. This new gelation chemistry may have great utilities in controlled release of multiple sensitive growth factors and encapsulation of multiple cell types for tissue regeneration.