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Immunoengineering Trainee Seminar
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Featured Speakers:
"Graph-based 2D and 3D Spatial Gene Neighborhood Networks of Single Cells in Gels and Tissues” - Zhou Fang, Ph.D. Student, Coskun Lab
Abstract
Spatially resolved transcriptomic technologies such as multiplexed error-robust fluorescence in situ hybridization (MERFISH) and sequential FISH generate high-dimensional datasets that reflect the organization of molecules within cells. Further advancements also allow the imaging of cells grown in 3D environments, such as hydrogel and Matrigel. Therefore, we developed the spatially-resolved gene neighborhood network (spaGNN) pipeline to identify subcellular spatially-resolved features that achieve cell-type identification and cell-cell communication (CCC) prediction. We first developed the spaGNN for 2D subcellular spatial transcriptomics data. This algorithm quantifies the physical proximity of RNA molecules. Spatially resolved gene neighborhoods are used to identify networks that are distinct at different parts of a single cell. We then examined the cell-type identification using the gene proximity features. We then extended the spaGNN pipeline into 3D environments and applied the pipeline to examine local CCC between MSCs in hydrogel, between MSCs and immune cells coculture in Matrigel, and between astrocytes and neurons in brain tissues.
"A Lymphoid–Gut-on-a-Chip Model to Recapitulate Human Immune Responses to Intestinal Inflammation” - Valeria Juarez, Ph.D. Student, Singh Lab
Abstract
The immune system plays a central role in maintaining intestinal homeostasis, and its dysregulation contributes to a range of chronic conditions, including inflammatory diseases, persistent infections, and cancer. While existing in vitro intestinal models capture epithelial differentiation, they lack a functional immune component, limiting their ability to model intestinal homeostasis and disease. Therefore, we developed a lymphoid–gut-on-a-chip platform that integrates a human B cell follicle organoid embedded within a fully synthetic hydrogel matrix and a perfusable intestinal epithelium derived from human induced pluripotent stem cells (iPSCs). Upon exposure to Escherichia coli (E. coli) lysate, the epithelial layer exhibits increased barrier permeability and pro-inflammatory cytokine secretion. In parallel, the lymphoid organoid shows enhanced antibody production, demonstrating immune–epithelial functional connectivity. Our lymphoid–gut-on-a-chip system provides a promising tool for investigating human gut–immune interactions and inflammatory responses in vitro.
The Immunoengineering Training Seminar Series is supported by the NIH T32 Research Training Program in Immunoengineering and housed within the Center for Immunoengineering at Georgia Tech.
Status
- Workflow Status:Published
- Created By:Christina Wessels
- Created:09/22/2025
- Modified By:Colly Mitchell
- Modified:10/02/2025
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