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Biology subjects

Filip, A. M.

Publications and source records attributed to Filip, A. M..

3 recordsLinked to original sources

Organoid-based colorectal tumor microenvironment model for immuno-oncology research

The development of cancer immunotherapies is hindered by the lack of human-relevant models that accurately translate to patient outcomes. We combine patient-derived colorectal tumor organoids (PDOs) and cancer-associated fibroblasts (CAFs) into floating extracellular matrix drops to form miniature colorectal tumors. These SHaking Organoid CO-cultures (SHOCOs) reproducibly capture key features of the tumor microenvironment (TME), including physiologically relevant ECM, hypoxic regions, and a diversified stromal compartment that captures primary CAF states. Compared with traditional PDO-based co-culture models, SHOCOs maintain immune cells in numbers, states and functional interactions that more closely reflect the physiological tumor microenvironment. The modularity of the system allowed controlled simulation of diverse patient tumor archetypes, and defining how TME components shape therapy response. Immune-rich SHOCOs treated with T-cell bispecific antibodies exhibited robust anti-tumor responses that were stronger and more rapid than their PDO-based counterparts. Stroma-rich tumors, on the other hand, diminished therapy responses by physically hindering both immune cell recruitment and limiting antibody penetration. Thus, SHOCOs enable the construction of modular tumor microenvironments, providing a versatile platform to dissect immune and stromal tumor biology and to catalyze the discovery of novel therapeutic approaches.

cancer biology↗

Modeling host-microbe interactions in immunocompetent engineered human gut tissues

The intestinal mucosal barrier contains microbial organisms within the lumen while preserving the ability to absorb nutrients. Dietary, microbial, and other exposures shaped human barrier evolution and continue to impact disease susceptibility. Here, we established engineered barrier models of the human small intestine and colon composed of a multilineage epithelium, mucus layer, accessible microbial compartment and autologous tissue-resident immune cells. The epithelium has crypt- and villus-like topological domains, with stem cells differentiating into absorptive and secretory lineages with region-specific identities. Secreted mucins accumulate apically, forming a dense mucus layer separating the epithelium from colonizing commensal and pathogenic bacteria. Intestinal memory T cells integrate into and interact with the epithelium. We use the engineered intestinal tissues to identify an epithelial gene regulatory network underlying response to Salmonella Typhimurium infection, and uncover epithelial-immune-pathogen crosstalk coordinating cytokine release and epithelial damage. Overall, this work allows for the modular integration of epithelial, microbial, and immune compartments providing a versatile system for studying human intestinal physiology and pathologies.

bioengineering↗

High-throughput histopathology for complex in vitro models

Human complex in vitro models (CIVMs) have demonstrated remarkable potential to study tissue development, physiology and disease at high-throughput. To effectively employ these miniaturized systems in translational preclinical research, their in-depth benchmarking is pivotal. Histology has been the core of tissue characterization for centuries and the foundation of spatial phenotyping. However, standard histology workflows are inherently low-throughput and centered on large tissue pieces. This does not match the high sample volumes and small sample sizes in CIVM research. Here, we introduce a holistic histo-workflow, utilizing 3D-printed histomolds that facilitate co-planar embedding of CIVMs at high-throughput, resulting in up to 48 samples in one section. We developed a variety of model-specific histomold designs that enable spatially controlled histological sectioning and downstream analyses. We describe these workflows, including mold generation, highplex staining and image analysis, and exemplify their application to histological analyses of various CIVMs. Altogether, the histomolds introduced here afford opportunities for CIVM processing and analysis, while significantly reducing labor and reagent resources, thereby democratizing high-throughput CIVM in histopathology.

pathology↗