Abstract Background T cell therapies are emerging as a new approach to treat and cure patients suffering from immune diseases where T cell homeostasis is no longer maintained. For the evaluation of treatments in pre-clinical rodent models, tools are required that enable fast, observer-independent and high-resolution analysis of different T cells in tissue sections. Multiplex staining of tissue samples provides a valuable opportunity for comprehensive analysis of cellular dynamics with enhanced spatial resolution and tissue context compared to traditional staining and flow cytometry methods. We have developed a high-throughput multiplex immunofluorescence panel for detecting different T cell types and activation status in mouse models of inflammatory bowel disease (IBD). Moreover, we used an AI-assisted method to enhance image analysis, enabling automated, accurate, and quantification of complex cellular interactions. Methods For the development and optimization of the various stainings we used formalin-fixed paraffin embedded (FFPE) mouse colon sections from an efficacy study with murine polyclonal regulatory T cells (Tregs) in the T cell transfer mouse model of IBD, enabling access to sections with healthy versus diseased pathology, as well as samples where Tregs were transferred to reduce colon pathology. Multiplex staining was performed with antibodies (such as CD3, FOXP3, CD25, CD69, CTLA-4 and KI67) using a Leica BOND RX autostainer, by applying sequential primary antibody staining, followed by secondary HRP-conjugated antibodies and Opal-TSA chemistry. Whole slide images (WSI) were generated by a Phenoimager HT (Akoya) and analyzed using Visiopharm software, with DAPI+ nuclei detection via AI-based application. Results We successfully developed a multiplex panel that enables high throughput staining and spatial resolution analysis of over six markers. We were able to determine the activation status of different subtypes of T cells and their specific localization in the colon. We could quantify infiltration of activated effector T cells (Teffs) in both the mucosa and submucosa in colon samples with high pathological scores, as well as FOXP3+ cells in samples from mice treated with Tregs. Conclusion We developed an Opal-based multiplex immunofluorescence method to detect T cells in mouse colon samples, focusing on activation and proliferation markers. Additionally, an AI-assisted image analysis tool that provided fast, reproducible, and quantitative results with spatial resolution. This innovative multiplex method holds promise for adaptation to different mouse models of colitis and other rodent models related to immune diseases, furthering its potential impact in the area of T cell therapy research.
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