Our overarching purpose is to develop new, minimally invasive diagnostic tools to differentiate idiopathic inflammatory bowel disease(IBD) from low-grade intestinal T-cell lymphoma (LGITL) in cats using multi-omics approaches, including whole-genome sequencing,spatial transcriptomics, and miRNA sequencing. The first aim involves identifying genomic mutations using next-generation sequencing(NGS). The second aim employs spatial transcriptomics to profile the gene expression in the spatial context of tissue architecture,uncovering crucial paracrine and juxtacrine signaling interactions that bulk transcriptomics cannot capture. The third aim focuses inmiRNA analysis to understand the role of epigenetic regulation. We will use FFPE samples of cat jejunum and ileum with IBD and LGITL,diagnosed by histopathology and confirmed with PCR for antigen receptor rearrangement PARR (n = 3 each segment and each condition,total 12 samples), in addition to three control animals. The proposed work is highly significant for veterinary medicine, as differentiatingIBD from LGITL remains clinically challenging due to overlapping symptoms and limitations in current diagnostic methods, and symptomscan be confounded with more aggressive neoplasms that require distinct therapy and hold poorer prognosis. Existing diagnostic toolsrequire invasive and expensive techniques, such as endoscopy or surgery for full-thickness biopsies, in addition to ancillary tests such ashistopathology, PARR, and immunohistochemistry (IHC) that can have results affected by the quality of the samples. By using cutting-edge sequencing technologies, this study seeks to develop more reliable, non-invasive diagnostic tools and provide novel insights intothe molecular differences between these two conditions. Spatial transcriptomics, for instance, has not being applied so far on research ofany feline condition.