Spatial transcriptomic analysis of low-grade intestinal T-cell lymphoma and lymphoplasmacytic inflammatory bowel disease in cats

Abstract

Alimentary lymphoma is the most prevalent neoplastic disease that affects the gastrointestinal tract of cats. In most cases, the neoplastic cell population is composed of small T lymphocytes primarily located in the intestinal mucosa, but can often invade deeper intestinal layers. It is a low-grade disease (LGITL), with chronic, even indolent behavior. Clinically, the disease is difficult to differentiate from inflammatory bowel disease (IBD), which is also a prevalent disease in adult and elderly cats. The currently available diagnostic techniques are invasive, as full-thickness biopsy is generally recommended. In some cases, histopathologic evaluation can provide a diagnosis, but in many others, the results are inconclusive, even after using complementary molecular techniques for clonality and immunophenotyping. To identify the differences in gene expression in intestinal samples from cats with LGITL and IBD using spatial transcriptomics, formalin-fixed paraffin-embedded cat jejunum and ileum samples were used, six with a diagnosis of LGITL and six with a diagnosis of IBD. Endoscopy biopsies and full-thickness biopsy and necropsy samples were included. Three ileum samples were prospectively collected as controls, to compare Peyer's patches of cats without gastrointestinal or neoplastic diseases with the LGITL and IBD samples. The spatial transcriptomics technique (GeoMx, Nanostring-Bruker) was successfully performed in T and B lymphocytes of cat samples for the first time, to our knowledge. The samples were assessed according to the diagnosis and compared among three different histologic areas: superficial epithelium, deep epithelium/submucosa, and Peyer's patches (when available). When comparing LGITL and IBD, all differences were found only in the T-cell population. Fourteen genes had higher expression in LGITL and six in the IBD samples. One gene was upregulated in Peyer's patches of LGITL versus the control, while one gene was downregulated and four were upregulated in IBD Peyer's patches when compared with the control samples. Transcriptional differences were also observed when comparing the histologic areas of samples from the same disease, in both B and T cells. These findings lay the foundation for future studies to fully validate the candidate genes.