Expanded T cell clones with lymphoma driver somatic mutations in refractory celiac disease

<p>Processed data and scripts for "Expanded T cell clones with lymphoma driver somatic mutations in refractory celiac disease".</p> <p>Intestinal inflammation continues in a subset of celiac disease (CD) patients despite a gluten-free<br>diet. Here, by applying multiomic single cell analysis to duodenal biopsies, we find low-grade<br>malignancies with lymphoma driver mutations in refractory CD type 2 (RCD2) patients comprise<br>surface CD3 negative (sCD3-) lymphocytes stalled at an innate lymphoid cell (ILC) - progenitor<br>T cell stage undergoing extensive TCR recombination. In people with refractory CD type 1<br>(RCD1), who currently lack explanation, we discover sCD3+ T cells with lymphoma driver<br>mutations forming large clones displaying inflammatory and cytotoxic molecular profiles in 6 of<br>10 individuals, and a single small clone in 1 of 4 active recently diagnosed CD cases. Accumulation<br>of driver-mutated T cells and sCD3- progenitors may explain chronic, non-responsive<br>autoimmunity.</p>