38Graft-versus-host-disease (GvHD) is the main complication of allogeneic hematopoietic stem cell 39 transplantation. GvHD patients have aberrant T cell expansions, which are thought to drive pathological 40 immune activation. Here we report mechanistic insights that somatic mutations may account for persistent 41 clonal T cell expansions in chronic GvHD (cGvHD). In an index patient suffering from cGVHD, we discovered 42 persisting somatic MTOR, NFKB2, and TLR2 mutations in an expanded CD4+ T clone. In the screening 43 cohort (n=135), the MTOR P2229R kinase domain mutation was detected in two additional cGvHD patients, 44but not in controls. Functional analysis of the discovered MTOR mutation indicated a gain-of-function 45 alteration in translational regulation yielding in up-regulation of phosphorylated S6K1, S6, and AKT. Paired 46 single-cell RNA and T cell receptor alpha and beta sequencing strongly supported cytotoxicity and 47 54 55Graft-versus host disease (GvHD) is the main complication of allogeneic hematopoietic stem cell 56 transplantation (allo-HSCT).(1) Chronic GvHD (cGvHD), that occurs more than 100 days after the 57 transplantation, develops in 30-70 % of allo-HSCT recipients. Affected patients frequently need 58 immunosuppressive treatment for years or even for a lifetime, and in many patients the condition is 59 fatal.(2) The genesis of cGvHD is multifactorial, but donor alloreactive lymphocytes are believed to be the 60 key pathogenetic drivers that target host tissues such as skin, soft tissues, oral mucosa, and eyes. In 61 particular, CD4+ T cells contribute to the early inflammation and tissue injury, to subsequent chronic 62 inflammation, and late aberrant tissue repair and fibrosis.(3) 63 During normal immune response, naïve T cells encounter their cognate antigen, get activated and 64 undergo a rapid clonal expansion.(4) The activation and proliferation of T cells are usually tightly regulated 65 processes, in which effector cells undergo apoptosis upon proper immune response. In many immune-66 system-mediated disorders, such as cGvHD, the immune homeostasis is disturbed, and the enormous 67 variability of different T cell clones is diminished. In some patients, the T cell receptor (TCR) repertoire is 68 heavily skewed, and clones comprising up to 20-40% of all T cells can exist.(5) The underlying mechanisms 69 for this phenomenon remain unknown. 70Here, we hypothesized that in cGvHD antigen-encountered T cells may acquire somatic mutations 71 due to constant immune-system activation and proliferation. Such mutations might lead to functional and 72 survival advantages of T cells that result in clonal expansion and aberrant immune responses. To explore 73 this theory, we sequenced purified CD4+ and CD8+ lymphocytes from an index patient suffering from 74 cGVHD with a custom deep-sequencing panel consisting of immunity and inflammation-related genes. 75 Mutation findings were confirmed in a validation cohort of 135 GVHD patients. Subsequently, the 76 functional consequences of the discovered...