32Acute gastrointestinal Graft-versus-Host-Disease (GVHD) is a primary determinant of mortality after 33 allogeneic hematopoietic stem-cell transplantation (alloSCT). It is mediated by alloreactive donor CD4 + T 34 cells that differentiate into pathogenic subsets expressing IFNγ, IL-17A or GM-CSF, and is regulated by 35 subsets expressing IL-10 and/or Foxp3. Developmental relationships between T-helper states during priming 36 in mesenteric lymph nodes (mLN) and effector function in the GI tract remain undefined at genome-scale. 37We used scRNA-seq and computational modelling to create an atlas of putative differentiation pathways 38 during GVHD. Computational trajectory inference suggested emergence of pathogenic and regulatory states 39 along a single developmental trajectory in mLN. Importantly, we identified an unexpected second trajectory, 40 categorised by little proliferation or cytokine expression, reduced glycolysis, and high TCF1 expression. 41 TCF1 hi cells upregulated α4β7 prior to gut migration and failed to express cytokines therein. Nevertheless, 42 they demonstrated recall potential and plasticity following secondary transplantation, including cytokine or 43Foxp3 expression, but reduced TCF1. Thus, scRNA-seq revealed divergence of allo-reactive CD4 + T cells 44into quiescent and effector states during gut GVHD, reflecting putative heterogenous priming in vivo. These 45 findings, the first at a single-cell level during GVHD over time, can now be used to interrogate T cell 46 differentiation in patients undergoing alloSCT. 47 25. Karmaus PWF, Chen X, Lim SA, Herrada AA, Nguyen TM, Xu B, et al. Metabolic heterogeneity underlies 608 reciprocal fates of TH17 cell stemness and plasticity. Nature. 2019;565(7737):101-5. 609 26. Pepper M, Pagan AJ, Igyarto BZ, Taylor JJ, and Jenkins MK. Opposing signals from the Bcl6 transcription factor 610 and the interleukin-2 receptor generate T helper 1 central and effector memory cells. Immunity. 2011;35(4):583-611 95.