Supplementary Figure 1 Histological staging criteria for acute GvHD Hepatic GVHD 1. Minimal periductal lymphoid cell infiltrates (5-10 cells) 2. Mild periductal.

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Supplementary Figure 1 Histological staging criteria for acute GvHD Hepatic GVHD 1. Minimal periductal lymphoid cell infiltrates (5-10 cells) 2. Mild periductal lymphoid cell infiltrates (10-20 cells) 3. Moderate periductal lymphoid cell infiltrates (20-40 cells), with intraepithelial lymphoid cells, single cell hepatocellular necrosis 4. Moderate to severe periductal lymphoid cell infiltrates (>40 cells), with intraepithelial lymphoid cells; single cell hepatocellular necrosis; some bridging of portal zones with lymphoid infiltrates Gastric GVHD 1. Squamous portion - small numbers of lymphocytes adjacent to basal epithelium 2. Squamous portion - small number of lymphocytes adjacent to basal epithelium and small numbers of intraepithelial lymphocytes; glandular portion -intraepithelial lymphocytes with degeneration of Parietal cells 3. Squamous portion - small to moderate number of lymphocytes adjacent to basal epithelium and small to moderate numbers of intraepithelial lymphocytes; glandular portion - intraepithelial lymphocytes with prominent degeneration of Parietal cells 4. Squamous portion - small to moderate number of lymphocytes adjacent to basal epithelium and small to moderate numbers of intraepithelial lymphocytes; glandular portion - intraepithelial lymphocytes with prominent degeneration of Parietal cells; mucosal erosion/ulceration Intestinal GVHD 1. Minimal to small numbers of infiltrating lymphocytes into crypt epithelium; rare degenerative epithelial cells 2. Small numbers of infiltrating lymphocytes into crypt epithelium; increased numbers of mitoses; rare to small numbers of degenerative epithelial cells in some crypts 3. Larger numbers of infiltrating lymphocytes into crypt epithelium; increased numbers of mitoses; small numbers of degenerative epithelial cells in most crypts; +/- mucosal ulceration 4. Larger numbers of infiltrating lymphocytes into crypt epithelium; increased numbers of mitoses; most crypts have evidence of degeneration of crypt epithelial cells; +/- mucosal ulceration Cutaneous GVHD 1. multifocal mild epidermal hyperplasia and hypekeratosis, minimal numbers of intraepithelial lymphocytes 2. multifocal mild epidermal hyperplasia and hypekeratosis, small numbers of intraepithelial lymphocytes, and rare degenerated epithelial cells 3. multifocal mild to moderate epidermal hyperplasia and hypekeratosis, small to moderate numbers of intraepithelial lymphocytes, and small to moderate numbers of degenerated epithelial cells 4. multifocal moderate epidermal hyperplasia and hypekeratosis, moderate numbers of intraepithelial lymphocytes, and moderate numbers of degenerated epithelial cells, microabscesses, skin erosion and/or ulceration

Supplementary Figure 2: Ruxolitinib does not impair post-transplant donor myeloid reconstitution and full donor chimerism. BM Only GVHD + vehicle GVHD+Ruxolitinib 90 mg/Kg GVHD+Ruxolitinib 45 mg/Kg ab 0 0,5 1,0 1,5 2,0 Donor CD3+ cells (*10^3)/ul blood p= p=0.01 p=NS Day +14 post- BMTDay +30 post- BMT cd Donor Gr-1+ cells (*10^3)/ul blood NS p=0.02 p=0.09 Day +14 post- BMTDay +30 post- BMT p=NS Donor B220+ cells (*10^3)/ul blood p< 0.05 Day +14 post- BMTDay +30 post- BMT p< ,5 1,0 1,5 2,0 Donor Ter119 cells (*10^3)/ul blood Day +14 post- BMTDay +30 post- BMT p=NS p=0.01 p=NS

Supplementary Figure 3: GVT effect against myeloid leukemia RMB-1 cell line is maintained in the presence of ruxolitinib p=0.01 p=0.003 p=0.2 % Bone Marrow RMB-1 cells BM Only+RMB-1 GVHD+ vehicle+ RMB-1 GVHD+Ruxolitinib 45 mg/Kg+ RMB p= p=0.002 p=0.1 % Spleen RMB-1 cells ab

Supplementary Figure 4: Ruxolitinib at the dose of 90 mg/Kg prevents acute GVHD without affecting T cell alloreactivity a c d b * % Spleen CD8 + IFN-γ + cells ** p=0.2 % Spleen CD4 + IFN-γ + cells p=0.3 % Spleen CD4 + IL-17 + cells e *** Naive T (CD62L+CD44-)CM T (CD62L+CD44+)EM T (CD62L-CD44+) % Spleen T cells NS * Total Spleen cellsCD3 + cellsCD4 + cellsCD8 + cells Cells per Spleen (*10^6) BM only GVHD+Vehicle GVHD+Ruxolitinib 90 mg/Kg % Spleen Treg cells p= p= ** p=0.3 p= ,1 0,2 0,3 0,4 0, ab

0 1,0 2,0 3,0 BM onlyGVHD + Vehicle GVHD +Ruxolitinib 45 mg/Kg # CD4 + IFN-γ + spleen cells (10^5) ** p=0.8 ** 0 1,0 2,0 3,0 4,0 5,0 BM onlyGVHD + Vehicle GVHD +Ruxolitinib 45 mg/Kg # CD8 + IFN-γ + spleen cells (10^5) ** p=0.4 ** 0 0,1 0,2 0,3 0,4 0,5 GVHD + Vehicle GVHD +Ruxolitinib 45 mg/Kg # Th17 spleen cells (10^5) p=0.4 Supplementary Figure 5: Ruxolitinib effect at 45 mg/Kg on absolute numbers of alloreactive T cells, Th17 and Treg cells. a bc GVHD + Vehicle GVHD +Ruxolitinib 45 mg/Kg # Treg spleen cells (10^5) p= ,5 1,0 1,5

Supplementary Figure 6: Representative Images of Ruxolitinb effect on T cells and macrophage infiltration of GVHD organs BM onlyGVHD + VehicleGVHD + Ruxolitinib T cells (CD3 epsilon +) Macrophages (Iba-1 +) a b c BM onlyGVHD + VehicleGVHD + Ruxolitinib T cells (CD3 epsilon +) Macrophages (Iba-1 +) BM onlyGVHD + VehicleGVHD + Ruxolitinib T cells (CD3 epsilon +) Macrophages (Iba-1 +) Sublobular/centrilobular veins: Leukocyte Rolling/Adhesion