Supplementary Materials

The PDF file includes:

• Materials and Methods
• Fig. S1. Liver function tests in recipients after autologous or allogeneic HCT in NHP.
• Fig. S2. Gating tree for flow cytometric identification and characterization of T cells within different spatiotemporal compartments using SIVS in NHP.
• Fig. S3. Phenotypic characteristics of liver intravascular compartment-1 T cells in NHP.
• Fig. S4. Compartmentalization of CD4⁺ T cells at steady state and after HCT in NHP.
• Fig. S5. Migration of CD4⁺ and CD8⁺ T cells at steady state and after HCT in NHP.
• Fig. S6. Phenotypic characterization of compartment-2 and compartment-3 CD8⁺ T cells in NHP.
• Fig. S7. Phenotypic characteristics of intestinal CD4⁺ T cells in NHP.
• Fig. S8. Transcriptomic identification of intestinal CD8⁺ T cells in NHP.
• Fig. S9. Transcriptomic identification of intestinal T_RM-high and T_RM-low CD8⁺ T cells from large intestine in NHP.
• Fig. S10. Immunophenotypic and transcriptomic characteristics of CD8⁺ T cells from the large intestine.
• Fig. S11. Threshold testing of T_RM-high and T_RM-low CD8⁺ T cells.
• Legends for tables S1 to S17
• Legend for data file S1
• References (87–91)

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Other Supplementary Material for this manuscript includes the following:

• Table S1 (Microsoft Excel format). Transplant characteristics.
• Table S2 (Microsoft Excel format). List of antibodies used, flow cytometry panels, and flow-based definitions of lymphocyte populations.
• Table S3 (Microsoft Excel format). scRNA-seq sample information and QC metrics.
• Table S4 (Microsoft Excel format). Differentially expressed genes between donor, host, and HC CD8⁺ T cells with high enrichment scores for the T_RM signature.
• Table S5 (Microsoft Excel format). Pathway analysis of differentially expressed genes between donor, host, and HC CD8⁺ T cells with high enrichment scores for the T_RM signature.
• Table S6 (Microsoft Excel format). Predicted activated upstream regulators in donor CD8⁺ T cells with high enrichment scores for the T_RM signature in comparison with their HC and host counterparts.
• Table S7 (Microsoft Excel format). Differentially expressed genes between donor, host, and HC CD8⁺ T cells with low enrichment scores for the T_RM signature.
• Table S8 (Microsoft Excel format). Pathway analysis of differentially expressed genes between donor, host, and HC CD8⁺ T cells with low enrichment scores for the T_RM signature.
• Table S9 (Microsoft Excel format). Predicted activated upstream regulators in donor CD8⁺ T cells with low enrichment scores for the T_RM signature in comparison with their HC and host counterparts.
• Table S10 (Microsoft Excel format). Differentially expressed genes between donor CD8⁺ T cells with low and high enrichment scores for the T_RM signature.
• Table S11 (Microsoft Excel format). Predicted activated upstream regulators in donor CD8⁺ T cells with low enrichment scores compared to cells with high enrichment scores for the T_RM signature.
• Table S12 (Microsoft Excel format). Gene signature of donor CD8⁺ T cells with low enrichment scores for the T_RM signature, defined as shown in Fig. 5B.
• Table S13 (Microsoft Excel format). Pathway analysis on the gene signature of donor CD8⁺ T cells with low enrichment scores for the T_RM signature.
• Table S14 (Microsoft Excel format). Predicted activated upstream regulators based on the gene signature of donor CD8⁺ T cells with low enrichment scores for the T_RM signature.
• Table S15 (Microsoft Excel format). Clinical characteristics of patients from the ABA2 clinical trial (NCT01743131), included in the current study.
• Table S16 (Microsoft Excel format). Results of GSEA analysis comparing patients from the ABA2 clinical trial (NCT01743131) with grade 2 to 4 and 3 to 4 aGVHD versus patients with grade 0 to 1 and 0 to 2 aGVHD, respectively.
• Table S17 (Microsoft Excel format). scRNA-seq–derived gene sets used for GSEA analysis.
• Data file S1 (Microsoft Excel format). Primary data.