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 TRM-high and TRM-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 TRM-high and TRM-low CD8+ T cells.
  • Legends for tables S1 to S17
  • Legend for data file S1
  • References (8791)

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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 TRM 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 TRM signature.
  • Table S6 (Microsoft Excel format). Predicted activated upstream regulators in donor CD8+ T cells with high enrichment scores for the TRM 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 TRM 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 TRM signature.
  • Table S9 (Microsoft Excel format). Predicted activated upstream regulators in donor CD8+ T cells with low enrichment scores for the TRM 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 TRM 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 TRM signature.
  • Table S12 (Microsoft Excel format). Gene signature of donor CD8+ T cells with low enrichment scores for the TRM 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 TRM 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 TRM 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.