Supplementary Materials

The PDF file includes:

  • Fig. S1. Immune gene signatures and survival in the AML discovery series.
  • Fig. S2. GeoMx DSP and ROI selection in a representative pretreatment BM trephine biopsy (SAL series) with high T cell infiltration.
  • Fig. S3. GeoMx DSP and ROI selection in a representative pretreatment BM trephine biopsy (SAL series) with low T cell infiltration.
  • Fig. S4. Highly multiplexed protein profiling in the SAL patient cohort.
  • Fig. S5. Correlation between CD3 infiltration and expression of IO-related proteins as revealed by GeoMx DSP of BM trephine biopsies (SAL series).
  • Fig. S6. Expression of SIG3 genes in TCGA-AML cases and in healthy tissues.
  • Fig. S7. Association between immune gene signatures and patients’ characteristics in the AML discovery series.
  • Fig. S8. Clinical outcomes of patients with immune-infiltrated and immune-depleted AML treated with allogeneic HSCT (PMCC cohort).
  • Fig. S9. Immune gene signatures in the CHOP and SAL cohorts.
  • Fig. S10. GO and pathway analyses.
  • Fig. S11. Immune scores in patients with AML (SAL cohort) at time of diagnosis and achievement of CR (paired samples).
  • Fig. S12. Intracellular cytokine staining of BM samples from patients with immune-infiltrated and immune-depleted AML.
  • Fig. S13. Immune subtypes associate with cancer driver gene mutations in TCGA-AML and Beat AML trial specimens.
  • Fig. S14. Genes implicated in IFN downstream signaling in Beat AML trial specimens with TP53 mutations.
  • Fig. S15. Selection of ROIs in BM biopsies from patients receiving flotetuzumab immunotherapy.
  • Table S1. DE genes (FDR < 0.05) between ELN favorable-risk and adverse-risk AML (HOVON discovery cohort).
  • Table S2. Competing risks analysis for OS prediction (PMCC discovery cohort).
  • Table S3. Causes of death in patients receiving allogeneic HSCT (PMCC cohort).
  • Table S4. GO of and KEGG pathways captured by DE genes between adult (SAL cohort) and childhood AML (CHOP cohort).
  • Table S5. GO of and KEGG pathways captured by DE genes between adult patients with AML at the time of diagnosis and achievement of CR (SAL cohort).
  • Table S6. GO of and KEGG pathways captured by DE genes between adult patients with AML at the time of relapse and achievement of CR (SAL cohort).
  • Table S7. Binary logistic regression predicting therapeutic resistance (PMCC cohort).
  • Table S8. Multinomial logistic regression predicting therapeutic response (HOVON cohort).
  • Table S9. Study participants in the CP-MGD006-01 clinical trial (NCT#02152956) of flotetuzumab immunotherapy.
  • Table S10. Protein panels used for GeoMx DSP of FFPE BM biopsies [SAL cohort (A) and flotetuzumab cohort (B)].
  • Table S11. Antibody panel used for intracellular cytokine staining of BM cell suspensions.
  • Reference (74)

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Other Supplementary Material for this manuscript includes the following:

  • Data S1 (Microsoft Excel format). Patient and disease characteristics (in silico data sources).