Fig. 1: Characterizing T cell infiltration in pediatric AML cases and non-leukemic controls.

A Schematic overview of the study population, used techniques, and the digital image analysis pipeline. AML cases are categorized in immune-infiltrated (red) and immune-depleted (blue) groups according to their T cell infiltration levels (above or below median of non-leukemic controls). Representative bone marrow biopsy images from a treatment-naïve pediatric AML case (B) and a non-leukemic control (C) showing H&E staining, CD3⁺ T cells, and CD8⁺ T cells. White lobules indicate adipocytes. Comparison of the normalized abundance of CD3⁺ T cells (D) and CD8⁺ T cells (E) in the bone marrow between pediatric AML cases and non-leukemic controls using the Mann–Whitney test. The dashed lines indicate the median CD3⁺ (D) and CD8⁺ (E) T cell abundance in non-leukemic controls, respectively. Normalized abundance of CD3⁺ (F) and CD8⁺ T cells (G) per cytogenetic subgroup. ‘Normal’ indicates normal karyotype, while ‘Others’ is a merge of cytogenetic abnormalities different from the five defined cytogenetic subgroups. See Table S1. ‘Complex’ indicates cases with complex karyotype AML (≥3 chromosomal abnormalities). The dashed lines shown in Fig. 1D, E are also shown in Fig. 1F-G. H Schematic overview of the TARGET-AML cohort, the additional non-leukemic control group, the performed analysis (CIBERSORTx), and the subsequent categorization of patients into the immune-infiltrated or immune-depleted groups (based on median T- and CD8⁺ T cell abundance in non-leukemic controls). Estimated absolute (ABS) abundance of T- (I) and CD8⁺ T (J) cells in the bone marrow of treatment-naïve pediatric AML cases in the TARGET-AML cohort. The dashed lines shown in Fig. 1I, J indicate the estimated median bone marrow T- and CD8⁺ T cell abundance in four non-leukemic controls.