Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia

Acute myeloid leukemia (AML) is an aggressive cancer which causes the rapid proliferation of immature myeloid-lineage blood cells (myeloblasts) in the bone marrow. These leukemic cells receive trophic signals from the bone marrow micro-environment (BMM) in which they reside, that are essential to the initiation and maintenance of the disease. Because this is a complex and heterogeneous tissue, many aspects of this environment remain poorly characterised due to experimental hurdles. Here we performed single-cell RNA-sequencing of bone marrow aspirates from 10 AML patients across multiple key timepoints in disease progression (diagnosis, post-treatment, relapse). Longitudinally-collected BM aspirates were obtained for 10 AML patients from the time of diagnosis, post-treatment/remission and at relapse from The Finnish Haematology Registry and Clinical Biobank. scRNAseq was performed on the mononuclear cell fraction using 10X Genomics Single Cell 3’ Solution, version 3.1 Libraries were sequenced an illumina NovaSeq 6000 with goal minimum sequencing depth of 50,000 reads/cell.