Genome-Wide Methylome and Transcriptome Profiling of Acute Myeloid Leukemia Derived Bone Marrow Mesenchymal Cells Identify Age Group Specific Biological Pathway Dysregulation in the Bone Marrow Microenvironment of AML

Adult patients with acute myeloid leukemia (AML) have a proportionate increase in mortality from their disease and therapy as age increases. In great part, this mortality is due to disease relapse that occurs at a higher rate irrespective of genetic assigned risk. While intensification of therapy in patients with favorable genomics such as core-binding-factor AML (CBF-AML) has yielded a high proportion of long-term remission and potential cure, this benefit has been less frequently observed in patients with AML age 60 and older despite receipt of similar therapy. Moreover, even less benefit has been observed in patients with unfavorable genomics such when bearing a complex karyotype (karyotype with ≥ 3 chromosome abnormalities). Reasons for this unfavorable outcome among older patients is unknown. We hypothesized that tumor-induced aging in cells of bone marrow microenvironment, specifically, in bone marrow mesenchymal stromal cells (BMSCs) plays a significant role in AML survival and progression in older compared to younger patients and that the difference in prognosis may depend on specific aging induced changes in the BMSCs. We expanded BMSCs under physiologic hypoxic conditions (91% nitrogen, 4% oxygen and 5% CO 2) to mimic the bone marrow microenvironment, isolated DNA and RNA from early passaged cells and performed methylation analysis using 850k Illumina DNAmehtylation arrays and gene expression analysis using mRNAseq. We used the Horvath Skin and Blood clock to calculate epigenetic age (DNA methylation age). We determined differentially expressed genes with increasing epigenetic or chronological age in the different AML genetic risk groups (n=9 CBF-AML, n=11 CK-AML and n=7 Normal donor BMSC) as well as in older (>60) and younger (