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

Abstract

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 (<60) AML-BMSCs, and performed Gene Set Enrichment Analysis (GSEA) for the Hallmarks as well as aging and senescence related genesets (n=33 genesets). We found that BMSCs derived from AML bone marrow cells are more age accelerated than normal donor BMSCs. Our GSEA analysis revealed enrichment for age-associated gene networks that reflected hallmarks of aging, including mitochondrial dysfunction, inflammation, and cellular senescence. Specifically, we observed a positive enrichment for the SenMayo gene signature ( Saul et al. 2022, Nature Communications) and a negative enrichment of proliferation and mitotic gene sets with increasing epigenetic and chronological age (padj<0.05). Gene sets that are related to inhibition of adipogenesis were positively enriched in the CBF-AML BMSCs compared to the CK-AML BMSCs. Our integrated analysis revealed novel observations regarding the cellular changes that occur in the AML stromal microenvironment with increasing age. Most interestingly, our findings suggest that AML derived BMSCs have increased epigenetic age compared to normal donor BMSCs. Additional experiments are ongoing to functionally validate the findings predicted by the enrichment analysis. Our study is the first to suggest an increased epigenetic age in the stromal bone marrow microenvironment of older AML patients.