Abstract 3756: Highly multiplexed proteomic assessment of the human acute myeloid leukemia bone marrow microenvironment
Authors: Bogdan Popescu, Katherine Lindblad, Giovanna Fantoni, Gege Gui, Janet Valdez, Meghali Goswami, Christin DeStefano, Catherine Lai, Angélique Biancotto, Julián Candia, Foo Cheung, Julie Thompson, Laura W. Dillon, Christopher S. Hourigan
Journal: Cancer Research (2019)

Abstract Acute myeloid leukemia (AML) is a genetically heterogenous and often fatal cancer of the hematopoietic system. Even after achieving an initial complete remission, more than half of such AML patients experience clinical relapse due to the persistence of “minimal” residual disease (MRD). Ex-vivo studies have hypothesized that the interactions between residual leukemic cells and the local microenvironment in the bone marrow may play a key role in their survival and chemoresistance. Therefore, we performed for the first time a global examination of the proteomic profile of the bone marrow microenvironment in AML patients using a highly multiplexed method based on the ability of slow off-rate modified aptamers (modified small single-stranded oligonucleotides) to bind target proteins with high specificity and affinity at slow dissociation rates. Ten relapsed/refractory adult AML patients and age-matched healthy subject controls were recruited, under an IRB-approved protocol, for research bone marrow aspirate (BMA) and blood serum collection. The supernatant resulting from centrifugation of BMA and serum samples were processed and analyzed on a SOMAscan™ hybridization microarray platform for the detection and quantification of 1,305 target proteins (Somalogic, CO). Data was corrected using Hybridization Control and Median Signal Normalization methods. Significant differences were found between AML and healthy donor bone marrow, such that 133 analytes were differentially expressed in the AML group (Wilcoxon rank sum test FDR p&amp;lt;0.05, fold change &amp;gt;1.5); 85 over-expressed and 48 under-expressed. In addition to proteins already known to be elevated in AML patients (eg: Erythropoietin, Thrombopoietin, Hepcidin and Ferritin) and dysregulation of pathways previously identified as disease relevant (eg: Arginase), we also discovered multiple statistically significant differences in levels of soluble proteins that are not currently known to be associated with AML pathogenesis or treatment. Comparative analysis between blood serum and bone marrow determined that 82 of the 133 candidates have differential expression that was specifically restricted to the bone marrow. The STRING database was queried for pathway analysis of enriched protein sets in the AML group and clustered analytes with molecular functions including cytokine activity (GO:0005125, n=11, p=1.93e-08), cytokine receptor binding (GO:0005126, n=12, p=3.17e-08) and signal transducer activity (GO:0004871, n=19, p=9.23e-05). Using a high-throughput proteomic technology we have identified an AML bone marrow microenvironment-specific profile comprised of both proteins with known implications in leukemic pathogenesis and also several novel candidates from biologically plausible pathways that, once validated, may provide mechanistic insight and opportunity for therapeutic targeting. Citation Format: Bogdan Popescu, Katherine Lindblad, Giovanna Fantoni, Gege Gui, Janet Valdez, Meghali Goswami, Christin DeStefano, Catherine Lai, Angélique Biancotto, Julián Candia, Foo Cheung, Julie Thompson, Laura W. Dillon, Christopher S. Hourigan. Highly multiplexed proteomic assessment of the human acute myeloid leukemia bone marrow microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3756.