Abstract About ten percent of infants with Down syndrome are born with a transient myeloproliferative disorder (DS-TMD) that spontaneously resolves within the first few months of life. Twenty to thirty percent of these infants subsequently develop acute megakaryoblastic leukemia (DS-AMKL), typically within a year or two following resolution of their DS-TMD. Recent work has shown that both DS-TMD and DS-AMKL cells harbor acquired mutations in the key megakaryocyte transcription factor GATA-1 that lead to the exclusive production of a short GATA-1 isoform (GATA-1s). The mechanism by which GATA-1s acts in DS-TMD/AMKL remains incompletely understood. Mice engineered to produce only GATA-1s exhibit hyperproliferation of fetal liver-derived megakaryocytes, but normal growth of post-natal bone marrow-derived megakaryocytes. This suggests that unique microenvironmental features of fetal liver compared to bone marrow differentially influence the effects of GATA-1s on megakaryopoiesis. In order to further understand the mechanisms involved in these stage-specific effects, we compared gene expression profiles of wild type megakaryocyte progenitors (MkPs) isolated directly from embryonic day 13.5 (e13.5) murine fetal liver (FL) and from adult bone marrow (BM). Cells were FACS sorted based on the immunophenotype lin-sca-1-c-kit+ CD41+ CD150+, which has recently been shown to mark megakaryocyte-selective progenitors. Colony forming assays of the sorted cells revealed 92–100% growth of megakaryocyte colonies in culture medium containing multilineage cytokines (SCF, IL3, IL11, GM-CSF, EPO and TPO), confirming strong enrichment for megakaryocyte lineage cells. RNA from sorted FL and BM MkPs was then used to perform Affymetrix 3′ cDNA expression microarray analysis. Expression of early-stage megakaryocyte factors, such as c-mpl, FOG1, GATA1, Runx-1 and Fli-1 were found in both sets of samples, confirming selection of megakaryocyte progenitor cells. Importantly, we observed a striking up regulation of interferon alpha (IFN alpha) inducible genes belonging to the p200 family in BM MkPs compared to FL MkPs. Gene set enrichment analyses (GSEA) confirmed broad up regulation of the IFN alpha pathway, and as well up regulation of the JAK-STAT pathway in BM MkPs compared to FL MkPs. These findings were validated by quantitative RT-PCR and in situ immunohistochemistry. Given that STAT1 is a direct GATA-1 target gene and a major downstream effector of IFN alpha signaling, we hypothesize that enhanced IFN alpha signaling in the bone marrow may compensate for potential deficiencies of STAT1 during fetal liver megakaryopoiesis in the setting of GATA-1s. Experiments are underway to test this hypothesis.