SY-1425 (tamibarotene), a potent and selective RAR alpha agonist, induces changes in the transcriptional regulatory circuit of AML cells leading to differentiation

SY-1425 (tamibarotene) is a potent and selective agonist of the transcription factor (TF) retinoic acid receptor alpha (RARα) that is currently being evaluated in a biomarker-directed Ph2 clinical study in AML and MDS. A subset of AML and MDS patients, referred to as RARA-high, has previously been found to have a large enhancer (super-enhancer) at the RARA locus or upregulation of IRF8, a RARα associated TF. Here, we profile the noncoding genome and transcriptional landscape in AML cells to define the circuitry of RARA-high AML characterized by RARα pathway activation. In addition, AML cell lines were profiled with and without SY-1425 treatment to query the perturbations of key regulatory connections by SY-1425. To better understand the regulatory circuitry of the RARα pathway in AML, we profiled RARA-high and RARA-low AML cell lines with a combination of ATAC-seq, H3K27ac ChIP-seq, and transcriptomic profiling. Using the enhancer landscape of these cell lines compared to a set of healthy human immune cells comprising hematopoietic stem and progenitor cells (HSPCs) as well as multiple myeloid lineages, we performed a non-negative least squares (NNLS) regression to determine the hematopoietic lineage components of these AML cell lines. We found that RARA-high cell lines sensitive to SY-1425 (THP-1, OCI-AML3, MV4-11, and EOL-1) tend to be most similar to monocytes, while RARA-low cell lines insensitive to SY-1425 (KG-1a, Kasumi-1, and OCI-M1) are more HSPC or erythroid-like. We then studied the effect of SY-1425 on the differentiation state of these AML cell lines by additionally profiling them with and without treatment. We find that the enhancer landscape of RARA-high AML cell lines was changed by SY-1425 toward one resembling more fully differentiated myeloid cells of different subtypes, including dendritic cells, granulocytic cells, and macrophages. This was in contrast to the well-characterized granulocytic differentiation of APL caused by retinoids. Functional validation by flow cytometry confirmed surface marker changes consistent with the observed epigenomic alterations. Comparable changes were not found in RARA-low AML cell lines. This effect supports the hypothesis that SY-1425 treatment relieves a RARα-mediated differentiation block of RARA-high AML. To understand the individual regulatory connections being modulated in response to SY-1425, we investigated the binding locations of TFs in the RARA-high cell lines with and without SY-1425 treatment. As expected, enhancers and genes bound by RARα were associated with upregulation of transcription in response to SY-1425. TF binding sites for IRF1 and IRF8 were also identified at induced enhancers. Conversely, known factors important for maintaining an immature/proliferative state were found associated with enhancers most deactivated by SY-1425 (as measured by H3K27ac loss). These included RUNX1, CEBP, and members of the FOS/JUN circuit (which were noted previously as a component of the oncogenic RARα circuit in patient samples). Taken together, these results support that the mechanism of action for SY-1425 is through perturbation of myeloid regulatory relationships in RARA-high AML blasts, leading to a more differentiated phenotype. Based on the understanding of AML- and RARα-driven tumor circuitry, we have generated insight into morphologic, lineage marker, and target-gene based measures to be used in conjunction with clinical studies. The ongoing Ph2 study of SY-1425 in AML and MDS (NCT02807558) will explore measurement of these features in patients. This abstract is also being presented as Poster 06. Citation Format: Christopher M. Fiore, Michael R. McKeown, Emily Lee, Matthew L. Eaton, Darren Smith, Kathryn Austgen, Mei Wei Chen, Matthew Guenther, M. Ryan Corces, Ravindra Majeti, Eric Olson, Christian C. Fritz. SY-1425 (tamibarotene), a potent and selective RARα agonist, induces changes in the transcriptional regulatory circuit of AML cells leading to differentiation [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr PR05.