Abstract 3173: Lymphocyte-specific chromatin accessibility predetermines glucocorticoid resistance in acute lymphoblastic leukemia

Glucocorticoids are well known for their immunosuppressive activity, and play a critical role in the treatment of lymphoid malignancies. However, the development of resistance remains a significant barrier to cure and the mechanisms are poorly defined. Moreover, glucocorticoids are rarely efficacious in treating myeloid and other non-lymphoid malignancies, and the mechanisms of lymphocyte-specific efficacy are unclear. To address these issues, we first carried out a global analysis of DNase I hypersensitive sites in 18 lymphoid and 64 non-lymphoid cell types to map lymphocyte-specific open chromatin domains (LSOs). We then integrated these domains with genome-wide glucocorticoid-induced gene transcription and epigenetic modulation in an in vivo patient-derived xenograft (PDX) model of acute lymphoblastic leukemia (ALL). Performing chromatin immunoprecipitation and assays for transposase-accessible chromatin (ATAC), we determined a strong correlation between glucocorticoid receptor (GR) binding and chromatin accessibility, acetylated histone marks and binding of a DNA structural protein (CTCF), and identified 1,536 GR bound LSOs. We next analyzed RNA-seq data in glucocorticoid sensitive and resistant ALL PDXs for expression changes in genes located within 100 kb of the LSOs after glucocorticoid treatment in vivo, and identified four groups comprising 389 genes that were significantly differentially expressed. Of the 198 up-regulated genes, 143 showed increased H3K27Ac enrichments at 177 LSOs. Forty-two LSOs showed the increase only in glucocorticoid sensitive but not resistant ALLs. Applying this to an extended panel of ALL PDXs, basal DNA methylation at the 42 LSOs was significantly higher in resistant ALLs despite no difference within the gene bodies, whereas the basal chromatin accessibility indicated by ATAC abundance was diminished. Pathway analysis indicated that the LSO regulated genes were involved in repressing B- and T- cell receptor signaling pathways and activating the apoptotic pathway. One such LSO was at the pro-apoptotic BIM gene locus, where CTCF binding was found only in lymphocytes but not in other cell types. The GR cooperated with CTCF to mediate interactions between the promoter and the BIM LSO to direct DNA looping, thus triggering BIM transcription. Importantly, this LSO was heavily methylated in resistant ALLs as well as non-lymphoid cells. Azacitidine, a DNA demethylating drug that is routinely used in the clinic, could partially reverse these changes and restore glucocorticoid sensitivity. Taken together, this study demonstrated for the first time that lymphocyte-specific epigenetic modifications pre-determine glucocorticoid resistance in ALL and may account for the lack of glucocorticoid sensitivity in other cell type. Reversal of these epigenetic changes may lead to improvements in the use of glucocorticoids in the clinic. Citation Format: Duohui Jing, Yizhou Huang, Xiaoyun Liu, Keith Sia, Rebecca C. Poulos, Miriam Span, Chao Zhang, Jianqing Mi, Jason WH Wong, Dominik Beck, John E. Pimanda, Richard B. Lock. Lymphocyte-specific chromatin accessibility predetermines glucocorticoid resistance in acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3173.