SUPER-ENHANCER ANALYSIS DEFINES NOVEL AML AND MDS SUB-TYPES SENSITIVE TO SY-1425, A POTENT AND SELECTIVE RARA AGONIST
EHA Library. McKeown M. Jun 12, 2016; 135301; S807
Dr. Michael McKeown
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Abstract
Abstract: S807
Type: Oral Presentation
Presentation during EHA21: On Sunday, June 12, 2016 from 09:00 - 09:15
Location: Hall A3
Background
Super-enhancers (SEs) are exceptionally large, highly active chromatin regions that are densely occupied by transcription factors. They have been implicated in directing gene expression programs that define cell identity and also regulate oncogenes critical to the pathogenesis of cancer. One such target, the retinoic acid receptor alpha (RARα) was identified by the asymmetric distribution of its enhancer in a cohort of 60 non-APL AML patient samples profiled by our gene control platform.
Aims
This study sought to characterize the relationship between a RARA super-enhancer and response to SY-1425, a potent and selective RARα agonist, in AML patient samples, cell lines, and mouse models. MDS patient samples were also tested for comparable RARA enhancer levels and elevated biomarker.
Methods
ChIP-seq and RNA-seq were used to study the presence of SEs and correlated mRNA in patient samples. ChIP-seq, RNA-seq, and expression arrays were used in AML cell lines for the same profiling in addition to characterization of the transcriptional and chromatin level response to SY-1425. The effect of SY-1425 was studied in proliferation assays for AML cell lines and in patient-derived murine xenograft models of AML.
Results
The presence of a SE at the RARA gene locus was found to predict anti-proliferative sensitivity to the potent, selective RARα agonist, SY-1425, both in vitro and in vivo. SY-1425 is a clinical stage RARα agonist with greater potency, selectivity, and improved PK over the pan-RAR agonist, ATRA. SY-1425 is not susceptible to auto-induced metabolism and markedly inhibited growth of RARA SE-selected patient-derived murine xenograft models in which ATRA had no significant benefit.Normal bone marrow blast cells have low levels of RARA enhancer activity. However, the formation of the SE at the RARA gene locus drives RARα transcription in excess of endogenous ligand level, favoring the unliganded, repressive state of the transcription factor that leads to myeloid differentiation block. SY-1425 treatment of SE-containing AML cells strongly induces activation of these formerly repressed genes, halting proliferation and promoting differentiation. To examine transcriptional response to SY-1425, ChIP-seq for enhancer (H3K27ac) and RARα binding was paired with mRNA profiling before and after treatment. Following treatment, loci with strong RARα peaks showed increased acetylation and there was formation of new enhancers where little acetylation was previously observed, consistent with RARα serving as a repressor when unliganded and as a transcriptional activator with SY-1425 bound. Moreover, the genes near the SY-1425-induced enhancers are found to be strongly upregulated. This effect is exemplified by enhancer and mRNA upregulation of TGM2, a canonical ATRA differentiation response gene in APL. This mechanism is similar to PML-RARα differentiation blockade and SY-1425-induced gene expression changes are very similar to those observed with retinoid treatment of APL cells.In addition to AML, a sub-population of MDS patient samples also contain elevated levels of RARA SE and associated biomarker, suggesting the potential utility of SY-1425 in this closely related disease. Furthermore, ChIP-seq analysis has established that SEs exist in MDS which are comparable to those in RARA SE-driven AML.
Conclusion
In summary, our gene control platform has identified novel subsets of non-APL AML and MDS patients who may respond to the selective RARa agonist, SY-1425. Based on these findings, a phase 2 clinical investigation of SY-1425 in AML and MDS patients, using an SE-derived biomarker to enrich for patients likely to respond, is planned for later this year.
Session topic: AML Biology - Novel targeted therapies
Keyword(s): AML, Epigenetic, MDS, Retinoic acid receptor (RAR)
Type: Oral Presentation
Presentation during EHA21: On Sunday, June 12, 2016 from 09:00 - 09:15
Location: Hall A3
Background
Super-enhancers (SEs) are exceptionally large, highly active chromatin regions that are densely occupied by transcription factors. They have been implicated in directing gene expression programs that define cell identity and also regulate oncogenes critical to the pathogenesis of cancer. One such target, the retinoic acid receptor alpha (RARα) was identified by the asymmetric distribution of its enhancer in a cohort of 60 non-APL AML patient samples profiled by our gene control platform.
Aims
This study sought to characterize the relationship between a RARA super-enhancer and response to SY-1425, a potent and selective RARα agonist, in AML patient samples, cell lines, and mouse models. MDS patient samples were also tested for comparable RARA enhancer levels and elevated biomarker.
Methods
ChIP-seq and RNA-seq were used to study the presence of SEs and correlated mRNA in patient samples. ChIP-seq, RNA-seq, and expression arrays were used in AML cell lines for the same profiling in addition to characterization of the transcriptional and chromatin level response to SY-1425. The effect of SY-1425 was studied in proliferation assays for AML cell lines and in patient-derived murine xenograft models of AML.
Results
The presence of a SE at the RARA gene locus was found to predict anti-proliferative sensitivity to the potent, selective RARα agonist, SY-1425, both in vitro and in vivo. SY-1425 is a clinical stage RARα agonist with greater potency, selectivity, and improved PK over the pan-RAR agonist, ATRA. SY-1425 is not susceptible to auto-induced metabolism and markedly inhibited growth of RARA SE-selected patient-derived murine xenograft models in which ATRA had no significant benefit.Normal bone marrow blast cells have low levels of RARA enhancer activity. However, the formation of the SE at the RARA gene locus drives RARα transcription in excess of endogenous ligand level, favoring the unliganded, repressive state of the transcription factor that leads to myeloid differentiation block. SY-1425 treatment of SE-containing AML cells strongly induces activation of these formerly repressed genes, halting proliferation and promoting differentiation. To examine transcriptional response to SY-1425, ChIP-seq for enhancer (H3K27ac) and RARα binding was paired with mRNA profiling before and after treatment. Following treatment, loci with strong RARα peaks showed increased acetylation and there was formation of new enhancers where little acetylation was previously observed, consistent with RARα serving as a repressor when unliganded and as a transcriptional activator with SY-1425 bound. Moreover, the genes near the SY-1425-induced enhancers are found to be strongly upregulated. This effect is exemplified by enhancer and mRNA upregulation of TGM2, a canonical ATRA differentiation response gene in APL. This mechanism is similar to PML-RARα differentiation blockade and SY-1425-induced gene expression changes are very similar to those observed with retinoid treatment of APL cells.In addition to AML, a sub-population of MDS patient samples also contain elevated levels of RARA SE and associated biomarker, suggesting the potential utility of SY-1425 in this closely related disease. Furthermore, ChIP-seq analysis has established that SEs exist in MDS which are comparable to those in RARA SE-driven AML.
Conclusion
In summary, our gene control platform has identified novel subsets of non-APL AML and MDS patients who may respond to the selective RARa agonist, SY-1425. Based on these findings, a phase 2 clinical investigation of SY-1425 in AML and MDS patients, using an SE-derived biomarker to enrich for patients likely to respond, is planned for later this year.
Session topic: AML Biology - Novel targeted therapies
Keyword(s): AML, Epigenetic, MDS, Retinoic acid receptor (RAR)
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