Therapeutic Targeting of EP300/CBP By Bromodomain Inhibition in Acute Myeloid Leukemia

CCS1477 (also known as inobrodib) is a potent and selective inhibitor of the bromodomains of EP300 and CBP, two homologous histone acetyltransferases with critical roles in cellular growth and differentiation.

In pre-clinical analyses we found that CCS1477 induced dose-dependent growth inhibition of a wide range of acute myeloid leukemia (AML) cell lines and primary patient samples of diverse molecular subtypes at low nanomolar concentrations. Growth inhibition was predominantly due to cell cycle arrest and differentiation; there was only modest apoptosis.

In vivo, in contrast to control mice which all developed short latency AML, all animals with experimentally initiated MLL-AF9 and MLL-AF10 driven AMLs (in a retroviral transduction and transplantation syngeneic model) treated with 30mg/kg daily PO CCS1477 survived to termination of the experiment at 220 days. In subcutaneous xenograft models, there was dose-dependent growth inhibition of MOLM16 AML cell tumours, with 20mg/kg daily for 21 days completely suppressing tumour growth and no tumour regrowth until 14 days following the end of treatment.

Mechanistically, we found that 100nM CCS1477 induced rapid and selective depletion of EP300 in particular from MYB binding sites in THP1 AML cells. ChIPseq demonstrated that in steady state the strongest recruitment of EP300 to chromatin in THP1 AML cells was at sites of MYB and CEBPA transcription factor occupancy, although EP300 was also found genome-wide at sites occupied by other factors including RUNX1 and ETS. Following CCS1477 treatment there was, within six hours, selective loss of EP300 at MYB occupied sites, co-localized reduced chromatin accessibility and histone H3K27 acetylation, and stalling of RNA polymerase at subordinate genes with reduced transcription. This was associated with a dose-dependent redistribution of EP300 to alternate sites and up regulation of differentiation genes.

In our ongoing phase I/IIa clinical trial investigating the safety and efficacy of CCS1477 in advanced haematological malignancies (NCT04068597), we have observed therapeutically beneficial granulocytic differentiation responses in patients with high-risk myelodysplasia or relapsed AML. For example, a patient with myelodysplasia with excess blasts 2 (MDS-EB2) evolving to AML who had received three cycles of azacitidine without response was treated with CCS1477 50mg PO (once daily, three days/week). Pre-CCS1477 treatment there was profound neutropenia and multiple admissions for sepsis. After CCS1477 treatment the neutrophil count rapidly normalized and, despite a brief admission for splenic infarction in the first week, the patient remained well for 5 months with no infective episodes. Treatment was stopped due to a rising leukocyte count. Similar responses were seen in other patients.

In one of these, single cell RNA sequencing of serial blood and bone marrow samples confirmed appearance of mature myeloid cells on CCS1477 treatment and, within the blast population, up regulation of a multilineage differentiation programme and down regulation of a stem cell programme. Reflecting our findings in cell line models, there was also up regulation of genes induced by MYB knockdown and concordant up and down regulation of genes regulated by CEBPA in THP1 AML cells.

Finally, we evaluated the activity of CCS1477 in xenograft models in combination with existing standard of care agents. Azacitidine and CCS1477 in particular demonstrated synergistic growth inhibitory activity in the MOLM16 model, as did venetoclax in MOLM16 and MV(4;11) models.

These encouraging pre-clinical and early phase clinical findings set the stage for the clinical trial evaluation of CCS1477 in combination with azacitidine and venetoclax.