Dual targeting of tyrosine kinase and BCL6 signaling for leukemia stem cell eradication

During the past reporting period (months 18-24 of this grant), we have made progress towards all three milestones. Major progress in Milestone 1 was made by identifying 391 compounds in 10 lead classes that will be developed further in a secondary fragment-based screen. While the goal of identifying lead class compounds with BCL6 inhibitory activity has already been met, we propose to run a secondary, fragment-based screen to refine the existing lead compounds and prioritize a small number for cell-based validation in Milestone 2. The success in Milestone 1 was based on computational modeling, HTS of 200,000 compounds and Fragment-based drug discovery (FBDD). For Milestone 2, we have successfully established POC analysis tools for validation of the ability of compounds to bind the BCL6 lateral groove and already produced 300 mg of BCL6-BTB domain protein needed for biochemical binding assays. Progress in Milestone 2 is based on surface plasmon resonance (SPR) and nuclear magnetic resonance (NMR) assays. In the coming months, we will use crystallographic fragment screening using a subset of our fragment library in addition to SPR and NMR, since crystallographic fragment screens have been shown to yield complimentary hits. For Milestone 3, we have now set up a reliable method to measure disease-modifying activity of BCL6-inhibitory compounds based on a newly generated knockin BCL6 reporter mouse model, in which transcriptional activation of the endogenous BCL6 promoter drives expression of mCherry. This addresses a main caveat of these measurements was that they were strongly influenced by the copy number of lentivector integrations. The BCL6fl/+-mCherry knockin BCL6 reporter system will provide a stable platform to study BCL6-expressing leukemia cells and effects of BCL6 small molecule inhibitors on survival and proliferation on BCL6-dependent leukemia cell populations. This will be a key requirement to measure disease-modifying activity of inhibitory compounds in large-scale assays in Milestone 3. Other requirements (e.g. leukemia xenografts) are already in place.

Reporting Period:

Year 3

During the past two years of this grant, we have generated compounds that have the ability to block the function of BCL6. In previous work, we had identified BCL6 as a key requirement for persistence of leukemia stem cells, which are the root cause of leukemia relapse and drug-resistance in patients. Over the past six months, we have focused on validating the new compounds based on functional tests that allow us to measure the depth and durability of BCL6 blockade in cell-based assay. To this end, we designed a large-scale petri-dish system in which we measured the efficacy of 11 lead compounds and their derivatives to abrogate the ability of leukemia cells to form colonies, a capability that reflects the activity of leukemia stem cells. This assay allowed us to prioritize 4 compounds for further testing. In parallel, we developed a biological assay to verify that the compounds are actually hitting their target, i.e. BCL6, by measuring the activity of genes that are typically regualted by BCL6. These genes include tumor suppressors like p53 and Arf and we measured the ability of our compounds to re-instate p53 and Arf expression. We found that p53 and Arf were reinstated only by 2 of our 4 lead candidates, so current trouble-shooting efforts will attempt to clarify why this is the case and whether we can modify these two compounds to improve their on-target efficacy. The other two compounds will move forward in the next derivative screen, in which we perform a fragment-based, screen, i.e. test multiple derivative based on addition and removal of small structural changes (fragments). Other caveats to address in the next year will be stability (half-life) of the lead compounds, bioavailability (how much and how long the compound will be available in the blood stream) and toxicity (how much of the compound will be tolerated by mice, is there indication of damage to tissues upon long-term treatment?).The goal of these studies will be to make a strong case for IND-enabling studies, i.e. to enter a formal, government-regulated process to convert the strongest of our compound into an FDA-approved drug for potential clinical testing in patients with drug-refractory AML and ALL.

Reporting Period:

NCE (Year 4)

For Milestone 1, we have successfully completed aa second focused screen of derivative compounds based on 6 leads in the first round. The fragment-based screen is currently in validation for structure-activity relationships (SAR; collaboration with Dr. Paul Workman, ICR, London). The proof-of-concept analysis for Milestone 2, and demonstration of specific interaction in the BCL6 lateral grove has been completed at the end of month 36 of this grant. Using computer-aided drug design (CADD), Dr. Melnick’s group and collaborators had previously identified a small molecule, 79-6, that bound to the BCL6-BTB domain. Thereby, 79-6 targeted the interaction of BCL6 and its co-repressors NCOR, BCOR and SMRT, and restored expression of BCL6 targets in leukemia cells, including Arf and p53. One caveat of the 79-6 compound that was identified by validation studies in Dr. Workman’s laboratory included the low degree of cell penetration and short half-life of the compound. To address these caveats, Dr. Cardenas applied a novel, CADD-based methodology based on “site identification by ligand competitive saturation” (SILCS). SILCS is a method for identifying a molecule’s binding site by simulating its physical movement. In this case, SILCS simulated the physical movement of 79-6 tool compound in solution to map the exact interaction interface between 79-6 and the BCL6 lateral groove. Thereby, SILCS produced a 3-dimensional map of the 79-6 molecule’s probable binding sites, which was then used to design 35 compounds to test in vitro. The new lead compound emerging from Dr. Melnick’s SILCS screen, FX-1085, is approximately 30-fold more effective than 79-6 and is now being validated in our studies on AML and ALL samples (Milestone 3). Results from this collaboration indicates that FX-1085 robustly prevents the formation of complexes between BCL6 and its co-repressors NCOR, BCOR and SMRT and, hence, re-activates BCL6 target genes, including Arf and p53. In the past six months (6-12 of the NCE), we have performed experiments to validate activity of BCL6 inhibition in vivo for the treatment of xenografted Ph+ ALL cells, MLL-rearranged ALL and RAS-driven acute leukemias.

Grant Application Details

Application Title:

Dual targeting of tyrosine kinase and BCL6 signaling for leukemia stem cell eradication

Public Abstract:

Leukemia is the most frequent form of cancer in children and teenagers, but is also common in adults. Chemotherapy has vastly improved the outcome of leukemia over the past four decades. However, many patients still die because of recurrence of the disease and development of drug-resistance in leukemia cells.
In preliminary studies for this proposal we discovered that in most if not all leukemia subtypes, the malignant cells can switch between an “proliferation phase” and a “quiescence phase”. The “proliferation phase” is often driven by oncogenic tyrosine kinases (e. g. FLT3, JAK2, PDGFR, BCR-ABL1, SRC kinases) and is characterized by vigorous proliferation of leukemia cells. In this phase, leukemia cells not only rapidly divide, they are also highly susceptible to undergo programmed cell death and to age prematurely. In contrast, leukemia cells in “quiescence phase” divide only rarely. At the same time, however, leukemia cells in "quiescence phase" are highly drug-resistant. These cells are also called 'leukemia stem cells' because they exhibit a high degree of self-renewal capacity and hence, the ability to initiate leukemia. We discovered that the BCL6 factor is required to maintain leukemia stem cells in this well-protected safe haven. Our findings demonstrate that the "quiescence phase" is strictly dependent on BCL6, which allows them to evade cell death during chemotherapy treatment. Once chemotherapy treatment has ceased, persisting leukemia stem cells give rise to leukemia clones that reenter "proliferation phase" and hence initiate recurrence of the disease. Pharmacological inhibition of BCL6 using inhibitory peptides or blocking molecules leads to selective loss of leukemia stem cells, which can no longer persist in a "quiescence phase".
In this proposal, we test a novel therapeutic concept eradicate leukemia stem cells: We propose that dual targeting of oncogenic tyrosine kinases (“proliferation”) and BCL6 (“quiescence”) represents a powerful strategy to eradicate drug-resistant leukemia stem cells and prevent the acquisition of drug-resistance and recurrence of the disease. Targeting of BCL6-dependent leukemia stem cells may reduce the risk of leukemia relapse and may limit the duration of tyrosine kinase inhibitor treatment in some leukemias, which is currently life-long.

Statement of Benefit to California:

Leukemia represents the most frequent malignancy in children and teenagers and is common in adults as well. Over the past four decades, the development of therapeutic options has greatly improved the prognosis of patients with leukemia reaching 5 year disease-free survival rates of ~70% for children and ~45% for adults. Despite its relatively favorable overall prognosis, leukemia remains one of the leading causes of person-years of life lost in the US (362,000 years in 2006; National Center of Health Statistics), which is attributed to the high incidence of leukemia in children. In 2008, the California Cancer Registry expected 3,655 patients with newly diagnosed leukemia and at total of 2,185 death resulting from fatal leukemia. In addition, ~23,300 Californians lived with leukemia in 2008, which highlights that leukemia remains a frequent and life-threatening disease in the State of California despite substantial clinical progress. Here we propose the development of a fundamentally novel treatment approach for leukemia that is directed at leukemia stem cells. While current treatment approaches effectively diminish the bulk of proliferating leukemia cells, they fail to eradicate the rare leukemia stem cells, which give rise to drug-resistance and recurrence of the disease. We propose a dual targeting approach which combines targeted therapy of the leukemia-causing oncogene and the newly discovered leukemia stem cell survival factor BCL6. The power of this new therapy approach will be tested in clinical trials to be started in the State of California.

Publications

Nat Med (2013): BACH2 mediates negative selection and p53-dependent tumor suppression at the pre-B cell receptor checkpoint. (PubMed: 23852341)
Nature (2011): BCL6 enables Ph(+) acute lymphoblastic leukaemia cells to survive BCR-ABL1 kinase inhibition. (PubMed: 21593872)
J Exp Med (2011): BCL6-mediated repression of p53 is critical for leukemia stem cell survival in chronic myeloid leukemia. (PubMed: 21911423)
Immunity (2011): Control of B cell development by the histone H2A deubiquitinase MYSM1. (PubMed: 22169041)
Cancer Cell (2015): Erk Negative Feedback Control Enables Pre-B Cell Transformation and Represents a Therapeutic Target in Acute Lymphoblastic Leukemia. (PubMed: 26073130)
Nat Commun (2015): Identification of FOXM1 as a therapeutic target in B-cell lineage acute lymphoblastic leukaemia. (PubMed: 25753524)
Nat Immunol (2015): Mechanisms of clonal evolution in childhood acute lymphoblastic leukemia. (PubMed: 25985233)
Proc Natl Acad Sci U S A (2014): Mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia. (PubMed: 24821775)
Blood (2015): Ph+ ALL: drawing strength from a benign past. (PubMed: 25953975)
Blood (2011): Pre-B cell receptor-mediated activation of BCL6 induces pre-B cell quiescence through transcriptional repression of MYC. (PubMed: 21856866)
Nat Genet (2014): RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia. (PubMed: 24413735)
Blood (2015): Rationale for targeting the pre-B-cell receptor signaling pathway in acute lymphoblastic leukemia. (PubMed: 25878119)
Cancer Cell (2015): Self-enforcing feedback activation between BCL6 and pre-B cell receptor signaling defines a distinct subtype of acute lymphoblastic leukemia. (PubMed: 25759025)
Nature (2015): Signalling thresholds and negative B-cell selection in acute lymphoblastic leukaemia. (PubMed: 25799995)
Blood (2012): Zebrafish screen identifies novel compound with selective toxicity against leukemia. (PubMed: 22490804)