Loss of COP9 signalosome genes at 2q37 is associated with IMiD resistance in multiple myeloma

The acquisition of a multidrug refractory state is a major cause of mortality in myeloma. Myeloma drugs that target the cereblon (CRBN) protein include widely used immunomodulatory drugs (IMiDs), and newer CRBN E3 ligase modulator drugs (CELMoDs), in clinical trials. CRBN genetic disruption causes resistance and poor outcomes with IMiDs. Here, we investigate alternative genomic associations of IMiD resistance, using large whole-genome sequencing patient datasets (n = 522 cases) at newly diagnosed, lenalidomide (LEN)-refractory and lenalidomide-then-pomalidomide (LEN-then-POM)-refractory timepoints. Selecting gene targets reproducibly identified by published CRISPR/shRNA IMiD resistance screens, we found little evidence of genetic disruption by mutation associated with IMiD resistance. However, we identified a chromosome region, 2q37, containing COP9 signalosome members COPS7B and COPS8, copy loss of which significantly enriches between newly diagnosed (incidence 5.5%), LEN-refractory (10.0%), and LEN-then-POM-refractory states (16.4%), and may adversely affect outcomes when clonal fraction is high. In a separate dataset (50 patients) with sequential samples taken throughout treatment, we identified acquisition of 2q37 loss in 16% cases with IMiD exposure, but none in cases without IMiD exposure. The COP9 signalosome is essential for maintenance of the CUL4-DDB1-CRBN E3 ubiquitin ligase. This region may represent a novel marker of IMiD resistance with clinical utility.

Multiple Myeloma Patient Tumors With High Levels of Cereblon Exon-10 Deletion Splice Variant Upregulate Clinically Targetable Pro-Inflammatory Cytokine Pathways

Immunomodulatory drugs (IMiDs), including lenalidomide and pomalidomide, are used in the routine treatment for multiple myeloma (MM) patients. Cereblon (CRBN) is the direct molecular target of IMiDs. While CRBN is not an essential gene for MM cell proliferation, the frequency of CRBN genetic aberrations, including mutation, copy number loss, and exon-10 (which includes a portion of the IMiD-binding domain) splicing, have been reported to incrementally increase in later-line patients. CRBN exon-10 splicing has also been shown to be associated with decreased progression-free survival in both newly diagnosed and relapsed refractory MM patients. Although we did not find significant general splicing defects among patients with CRBN exon-10 splice variant when compared to those expressing the full-length transcript, we identified upregulated TNFA signaling via NFKB, inflammatory response, and IL-10 signaling pathways in patients with exon-10 splice variant across various data sets—all potentially promoting tumor growth via chronic growth signals. We examined master regulators that mediate transcriptional programs in CRBN exon-10 splice variant patients and identified BATF, EZH2, and IKZF1 as the key candidates across the four data sets. Upregulated downstream targets of BATF, EZH2, and IKZF1 are components of TNFA signaling via NFKB, IL2/STAT5 signaling pathways, and IFNG response pathways. Previously, BATF-mediated transcriptional regulation was associated with venetoclax sensitivity in MM. Interestingly, we found that an EZH2 sensitivity gene expression signature also correlated with high BATF or venetoclax sensitivity scores in these tumors. Together, these data provide a rationale for investigating EZH2 inhibitors or venetoclax in combination with the next generation CRBN-targeting agents, such as CELMoDs, for patients overexpressing the CRBN exon-10 splice variant.

Cereblon pathway biomarkers and immune profiles in patients with myeloma receiving post-ASCT lenalidomide maintenance (LEOPARD)

LEOPARD was a single arm, phase II study of lenalidomide (LEN) and alternate day prednisolone maintenance in patients with newly diagnosed multiple myeloma (MM) following autologous stem cell transplantation (ASCT). Sixty patients were enrolled. Estimated median potential follow-up was 44 m, median PFS was 38.3 m, median OS was not reached (landmark 36 m OS: 71.4%). Correlative immunohistochemistry performed on pre-ASCT trephines demonstrated high MM tumor cereblon (total/cytoplasmic) was associated with superior OS (p = .045, p = .031, respectively), whereas high c-Myc was associated with inferior PFS (p = .04). Patients with high cereblon (total/nuclear) were more likely to improve depth of response, whereas patients with high c-Myc were less likely, suggesting alternative/more effective post-ASCT strategies for patients with high c-Myc need identification. Peripheral blood immune profiling (mass cytometry) informed a more sustained response to LEN maintenance, demonstrating enrichment of activated/cytotoxic NK cells and cytotoxic T cells in patients with durable responses, contrasting with enrichment of B-regs in early relapsers.

Abstract A082: A phase I study of the MDM2 antagonist RO6839921, a pegylated intravenous prodrug of idasanutlin, in patients with AML

Background: Activation of the p53 pathway by inhibiting MDM2 has been proposed as a novel strategy for cancer therapy. We previously reported the phase 1 results in solid tumor patients (pts) of RO6839921, a small-molecule pegylated IV prodrug of the MDM2 antagonist idasanutlin (active principle = AP), which was developed with the goal of reducing exposure variability to improve the therapeutic index. We report here on the safety, PK, PD, and activity in AML pts. Methods: This was an open-label phase I monotherapy study evaluating RO6839921 in R/R AML pts on a 5-day dosing schedule. Primary objectives were to identify dose-limiting toxicities (DLTs) and the maximum tolerated dose (MTD, DLT rate ≤ 33%). Secondary objectives were to assess PK, PD, and preliminary activity. Maximum escalation increments followed a Modified Fibonacci sequence. TP53 mutational status was assessed by next-generation sequencing from bone marrow samples. Serum MIC-1 (macrophage inhibitory cytokine-1), a p53 transcriptional target, was analyzed by Elecsys® ECL as a PD marker of p53 activation. Results: 26 DLT-evaluable pts were treated at doses between 120-300 mg AP. The MTD was 250 mg with DLTs reported at 250 mg (2/8 pts, 25%) and 300 mg (2/5 pts, 40%) (table). Related AEs ≥ G3 in >5% of pts included febrile neutropenia (3/26, 11.5%), epistaxis and platelet count decreased (both 2/26, 7.7%). Related AEs of all grades observed in > 20% pts were diarrhea, nausea, vomiting, decreased appetite, and fatigue. PK analyses showed rapid and near-complete conversion of prodrug to AP and dose-proportional exposure across the doses tested (table). Variability ranged from 30-47% (22-54% for idasanutlin). 11/26 pts had evidence of antileukemic activity (CR, CRi/MLFS, PR, HI/SD) for a disease control rate of 42%, with a composite CR rate of 7.7% (1 CR, 1 CRi/MLFS; 2/26); TP53 was evaluable in 24 pts; 21 (87.5%) were wild type and 3 mutant (12.5%). 10/11 pts with activity were wild type and 1 did not have a sample. p53 activation was demonstrated by MIC-1 induction in serum and was associated with AP exposure. Conclusions: RO6839921 shows a PK profile similar to idasanutlin. The MTD of 250 mg AP qd x 5 days has a manageable safety profile in R/R AML at ~25% of the idasanutlin dose identified for development in this population. Single-agent antileukemic activity is observed in 42% pts overall, including 4 of 8 pts (50%) at the MTD. NCT02098967. Arm B Cohort(n)Dose(mg AP)Prior AML induction regimens (median and range)ELN risk at initial diagnosis (Favorable, Int-1, Int-2, Adverse)TP53 status (Wild Type, Mutant, or Not Evaluable)PK (AP on D5)DLT eventsAnti-leukemicactivity*FI-1I-2AdvCmax (µg/ml)AUC0-24 (hr*µg/ml)Cohort 1 (n = 6)1202 (0-4)00155 WT, 1 NE18 ± 690 ± 30none2 HI/SDCohort 2 (n = 7)2001 (1-4)13215 WT / 1 MT / 1 NE32 ± 3164 ± 41none1 PR, 2 HI/SDCohort 3 (n = 5)3002 (0-3)01133 WT / 2 MT42 ± 8335 ± 93G4 QTcF prolongation, G3 colitis1 CRi/MLFS, 1 HI/SDCohort 4MTD(n = 8)2501 (0-2)13138 WT43 ± 9 (n=3)278 ± 72 (n=3)G3 stomatitis, G3 diarrhea1 CR, 1 PR, 2 HI/SDTotal(n = 26)11 (42%)

Citation Format: Karen Yee, Geoffrey Uy, Sarit Assouline, Carolyn D. Britten, Jianguo Zhi, Steven Blotner, William Pierceall, Brian Higgins, Lin-Chi Chen. A phase I study of the MDM2 antagonist RO6839921, a pegylated intravenous prodrug of idasanutlin, in patients with AML [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A082.

Abstract 340: Mitochondrial priming of new targeted agents in acute myeloid leukemia

As numerous molecularly targeted agents are entering clinical trials, predictive testing is highly desirable. We investigated if response to certain agents correlates with the recently reported method of BH3 profiling (Chonghaile TN et al, Science, 2011), a functional assay developed by Letai's group that measures tumor cell mitochondrial priming by measuring mitochondrial outer membrane permeabilization (MOMP) following exposure to the peptide-mimicking BH3 domains of BH3-only proteins. Mitochondrial priming has been reported to be correlated with clinical responses to conventional chemotherapy in solid tumors and hematological malignancies (Vo TT et al, Cell, 2012, Pierceall W et al, Mol Cancer Ther, 2013).

Twenty-two AML lines were tested. Cells were permeabilized with digitonin and exposed to standardized doses of BH3 peptides (BIM, PUMA, NOXA, BAD, BMF, HRK, or PUMA2A). JC-1 was used for detection of MOMP and served as a measure of sensitivity to each peptide (reported as %[BH3 peptide]). Also, BCL-2, BCL-XL and MCL-1 expression levels were determined by Western blot. In addition to studies of untreated cells, treatment effects of different anti-leukemia drugs (AraC, Nutlin-3a, KPT-330 [Selinexor] and ABT-199) were determined over a wide dose range and denoted as ([specific apoptosis] = [(%Annexin V+ cells at each dose) - (%Annexin V+ cells at 0 μM)]/[100- (%Annexin V+ cells at 0 μM)]). Mixed linear models were used for analysis. As expected, ABT-199 sensitivity positively correlated with %[BAD]-%[HRK] (|β| = 3.22, p < 0.001), which is compatible with BCL-2 dependency of ABT-199 (while BAD is binding to BCL-2 and BCL-XL, HRK is binding to BCL-XL only and the difference is therefore BCL-2-specific). This was supported by the observed correlation between %[BAD]-%[HRK] and BCL-2 protein expression levels (r=0.619; p = 0.018). AraC sensitivity showed a similar correlation with %[BAD]-%[HRK] (|β| = 1.61, P < 0.05). KPT-330 sensitivity in p53 wild-type cell lines positively correlated with %[PUMA] (|β| = 0.92, P = 0.054), consistent with the notion that KPT-330 induces PUMA through p53 activation. Unexpectedly, Nutlin-3a activity did not correlate with any of the BH3 peptides. Results indicate that ABT-199, KPT-330 and Nutlin-3a show different modes of action in terms of BH3 peptide dependency, supporting potential combination effects of these agents. For ABT-199, increased MCL1 levels were associated with diminished cytotoxicity (r=0.532; p=0.05), as expected. For Ara-C, a similar correlation with MCL-1 was noted (r=0.505; p=0.06), but no correlations were observed for Nutlin-3a and KPT-330.

In conclusion, BH3 profiling is a promising tool to predict the BH3 peptide dependency of the BH3-mimetic ABT-199 and the XPO1-inhibitor KPT-330. Functional BH3-profiling appears to be superior to the static quantitation of Bcl-2 family protein levels in AML. Furthermore, mitochondrial priming may be useful for the rational design of new combination therapies.

Citation Format: Jo Ishizawa, Kensuke Kojima, Seshagiri R. Duvvuri, Teresa McQueen, Vivian R. Ruvolo, Graciela M. Nogueras-Gonzalez, Xuelin Huang, William Pierceall, Michael Cardone, Ryan Lena, Camille Doykan, Sharon Shacham, Michael Kauffman, Marina Konopleva, Michael Andreeff. Mitochondrial priming of new targeted agents in acute myeloid leukemia. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 340. doi:10.1158/1538-7445.AM2014-340

Abstract 2466: Characterization and development of on-target Mcl-1 inhibitors; BH3 profiling provides a valuable drug discovery tool

Anti-apoptotic Bcl-2 family proteins are central to the regulation of the intrinsic apoptotic pathway, and as such constitute an important group of targets with great potential as oncology therapeutics. The Bcl-2 family protein Mcl-1 has been demonstrated to facilitate survival and chemoresistance in multiple myeloma, AML, and other cancers, and agents which affect this pathway have become highly sought after. Currently, however, no therapies exist which directly target Mcl-1. We have identified compounds that target Mcl-1 which may be characterized as both Mcl-1-selective and pan-Mcl-1/Bcl-2 inhibitors. This effort has been facilitated by utilization of the BH3 profiling technology to guide SAR. This assay allows for determination of the mitochondrial priming state of both cell culture samples and primary patient samples. We have demonstrated a correlation between myeloma and leukemia cell line response to treatment with our inhibitors and the mitochondrial priming state of such cell lines. Such correlations have also been shown with respect to the extent of cytochrome C release. In the case of the selective Mcl-1 inhibitor, we have shown that cytochrome C release occurs preferentially in leukemia cell lines which are highly primed for Mcl-1 rather than Bcl-2. In addition, our Mcl-1 selective inhibitor demonstrates enhanced cell killing ability in leukemia cells which have been engineered to selectively express Mcl-1, Bcl-2, and Bcl-xL. Our current lead candidate possesses excellent drug-like properties and displays impressive efficacy in a multiple myeloma disseminated xenograft model. This work demonstrates the utility of the BH3 profiling assay as providing a functional biomarker for drug discovery tool and its ability to validate the on-target activity of Mcl-1 and Bcl-2 inhibitors.

Citation Format: David J. Richard, Nicole Carlson, William Pierceall, Ryan Lena, Thomas Bannister, Peter Hodder, Timothy Spicer, Michael Andreeff, Joseph Opferman, Brian Koss, Andrew Kung, Michael Cardone. Characterization and development of on-target Mcl-1 inhibitors; BH3 profiling provides a valuable drug discovery tool. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2466. doi:10.1158/1538-7445.AM2013-2466