Blake, Maja K.

Abstract Background: Waldenstršms macroglobulinemia (WM) is an indolent B-lymphoplasmacytic lymphoma, which is highly sensitive to 20S proteasome inhibitors such as bortezomib. However, clinical resistance to the drug can be observed early at onset of therapy (primary or inherent resistance) or develop over time, through repeated exposure to the drug (acquired resistance). Although prior investigations into the biological mechanisms associated with bortezomib resistance (BR) have identified aberrations at the genomic (PSMB5 mutation) and transcriptional level (loss of XPB-1), there is limited data on the epigenetic abnormalities that support resistance to 20S proteasome inhibition. With this in mind, we conducted a comprehensive methylation and mRNA expression analysis in WM cells focusing on the molecular patterns that characterize inherent BR (iBR) as well as acquired BR (aBR). Materials and Methods: Bortezomib sensitive (BS) human WM cell lines, BCWM.1 and MWCL-1, the iBR WM cell line RPCI-WM1 (developed from a bortezomib-refractory WM patient) as well as aBR subclones (BCWM.1/BR, MWCL-1/BR) were used in the study. Methylation status of WM cells was profiled by Illumina Infinium 450k methylation array. Methylation IDAT files were background subtracted using GenomeStudio v1.9. Beta mixture quantile dilation (BMIQ) method in R watermelon package was used to adjust type II probes into distribution characteristic of type I probes. For each gene, probes were partitioned into 6 regions using R IMA package and the ones belonging to the same region were averaged, including transcription start sites (TSS; both 200 bp and 1500 bp upstream), 5' untranslated region (UTR), and 3'UTR, the first exon, and genebody. Gene regions showing a significant adjusted p-value and a beta difference of >0.1 or <-0.1 were selected for differential hypermethylation and hypomethylation, respectively. Correlation with gene expression was conducted only on genes showing >1.5 fold change in expression. Overview of methodology is shown in Figure 1. Results: We first assessed the differential methylation pattern (TSS, 200bp upstream of gene body) of bortezomib-sensitive (BS, BCWM.1, IC50 6nM) and iBR cells, (RPCI-WM1). A total of 3,801 hypermethylated and 1,865 hypomethylated DNA regions were observed in iBR cells relative to BS cells (Figure 2A). In iBR cells, a negative correlation between hypermethylated DNA and corresponding gene expression was found in 1,039 genes (Spearman r = -0.12) (Figure 2B). In parallel, we compared the methylation pattern (TSS 200bp) of BS WM cells (BCWM.1 and MWCL-1) with their aBR derivatives, which display ~20 – 50 fold resistance to bortezomib. aBR subclones showed differential hypermethylation of 1,521 DNA regions and hypomethylation of 651 genomic regions relative to BS WM cells. These findings were not unexpected as aBR cell lines, being derivatives of BS WM cells, are clonally related to the former, whereas iBR cells are derived from a different clone. Meta-analysis of iBR and aBR followed by pathway enrichment (NextBio, Illumina Inc), revealed a significant clustering of commonly hypermethylated genes within the Validated Transcriptional Targets of TP63 isoforms Canonical Pathway (p<1.9-E5, Figure 2C) and the CEBPA binding site Geneset 2 (p<8.2-E9, Figure 2D); pathways whose genes are actively involved in suppression of cell growth and differentiation. Further validation and functional relevance of candidate gene targets from this analysis, which are relevant to WM pathobiology, are currently being investigated. Conclusion: This is the first study to examine and correlate the global methylation and gene expression profiles in WM tumor cells that are inherently wired to resist 20S proteasome inhibition as well as tumor cells, which have acquired resistance through continuous exposure to bortezomib. Although considerable differences were observed in the methylation profiles of WM cells displaying inherent vs. acquired resistance, a number of common genes emerged and pointed towards transcriptional repressors, whose inactivation through methylation has been linked to other cancers. Altogether, these findings uncover cellular systems in WM cells, which are affected by DNA methylation, subsequent mRNA suppression and which may be associated as a whole with both inherent and acquired forms of bortezomib resistance. Disclosures No relevant conflicts of interest to declare.

Abstract Background: Deubiquitinating enzyme (DUB) inhibitors are an emerging class of compounds, which are increasingly being regarded for their anti-cancer activity and therapeutic potential. The 19S regulatory particle of the proteasome contains two DUBs, USP14 and UCHL5, which are critical for the proper unfolding and deubiquitination of proteins prior to their entry into the 20S proteasome β-catalytic core. In B/plasma cell malignancies such as Waldenströms macroglobulinemia (WM) and multiple myeloma (MM), protein homeostasis and optimal proteasome functionality are paramount for tumor survival. This is evidenced by the success of 20S proteasome inhibition with bortezomib and carfilzomib, which have demonstrated remarkable clinical benefit in patients with WM or MM. As such, the proteasome degradation pathway represents a highly attractive and clinically validated, yet still largely unexplored therapeutic target. Here, we provide first evidence of the cytotoxic effects and molecular sequelae associated with a novel 19S proteasome DUB inhibitor, VLX1570, which selectively targets USP14 and UCHL5, in preclinical models of B/plasma cell cancers and their drug resistant tumor subclones. Materials: VLX1570 was obtained from Vivolux AB, Sweden. Bortezomib was purchased from Sellekchem, Houston TX. Human myeloma cell lines (OPM2, U266, KMS11), human WM cell lines (BCWM.1, MWCL-1 and RPCI-WM1), their respective bortezomib-resistant (BR) subclones as well as ibrutinib-resistant (IR) derivatives of BCWM.1 and RPCI-WM1 were used in experiments (total n=12). Peripheral blood mononuclear cells (PBMCs) from healthy donors were used to assess for cytotoxicity of VLX1570 in non-tumor cells. Results: A 72hr MTS assay first established sensitivity of plasma cell cancer models towards VLX1570, including drug resistant subclones (EC50 range, 20 – 90nM). Next we assessed whether loss of viability was due to apoptosis and observed dose-dependent annexin-V staining in ~50 – 70% of wild-type MM and WM cells, ~45 – 55% in corresponding BR models and ~50% in IR subclones when exposed to VLX1570 (100nm – 500nM) for 24hrs. VLX1570 was tested at similar concentrations in PBMCs and induced minimal cell death. To understand if VLX1570-induced apoptosis was mitochondrial mediated, we assessed mitochondrial outer membrane permeability (MOMP) in all plasma cell cancer models treated with the DUB inhibitor (100 – 500nM) and found a dose-dependent increase in MOMP (p<0.00025 – 0.000001). Activation of the mitochondrial/intrinsic apoptotic pathway was also evidenced by cleavage of caspase-9 and 3 on immunoblot analysis. As inhibition of protein deubiquitination results in accumulation of polyubiquitinated protein conjugates, we examined global ubiquitinated protein levels and found increasing amounts of high molecular weight poly-ubiquitinated protein in VLX1570 treated tumor cells in a dose-dependent manner. This prompted us to further delineate the potential cellular response mechanisms that relay the antitumor activity of VLX1570 in malignant plasma cells. Immunoblot analysis of drug sensitive and (bortezomib or ibrutinib) resistant MM and WM cell lines revealed several changes in ER stress response proteins, notably induction of HSP70 and splicing of XBP1; the latter event which was less prominent in BR cell lines treated with bortezomib. This suggested the ability of VLX1570 to overcome resistance through a rapid and potent proteotoxic effect, which overwhelmed the tumor cells stress response mechanisms beyond its capacity for survival. Finally, as abnormalities in the NFkB signaling pathway are implicated in malignant plasma cell survival, we found markedly decreased nuclear translocation of NFkB (p-P65) protein in tumor cells treated with VLX1570. Conclusions: The DUBs of the 19S proteasome cap offer an attractive target within the proteasome degradation system and whose inhibition by VLX1570 is able to circumvent mechanisms that support resistance to b-catalytic PI (bortezomib) or BTK inhibitor (ibrutinib) therapy. The studies undertaken thus far, coupled with more rigorous mechanistic and in vivo efficacy analyses currently underway, provides rational for the clinical development of DUB inhibitors for use in malignant B/plasma cell malignancies. Disclosures Martin: Janssen: Honoraria.

Abstract Background: While B-cell receptor (BCR) signaling is essential for the development, of normal B cells, its aberrant hyper-activation results in neoplastic transformation of B-lymphocytes. Recent investigations using small molecule inhibitors validate the BCR pathway as a valuable target. Bruton’s tyrosine kinase (BTK) is one of the components of a signaling hub that transduces signals from the BCR into the cell for its activation and has been shown to be a therapeutic target. Ibrutinib (PCI-32765), an irreversible BTK inhibitor has shown clinical efficacy in CLL, mantle cell lymphoma (MCL) and Waldenströms macroglobulinemia (WM). Ibrutinib binds to cysteine-481 of the BTK protein and blocks its phosphorylation, resulting in termination of BCR-mediated activation of cells with a concomitant induction of death. Despite the clinical success of ibrutinib, a high percentage of patients achieve only partial response and eventually acquire resistance to the drug, resulting in aggressive relapse of the disease. A mutation of Cys481-Ser in BTK (ibrutinib-BTK binding site) has been reported to be one of the reasons for the development of ibrutinib resistance (IR). To understand the mechanisms resulting in acquisition of IR, we developed preclinical models of IR in WM and MCL. Materials: Ibrutinib was obtained from Pharmacyclics, CA. Validated human WM models (BCWM.1, RPCI-WM1 and MWCL.1 cell lines) and human MCL models (Jeko-1 and Maver cell lines) were used for the study. Results: BTK was constitutively phosphorylated at Y223 and Y551 in all the cell lines tested and this was inhibited by ibrutinib in a dose dependent manner. Phosphorylation of other kinases in the cascade such as SYK (Y323 and Y525/526) and PLCg2 (Y759 and Y1217) were also inhibited while AKT phosphorylation at both Ser473 and Thr308 was consistently increased in presence of ibrutinib. Treatment with ibrutinib induced cell cycle arrest in the G1 phase by 24h followed by apoptosis. Cell growth assays (MTS assay) showed that BCWM.1 was the most sensitive cell line followed by MWCL-1, RPCI-WM1, Maver and Jeko-1. Exposure of WM and MCL cells for prolonged periods of time with progressively increasing concentrations of ibrutinib resulted in outgrowth of clones (IR WM and MCL cell lines) that were resistant to apoptosis with a slow growth rate as compared to wild type parental cells. IR cells attained 2 – 20 fold resistance to ibrutinib as compared to the respective parental lines as determined by MTS assay. Sequence analysis of the BTK gene in all the cell lines revealed no mutation in IR cells at Cys481 suggesting that in an acquired IR state, resistance to ibrutinib can be developed independent of BTK Cys481 mutation. Interestingly, we found p-BTK levels to be markedly reduced in IR cells. Ibrutinib reversal experiments suggested that while a continuous presence of ibrutinib is needed for inhibition of BTK phosphorylation, a stable IR state could be maintained (for >1 month) in the absence of ibrutinib. This suggested the cells reliance on a parallel survival pathway, independent of BTK phosphorylation. Focused mRNA (Nanostring nCounter assay) and immunoblot analysis revealed significant changes in the expression profiles of several cellular elements. These included transcription factors such as PU.1, IRF4, BLIMP1, BCL-6 b-catenin as well as the phosphorylated ERK1/2, STAT1 and 3 suggesting a reprogramming of critical cellular networks, which IR tumor cells might be utilizing to overcome ibrutinib-induced cytotoxicity. Importantly, we observed that IR cells retained high levels of p-AKT and showed an increase in expression of BCL2 family members, as well as BCL-2 itself. Treatment of IR cells with ibrutinib +/- MK2206 (AKT inhibitor), or ABT-199 (BCL-2 inhibitor), synergistically induced cytotoxicity in IR cells, suggesting the importance of these parallel survival pathways (AKT/BCL2) in maintaining an IR state. Conclusion: Here we demonstrate that in the absence of BTK Cys481 mutation, an IR state is associated with reprogramming of transcriptional networks countering ibrutinib-induced toxicity by activation of AKT and BCL-2. Our current data exposes multiple vulnerabilities within IR cells, which can be therapeutically exploited to potentially delay onset of IR, by targeting alternative oncogenic mechanisms that are activated in presence of sustained BTK inhibition. Disclosures No relevant conflicts of interest to declare.

SummaryDeubiquitinase enzymes (DUBs) of the proteasomal 19S regulatory particle are emerging as important therapeutic targets in several malignancies. Here we demonstrate that inhibition of two proteasome‐associated DUBs (USP14 and UCHL5) with the small molecule DUB inhibitor b‐AP15, results in apoptosis of human Waldenström macroglobulinaemia (WM) cell lines and primary patient‐derived WM tumour cells. Importantly, b‐AP15 produced proteotoxic stress and apoptosis in WM cells that have acquired resistance to the proteasome inhibitor bortezomib. In silico modelling identified protein residues that were critical for the binding of b‐AP15 with USP14 or UCHL5 and proteasome enzyme activity assays confirmed that b‐AP15 does not affect the proteolytic capabilities of the 20S proteasome β‐subunits. In vitro toxicity from b‐AP15 appeared to result from a build‐up of ubiquitinated proteins and activation of the endoplasmic reticulum stress response in WM cells, an effect that also disrupted the mitochondria. Focused transcriptome profiling of b‐AP15‐treated WM cells revealed modulation of several genes regulating cell stress and NF‐κB signalling, the latter whose protein translocation and downstream target activation was reduced by b‐AP15 in vitro. This is the first report to define the effects and underlying mechanisms associated with inhibition of USP14 and UCHL5 DUB activity in WM tumour cells.