A structure-based designed small molecule depletes hRpn13Pru and a select group of KEN box proteins

Proteasome subunit hRpn13 is partially proteolyzed in certain cancer cell types to generate hRpn13Pru by degradation of its UCHL5/Uch37-binding DEUBAD domain and retention of an intact proteasome- and ubiquitin-binding Pru domain. By using structure-guided virtual screening, we identify an hRpn13 binder (XL44) and solve its structure ligated to hRpn13 Pru by integrated X-ray crystallography and NMR to reveal its targeting mechanism. Surprisingly, hRpn13Pru is depleted in myeloma cells following treatment with XL44. TMT-MS experiments reveal a select group of off-targets, including PCNA clamp-associated factor PCLAF and ribonucleoside-diphosphate reductase subunit M2 (RRM2), that are similarly depleted by XL44 treatment. XL44 induces hRpn13-dependent apoptosis and also restricts cell viability by a PCLAF-dependent mechanism. A KEN box, but not ubiquitination, is required for XL44-induced depletion of PCLAF. Here, we show that XL44 induces ubiquitin-dependent loss of hRpn13Pru and ubiquitin-independent loss of select KEN box containing proteins.

Use of CRISPR-based screens to identify mechanisms of chemotherapy resistance

Despite the development of new classes of targeted anti-cancer drugs, the curative treatment of metastatic solid tumors remains out of reach owing to the development of resistance to current chemotherapeutics. Although many mechanisms of drug resistance have been described, there is still a general lack of understanding of the many means by which cancer cells elude otherwise effective chemotherapy. The traditional strategy of isolating resistant clones in vitro, defining their mechanism of resistance, and testing to see whether these mechanisms play a role in clinical drug resistance is time-consuming and in many cases falls short of providing clinically relevant information. In this review, we summarize the use of CRISPR technology, including the promise and pitfalls, to generate libraries of cancer cells carrying sgRNAs that define novel mechanisms of resistance. The existing strategies using CRISPR knockout, activation, and inhibition screens, and combinations of these approaches are described. In addition, specialized approaches to identify more than one gene that may be contributing to resistance, as occurs in synthetic lethality, are described. Although these CRISPR-based approaches to cataloguing drug resistance genes in cancer cells are just beginning to be utilized, appropriately used they promise to accelerate understanding of drug resistance in cancer.

Drug combinations identified by high-throughput screening promote cell cycle transition and upregulate Smad pathways in myeloma

Drug resistance and disease progression are common in multiple myeloma (MM) patients, underscoring the need for new therapeutic combinations. A high-throughput drug screen in 47 MM cell lines and in silico Huber robust regression analysis of drug responses revealed 43 potentially synergistic combinations. We hypothesized that effective combinations would reduce MYC expression and enhance p16 activity. Six combinations cooperatively reduced MYC protein, frequently over-expressed in MM and also cooperatively increased p16 expression, frequently downregulated in MM. Synergistic reductions in viability were observed with top combinations in proteasome inhibitor-resistant and sensitive MM cell lines, while sparing fibroblasts. Three combinations significantly prolonged survival in a transplantable Ras-driven allograft model of advanced MM closely recapitulating high-risk/refractory myeloma in humans and reduced viability of ex vivo treated patient cells. Common genetic pathways similarly downregulated by these combinations promoted cell cycle transition, whereas pathways most upregulated were involved in TGFβ/SMAD signaling. These preclinical data identify potentially useful drug combinations for evaluation in drug-resistant MM and reveal potential mechanisms of combined drug sensitivity.

Structural Optimization and Anticancer Activity of Polo-like Kinase 1 (Plk1) Polo-Box Domain (PBD) Inhibitors and Their Prodrugs

Polo-like kinase 1 (Plk1), a mitotic kinase whose activity is widely upregulated in various human cancers, is considered an attractive target for anticancer drug discovery. Aside from the kinase domain, the C-terminal noncatalytic polo-box domain (PBD), which mediates the interaction with the enzyme's binding targets or substrates, has emerged as an alternative target for developing a new class of inhibitors. Various reported small molecule PBD inhibitors exhibit poor cellular efficacy and/or selectivity. Here, we report structure-activity relationship (SAR) studies on triazoloquinazolinone-derived inhibitors, such as 43 (a 1-thioxo-2,4-dihydrothieno[2,3-e][1,2,4]triazolo[4,3-a]pyrimidin-5(1H)-one) that effectively block Plk1, but not Plk2 and Plk3 PBDs, with improved affinity and drug-like properties. The range of prodrug moieties needed for thiol group masking of the active drugs has been expanded to increase cell permeability and mechanism-based cancer cell (L363 and HeLa) death. For example, a 5-thio-1-methyl-4-nitroimidazolyl prodrug 80, derived from 43, showed an improved cellular potency (GI50 4.1 μM). As expected, 80 effectively blocked Plk1 from localizing to centrosomes and kinetochores and consequently induced potent mitotic block and apoptotic cell death. Another prodrug 78 containing 9-fluorophenyl in place of the thiophene-containing heterocycle in 80 also induced a comparable degree of anti-Plk1 PBD effect. However, orally administered 78 was rapidly converted in the bloodstream to parent drug 15, which was shown be relatively stable toward in vivo oxidation due to its 9-fluorophenyl group in comparison to unsubstituted phenyl. Further derivatization of these inhibitors, particularly to improve the systemic prodrug stability, could lead to a new class of therapeutics against Plk1-addicted cancers.

mTOR inhibition overcomes RSK3-mediated resistance to BET inhibitors in small cell lung cancer

Small cell lung cancer (SCLC) is a recalcitrant malignancy with limited treatment options. Bromodomain and extraterminal domain inhibitors (BETis) have shown promising preclinical activity in SCLC, but the broad sensitivity spectrum limits their clinical prospects. Here, we performed unbiased high-throughput drug combination screens to identify therapeutics that could augment the antitumor activities of BETis in SCLC. We found that multiple drugs targeting the PI-3K-AKT-mTOR pathway synergize with BETis, among which mTOR inhibitors (mTORis) show the highest synergy. Using various molecular subtypes of the xenograft models derived from patients with SCLC, we confirmed that mTOR inhibition potentiates the antitumor activities of BETis in vivo without substantially increasing toxicity. Furthermore, BETis induce apoptosis in both in vitro and in vivo SCLC models, and this antitumor effect is further amplified by combining mTOR inhibition. Mechanistically, BETis induce apoptosis in SCLC by activating the intrinsic apoptotic pathway. However, BET inhibition leads to RSK3 upregulation, which promotes survival by activating the TSC2-mTOR-p70S6K1-BAD cascade. mTORis block this protective signaling and augment the apoptosis induced by BET inhibition. Our findings reveal a critical role of RSK3 induction in tumor survival upon BET inhibition and warrant further evaluation of the combination of mTORis and BETis in patients with SCLC.

Deep phenotyping and lifetime trajectories reveal limited effects of longevity regulators on the aging process in C57BL/6J mice

Current concepts regarding the biology of aging are primarily based on studies aimed at identifying factors regulating lifespan. However, lifespan as a sole proxy measure for aging can be of limited value because it may be restricted by specific pathologies. Here, we employ large-scale phenotyping to analyze hundreds of markers in aging male C57BL/6J mice. For each phenotype, we establish lifetime profiles to determine when age-dependent change is first detectable relative to the young adult baseline. We examine key lifespan regulators (putative anti-aging interventions; PAAIs) for a possible countering of aging. Importantly, unlike most previous studies, we include in our study design young treated groups of animals, subjected to PAAIs prior to the onset of detectable age-dependent phenotypic change. Many PAAI effects influence phenotypes long before the onset of detectable age-dependent change, but, importantly, do not alter the rate of phenotypic change. Hence, these PAAIs have limited effects on aging.

Identification of markers for tumor- and immune-derived extracellular vesicles (EVs) in preclinical models

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Background: Extracellular Vesicles (EV) are of broad interest as carriers of molecular signatures of tumor progression and cancer treatment response. EVs, which contain nucleic acids, lipids, and proteins, are released from cells for waste excretion and communication. Numerous proteins and markers are expressed within and on the surface of EVs, but classification markers for murine EV subsets are lacking. To identify tumor and dendritic cell- derived EV markers for preclinical models of breast cancer, we investigated surface marker repertoires of EVs produced by the murine breast cancer and dendritic cell lines, 4T1 and DC2.4. Methods: Cells were cultured in serum free media for 2 days. EVs were harvested and isolated by ultrafiltration followed by size exclusion chromatography. EV particle size and concentration were estimated by nanoparticle tracking analysis and microBCA. To identify highly expressed EV markers, a mouse EV multiplex flow cytometry assay was performed using detection antibodies, CD9, CD63, and CD81, with sets of >35 barcoded capture beads, representing more than 100 specific capture: detection combinations. EV marker expression was analyzed using the FCMPASS/MPAPASS software (nano.ccr.cancer.gov). > 250 beads were assessed for each capture- and detection- antibody combination for each EV type and dilution tested; mean fluorescent intensity was determined; and pairwise comparisons between test and control sample sets were evaluated by t-tests. Results: Breast cancer (4T1)-derived EVs but not dendritic cell (DC2.4)-derived EVs were strongly detected with CD326 (EpCAM) and CD49b (integrin alpha5, VLA-2) capture beads, using each of the three tetraspanin antibodies. Both types of EVs were detected with anti-CD9 and anti-CD81 when captured by anti-CD44 and anti-CD49e (integrin beta1, VLA-5) beads. DC2.4 EVs were distinctively identified by CD11b capture. CD63 capture and detection antibodies robustly recognized EVs from 4T1 but provided minimal recognition of DC2.4 EVs. Mouse serum EVs from non-tumor bearing mice, showed minimal or no detectable CD326 or CD11b. Conclusions: Multiparametric MPAPASS-processed EV repertoire analysis of EVs from murine breast cancer and dendritic cell lines identified CD9, CD81, CD44, and CD49e as common epitopes among both types of evaluated EVs. CD326, CD49b, and CD63 distinguished 4T1 from DC2.4 EVs, and CD11b distinctively identified the DC2.4 EVs. The absence of detected CD326+ and CD11b+ in the serum of non-tumor bearing mice indicates the potential of these two markers for detection of specific tumor and antigen presenting cell EV subsets in serum from mice bearing CD326+ tumors such as 4T1. These results establish a foundation for further tests of detection and tracking of tumor-specific CD326+ EVs as "liquid biopsies" in blood samples as correlates to tumor progression and/or response to treatment.

Conditional deletion of mTOR discloses its essential role in early B-cell development

Mechanistic target of rapamycin (mTOR) is a serine-threonine kinase and central regulator of cell growth, differentiation, and survival. mTOR is commonly hyperactivated in a diverse number of cancers and critical roles for mTOR in regulating immune cell differentiation and function have been demonstrated. However, there is little work investigating the roles of mTOR in early B-cell development. Here we demonstrate that conditional disruption of mTOR in developing mouse B cells results in reduced pre-B-cell proliferation and survival, as well as a developmental block at the pre-B-cell stage, with a corresponding lack of peripheral B cells. Upon immunization with NP-CGG antigen, mice with Mtor conditional disruption in early B cells lost their ability to form germinal centers and produce specific antibodies. In competitive BM repopulation assays, donor BM cells from conditional knock-out mice were completely impaired in their ability to reconstitute B cells. Our data reveal the essential role of mTOR in early pre-B-cell development and survival.

Fatty acid oxidation is required for embryonic stem cell survival during metabolic stress

Metabolic regulation is critical for the maintenance of pluripotency and the survival of embryonic stem cells (ESCs). The transcription factor Tfcp2l1 has emerged as a key factor for the naïve pluripotency of ESCs. Here, we report an unexpected role of Tfcp2l1 in metabolic regulation in ESCs-promoting the survival of ESCs through regulating fatty acid oxidation (FAO) under metabolic stress. Tfcp2l1 directly activates many metabolic genes in ESCs. Deletion of Tfcp2l1 leads to an FAO defect associated with upregulation of glucose uptake, the TCA cycle, and glutamine catabolism. Mechanistically, Tfcp2l1 activates FAO by inducing Cpt1a, a rate-limiting enzyme transporting free fatty acids into the mitochondria. ESCs with defective FAO are sensitive to cell death induced by glycolysis inhibition and glutamine deprivation. Moreover, the Tfcp2l1-Cpt1a-FAO axis promotes the survival of quiescent ESCs and diapause-like blastocysts induced by mTOR inhibition. Thus, our results reveal how ESCs orchestrate pluripotent and metabolic programs to ensure their survival in response to metabolic stress.

Mouse tumor susceptibility genes identify drug combinations for multiple myeloma

Long-term genetic studies utilizing backcross and congenic strain analyses coupled with positional cloning strategies and functional studies identified Cdkn2a, Mtor, and Mndal as mouse plasmacytoma susceptibility/resistance genes. Tumor incidence data in congenic strains carrying the resistance alleles of Cdkn2a and Mtor led us to hypothesize that drug combinations affecting these pathways are likely to have an additive, if not synergistic effect in inhibiting tumor cell growth. Traditional and novel systems-level genomic approaches were used to assess combination activity, disease specificity, and clinical potential of a drug combination involving rapamycin/everolimus, an Mtor inhibitor, with entinostat, an histone deacetylase inhibitor. The combination synergistically repressed oncogenic MYC and activated the Cdkn2a tumor suppressor. The identification of MYC as a primary upstream regulator led to the identification of small molecule binders of the G-quadruplex structure that forms in the NHEIII region of the MYC promoter. These studies highlight the importance of identifying drug combinations which simultaneously upregulate tumor suppressors and downregulate oncogenes.

Hypomorphic mTOR Downregulates CDK6 and Delays Thymic Pre-T LBL Tumorigenesis

PI3K/AKT/mTOR pathway hyperactivation is frequent in T-cell acute lymphoblastic leukemia/lymphoma (T-ALL/LBL). To model inhibition of mTOR, pre-T-cell lymphoblastic leukemia/lymphoma (pre-T LBL) tumor development was monitored in mice with T lymphocyte-specific, constitutively active AKT (Lck-MyrAkt2) that were either crossed to mTOR knockdown (KD) mice or treated with the mTOR inhibitor everolimus. Lck-MyrAkt2;mTOR KD mice lived significantly longer than Lck-MyrAkt2;mTOR wild-type (WT) mice, although both groups ultimately developed thymic pre-T LBL. An increase in survival was also observed when Lck-MyrAkt2;mTOR WT mice were treated for 8 weeks with everolimus. The transcriptional profiles of WT and KD thymic lymphomas were compared, and Ingenuity Pathway Upstream Regulator Analysis of differentially expressed genes in tumors from mTOR WT versus KD mice identified let-7 and miR-21 as potential regulatory genes. mTOR KD mice had higher levels of let-7a and miR-21 than mTOR WT mice, and rapamycin induced their expression in mTOR WT cells. CDK6 was one of the most downregulated targets of both let-7 and miR21 in mTOR KD tumors. CDK6 overexpression and decreased expression of let-7 in mTOR KD cells rescued a G₁ arrest phenotype. Combined mTOR (rapamycin) and CDK4/6 (palbociclib) inhibition decreased tumor size and proliferation in tumor flank transplants, increased survival in an intravenous transplant model of disseminated leukemia compared with single agent treatment, and cooperatively decreased cell viability in human T-ALL/LBL cell lines. Thus, mTOR KD mice provide a model to explore drug combinations synergizing with mTOR inhibitors and can be used to identify downstream targets of inhibition.

Attenuation of immune-mediated bone marrow damage in conventionally housed mice

In humans, bone marrow (BM) failure syndromes, both constitutional and acquired, predispose to myeloid malignancies. We have modeled acquired immune aplastic anemia, the paradigmatic disease of these syndromes, in the mouse by infusing lymph node cells from specific pathogen-free (SPF) CD45.1 congenic C57BL/6 (B6) donors into hybrid CByB6F1 recipients housed either in conventional (CVB) or SPF facilities. The severity of BM damage was reduced in CVB recipients; they also had reduced levels of CD44⁺ CD62L^- effector memory T cells, reduced numbers of donor-type CD44⁺ T cells, and reduced expansion of donor-type CD8 T cells carrying T-cell receptor β-variable regions 07, 11, and 17. Analyses of fecal samples through 16S ribosomal RNA amplicon sequencing revealed greater gut microbial alpha diversity in CVB mice relative to that of SPF mice. Thus, the presence of a broader spectrum of gut microorganisms in CVB-housed CByB6F1 could have primed recipient animal's immune system leading to suppression of allogeneic donor T-cell activation and expansion and attenuation of host BM destruction. These results suggest the potential benefit of diverse gut microbiota in patients receiving BM transplants.

The transcription factor MZF1 differentially regulates murine Mtor promoter variants linked to tumor susceptibility

Mechanistic target of rapamycin (MTOR) is a highly conserved serine/threonine kinase that critically regulates cell growth, proliferation, differentiation, and survival. Previously, we have implicated Mtor as a plasmacytoma-resistance locus, Pctr2, in mice. Here, we report that administration of the tumor-inducing agent pristane decreases Mtor gene expression to a greater extent in mesenteric lymph nodes of BALB/cAnPt mice than of DBA/2N mice. We identified six allelic variants in the Mtor promoter region in BALB/cAnPt and DBA/2N mice. To determine the effects of these variants on Mtor transcription, we constructed a series of luciferase reporters containing these promoter variants and transfected them into mouse plasmacytoma cells. We could attribute the differences in Mtor promoter activity between the two mouse strains to a C → T change at the -6 position relative to the transcriptional start site Tssr 40273; a T at this position in the BALB promoter creates a consensus binding site for the transcription factor MZF1 (myeloid zinc finger 1). Results from electrophoretic mobility shift assays and DNA pulldown assays with ChIP-PCR confirmed that MZF1 binds to the cis-element TGGGGA located in the -6/-1 Mtor promoter region. Of note, MZF1 significantly and differentially down-regulated Mtor promoter activity, with MZF1 overexpression reducing Mtor expression more strongly in BALB mice than in DBA mice. Moreover, MZF1 overexpression reduced Mtor expression in both fibroblasts and mouse plasmacytoma cells, and Mzf1 knockdown increased Mtor expression in BALB3T3 and NIH3T3 fibroblast cells. Our results provide evidence that MZF1 down-regulates Mtor expression in pristane-induced plasmacytomas in mice.

Characterization of clinically used oral antiseptics as quadruplex-binding ligands

Approaches to characterize the nucleic acid-binding properties of drugs and druglike small molecules are crucial to understanding the behavior of these compounds in cellular systems. Here, we use a Small Molecule Microarray (SMM) profiling approach to identify the preferential interaction between chlorhexidine, a widely used oral antiseptic, and the G-quadruplex (G4) structure in the KRAS oncogene promoter. The interaction of chlorhexidine and related drugs to the KRAS G4 is evaluated using multiple biophysical methods, including thermal melt, fluorescence titration and surface plasmon resonance (SPR) assays. Chlorhexidine has a specific low micromolar binding interaction with the G4, while related drugs have weaker and/or less specific interactions. Through NMR experiments and docking studies, we propose a plausible binding mode driven by both aromatic stacking and groove binding interactions. Additionally, cancer cell lines harbouring oncogenic mutations in the KRAS gene exhibit increased sensitivity to chlorhexidine. Treatment of breast cancer cells with chlorhexidine decreases KRAS protein levels, while a KRAS gene transiently expressed by a promoter lacking a G4 is not affected. This work confirms that known ligands bind broadly to G4 structures, while other drugs and druglike compounds can have more selective interactions that may be biologically relevant.

Abstract 5113: A flexible pipeline for precision medicine biomarker detection and prediction of treatment response

Recent years have seen an explosion in the availability of paired molecular profiling and drug screen data, providing an unprecedented opportunity for the development of targeted therapies based on an individual’s genetic background. Despite a number of recent successes in diseases ranging from cystic fibrosis to cancer, significant hurdles remain in our ability to accurately predict treatments based on molecular profiling data. In particular, few such tools exist that allow the integration of heterogeneous data types (e.g. genomic, transcriptomic, and somatic mutations), along with high-throughput drug screen data to make predictions about treatment efficacy. Here, we describe a generalized open-source pipeline developed for the analysis of precision medicine data, Pharmacogenomics Prediction Pipeline, or “P3”. The modular design of P3 enables the inclusion of arbitrary input data types and the selection from multiple alternative machine learning algorithms, while automated statistical and visualization reporting steps incorporated throughout the pipeline assist in parameter tuning and early detection of problematic data components. Molecular profiling data is further enriched by the incorporation of external biological information in the form of pathway and gene set annotations such and Gene Ontology (GO) and The Molecular Signatures Database (MSigDB). To demonstrate the use of P3 for preclinical biomarker prediction, we applied P3 to an unpublished multiple myeloma dataset consisting of exome, RNA-Seq, CNV, and drug screen data for 1,912 compounds across 47 tumor cell lines. Specifically, P3 was used to predict molecular features associated with response to treatment for all drugs where a differential response to treatment was observed across patients. Furthermore, molecular profiling and drug screen data for 267 drugs and over a thousand cell lines spanning multiple cancer types from the Genomics of Drug Sensitivity in Cancer (GDSC) project were analyzed using P3, providing insights into shared mechanisms of drug sensitivity and resistance across different cancer and treatment types.

Citation Format: V Keith Hughitt, Sayeh Gorjifard, Aleksandra M. Michalowski, John K. Simmons, Ryan Dale, Eric C. Polley, Jonathan J. Keats, Beverly A. Mock. A flexible pipeline for precision medicine biomarker detection and prediction of treatment response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5113.

The transcription factor CBFB suppresses breast cancer through orchestrating translation and transcription

Translation and transcription are frequently dysregulated in cancer. These two processes are generally regulated by distinct sets of factors. The CBFB gene, which encodes a transcription factor, has recently emerged as a highly mutated driver in a variety of human cancers including breast cancer. Here we report a noncanonical role of CBFB in translation regulation. RNA immunoprecipitation followed by deep sequencing (RIP-seq) reveals that cytoplasmic CBFB binds to hundreds of transcripts and regulates their translation. CBFB binds to mRNAs via hnRNPK and enhances translation through eIF4B, a general translation initiation factor. Interestingly, the RUNX1 mRNA, which encodes the transcriptional partner of CBFB, is bound and translationally regulated by CBFB. Furthermore, nuclear CBFB/RUNX1 complex transcriptionally represses the oncogenic NOTCH signaling pathway in breast cancer. Thus, our data reveal an unexpected function of CBFB in translation regulation and propose that breast cancer cells evade translation and transcription surveillance simultaneously through downregulating CBFB.

CBFB is highly mutated in breast cancers and is known to interact with RUNX proteins to regulate transcription. Here, the authors describe a non-canonical role of CBFB in translation regulation in which it binds to mRNAs through hnRNPK, facilitating translation by eIF4B.

Chemical and structural studies provide a mechanistic basis for recognition of the MYC G-quadruplex

G-quadruplexes (G4s) are noncanonical DNA structures that frequently occur in the promoter regions of oncogenes, such as MYC, and regulate gene expression. Although G4s are attractive therapeutic targets, ligands capable of discriminating between different G4 structures are rare. Here, we describe DC-34, a small molecule that potently downregulates MYC transcription in cancer cells by a G4-dependent mechanism. Inhibition by DC-34 is significantly greater for MYC than other G4-driven genes. We use chemical, biophysical, biological, and structural studies to demonstrate a molecular rationale for the recognition of the MYC G4. We solve the structure of the MYC G4 in complex with DC-34 by NMR spectroscopy and illustrate specific contacts responsible for affinity and selectivity. Modification of DC-34 reveals features required for G4 affinity, biological activity, and validates the derived NMR structure. This work advances the design of quadruplex-interacting small molecules to control gene expression in therapeutic areas such as cancer.

Targeting noncoding nucleic acids with small molecules represents an important and significant challenge in chemical biology and drug discovery. Here the authors characterize DC-34, a small molecule that exhibits selective binding to specific G4 structures, and provide a structural basis for its selectivity

mTOR intersects antibody-inducing signals from TACI in marginal zone B cells

Mechanistic target of rapamycin (mTOR) enhances immunity in addition to orchestrating metabolism. Here we show that mTOR coordinates immunometabolic reconfiguration of marginal zone (MZ) B cells, a pre-activated lymphocyte subset that mounts antibody responses to T-cell-independent antigens through a Toll-like receptor (TLR)-amplified pathway involving transmembrane activator and CAML interactor (TACI). This receptor interacts with mTOR via the TLR adapter MyD88. The resulting mTOR activation instigates MZ B-cell proliferation, immunoglobulin G (IgG) class switching, and plasmablast differentiation through a rapamycin-sensitive pathway that integrates metabolic and antibody-inducing transcription programs, including NF-κB. Disruption of TACI-mTOR interaction by rapamycin, truncation of the MyD88-binding domain of TACI, or B-cell-conditional mTOR deficiency interrupts TACI signaling via NF-κB and cooperation with TLRs, thereby hampering IgG production to T-cell-independent antigens but not B-cell survival. Thus, mTOR drives innate-like antibody responses by linking proximal TACI signaling events with distal immunometabolic transcription programs.

Abstract 194: Effective targeting of MYC expression with a novel nucleic acid binding (G4-quadruplex) small molecule coupled with HDAC inhibition synergizes to limit myeloma growth

MYC is deregulated in many malignancies and its aberrant expression is associated with tumorigenesis and tumor maintenance. We employed a therapeutic strategy to target both MYC transcription, and protein stability. Previously, we developed a small molecule microarray and screened it for MYC G4-binding compounds. The stabilization of G-quadraplex (G4) structures by nucleic acid binding small molecules in the NHE III region of the MYC promoter slows MYC transcription. We identified a benzofuran containing small molecule that could selectively and reversibly stabilize MYC-G4 DNA and reduce MYC expression. This compound demonstrated a G4-dependent mechanism of action showing toxicity in multiple myeloma cell lines containing a G4 in their MYC promoter whereas minimal effects were seen in a Burkitt’s lymphoma line lacking the MYC G4 sequence. Gene expression analysis validated that this compound selectively inhibited MYC and other MYC effectors, but did little to limit the expression of other G4 containing genes. The synthesis of more than 15 analogs identified a new benzofuran-containing analog with enhanced inhibitory activity in a diverse panel of human cancer cell lines (NCI-60), including a number of myeloma cell lines. EDGE-seq data confirmed that the new analog is similar to the original compound in having higher affinity for the G4 in MYC compared to the G4 in BCL2, KRAS, VEGFA and HIF1A. In addition, the analog was synergistic with entinostat, an HDAC inhibitor that can affect MYC protein stability, in limiting myeloma cells, but not PBMCs. The more potent growth inhibitory activity of the new analog allowed us to generate sufficient quantities to evaluate its pharmacokinetics and toxicity in mice. The compound was well tolerated in a dose-escalation toxicity study; no adverse effects were observed and preliminary pharmacokinetic studies showed promising serum bioavailability and exposure properties when administered either intravenously, intraperitoneally or orally. In an assessment of short term in vivo activity, MYC protein expression was inhibited in multiple myeloma xenografts. Longer term studies to evaluate the anti-tumor activity of the compound are currently in progress. Thus, our data provide evidence that small molecule stabilization of the MYC G4 can drive transcriptional silencing of oncogenic MYC both in vitro and in vivo. Furthermore, synergistic tumor cell killing was achieved when the MYC G4 inhibitor was coupled with HDAC inhibition.

Citation Format: Snehal M. Gaikwad, David R. Calabrese, Elena C. Leon, John K. Simmons, Shuling Zhang, Aleksandra Michalowski, Sayeh Gorjifard, Zaw Phyo, Daniel Connors, John S. Schneekloth, Beverly A. Mock. Effective targeting of MYC expression with a novel nucleic acid binding (G4-quadruplex) small molecule coupled with HDAC inhibition synergizes to limit myeloma growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 194. doi:10.1158/1538-7445.AM2017-194

Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation

Cancer treatments often require combinations of molecularly targeted agents to be effective. mTORi (rapamycin) and HDACi (MS-275/entinostat) inhibitors have been shown to be effective in limiting tumor growth, and here we define part of the cooperative action of this drug combination. More than 60 human cancer cell lines responded synergistically (CI<1) when treated with this drug combination compared with single agents. In addition, a breast cancer patient-derived xenograft, and a BCL-XL plasmacytoma mouse model both showed enhanced responses to the combination compared with single agents. Mice bearing plasma cell tumors lived an average of 70 days longer on combination treatment compared with single agents. A set of 37 genes cooperatively affected (34 downregulated; 3 upregulated) by the combination responded pharmacodynamically in human myeloma cell lines, xenografts, and a P493 model, and were both enriched in tumors, and correlated with prognostic markers in myeloma patient datasets. Genes downregulated by the combination were overexpressed in several untreated cancers (breast, lung, colon, sarcoma, head and neck, myeloma) compared with normal tissues. The MYC/E2F axis, identified by upstream regulator analyses and validated by immunoblots, was significantly inhibited by the drug combination in several myeloma cell lines. Furthermore, 88% of the 34 genes downregulated have MYC-binding sites in their promoters, and the drug combination cooperatively reduced MYC half-life by 55% and increased degradation. Cells with MYC mutations were refractory to the combination. Thus, integrative approaches to understand drug synergy identified a clinically actionable strategy to inhibit MYC/E2F activity and tumor cell growth in vivoMol Cancer Ther; 16(9); 2008-21. ©2017 AACR.

Abstract 2833: Genetic and pharmacologic inhibition of mTOR delays mortality due to thymc lymphoma formation in mice and is associated with decreases in cell cycle proteins

The AKT/mTOR pathway is frequently hyperactivated in T-cell acute lymphoblastic leukemia (T-ALL). To model inhibition of this pathway in lymphoma, mice with T-lymphocyte-specific, constitutively active AKT (Lck-MyrAkt2) were crossed to mice with genetically reduced mTOR expression (knock-down, KD). Mice with genetic reduction of mTOR had increased survival by 10 weeks relative to wild type mTOR mice, though both developed thymic pre-T-cell lymphoblastic leukemia/lymphoma (pre-T LBL). Similarly, when mTOR wild type Lck-MyrAkt2 mice were treated for 8 weeks with the rapamycin analog, everolimus, an inhibitor of the mTOR TORC1 complex, survival was also increased. Gene expression profiling of thymic lymphomas from the mice revealed that mTOR KD was associated with decreased expression of Cdk6, a critical proliferative control node in T-cell development and oncogenic transformation. Pharmacologic inhibition of mTOR in tumor cells also decreased CDK6. The combination of a mTOR inhibitor (rapamycin) and a CDK4/6 inhibitor (PD-0332991, Palbociclib) synergistically decreased the overall viability and signaling downstream of drug targets in mouse lymphoma cells and in human T-ALL/LBL cell lines. This combination was also evaluated in mice using a disseminated leukemia model. In vivo treatment with this combination not only reduced tumor size by inhibiting tumor cell proliferation and arresting tumor cell cycle, but also increased overall survival. We are currently validating upstream regulators of Cdk6 as well as downstream targets in the pre-T LBL tumors from the mTOR deficient mice.

Citation Format: Shuling Zhang, Joy M. Gary, John K. Simmons, Jinfei Xu, Benjamin J. Gamache, Ke Zhang, Nicholas Watson, Alexander L. Kovalchuk, Aleksandra M. Michalowski, Jin-Qiu Chen, Michelle A. Herrmann, Tuddow Thaiwong, Matti Kiupel, Wendy Dubois, Joseph R. Testa, Beverly A. Mock. Genetic and pharmacologic inhibition of mTOR delays mortality due to thymc lymphoma formation in mice and is associated with decreases in cell cycle proteins. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2833.

Small Molecule Microarrays Enable the Identification of a Selective, Quadruplex-Binding Inhibitor of MYC Expression

The transcription factor MYC plays a pivotal role in cancer initiation, progression, and maintenance. However, it has proven difficult to develop small molecule inhibitors of MYC. One attractive route to pharmacological inhibition of MYC has been the prevention of its expression through small molecule-mediated stabilization of the G-quadruplex (G4) present in its promoter. Although molecules that bind globally to quadruplex DNA and influence gene expression are well-known, the identification of new chemical scaffolds that selectively modulate G4-driven genes remains a challenge. Here, we report an approach for the identification of G4-binding small molecules using small molecule microarrays (SMMs). We use the SMM screening platform to identify a novel G4-binding small molecule that inhibits MYC expression in cell models, with minimal impact on the expression of other G4-associated genes. Surface plasmon resonance (SPR) and thermal melt assays demonstrated that this molecule binds reversibly to the MYC G4 with single digit micromolar affinity, and with weaker or no measurable binding to other G4s. Biochemical and cell-based assays demonstrated that the compound effectively silenced MYC transcription and translation via a G4-dependent mechanism of action. The compound induced G1 arrest and was selectively toxic to MYC-driven cancer cell lines containing the G4 in the promoter but had minimal effects in peripheral blood mononucleocytes or a cell line lacking the G4 in its MYC promoter. As a measure of selectivity, gene expression analysis and qPCR experiments demonstrated that MYC and several MYC target genes were downregulated upon treatment with this compound, while the expression of several other G4-driven genes was not affected. In addition to providing a novel chemical scaffold that modulates MYC expression through G4 binding, this work suggests that the SMM screening approach may be broadly useful as an approach for the identification of new G4-binding small molecules.

Molecular Pathways: Increased Susceptibility to Infection Is a Complication of mTOR Inhibitor Use in Cancer Therapy

As one of the earliest examples of "chemical biology," the M: echanistic T: arget of R: apamycin (mTOR) protein and its chemical inhibitors have been extensively studied across a spectrum of physiologic and pathologic processes at the molecular, organismal, and patient population levels. There are several FDA-approved mTOR inhibitors (sirolimus, everolimus, and temsirolimus) with indications for cancer treatment and for prevention of solid organ rejection. Dozens of mTOR inhibitors are currently being evaluated in hundreds of ongoing clinical trials across a spectrum of diseases, including numerous cancer indications, autoimmune diseases, and a number of congenital disorders. As many of the approved and investigational indications for mTOR inhibitors require long-term treatment, the magnitude and incidence of particular side effects differ from those observed in shorter-term treatments. Here, we focus on the increased risk of infections in patients being treated with mTOR inhibitors. While increased infection rates might be expected from a class of drugs approved as posttransplant immunosuppressants, we review reports from clinical, mechanistic, and genetically engineered mouse model studies detailing a much more nuanced view of mTOR inhibitor drug action and target biology.

Abstract 2309: Murine model of dual mTORC kinase inhibition identifies CDK6 as a synergistic target in T-ALL

The PI3K/AKT/mTOR pathway is frequently hyperactivated in T- cell acute lymphoblastic leukemia (T-ALL). To model inhibition of this pathway in lymphoma, mice with constitutively-active AKT specific to T-lymphocytes (Lck-MyrAkt2) were crossed with mice that have genetically-reduced mTOR expression (mTOR knock-down, KD). Lck-MyrAkt2 mice with mTOR KD had altered thymic T-lymphocyte development; these mice also had delayed thymic pre-T cell lymphoblastic leukemia/lymphoma (pre-T LBL) progression and increased survival relative to wild type (WT) mTOR/ Lck-MyrAkt2 mice (average survival of 24 versus 14 weeks, respectively). Delayed pre-T LBL formation was also observed when WT mTOR/Lck-MyrAkt2 mice were treated for 8 weeks with the rapamycin analog, everolimus, an inhibitor of the mTOR TORC1 complex. Transcriptional profiling of thymic lymphomas from the WT vs KD mTOR/ Lck-MyrAkt2 mice revealed that mTOR KD was associated with decreased expression of Cdk6, a critical proliferative control node in T- cell development and oncogenic transformation. Pharmacologic inhibition of mTOR in tumor cells also decreased CDK6. Tumor cells from WT mTOR/Lck-MyrAkt2 mice were more sensitive to CDK4/6 inhibitors than tumor cells from KD mTOR/Lck-MyrAkt2 mice. Combining an mTOR inhibitor (rapamycin) with a CDK4/6 inhibitor (PD-0332991) synergistically inhibited the viability and decreased downstream signaling in both mouse lymphoma cells and human T-cell acute lymphoblastic leukemia (T-ALL) cell lines. Combining a dual mTORC inhibitor (PP242) with a CDK4/6 inhibitor decreased downstream signaling to an even greater extent in human T-ALL cell lines. Our results suggest that an mTORi/CDKi combination may be beneficial in the treatment of human T-ALL.

Citation Format: Joy M. Gary, Jinfei Xu, John Simmons, Shuling Zhang, Benjamin Gamache, Ke Zhang, Alexander Kovalchuk, Aleksandra Michalowski, Jin-Qiu Chen, Michelle Herrmann, Wendy Dubois, Joseph Testa, Beverly A. Mock. Murine model of dual mTORC kinase inhibition identifies CDK6 as a synergistic target in T-ALL. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2309. doi:10.1158/1538-7445.AM2015-2309

Abstract A73: De-convoluting therapeutic resistance in a pancreatic cancer model: Pharmacogenomic evaluation of intratumoral clonal heterogeneity

Background: The duration of therapeutic response in pancreatic adenocarcinoma to both targeted therapies and conventional chemotherapeutics is abysmal, greatly contributing to the 5-year survival rate of this disease remaining in the single digits. Given the high proliferative rate of these tumors, and the frequent occurrence of mutations in genes critical for maintaining genomic integrity, we hypothesized that rapid therapeutic resistance may largely be the consequence of intratumoral heterogeneity present at the onset of therapy.

Materials and Methods: To address this question, an integrated genomic and pharmacologic survey was performed on a panel of clonal cell lines generated from a tumor arising in a Kras/Trp53 mutant mouse model (p48-Cre; LSL-KrasG12D; LSL-Trp53R172H).

Results: All lines screened maintained tumorigenicity upon allografting, and exhibited metastatic capacity. Whole exome sequencing confirmed that 94% of driver mutations found in the clonal lines were also present in the tumor. Importantly, each clonal line contains unique passenger mutations. Exposure of these lines to conventional chemotherapeutics in vitro (i.e. gemcitabine, doxorubicin, and vincristine) showed high variance in sensitivity, with 10-fold ranges of IC50s among the lines. Screening of the clonal cell lines with a kinase inhibitor library of 200 compounds, showed distinct vulnerabilities to targeted pathways between the lines. Gene expression profiling and pathway analysis highlighted variation in critical cellular pathways between the lines.

Conclusions: Our results in this model system implicate ab initio drug resistance in these heterogeneous tumors as a major contributor to the poor therapeutic outcomes in this disease. This applies to conventional chemotherapy as well as targeted inhibitors.

Citation Format: Eveline E. Vietsch, John K. Simmons, Ivana Peran, Marianne Stenstra, Beverly A. Mock, Anton Wellstein. De-convoluting therapeutic resistance in a pancreatic cancer model: Pharmacogenomic evaluation of intratumoral clonal heterogeneity. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr A73.

Loss-of-function RNAi screens in breast cancer cells identify AURKB, PLK1, PIK3R1, MAPK12, PRKD2, and PTK6 as sensitizing targets of rapamycin activity

The use of molecularly targeted drugs as single agents has shown limited utility in many tumor types, largely due to the complex and redundant nature of oncogenic signaling networks. Targeting of the PI3K/AKT/mTOR pathway through inhibition of mTOR in combination with aromatase inhibitors has seen success in particular sub-types of breast cancer and there is a need to identify additional synergistic combinations to maximize the clinical potential of mTOR inhibitors. We have used loss-of-function RNAi screens of the mTOR inhibitor rapamycin to identify sensitizers of mTOR inhibition. RNAi screens conducted in combination with rapamycin in multiple breast cancer cell lines identified six genes, AURKB, PLK1, PIK3R1, MAPK12, PRKD2, and PTK6 that when silenced, each enhanced the sensitivity of multiple breast cancer lines to rapamycin. Using selective pharmacological agents we confirmed that inhibition of AURKB or PLK1 synergizes with rapamycin. Compound-associated gene expression data suggested histone deacetylation (HDAC) inhibition as a strategy for reducing the expression of several of the rapamycin-sensitizing genes, and we tested and validated this using the HDAC inhibitor entinostat in vitro and in vivo. Our findings indicate new approaches for enhancing the efficacy of rapamycin including the use of combining its application with HDAC inhibition.

Abstract 1629: Identification and biological characterization of a novel class of small molecules to inhibit c-myc transcription

The transcription factor c-myc, deregulated in ∼70% of all cancer cases, facilitates tumor initiation and promotion most frequently in colon, breast, lung, ovarian, and lymphoid malignancies, and acts as a universal amplifier of aberrant growth-related cell signaling. Due to its helix-loop helix topology, short protein half-life, and rapid replenishment within the cancer cell, c-myc was long considered to be ‘undruggable.’ Recently, much attention has focused on inhibiting c-myc either through indirect pathway modulation, or on the transcriptional level. 85-90% of c-myc gene expression is controlled by a G-quadruplex (G4) DNA structure found in the nuclease hypersensitive element III(1) region (NHEIII1) of its promoter, which, when stabilized with a chemical agent, would theoretically inhibit myc transcription by preventing normal polymerase function. In this study, we report the identification and biological characterization of a novel chemical class to directly bind the c-myc G4 DNA. The chemical motif discussed here was identified from a highly selective (hit rate of 0.16%, with few false positives) small molecule microarray screen of 20,000 compounds. A panel of the 12 most promising hits was chosen for biological and biochemical secondary validation in a variety of in vitro and cell based assays to confirm mechanism of action and functional effects in biological systems. Of note, numerous compounds from the initial panel of hits exhibited effects with a range of potency in comparison with untreated and non quadruplex forming nucleic acid controls, thereby validating the original screening method. For prioritization, hits were further evaluated for their capacity to preferentially induce myc-dependent cell death in a tetracycline controlled c-myc stable cell line. A top lead was identified, and structure-activity relationship was preliminarily evaluated with a small panel of analogues, leading to a final compound with three times greater potency. The chosen compound exhibited strong dose-dependent cell killing activity, in human multiple myeloma with high levels of c-myc, with an IC50 in the single digit micromolar range. Additionally, the compound reduced c-myc gene expression in a series of B cell neoplasms to near the limit of detection, both transcriptionally and translationally. The mechanism of action was confirmed in a Burkitt's Lymphoma model through a quadruplex promoter-specific comparative analysis of myc transcript copy numbers in the presence or absence of treatment. Continuing studies will focus on further structural optimization of the ligand, a thorough examination of its genome-wide effects, and tolerability in animal models.

Citation Format: Kenneth M. Felsenstein, John K. Simmons, Peter Gareiss, Beverly A. Mock, John ‘Jay’ S. Schneekloth. Identification and biological characterization of a novel class of small molecules to inhibit c-myc transcription. [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 1629. doi:10.1158/1538-7445.AM2014-1629

TORC1 and class I HDAC inhibitors synergize to suppress mature B cell neoplasms

Enhanced proliferative signaling and loss of cell cycle regulation are essential for cancer progression. Increased mitogenic signaling through activation of the mTOR pathway, coupled with deregulation of the Cyclin D/retinoblastoma (Rb) pathway is a common feature of lymphoid malignancies, including plasmacytoma (PCT), multiple myeloma (MM), Burkitt's lymphoma (BL), and mantle cell lymphoma (MCL). Here we evaluate the synergy of pharmacologically affecting both of these critical pathways using the mTOR inhibitor sirolimus and the histone deacetylase inhibitor entinostat. A dose-matrix screening approach found this combination to be highly active and synergistic in a panel of genetically diverse human MM cell lines. Synergy and activity was observed in mouse PCT and human BL and MCL cell lines tested in vitro, as well as in freshly isolated primary MM patient samples tested ex vivo. This combination had minimal effects on healthy donor cells and retained activity when tested in a co-culture system simulating the protective interaction of cancer cells with the tumor microenvironment. Combining sirolimus with entinostat enhanced cell cycle arrest and apoptosis. At the molecular level, entinostat increased the expression of cell cycle negative regulators including CDKN1A (p21) and CDKN2A (p16), while the combination decreased critical growth and survival effectors including Cyclin D, BCL-XL, BIRC5, and activated MAPK.

B cell-specific deficiencies in mTOR limit humoral immune responses

Generation of high-affinity Abs in response to Ags/infectious agents is essential for developing long-lasting immune responses. B cell maturation and Ab responses to Ag stimulation require Ig somatic hypermutation (SHM) and class-switch recombination (CSR) for high-affinity responses. Upon immunization with either the model Ag 4-hydroxy-3-nitrophenylacetyl hapten (NP) conjugated to chicken γ globulin lysine (NP-CGG) or heat-killed Streptococcus pneumoniae capsular type 14 protein (Pn14), knock-in (KI) mice hypomorphic for mTOR function had a decreased ability to form germinal centers, develop high-affinity anti-NP-specific or anti-Pn14-specific Abs, and perform SHM/CSR. Hypomorphic mTOR mice also had a high mortality (40%) compared with wild-type (WT) (0%) littermates and had lower pneumococcal surface protein A-specific Ab titers when immunized and challenged with live S. pneumoniae infection. Mice with mTOR deleted in their B cell lineage (knockout [KO]) also produced fewer splenic germinal centers and decreased high-affinity Ab responses to NP-CGG than did their WT littermates. CSR rates were lower in mTOR KI and KO mice, and pharmacologic inhibition of mTOR in WT B cells resulted in decreased rates of ex vivo CSR. RNA and protein levels of activation-induced cytidine deaminase (AID), a protein essential for SHM and CSR, were lower in B cells from both KI and B cell-specific KO mice, concomitant with increases in phosphorylated AKT and FOXO1. Rescue experiments increasing AID expression in KI B cells restored CSR levels to those in WT B cells. Thus, mTOR plays an important immunoregulatory role in the germinal center, at least partially through AID signaling, in generating high-affinity Abs.

Abstract 2217: A systems pharmacogenomic approach to identify synergistic molecular mechanisms of combined mTOR/HDAC inhibition

The necessity of combining targeted therapeutics to achieve optimal, lasting clinical benefit is clear, but standardized approaches for identifying the interactive effects of these combinations are not yet established. Discerning drug synergy at the molecular level has proven particularly challenging, yet identification of cooperatively responding, biologically-relevant targets could be useful for defining patient subsets for which the combination would be active. Here we used a transcriptional co-expression systems-level analysis to define the cooperative molecular response to the synergistic combination of mTOR/HDAC inhibitors in multiple myeloma (MM), and in other tumor types including triple negative breast cancer. Co-expression analysis of cells treated individually and in combination defined the contribution of each drug to the combination, and identified a distinct network of 126 genes cooperatively targeted by both drugs. We interrogated the cooperative network genes for differential expression between normal and malignant cells, as well as for correlation with survival in a large patient dataset. 37 of the cooperatively affected genes were both differentially expressed in MM and predictive of survival (p&lt;0.01). Analysis of additional tumor types showed similar results. The pharmacodynamic response of the survival-linked signature to the drug combination was evaluated using the NanoString gene expression platform in a large number of cell lines from multiple tumor types and in ex vivo-treated primary patient samples before and after treatment. We found the expression change of signature genes to be highly specific for biological response to the drug combination across tumor types. Additionally, to link the response signature to a central molecular effect of combination treatment, Ingenuity transcription factor enrichment testing was performed. Based on these predictions, subsequent analysis of CHIP-Seq datasets was performed, and two oncogenic transcription factors (TFs) were found to bind nearly all genes of this signature. We then experimentally linked drug combination response to diminished expression of these TFs at the protein level ahead of cell cycle and apoptotic changes. Further experiments have been performed to establish a direct link between these TFs, our gene signature, and drug response. Thus, a systems-level genomic approach has identified a gene signature indicative of drug combination activity, mechanism, disease specificity, and clinical potential.

Citation Format: John K. Simmons, Aleksandra M. Michalowski, Ben Gamache, Jyoti Patel, Adriana Zingone, Ke Zhang, Michael Kuehl, Jing Huang, Ola Landgren, Beverly A. Mock. A systems pharmacogenomic approach to identify synergistic molecular mechanisms of combined mTOR/HDAC inhibition. [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 2217. doi:10.1158/1538-7445.AM2013-2217

A novel KIT-deficient mouse mast cell model for the examination of human KIT-mediated activation responses

Activation of KIT, by its ligand, stem cell factor (SCF), results in the initiation of signal transduction pathways that influence mast cell survival and proliferation. Activating mutations in KIT have thus been linked to clonal MC proliferation associated with systemic mastocytosis. SCF also modulates MC function by inducing MC chemotaxis and by potentiating antigen (Ag)/IgE-mediated MC degranulation. Thus, mutations in KIT also have the potential to affect these processes in allergic and other mast cell-related diseases. Studies to determine how native and mutated KIT may modulate MC chemotaxis and activation have, however, been limited due to the lack of availability of a suitable functional MC line lacking native KIT which would allow transduction of KIT constructs. Here we describe a novel mouse MC line which allows the study of normal and mutated KIT constructs. These cells originated from a bone marrow-derived mouse MC culture out of which a rapidly dividing mast cell sub-population spontaneously arose. Over time, these cells lost KIT expression while continuing to express functional high affinity receptors for IgE (FcεRI). As a consequence, these cells degranulated in response to Ag/IgE but did not migrate nor show any evidence of potentiation of Ag/IgE degranulation in response to SCF. Retroviral transduction of the cells with a human (hu)KIT construct resulted in surface expression of huKIT which responded to huSCF by potentiation of Ag/IgE-induced degranulation and chemotaxis. This cell line thus presents a novel system to delineate how MC function is modulated by native and mutated KIT and for the identification of novel inhibitors of these processes.

Abstract PR6: A cooperative molecular response to combined mTOR/HDAC inhibition revealed by transcriptional co-expression analysis

Identification of biologically relevant molecular targets responding cooperatively to drug combinations is challenging, yet potentially useful in predicting clinical outcomes. We found that combining sirolimus (rapamycin), an inhibitor of mechanistic target of rapamycin (mTOR), with entinostat (MS-275), a selective class I histone deacytlase (HDAC) inhibitor, was synergistic in controlling 90% of tested cell lines derived from B cell malignancies, including multiple myeloma, mantle cell lymphoma, and murine plasmacytoma, in vitro, and effective in limiting xenograft growth in vivo. To understand the transcriptional underpinnings of the drug synergy, weighted gene co-expression analysis (WGCNA) was adapted to analyze gene expression profile data from cells treated with sirolimus and entinostat individually and in combination. WGCNA delineated the contribution of each inhibitor to the overall gene expression change of the combination by considering not only measures of fold-change and significance testing, but also the degree of gene expression interconnectedness. A co-expression network consisting of five gene modules was defined, where each module represents a unique transcriptional effect of the drug combination. In the next phase of analysis, each gene module was individually tested for functional and clinical enrichment. The module containing genes cooperatively affected by both compounds was highly enriched (p&lt;0.001) for genes involved in cell cycle, immune recognition, and DNA damage/repair, which we have validated. Gene set enrichment analysis of each drug-induced gene expression module demonstrated that genes of all five modules were significantly enriched when healthy donors were compared to MM patients. Finally, interrogation of the cooperative drug signature in patient GEP datasets with survival annotation found it predictive of increased survival (p&lt;0.01), thus linking the drug combination-induced transcriptional changes to predictions for enhanced survival. Thus, systems-level genomic approaches identified markers and a gene signature associated with drug combination activity, disease specificity, and clinical potential.

This proffered talk is also presented as Poster A16.

Citation Format: John Kyle Simmons, Beverly A. Mock, Aleksandra Michalowski, Jyoti Patel, Bih-Rong Wei, R. Mark Simpson, W. Michael Kuehl, Shuling Zhang, Ke Zhang, Ola Landgren. Sorger. A cooperative molecular response to combined mTOR/HDAC inhibition revealed by transcriptional co-expression analysis [abstract]. In: Proceedings of the AACR Special Conference on Chemical Systems Biology: Assembling and Interrogating Computational Models of the Cancer Cell by Chemical Perturbations; 2012 Jun 27-30; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2012;72(13 Suppl):Abstract nr PR6.

Abstract 4734: Genes cooperatively downregulated by combined mTOR/histone deactylase (HDAC) inhibition are overexpressed in myeloma patients with lower survival

The molecular pathogenesis of many cancer types, including multiple myeloma (MM) and mantle cell lymphoma (MCL), involves alterations in the PI3K/Akt/mTOR and cyclin/CDK/CDKI/Rb (Rb) pathways. Previously, we showed that the combination of an HDAC inhibitor (HDACi) with rapamycin synergistically inhibited proliferation in 88% of human MM cell lines tested, and effectively controlled tumor growth in preclinical studies. To gain an initial understanding of the molecular mechanism of the synergistic action of the drug combination, we used an unbiased systems-level approach to analyze our gene expression profile (GEP) data with weighted gene co-expression network analysis (WGCNA). This analysis delineated the contribution of HDACi and rapamycin, singly and in combination, to the overall gene expression change of the combination by considering not only measures of fold-change and significance testing, but also the degree of gene expression inter-connectedness. WGCNA identified five gene modules, each representing a particular gene expression effect of the combination. Each gene module was individually tested for functional and clinical enrichment using gene set enrichment analysis (GSEA) and survival analyses with Cox regression. Of particular interest, the module containing genes cooperatively affected by both compounds was highly enriched (p&lt;0.001) for genes involved in cell cycle (especially mitotic processes), immune recognition, and DNA damage/repair, which we investigated further. Genes down-regulated by the drug combination were most significantly correlated with genes over-expressed in MM patients. Furthermore, analysis of the cooperative drug signature in publicly available patient GEP datasets with survival annotation found it predictive of increased survival (p&lt;0.01), thus linking the drug combination-induced transcriptional changes to predictions for enhanced survival.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4734. doi:1538-7445.AM2012-4734

Abstract C111: Genes cooperatively targeted by combined mTOR/histone deactylase (HDAC) inhibition are predictive of increased multiple myeloma patient survival

The molecular pathogenesis of many cancer types, including multiple myeloma (MM), involves alterations in the PI3K/Akt/mTOR and cyclin/CDK/CDKI/Rb (Rb) pathways. Targeting these pathways individually has shown limited efficacy. Here, however, we show the combination of an HDAC inhibitor with rapamycin synergistically inhibits proliferation in 88% of human myeloma cell lines tested (p&lt;0.01), as well as effectively controlling tumor growth in long-term preclinical studies. To understand the synergistic molecular mechanism of this combination, candidate pathway analysis and a systems-level approach were taken. We found the combination antagonized the oncogenic activation of the AKT pathway associated with single-agent rapamycin treatment, along with inhibiting the ERK/MAPK pathway to a much greater extent than either single agent alone. For a more unbiased approach, gene expression profiling (GEP) was coupled with a systems-level gene co-expression network analysis. This analysis delineated the contribution of each inhibitor to the overall gene expression change of the combination by considering not only measures of fold-change and significance testing, but also the degree of gene expression inter-connectedness. With these findings, a network of five gene modules was constructed, where each module represents a particular gene expression effect of the combination. Each module of genes was then individually tested for functional and clinical enrichment. Of particular interest, the module containing genes cooperatively affected by both compounds was highly enriched (p&lt;0.001) for genes involved in cell cycle (especially mitotic processes), immune recognition, and DNA damage/repair, which we have investigated further. Specifically, we confirmed the down-regulation of RRM2, a gene involved in DNA synthesis and repair, by western blot and validated an increase in DNA damage markers with combination treatment. Additionally, we determined that specific RRM2 inhibition decreased MM cell viability, which decreased further when combined with rapamycin. Gene Set Enrichment Analysis of drug-induced gene expression profiles demonstrated that all gene expression modules associated with the drug combination were significantly enriched (p&lt;0.01) when comparing healthy donors to MM patients in a large, publicly available GEP dataset. Finally, interrogation of the cooperative drug signature in publicly available patient GEP datasets with survival annotation found it predictive of increased survival (p&lt;0.01), thus linking the drug combination-induced transcriptional changes to predictions for enhanced survival.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr C111.

Abstract 805: mTORC protein levels affect class switch recombination, somatic hypermutation, and antibody production

Mammalian target of rapamycin (mTOR) regulates cell growth, cell cycle, and survival through two main complexes, mTORC1 and mTORC2. In our previous studies, striking decreases in both size and number of B cells were seen in mice with constitutive reductions in protein levels of both mTOR complexes. In addition, there were alterations in B cell differentiation with partial blocks in B cell development in the bone marrow. In our current studies, we have focused on their defect in antibody production. When challenged with either NP-CGG (T-dependent antigen) or NP-LPS (T-independent antigens), reduced IgG antibody titers to NP antigens were seen in mice with constitutive reductions in mTOR protein levels, despite equivalent levels of total antibody production; high affinity antibody production was also less. The numbers of germinal centers were reduced in the spleens of the mTORC1/2-compromised mice compared to their wild-type littermates. Fewer B cells from the mTORC1/2-compromised mice were able to undergo class switching from IgM to IgG. In addition, germinal center B cells from these mice exhibited reductions in somatic hypermutation rates of their immunoglobulin loci. Studies are currently underway to evaluate the ability of these mice to respond to an in vivo challenge of live bacteria.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 805. doi:10.1158/1538-7445.AM2011-805

The role of plasmacytoma growth factor in the in vitro responses of murine plasmacytoma cells

Many plasmacytomas arising in BALB/c mice are dependent upon a specific, macrophage-derived plasmacytoma growth factor for survival and proliferation in vitro. Adherent cells taken from the peritoneal oil granuloma in which the early plasmacytomas arise and proliferate produce 50 times more PCT-GF activity in vitro than do normal peritoneal cells, thus suggesting a possible in vivo role for PCT-GF. Purification and amino acid sequencing of PCT-GF derived from the murine macrophage cell line, P388D1, have identified a 23 kDa protein with a unique NH2-terminal sequence. This molecule is now known as murine IL6. As part of the characterization of murine Il-6, genomic sequences have been localized to the proximal end of mouse chromosome 5 via Southern analysis of restriction fragment length polymorphisms. The removal of IL6 from IL6-dependent PCT cell lines results in a growth arrest in early G1. This is accompanied by a rapid and specific loss of transferrin receptor expression and results in eventual cell death. It appears that the response to IL6 is at least partially dependent on Ca++ because functional Ca++ channels are necessary for the PCT cells to pass through G1 and to maintain transferrin receptor expression.

The Collaborative Cross, a community resource for the genetic analysis of complex traits

The goal of the Complex Trait Consortium is to promote the development of resources that can be used to understand, treat and ultimately prevent pervasive human diseases. Existing and proposed mouse resources that are optimized to study the actions of isolated genetic loci on a fixed background are less effective for studying intact polygenic networks and interactions among genes, environments, pathogens and other factors. The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease.

The nature and identification of quantitative trait loci: a community's view

This white paper by eighty members of the Complex Trait Consortium presents a community's view on the approaches and statistical analyses that are needed for the identification of genetic loci that determine quantitative traits. Quantitative trait loci (QTLs) can be identified in several ways, but is there a definitive test of whether a candidate locus actually corresponds to a specific QTL?

Frap, FKBP12 rapamycin-associated protein, is a candidate gene for the plasmacytoma resistance locus Pctr2 and can act as a tumor suppressor gene

Susceptibility to mouse plasmacytomagenesis is a complex genetic trait controlled by several Pctr loci (Pctr1, Pctr2, etc). Congenic strain analysis narrowed the genetic interval surrounding the Pctr2 locus, and genes identified in the interval were sequenced from susceptible BALB/c and resistant DBA/2 mice. Frap (FKBP12 rapamycin-associated protein, mTOR, RAFT) was the only gene differing in amino acid sequence between alleles that correlated with strain sensitivity to tumor development. The in vitro kinase activity of the BALB/c FRAP allele was lower than the DBA/2 allele; phosphorylation of p53 and PHAS1/4EBP1 (properties of heat and acid stability/eukaryotic initiation factor 4E-binding protein) and autophosphorylation of FRAP were less efficient with the BALB/c allele. FRAP also suppressed transformation of NIH 3T3 cells by ras, with DBA/2 FRAP being more efficient than BALB/c FRAP. Rapamycin, a specific inhibitor of FRAP, did not inhibit growth of plasmacytoma cell lines. These studies identify Frap as a candidate tumor suppressor gene, in contrast to many reports that have focused on its prooncogenic properties. Frap may be similar to Tgfb and E2f in exerting both positive and negative growth-regulatory signals, depending on the timing, pathway, or tumor system involved. The failure of rapamycin to inhibit plasma cell tumor growth suggests that FRAP antagonists may not be appropriate for the treatment of plasma cell tumors. Pctr2 joins Pctr1 in possessing alleles that modify susceptibility to plasmacytomagenesis by encoding differences in efficiency of function (efficiency alleles), rather than all-or-none, gain-of-function, or loss-of-function alleles. By analogy, human cancer may also result from the combined effects of several inefficient alleles.

p16 INK4a gene promoter variation and differential binding of a repressor, the ras-responsive zinc-finger transcription factor, RREB

BALB/c mice are susceptible to the development of pristane-induced plasma cell tumors, and have a rare allelic variant in the coding region of the p16(INK4a) (p16) tumor suppressor gene that produces a protein with impaired activity. We have now found that the BALB/c p16 promoter has an allelic variant that may also compromise p16 activity. Following pristane treatment, BALB/c p16 mRNA levels in B cells were lower than that in DBA/2 or C.D2-Pctr1, a resistant BALB/c congenic strain that harbors DBA/2 chromatin surrounding the p16 locus. Four sequence variants were found between BALB/c and DBA/2 in the p16 promoter region. In reporter assays, the DBA promoter was at least four times more active in driving luciferase expression than the BALB/c promoter. Most of the difference in activity was localized to a single nucleotide deletion in BALB/c. This deletion created a consensus binding site for RREB, a ras-responsive transcriptional element with zinc-finger binding motifs. Transient transfections with RREB confirmed that the p16 promoter can be downregulated by RREB, in a Ras- or Mek-dependent manner, and that the BALB/c promoter is more sensitive than DBA/2 to regulation by RREB. BALB/c mice have both regulatory and coding region defects that may contribute to the impairment of p16 gene function.

Efficiency alleles of the Pctr1 modifier locus for plasmacytoma susceptibility

The susceptibility of BALB/c mice to pristane-induced plasmacytomas is a complex genetic trait involving multiple loci, while DBA/2 and C57BL/6 strains are genetically resistant to the plasmacytomagenic effects of pristane. In this model system for human B-cell neoplasia, one of the BALB/c susceptibility and modifier loci, Pctr1, was mapped to a 5.7-centimorgan (cM) chromosomal region that included Cdkn2a, which encodes p16(INK4a) and p19(ARF), and the coding sequences for the BALB/c p16(INK4a) and p19(ARF) alleles were found to be polymorphic with respect to their resistant Pctr1 counterparts in DBA/2 and C57BL/6 mice (45). In the present study, alleles of Pctr1, Cdkn2a, and D4Mit15 from a resistant strain (BALB/cDAG) carrying DBA/2 chromatin were introgressively backcrossed to the susceptible BALB/c strain. The resultant C.DAG-Pctr1 Cdkn2a D4Mit15 congenic was more resistant to plasmacytomagenesis than BALB/c, thus narrowing Pctr1 to a 1.5-cM interval. Concomitantly, resistant C57BL/6 mice, from which both gene products of the Cdkn2a gene have been eliminated, developed pristane-induced plasma cell tumors over a shorter latency period than the traditionally susceptible BALB/cAn strain. Biological assays of the p16(INK4a) and p19(ARF) alleles from BALB/c and DBA/2 indicated that the BALB/c p16(INK4a) allele was less active than its DBA/2 counterpart in inducing growth arrest of mouse plasmacytoma cell lines and preventing ras-induced transformation of NIH 3T3 cells, while the two p19(ARF) alleles displayed similar potencies in both assays. We propose that the BALB/c susceptibility/modifier locus, Pctr1, is an "efficiency" allele of the p16(INK4a) gene.

[Specific immunotherapy (hyposensitization) with insect venom in pregnancy]

BACKGROUND

Pregnancy typically prohibits the specific immunotherapy (SIT) of various allergic conditions, with the exception of pre-existing Hymenoptera venom allergies. International consensus currently recommends the continuation of a well-tolerated SIT with insect venom during pregnancy, since there is a significant risk of anaphylaxis after insect stings with potentially dismal outcomes for mother and fetus.

CASE REPORT

We report on a 28-year old woman, becoming pregnant during specific immunotherapy with Hymenoptera venom. SIT was continued during pregnancy and a premature birth occurred at the 24th week.

DISCUSSION AND CONCLUSION

Unfortunately, there are still conflicting opinions in Germany regarding SIT during pregnancy, and the decision to perform such therapy is entirely based on knowledge and/or level of comfort of the primary physician. Thus, obstetricians should closely work together with an allergologist in cases of pregnant women with insect sting allergies.

Structure and localization of mouse Pmscl1 and Pmscl2 genes

Sera from some patients with polymyositis-scleoderma overlap syndrome (PM-SCL) recognize two antigenically unrelated proteins, PMSCL1 and PMSCL2. Complete mouse Pmscl1 and Pmscl2 cDNA sequences, chromosomal localizations, exon/intron structure, and promoter region sequences of the mouse Pmscl2 gene are presented. The PMSCL1 gene was found to overlap significantly with cyclin A2 in both human and mouse. As such, it may be deduced that PMSCL1 sequences map to human chromosome 4q27 and the proximal portion of mouse chromosome (Chr) 3 where human and mouse cyclin A2 genes reside. Analysis of human and mouse PMSCL1 cDNA sequences provides evidence that the PMSCL1 protein is 68 amino acids longer than previously thought. A BAC containing mouse Pmscl2 was localized to distal mouse Chr 4 by FISH. This BAC contains the microsatellite D4Mit310. D4Mit310 colocalizes with a number of genes that map to human 1p36. In fact, a STS (G25404) located 54.6 cR from the top of human chromosome 1 was found to contain PMSCL2 sequence upon BLAST search.

Mapping of the SWAP70 gene to mouse chromosome 7 and human chromosome 11p15

The protein SWAP-70 was isolated as part of a DNA recombination complex in B lymphocytes, where it is predominantly expressed. In resting B cells, SWAP-70 is found in the cytoplasm; upon B-cell activation, it is transported both into the nucleus and to the cell membrane, where it is associated with the B-cell receptor complex and may play a role in signal transduction. In the nucleus, its involvement in heavy-chain class switch recombination has been suggested. In this report, using restriction fragment length polymorphism, simple sequence length polymorphism, and fluorescence in situ hybridization, we map the chromosomal localization of the mouse and the human genes to syntenic regions of mouse mid Chromosome (Chr) 7 and human Chr 11p15.