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.

Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells

PURPOSE

Circulating tumor DNA (ctDNA) has the potential to guide therapy selection and monitor treatment response in patients with metastatic cancer. However, germline and clonal hematopoiesis-associated alterations can confound identification of tumor-specific mutations in cell-free DNA (cfDNA), often requiring additional sequencing of tumor tissue. The current study assessed whether ctDNA-based treatment response monitoring could be performed in a tumor tissue-independent manner by combining ultra-deep targeted sequencing analyses of cfDNA with patient-matched white blood cell (WBC)-derived DNA.

EXPERIMENTAL DESIGN

In total, 183 cfDNA and 49 WBC samples, along with 28 tissue samples, from 52 patients with metastatic colorectal cancer participating in the prospective phase III CAIRO5 clinical trial were analyzed using an ultra-deep targeted sequencing liquid biopsy assay.

RESULTS

The combined cfDNA and WBC analysis prevented false-positives due to germline or hematopoietic variants in 40% of patients. Patient-matched tumor tissue sequencing did not provide additional information. Longitudinal analyses of ctDNA were more predictive of overall survival than standard-of-care radiological response evaluation. ctDNA mutations related to primary or acquired resistance to panitumumab were identified in 42% of patients.

CONCLUSIONS

Accurate calling of ctDNA mutations for treatment response monitoring is feasible in a tumor tissue-independent manner by combined cfDNA and patient-matched WBC genomic DNA analysis. This tissue biopsy-independent approach simplifies sample logistics and facilitates the application of liquid biopsy ctDNA testing for evaluation of emerging therapy resistance, opening new avenues for early adaptation of treatment regimens.

Characterization of tumor mutation burden, PD-L1 and DNA repair genes to assess relationship to immune checkpoint inhibitors response in metastatic renal cell carcinoma

Background

Immune checkpoint inhibitors (ICIs) have expanded treatment options for metastatic renal cell carcinoma (mRCC); however, there are limited predictive biomarkers for response to ICIs in this indication, with programmed death-ligand 1 (PD-L1) status demonstrating little predictive utility in mRCC. While predictive of ICI response in other tumor types, the utility of tumor mutation burden (TMB) in mRCC is unclear. Here, we assess TMB, loss of antigen presentation genes and PD-L1 status correlated with outcomes to ICI treatment in mRCC.

Methods

Tumor samples from 34 patients with mRCC treated with ICI therapy at Duke Cancer Institute were retrospectively evaluated using Personal Genome Diagnostics elio tissue complete (RUO version), a tumor genomic profiling assay for somatic variants, TMB, microsatellite status and genomic status of antigen presentation genes. Tumor samples were also analyzed with the Dako 28-8 PD-L1 immunohistochemistry assay. Deidentified clinical information was extracted from the medical record, and tumor response was evaluated based on the Response Evaluation Criteria In Solid Tumors (RECIST) V.1.1 criteria.

Results

Patients were stratified by overall response following ICI therapy and designated as progressive disease (PD; n=18) or disease control groups (DC; n=16). TMB scores ranged from 0.36 to 12.24 mutations/Mb (mean 2.83 mutations/Mb) with no significant difference between the PD and DC groups (3.01 vs 2.63 mutations/Mb, respectively; p=0.7682). Interestingly, 33% of PD patients displayed loss of heterozygosity of major histocompatibility complex class I genes (LOH-MHC) vs 6% of DC patients. Nine of 34 samples were PD-L1-positive (4 in the PD group; 5 in the DC group), suggesting no correlation between PD-L1 expression and response to ICI therapy. Notably, the DC group displayed an enrichment of mutations in DNA repair genes (p=0.04), with 68.8% exhibiting at least one mutated homologous recombination repair (HRR)-related gene compared with only 38.9% of the PD group (p=0.03).

Conclusions

Overall, neither TMB nor PD-L1 correlated with ICI response and TMB was not significantly associated with PD-L1 expression. The higher incidence of LOH-MHC in PD group suggests that loss of antigen presentation may restrict response to ICIs. Separately, enrichment of HRR gene mutations in the DC group suggests potential utility in predicting ICI response and a potential therapeutic target, warranting future studies.

Abstract 540: Molecular response evaluation of patients with metastatic colorectal cancer using circulating tumor DNA

Introduction: Patients with colorectal cancer with unresectable and isolated liver metastases (CRLM) are mostly treated with chemotherapy and targeted treatments like anti-epidermal growth factor receptor (EGFR) monoclonal antibody therapy. Clinical response evaluation of systemic treatment is performed by radiological CT imaging, which can detect disease progression. However, CT imaging does not always give information about the viability of the tumor tissue nor does it constitute the genomic changes of the tumor, i.e. development of sub-clones following the pressure of treatment. Cell-free circulating tumor DNA (ctDNA) derived from liquid biopsies is a minimally invasive biomarker that has great potential for tumor detection and is present in relatively high levels in the plasma of patients with CRLM. Liquid biopsy ctDNA allows for longitudinal follow-up and gives the possibility to track intratumor heterogeneity caused by different sub-clones without a repeated tumor biopsy. Here, we aim to assess the use of molecular profiling using serial liquid biopsies as a biomarker for treatment response evaluation.

Methods: Tumor tissue obtained prior to treatment as well as longitudinal liquid biopsies were collected from patients with CRLM who participated in a prospective clinical trial with CRC and were treated with panitumumab and doublet chemotherapy. Liquid biopsy ctDNA was isolated and analyzed by targeted sequencing using a panel of 33-genes, allowing to map dynamic molecular changes during treatment. ctDNA sequencing results were corrected for germline variants and clonal hematopoiesis variants by using targeted sequencing data of patient-matched tumor tissue DNA and white blood cell (WBC) genomic DNA, respectively. ‘Molecular response' was defined as the elimination of more than 95% of ctDNA after treatment compared to the measurement before treatment initiation. Detection of disease progression by ctDNA was compared to CT imaging.

Results: At present, 110 longitudinal plasma samples as well as WBC genomic DNA and tumor tissue DNA are analyzed from a cohort of 33 patients. Currently, we are expanding the number of patients and samples. Molecular responders to treatment showed a significantly longer overall survival than non-responders (median 51 vs 25 months; p=0.033; HR=3.7). In addition, significantly earlier detection of disease progression was observed using ctDNA compared to radiological imaging (median difference of 4.8 months; p=0.006).

Conclusion: Serial plasma ctDNA analyses in patients with mCRC provide a minimally-invasive tool for longitudinal treatment response evaluation of dynamic genomic alterations and creates an opportunity for patient subset selection for possible adaptation of the treatment regimen.

Citation Format: Iris van 't Erve, Jamie E. Medina, Alessandro Leal, Eniko Papp, Karen Bolhuis, John K. Simmons, Samuel Angiuoli, Cornelis J. Punt, Gerrit A. Meijer, Victor E. Velculescu, Remond J. Fijneman. Molecular response evaluation of patients with metastatic colorectal cancer using circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 540.

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.

Abstract 3096: Liquid biopsy cell-free circulating tumor DNA as prognostic biomarker for stage III colon cancer patients

Introduction: Stage III colon cancer patients undergo surgery followed by adjuvant chemotherapy (ACT) according to clinical guidelines. However, 50% would be cured by surgery alone and are being overtreated, while 30-35% will relapse despite adjuvant treatment. This means that only 15-20% of the patients benefit from ACT. Therefore, there is a need for better prognostic biomarkers to stratify patients for ACT. Detection of cell-free circulating tumor DNA (ctDNA) in blood after surgery is indicative of minimal residual disease and highly prognostic for disease recurrence. Hence, detecting liquid biopsy ctDNA is a promising approach to guide treatment decisions in stage III colon cancer.

Aim: Determine prognostic value of ctDNA in stage III colon cancer patients treated with ACT in order to reduce futile treatment.

Methods: 315 stage III colon cancer patients treated with ACT will be included in the prospective observational study “PROVENC3” (PROgnostic Value of Early Notification by Ctdna in Colon Cancer stage 3). The Prospective Dutch Colorectal Cancer Cohort (PLCRC) infrastructure organizes accrual of colorectal cancer patients in more than 50 hospitals in the Netherlands, among which 25 hospitals that accrue patients for PROVENC3. If informed consent is provided, blood is collected at baseline, post-surgery, post-ACT and every six months up to 3 years, and shipped to a central location. Tumor-informed detection of mutations in ctDNA will be performed by combined analysis of targeted sequencing of a panel of >30 genes in cfDNA (PGDx elio plasma test) and a panel of >500 genes in DNA from formalin-fixed paraffin-embedded tumor tissue (PGDx elio tissue complete assay). The clinical, pathological, and molecular data will be handled according to the FAIR (findable, accessible, interoperable and reusable) principles and integrated in cBioPortal.

Results and future directions: Around 125 patients and 400 blood samples included to date. Once sequencing data are obtained we will determine: 1) the proportion of ctDNA-positive and ctDNA-negative patients after surgery and the corresponding recurrence rates; 2) the prognostic value of ctDNA pre-surgery; and 3) the lead time between ctDNA detection and recurrence. Ultimately, the results of this study will be used to model and design an ethically acceptable and cost-effective ctDNA-guided interventional trial, to reduce futile ACT and its associated side-effects in stage III colon cancer patients.

Citation Format: Carmen Rubio Alarcón, Dave E. van der Kruijssen, Lana Meiqari, Linda J. Bosch, John K. Simmons, Victor E. Velculescu, Daan van den Broek, Cornelis J. Punt, Veerle M. Coupé, Miriam Koopman, Gerrit A. Meijer, Geraldine R. Vink, Remond J. Fijneman. Liquid biopsy cell-free circulating tumor DNA as prognostic biomarker for stage III colon cancer patients [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3096.

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.

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.

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

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.

Abstract LB-281: Elucidating potential therapeutic targets in a model of Pten/Tp53 null prostate cancer using high-throughput screening technology

Prostate cancer (PCa) demonstrates significant intra and inter tumor heterogeneity, similar to many other solid tumors. The “gold standard” of therapy for metastatic prostate cancer is androgen deprivation therapy (ADT). Although ADT is initially effective, acquired resistance, termed castration resistant prostate cancer (CRPC), almost always occurs. It is believed that development of CRPC is governed by both intrinsically resistant progenitor cells and by acquired genomic mutations. Clinically advanced CRPC tumors often display loss of PTEN (40%) and aberrations in TP53 (50%), the presence of which in primary prostate cancer are associated with poor clinical prognosis. Our goal is to identify novel targeted therapies against progenitor cells harboring Pten/Tp53 mutations.

To enable high throughput screening, we derived multiple cell lines from a PB-Cre4 Ptenfl/fl;Tp53fl/fl mouse model before (intact) and after (castrate) castration. The RNA-seq analyses of the 8 resultant cell lines revealed distinct clustering of intact and castrate lines as well as patterns of expression characteristic of progenitor cells. Cell lineage marker analysis showed strong KRT8 and minimal KRT5 expression. Using these 8 distinct luminal cell lines, we performed the mechanism interrogation plate (MIPe) screen, a high throughput 1,912 compound screening assay at the National Center for Advancing Translational Science (NCATS). Post-screen informatics data processing and subsequent analysis sorted out compounds that displayed strong activity (1.1 and 1.2 curve class). Multiple compounds were unique to each cell line, however, no difference in sensitivity between the two groups of intact and castrate cell types was observed. Grouping of intact and castrate cell lines together as one population identified a diverse array of 235 compounds (12% of MIPe library) with robust activity against most of the cell lines. Some of these compounds are redundant for specific targets that are key regulators of a multitude of signaling pathways, such as the heat shock protein HSP90AB1, which was targeted by 11 different compounds. In contrast, other targets, like BIRC5, were potently targeted by only one compound. A majority of the 235 compounds targeted components of signaling pathways important in PCa, including: 28 compounds targeting PI3K/AKT/mTOR signaling (AKT1, PIK3CA, mTORc 1/2), 13 compounds targeting cell cycle regulators (CDK1, CDK4), 13 compounds targeting DNA repair and replication (CHEK1, TOP2A), 6 compounds targeting NFKB signaling (IKBKB,ITK) and 5 compounds targeting MAPK signaling (MAPK8, MAP2K1). Using high throughput screening technology to sort for compounds based on potency and activity identified clinically and biologically relevant therapeutic applications for existing compounds in a novel context, Pten/Tp53 null PCa progenitor cells.

Citation Format: Keith H. Jansson, John K. Simmons, Caitlyn Fuller, Supreet Agarwal, Paul G. Hynes, Lei Fang, Ross Lake, Jacob Cawley, Lauren Stahl, Xiaohu Zhang, Rajarshi Guha, Craig Thomas, Kathleen Kelly. Elucidating potential therapeutic targets in a model of Pten/Tp53 null prostate cancer using high-throughput screening technology. [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 LB-281.

Feline Mammary Cancer

Feline mammary carcinoma (FMC) is similar to human breast cancer in the late age of onset, incidence, histopathologic features, biological behavior, and pattern of metastasis. Therefore, FMC has been proposed as a relevant model for aggressive human breast cancer. The goals of this study were to develop a nude mouse model of FMC tumor growth and metastasis and to measure the expression of genes responsible for lymphangiogenesis, angiogenesis, tumor progression, and lymph node metastasis in FMC tissues and cell lines. Two primary FMC tissues were injected subcutaneously, and 6 FMC cell lines were injected into 3 sites (subcutaneous, intratibial, and intracardiac) in nude mice. Tumors and metastases were monitored using bioluminescent imaging and characterized by gross necropsy, radiology, and histopathology. Molecular characterization of invasion and metastasis genes in FMC was conducted using quantitative real-time reverse transcription polymerase chain reaction in 6 primary FMC tissues, 2 subcutaneous FMC xenografts, and 6 FMC cell lines. The histologic appearance of the subcutaneous xenografts resembled the primary tumors. No metastasis was evident following subcutaneous injection of tumor tissues and cell lines, whereas lung, brain, liver, kidney, eye, and bone metastases were confirmed following intratibial and intracardiac injection of FMC cell lines. Finally, 15 genes were differentially expressed in the FMC tissues and cell lines. The highly expressed genes in all samples were PDGFA, PDGFB, PDGFC, FGF2, EGFR, ERBB2, ERBB3, VEGFD, VEGFR3, and MYOF. Three genes ( PDGFD, ANGPT2, and VEGFC) were confirmed to be of stromal origin. This investigation demonstrated the usefulness of nude mouse models of experimental FMC and identified molecular targets of FMC progression and metastasis.

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 B40: Selective suppression of Myc transcription with a G-quadruplex stabilizing small molecule

The transcription factor Myc is disregulated in some 70% of human cancers, where it triggers aberrant growth and signaling, and contributes to tumorigenesis. Thus, Myc is a highly sought after drug target. However, targeting the Myc protein directly with small molecules has proven to be a significant challenge due to a lack of small molecule binding sites and rapid protein turnover in the cell. To date, most successes in inhibiting Myc function have come through alternative indirect approaches such as BET bromodomain inhibition. Here, we present a novel class of small molecules that silences Myc expression by stabilization of the G-quadruplex structure present in the NHEIII region of the Myc promoter. We used a small molecule microarray screen to identify molecules that selectively bind to the Myc G-quadruplex. Biophysical studies, including thermal melt and SPR analysis, demonstrated that the compound binds reversibly to the quadruplex structure with low micromolar affinity. Next, we demonstrated that the compound inhibited polymerase progression in an in vitro PCR-stop assay in a dose dependent fashion, while the compound had no effect on amplification of an oligo incapable of forming a quadruplex. Target specificity was demonstrated using a cell-based assay where one copy of the Myc gene has a translocation and is no longer under the control of a quadruplex. In this assay, Myc is only silenced upon treatment when there is a quadruplex in the promoter. Further studies demonstrate dose- and time-dependent effects on cell viability and Myc protein levels in a panel of myeloma cells. The compound also had minimal effects on viability of PBMCs from a healthy donor. Finally, gene expression analysis demonstrated that in contrast to other quadruplex-stabilizing small molecules, the compound reported here does not silence several other genes that are also under the control of quadruplexes.

Citation Format: John K. Simmons, Lindsey B. Saunders, Kenneth Felsenstein, Peter Gareiss, Shuling Zhang, Beverly Mock, John S. Schneekloth, Jr.. Selective suppression of Myc transcription with a G-quadruplex stabilizing small molecule. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr B40.

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.

Animal Models of Bone Metastasis

Bone is one of the most common sites of cancer metastasis in humans and is a significant source of morbidity and mortality. Bone metastases are considered incurable and result in pain, pathologic fracture, and decreased quality of life. Animal models of skeletal metastases are essential to improve the understanding of the molecular pathways of cancer metastasis and growth in bone and to develop new therapies to inhibit and prevent bone metastases. The ideal animal model should be clinically relevant, reproducible, and representative of human disease. Currently, an ideal model does not exist; however, understanding the strengths and weaknesses of the available models will lead to proper study design and successful cancer research. This review provides an overview of the current in vivo animal models used in the study of skeletal metastases or local tumor invasion into bone and focuses on mammary and prostate cancer, lymphoma, multiple myeloma, head and neck squamous cell carcinoma, and miscellaneous tumors that metastasize to bone.

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

Abstract 5472: Systems pharmacogenomics approach identifies synergistic molecular action of combined MTOR/HDAC inhibition on MYC

Multiple myeloma (MM) and murine plasmacytoma (PCT) are rare mature B-lymphoid malignancies. Allelic variants of Mtor and Cdkn2a affect susceptibility to PCT, and functional alterations in the PI3K/MTOR and CYCLIN/CDK/CDKI/RB (RB) pathways are common to both malignancies. 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 in vitro, effective in limiting xenograft growth in vivo, and diminished cellular viability in ex vivo patient samples. Similarly, the combination reduced tumor burden and volume and increased survival in a long-term, in-vivo study in C.B6-Bcl2l1 mice. To examine the core synergistic consequence of combining entinostat with sirolimus, an integrated, systems-level approach was used. Weighted gene co-expression analysis (WGCNA) of GEP data from MM cells treated individually and in combination was used to identify a distinct module of 126 genes cooperatively affected by both drugs. Of the cooperatively affected genes, 37 were found to be differentially expressed in MM and predictive of survival (p&lt;0.01). Ingenuity upstream analysis identified MYC as a potential core regulator of the synergistic transcriptional response. MYC protein, but not mRNA, decreased in response to the drug combination when examined by Western blot and NanoString analyses, respectively. Using tet-off, MYC-inducible transformed P493 cells, the necessity of MYC for the drop in cellular viability and response of the gene signature to the combination was evident. Using the translational and proteasomal inhibitors, cycloheximide and MG132, respectively, it was determined that MYC protein half-life decreased with the combination, largely due to proteasomal degradation. Utilizing a systems-level approach and biological filters, an alternative route to MYC inhibition was determined. Biologically relevant, this methodology can be used to define the molecular underpinnings of drug combinations, applicable to many diseases.

Citation Format: Benjamin J. Gamache, John K. Simmons, Aleksandra Michalowski, Jyoti Patel, Ke Zhang, Shuling Zhang, Wendy DuBois, Adriana Zingone, Michael Kuehl, Jing Huang, Ola Landgren, Beverly Mock. Systems pharmacogenomics approach identifies synergistic molecular action of combined MTOR/HDAC inhibition on MYC. [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 5472. doi:10.1158/1538-7445.AM2014-5472

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.

Combined zoledronic acid and meloxicam reduced bone loss and tumour growth in an orthotopic mouse model of bone-invasive oral squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) is common in cats and humans and invades oral bone. We hypothesized that the cyclooxygenase (COX)-2 inhibitor, meloxicam, with the bisphosphonate, zoledronic acid (ZOL), would inhibit tumour growth, osteolysis and invasion in feline OSCC xenografts in mice. Human and feline OSCC cell lines expressed COX-1 and COX-2 and the SCCF2 cells had increased COX-2 mRNA expression with bone conditioned medium. Luciferase-expressing feline SCCF2Luc cells were injected beneath the perimaxillary gingiva and mice were treated with 0.1 mg kg(-1) ZOL twice weekly, 0.3 mg kg(-1) meloxicam daily, combined ZOL and meloxicam, or vehicle. ZOL inhibited osteoclastic bone resorption at the tumour-bone interface. Meloxicam was more effective than ZOL at reducing xenograft growth but did not affect osteoclastic bone resorption. Although a synergistic effect of combined ZOL and meloxicam was not observed, combination therapy was well-tolerated and may be useful in the clinical management of bone-invasive feline OSCC.

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

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.

Loss of tumor progression locus 2 (tpl2) enhances tumorigenesis and inflammation in two-stage skin carcinogenesis

Tumor progression locus 2 (Tpl2) is a serine/threonine kinase in the mitogen-activated protein kinase signal transduction cascade known to regulate inflammatory pathways. Previously identified as an oncogene, its mutation or overexpression is reported in a variety of human cancers. To address its role in skin carcinogenesis, Tpl2(-/-) or wild-type (WT) C57BL/6 mice were subjected to a two-stage dimethylbenzanthracene/12-O-tetradecanoylphorbol-13-acetate (TPA) mouse skin carcinogenesis model. Tpl2(-/-) mice developed a significantly higher incidence of tumors (80%) than WT mice (17%), as well as a reduced tumor latency and a significantly higher number of total tumors (113 vs 6). Moreover, Tpl2(-/-) mice treated with TPA experienced significantly higher nuclear factor kappaB (NF-κB) activation, edema, infiltrating neutrophils and production of proinflammatory cytokines than did WT mice. We investigated the role of the p38, JNK, MEK and NF-κB signaling pathways both in vitro and in vivo in WT and Tpl2(-/-) mice by using inhibitors for each of these pathways. We confirmed that the proinflammatory effect in Tpl2(-/-) mice was due to heightened activity of the NF-κB pathway. These studies indicate that Tpl2 may serve more as a tumor suppressor than as an oncogene in chemically induced skin carcinogenesis, with its absence contributing to both tumorigenesis and inflammation.