Pleckstrin Homology [PH] domain, structure, mechanism, and contribution to human disease

The pleckstrin homology [PH] domain is a structural fold found in more than 250 proteins making it the 11th most common domain in the human proteome. 25% of family members have more than one PH domain and some PH domains are split by one, or several other, protein domains although still folding to give functioning PH domains. We review mechanisms of PH domain activity, the role PH domain mutation plays in human disease including cancer, hyperproliferation, neurodegeneration, inflammation, and infection, and discuss pharmacotherapeutic approaches to regulate PH domain activity for the treatment of human disease. Almost half PH domain family members bind phosphatidylinositols [PIs] that attach the host protein to cell membranes where they interact with other membrane proteins to give signaling complexes or cytoskeleton scaffold platforms. A PH domain in its native state may fold over other protein domains thereby preventing substrate access to a catalytic site or binding with other proteins. The resulting autoinhibition can be released by PI binding to the PH domain, or by protein phosphorylation thus providing fine tuning of the cellular control of PH domain protein activity. For many years the PH domain was thought to be undruggable until high-resolution structures of human PH domains allowed structure-based design of novel inhibitors that selectively bind the PH domain. Allosteric inhibitors of the Akt1 PH domain have already been tested in cancer patients and for proteus syndrome, with several other PH domain inhibitors in preclinical development for treatment of other human diseases.

PLEKHA7 signaling is necessary for the growth of mutant KRAS driven colorectal cancer

Plekha7 (Pleckstrin homology [PH] domain containing, family A member 7) regulates the assembly of proteins of the cytoplasmic apical zonula adherens junction (AJ), thus ensuring cell-cell adhesion and tight-junction barrier integrity. Little is known of Plekha7 function in cancer. In colorectal cancer (CRC) Plekha7 expression is elevated compared to adjacent normal tissue levels, increasing with clinical stage. Plekha7 was present at plasma membrane AJ with wild-type KRas (wt-KRas) but was dispersed in cells expressing mutant KRas (mut-KRas). Fluorescence lifetime imaging microscopy (FLIM) indicated a direct Plekha7 interaction with wt-KRas but scantily with mut-KRas. Inhibiting Plekha7 specifically decreased mut-KRas cell signaling, proliferation, attachment, migration, and retarded mut-KRAS CRC tumor growth. Binding of diC8-phosphoinositides (PI) to the PH domain of Plekha7 was relatively low affinity. This may be because a D175 amino acid residue plays a "sentry" role preventing PI(3,4)P₂ and PI(3,4,5)P₃ binding. Molecular or pharmacological inhibition of the Plekha7 PH domain prevented the growth of mut-KRas but not wt-KRas cells. Taken together the studies suggest that Plekha7, in addition to maintaining AJ structure plays a role in mut-KRas signaling and phenotype through interaction of its PH domain with membrane mut-KRas, but not wt-KRas, to increase the efficiency of mut-KRas downstream signaling.

Structural basis for the association of PLEKHA7 with membrane-embedded phosphatidylinositol lipids

PLEKHA7 (pleckstrin homology domain containing family A member 7) plays key roles in intracellular signaling, cytoskeletal organization, and cell adhesion, and is associated with multiple human cancers. The interactions of its pleckstrin homology (PH) domain with membrane phosphatidyl-inositol-phosphate (PIP) lipids are critical for proper cellular localization and function, but little is known about how PLEKHA7 and other PH domains interact with membrane-embedded PIPs. Here we describe the structural basis for recognition of membrane-bound PIPs by PLEHA7. Using X-ray crystallography, nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration calorimetry, we show that the interaction of PLEKHA7 with PIPs is multivalent, distinct from a discrete one-to-one interaction, and induces PIP clustering. Our findings reveal a central role of the membrane assembly in mediating protein-PIP association and provide a roadmap for understanding how the PH domain contributes to the signaling, adhesion, and nanoclustering functions of PLEKHA7.

Abstract PO014: PSGL-1 is an early T cell signaling regulator that drives immunometabolism and terminal differentiation in tumor-specific CD8 T cells

We previously identified that the adhesion molecule P-selectin glycoprotein ligand-1 (PSGL-1) regulates T cell function and exhaustion in responses to chronic viral infection and melanoma tumors. Subsequently, our studies have focused on investigating the mechanisms by which PSGL-1 regulates T cell activation and exhaustion and evaluating PSGL-1 as a target for cancer immunotherapy. Using the CD4cre system in combination with PSGL-1-floxed mice, we find that T cell intrinsic deletion of PSGL-1 is sufficient to promote enhanced tumor growth control of mesothelioma as well as melanoma tumors. We have found that in vivo PSGL-1 blockade recapitulates the enhanced melanoma tumor growth control observed with PSGL-1-/- CD8+ T cells and limits the development of T cell exhaustion during chronic LCMV Clone 13 viral infection. Conversely, ligation of PSGL-1 in vitro or in vivo drives enhanced upregulation T cell exhaustion markers, most notably PD-1 expression. Phosphoproteomic analysis of early T cell activation revealed the rapid upregulation of more than 30 phosphorylated proteins with significantly enhanced expression following PSGL-1 ligation during T cell activation than T cell activation alone. GSEA and western blot analysis confirmed the increased expression of several regulators of T cell signaling including pAkt1 and pErk in both activated PSGL-1-/- T cells and following PSGL-1 ligation during T cell activation. Single-cell RNA-sequencing of melanoma tumor-specific PSGL-1-/- CD8+ T cells identified differential modulation of genes associated with T cell metabolism and effector responses, including increased Mtor and Hif1a in tumors and Tcf7 in tumor-draining lymph nodes. The Seahorse glycolysis stress test identified that PSGL-1-/- T cells show increased glycolysis after 72 hours of in vitro activation at both sub-optimal and optimal levels of αCD3 stimulation, and 2-NBDG glucose uptake assays confirmed increased glucose uptake by PSGL-1-/- CD8+ T cells within two hours of stimulation. Further, 2-NBDG uptake was increased by PSGL-1-/- CD8+ T cells ex vivo from melanoma tumors. Importantly, this increased glycolytic phenotype does not come at the cost of CD8+ T cell stemness, as determined by TCF-1 staining. We hypothesize that PSGL-1 serves as a key regulator of early T cell activation and repeated signaling through PSGL-1 promotes differentiation into exhausted CD8+ T cells by sustaining TCR signaling. Conversely, we hypothesize that the absence of PSGL-1 allows for faster initiation and termination of TCR signaling, inhibiting differentiation into exhausted CD8+ T cells. Taken together, these data show that PSGL-1 signaling has an intrinsic and immediate role in the development of T cell responses and their metabolic profile which may drive their enhanced responses to tumors.

Citation Format: Jennifer L. Hope, Dennis C. Otero, Eun-ah Bae, Christopher J Stairiker, Ashley B. Palete, Hannah A. Faso, Petrus de Jong, Garth Powis, Linda M. Bradley. PSGL-1 is an early T cell signaling regulator that drives immunometabolism and terminal differentiation in tumor-specific CD8 T cells [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2020 Oct 19-20. Philadelphia (PA): AACR; Cancer Immunol Res 2021;9(2 Suppl):Abstract nr PO014.

A Robust and Cost-Effective Luminescent-Based High-Throughput Assay for Fructose-1,6-Bisphosphate Aldolase A

Hypoxic solid tumors induce the stabilization of hypoxia-inducible factor 1 alpha (HIF1α), which stimulates the expression of many glycolytic enzymes and hypoxia-responsive genes. A high rate of glycolysis supports the energetic and material needs for tumors to grow. Fructose-1,6-bisphosphate aldolase A (ALDOA) is an enzyme in the glycolytic pathway that promotes the expression of HIF1α. Therefore, inhibition of ALDOA activity represents a potential therapeutic approach for a range of cancers by blocking two critical cancer survival mechanisms. Here, we present a luminescence-based strategy to determine ALDOA activity. The assay platform was developed by integrating a previously established ALDOA activity assay with a commercial NAD/NADH detection kit, resulting in a significant (>12-fold) improvement in signal/background (S/B) compared with previous assay platforms. A screening campaign using a mixture-based compound library exhibited excellent statistical parameters of Z' (>0.8) and S/B (~20), confirming its robustness and readiness for high-throughput screening (HTS) application. This assay platform provides a cost-effective method for identifying ALDOA inhibitors using a large-scale HTS campaign.

Immunometabolism regulation by PSGL-1 signaling in tumor-specific CD8 T cells

We previously identified that the adhesion molecule P-selectin glycoprotein ligand-1 (PSGL-1) regulates T cell function and exhaustion in response to chronic viral infection and tumors. Subsequent studies have focused on investigating the role of PSGL-1 signaling in T cell responses, with an emphasis on understanding the mechanisms by which PSGL-1 regulates T cell exhaustion. Single-cell RNA-sequencing of tumor infiltrating PSGL-1−/− CD8+ T cells identified the upregulation and differential modulation of several genes associated with T cell metabolism and enhanced intratumoral responses, including Mtor, Hif1a, and Mki67 in Gzmb/Ifng double-positive cells from tumors and Tcf7 in both tumor draining and non-draining inguinal lymph nodes. These data suggest an important role for PSGL-1 signaling in the development and maintenance of effective anti-tumor T cell responses to melanoma. Using the Seahorse glycolysis stress test, we identified that both CD4+ and CD8+ PSGL-1−/− T cells demonstrate increased glycolysis after 72 hours of in vitro activation compared to wild-type T cells. In situ activation of PSGL-1−/− CD8+ T cells demonstrated that PSGL-1−/− CD8+ T cells have increased glycolysis and increased glycolytic capacity at both sub-optimal and optimal levels of α-CD3 stimulation, and 2-NBDG glucose uptake assays confirmed increased glucose uptake by PSGL-1−/− CD8+ T cells within two hours of stimulation. Importantly, this increased glycolytic phenotype does not come at the cost of CD8+ T cell stemness, as determined by TCF-1 staining. Taken together, these data show that PSGL-1 signaling has an intrinsic and immediate role in the development of T cell responses and their metabolic profile in response to melanoma tumors.

Absence of HIF1A Leads to Glycogen Accumulation and an Inflammatory Response That Enables Pancreatic Tumor Growth

Cancer cells respond to hypoxia by upregulating the hypoxia-inducible factor 1α (HIF1A) transcription factor, which drives survival mechanisms that include metabolic adaptation and induction of angiogenesis by VEGF. Pancreatic tumors are poorly vascularized and severely hypoxic. To study the angiogenic role of HIF1A, and specifically probe whether tumors are able to use alternative pathways in its absence, we created a xenograft mouse tumor model of pancreatic cancer lacking HIF1A. After an initial delay of about 30 days, the HIF1A-deficient tumors grew as rapidly as the wild-type tumors and had similar vascularization. These changes were maintained in subsequent passages of tumor xenografts in vivo and in cell lines ex vivo. There were many cancer cells with a "clear-cell" phenotype in the HIF1A-deficient tumors; this was the result of accumulation of glycogen. Single-cell RNA sequencing (scRNA-seq) of the tumors identified hypoxic cancer cells with inhibited glycogen breakdown, which promoted glycogen accumulation and the secretion of inflammatory cytokines, including interleukins 1β (IL1B) and 8 (IL8). scRNA-seq of the mouse tumor stroma showed enrichment of two subsets of myeloid dendritic cells (cDC), cDC1 and cDC2, that secreted proangiogenic cytokines. These results suggest that glycogen accumulation associated with a clear-cell phenotype in hypoxic cancer cells lacking HIF1A can initiate an alternate pathway of cytokine and DC-driven angiogenesis. Inhibiting glycogen accumulation may provide a treatment for cancers with the clear-cell phenotype. SIGNIFICANCE: These findings establish a novel mechanism by which tumors support angiogenesis in an HIF1α-independent manner.

Fluorescent probes towards selective cathepsin B detection and visualization in cancer cells and patient samples

Highly selective fluorescent activity-based probe for the visualization of cathepsin B in cancer cells.

Human cysteine cathepsins constitute an 11-membered family of proteases responsible for degradation of proteins in cellular endosomal–lysosomal compartments as such, they play important roles in antigen processing, cellular stress signaling, autophagy, and senescence. Moreover, for many years these enzymes were also linked to tumor growth, invasion, angiogenesis and metastasis when upregulated. Individual biological roles of each cathepsin are difficult to establish, because of their redundancy and similar substrate specificities. Selective chemical tools that enable imaging of individual cathepsin activities in living cells, tumors, and the tumor microenvironment may provide a better insight into their functions. In this work, we used HyCoSuL technology to profile the substrate specificity of human cathepsin B. The use of unnatural amino acids in the substrate library enabled us to uncover the broad cathepsin B preferences that we utilized to design highly-selective substrates and fluorescent activity-based probes (ABPs). We further demonstrated that Cy5-labeled MP-CB-2 probe can selectively label cathepsin B in eighteen cancer cell lines tested, making this ABP highly suitable for other biological setups. Moreover, using Cy5-labelled MP-CB-2 we were able to demonstrate by fluorescence microscopy that in cancer cells cathepsins B and L share overlapping, but not identical subcellular localization.

Abstract 3550: microRNA-211 promotes aggressive melanoma growth in vivo by epigenetic modification, and contributes to BRAFV600E inhibitor resistance via ERK5 signaling

The microRNA miR-211 is an established participant in melanomagenesis, but controversy exists as to whether it acts as a bone fide tumor suppressor or oncogene. Here we ectopically expressed miR-211 in the BRAF v600E-mutant A375 melanoma cell line and examined its effect in xenografts in vivo. The miR-211 ectopic expression promoted aggressive tumor xenograft growth with extensive cell proliferation, and angiogenesis. ChIP-seq and single cell sequencing analysis of xenograft tissues demonstrated that aggressive tumor formation is partly associated with H3K27me3 and H3K4me3, and migration of cells from mouse tissues to tumor locus. Interrogation of xenograft transcriptomics data revealed activation of the ERK5 pathway, itself negatively regulated by miR-211 target genes, BIRC2 and DUSP6, further confirmed as direct miR-211 target genes by RNA immunopurification with RNA-seq (RIP-seq) and site-directed mutagenesis. miR-211 conferred resistance to the BRAF inhibitor vemurafenib, and MEK inhibitor cobimetinib with corresponding increases in ERK5 phosphorylation. The miR-211-ERK5 axis may represent a novel therapeutic target, but however, miR-211 is exquisitely pleiotropic in the complex in vivo tumor environment and its context must be considered carefully in diagnostic and therapeutic development.

Citation Format: Bongyong Lee, Anupama Sahoo, Junko Sawada, Dimitrios G. Zisoulis, John Marchica, Sanjay Sahoo, Fabiana I Alves De Lima Layng, Darren Finlay, Joseph Mazar, Piyush Joshi, Masanobu Komatsu, Kristiina Vuori, Garth Powis, Petrus R. de Jong, Animesh Ray, Ranjan J. Perera. microRNA-211 promotes aggressive melanoma growth in vivo by epigenetic modification, and contributes to BRAFV600E inhibitor resistance via ERK5 signaling [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 3550.

Intrinsic Alteration of Differentiation and Glycolysis in T Lymphocytes Immediately After TCR Activation Through PSGL-1 Signaling

P-selectin glycoprotein ligand-1 (PSGL-1) is an adhesion molecule expressed on the surface of naïve, effector, and memory CD4+ and CD8+ T cells. We identified PSGL-1 to be an immune checkpoint inhibitor as antibody-mediated ligation of PSGL-1 promotes T cell exhaustion and deletion of PSGL-1 prevents chronic viral infection and inhibits tumor. To investigate the role of PSGL-1 signaling in the development of T cell responses, we assessed the differentiation state, expansion capacity, and glycolytic profile of PSGL-1-deficient T cells. PSGL-1+/− OT-II CD4+ T cells demonstrated increased skewing towards IL-17A+ T cells compared to wild-type OT-II CD4+ T cells under TH17 conditions, and reduced IFNg+ cells under both TH0 and TH1 conditions. In a B16-OVA tumor model, we observed increased IL-13+ CD4+ T cells among the intratumoral T cell compartment in PSGL-1−/− mice. In vitro activation with a sub-optimal dose of αCD3 of PSGL-1−/− OT-II CD4+ T cells demonstrated increased expansion and expression of CD25 compared to wild-type OT-II CD4+ T cells. Further, adoptively transferred in vitro-activated PSGL-1−/− CD4+ T cells demonstrated greater expansion in vivo upon adoptive transfer into RAG−/− host mice. Using the Seahorse glycolysis stress test, we identified that both CD4+ and CD8+ PSGL-1−/− T cells demonstrate increased glycolysis after 72 hours of in vitro activation compared to wild-type T cells. Further, in situ activation of PSGL-1−/− CD8+ T cells demonstrates that at both sub-optimal and optimal levels of αCD3 stimulation, PSGL-1−/− CD8+T cells have increased glycolysis and increased glycolytic capacity. Taken together, these data show that PSGL-1 signaling has an intrinsic and immediate role in the development of T cell responses.

An Inhibitor of the Pleckstrin Homology Domain of CNK1 Selectively Blocks the Growth of Mutant KRAS Cells and Tumors

Cnk1 (connector enhancer of kinase suppressor of Ras 1) is a pleckstrin homology (PH) domain-containing scaffold protein that increases the efficiency of Ras signaling pathways, imparting efficiency and specificity to the response of cell proliferation, survival, and migration. Mutated KRAS (mut-KRAS) is the most common proto-oncogenic event, occurring in approximately 25% of human cancers and has no effective treatment. In this study, we show that selective inhibition of Cnk1 blocks growth and Raf/Mek/Erk, Rho and RalA/B signaling in mut-KRAS lung and colon cancer cells with little effect on wild-type (wt)-KRAS cells. Cnk1 inhibition decreased anchorage-independent mut-KRas cell growth more so than growth on plastic, without the partial "addiction" to mut-KRAS seen on plastic. The PH domain of Cnk1 bound with greater affinity to PtdIns(4,5)P2 than PtdIns(3,4,5)P3, and Cnk1 localized to areas of the plasma membranes rich in PtdIns, suggesting a role for the PH domain in the biological activity of Cnk1. Through molecular modeling and structural modification, we identified a compound PHT-7.3 that bound selectively to the PH domain of Cnk1, preventing plasma membrane colocalization with mut-KRas. PHT-7.3 inhibited mut-KRas, but not wild-type KRas cancer cell and tumor growth and signaling. Thus, the PH domain of Cnk1 is a druggable target whose inhibition selectively blocks mutant KRas activation, making Cnk1 an attractive therapeutic target in patients with mut-KRAS-driven cancer. SIGNIFICANCE: These findings identify a therapeutic strategy to selectively block oncogenic KRas activity through the PH domain of Cnk1, which reduces its cell membrane binding, decreasing the efficiency of Ras signaling and tumor growth.

Abstract 2428: Redox regulation of β-catenin in colorectal cancer

Colorectal cancer (CRC) is the second most newly diagnosed cancer in the United States. β-catenin is the downstream effector of the Wnt/β-catenin signaling pathway. Loss of function (LOF) mutations on adenomatous polyposis coli (APC), a critical member of the β-catenin degradation complex leads to constitutively elevated β-catenin as an early oncogenic event in 85% of CRCs and is associated with decreased CRC patient survival. Increased level of β-catenin augments the nuclear accumulation of β-catenin, where it acts a co-activator of a number of transcription factors leading to the expression of downstream target genes that promote cancer cell proliferation, survival, and migration. There is no effective therapy for β-catenin as a cause of cancer. In addition to CRC, elevated levels of Wnt signaling have been reported in leukemia, melanoma, and breast cancers highlighting the need for novel therapies that attenuate aberrant β-catenin mediated transcription. Here we report on the redox dependency of the Wnt/β-catenin signaling pathway, identified through a forward genetic screen in Drosophila, and identify thioredoxin reductase-1 (TXNR1) as a potential target for the inhibition of aberrant β-catenin transcriptional activity through in vivo studies with the APCmin/+ mouse model. Drosophila harboring a mutation in their thioredoxin reductase (trxr-1) gene and a partial lethality phenotype were used in an enhancer/suppressor forward genetic screen. Increased lethality was observed when the trxr-1 mutation (trxr-1481) was combined with heterozygous mutations and deletions in wnt2, while wnt2 deletion and mutations alone had no effect on lethality. To test the translational value of these findings, APCmin/+ mice were treated with PX-12, a human TXNR1 inhibitor, daily by gavage from day 40 to time of death. We observed a dose dependent reduction in the number and size of intestinal polyps by PX-12 treatment, and an increased survival in treated mice. Furthermore, mechanistic studies utilizing human CRC cell lines harboring LOF mutations to the β-catenin degradation complex revealed β-Catenin mediated transcription, as measured by TOP Flash luciferase assay, was diminished when TXNR1 was silenced by siRNA. Additionally, we observed decreased β-catenin protein level in CRC cell lines treated with PX-12 or siRNA targeting TXNRD1 and its functional partner thioredoxin (TXN). The addition of the pan caspase inhibitor ZVAD but not the proteasome inhibitor MG132 was able to stabilize β-catenin protein upon treatment with PX-12 suggesting β-catenin destabilization is occurring via a caspase dependent mechanism. These results suggest a conserved mechanism for the redox regulation of β-catenin involving TXNR1; furthermore, inhibition of TXNR1 activity destabilizes β-catenin protein and decreases β-catenin mediated transcription in human CRC cell lines and inhibits intestinal neoplasia development in an experimental mouse model for CRC.

Citation Format: Alejandro D. Campos, Brian James, Petrus De Jong, Robert Lemos, Nikolas Marino, Garth Powis. Redox regulation of β-catenin in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2428.

Abstract 2916: Targeting lysophospholipid metabolism inhibits pancreatic cancer cell proliferation under nutrient-limiting conditions

Patients with pancreatic ductal adenocarcinoma (PDAC) have a poor prognosis, and more effective systemic treatments for patients with local progression or metastasis (85% of cases) are needed. The pancreatic tumor microenvironment provides a rich source for novel drug targets. We aimed to identify and validate novel metabolic drug targets that are unique to hypoxic PDAC cells. Using bulk RNA sequencing in combination with metabolomics analyses in vitro, we previously found that PDAC cells negate the loss of intracellular unsaturated fatty acids in hypoxia by orchestrating the release of lysophospholipids (lyso-PLs) by cancer-associated fibroblasts, which are then taken up and stored in intracellular lipid droplets in hypoxic cancer cells. To confirm the relevance of these findings in vivo, we performed 3' droplet based single-cell RNA sequencing (scRNA-seq) combined with metabolomics analyses of intracellular and extracellular (tumor interstitial fluid) metabolites of MIAPaCa2 and patient-derived xenografts (PDX). Identification of cell lineages and subpopulations with hypoxic gene signatures was performed to correlate changes in metabolite levels with metabolic gene expression in vivo. This approach confirmed differential expression of lipid droplet-associated enzymes in hypoxic areas of the tumor, including lyso-PL acyl transferases (LPCAT1, LPCAT3), and phospholipases (LYPLA1, PLA2G15). We found that resistance of PDAC cell lines to pharmacologic treatment with inhibitors of fatty acid desaturases (FADS), reminiscent of hypoxia and nutrient starvation in vivo, was mediated by uptake of lyso-PLs from the medium. Importantly, genetic knockdown of LPCAT and LYPLA isoforms reversed the resistance to FADS inhibitors in culture in vitro and in vivo. Clinical relevance was demonstrated by mRNA expression analysis of PDAC patients from The Cancer Genome Atlas (TCGA) database, which showed that the expression of lyso-PL metabolizing genes is correlated with a significant worse prognosis (log-rank test, P=0.008). We are currently developing pharmacologic approaches to target LPCAT and LYPLA enzymes in hypoxic cancer cells as a novel approach for PDAC patients with unresectable disease.

Citation Format: Petrus R. de Jong, Marco Maruggi, Alejandro D. Campos, Morgan A. Brand, Robert Lemos, David A. Scott, Sally A. Litherland, J. Pablo Arnoletti, Brian P. James, Garth Powis. Targeting lysophospholipid metabolism inhibits pancreatic cancer cell proliferation under nutrient-limiting conditions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2916.

Recent Advances in the Development of Anticancer Drugs that Act against Signalling Pathways

Cancer can be considered a disease of deranged intracellular signalling. The intracellular signalling pathways that mediate the effects of oncogenes on cell growth and transformation present attractive targets for the development of new classes of drugs for the prevention and treatment of cancer. This is a new approach to developing anticancer drugs and the potential, as well as some of the problems, inherent in the approach are discussed. Anticancer drugs that produce their effects by disrupting signalling pathways are already in clinical trial. Some properties of these drugs, as well as other inhibitors of signalling pathways under development as potential anticancer drugs, are reviewed.

A Fluorescence-Based High-Throughput Assay for the Identification of Anticancer Reagents Targeting Fructose-1,6-Bisphosphate Aldolase

A high rate of glycolysis, which supplies energy and materials for anabolism, is observed in a wide range of tumor cells, making it a potential pathway to control cancer growth. ALDOA is a multifunctional enzyme in the glycolytic pathway and also promotes HIF-1α, which is of importance in hypoxic solid tumors. The current method for assaying ALDOA activity involves monitoring the consumption of NADH in vitro using absorbance or intrinsic fluorescence via a coupled enzymatic reaction. Here, we report the development of a homogeneous biochemical assay that can overcome limitations of current methods, in particular for the application of high-throughput drug screening. The assay utilizes the commercially available Elite NADH Assay Kit, which incorporates an enzymatic reaction to measure the level of NADH using a fluorescent probe. Assay optimization and validation are discussed. Its feasibility for high-throughput screening (HTS) was demonstrated by screening 65,000 compounds for the identification of small molecules that inhibit ALDOA. Through a validation screen and dose-response evaluation, four inhibitors with IC₅₀ below 10 µM were identified. In conclusion, we demonstrate that a traditional ALDOA assay can be transformed readily into a fluorescence-based assay utilizing a commercial NADH detection kit that is rapid, sensitive, inexpensive, and HTS friendly.

Abstract 2967: Pancreatic cancer cell growth requires lipids released by tumor-induced stroma autophagy

Pancreatic ductal adenocarcinoma (PDAC) is non-resectable in the majority of patients and highly resistant to chemotherapy, resulting in a poor survival. The tumor microenvironment and hypoxia are important modifiers of cancer progression in PDAC. Understanding the metabolic vulnerabilities of PDAC in the harsh tumor microenvironment may lead to novel therapeutic approaches with improved clinical efficacy. First, we found that PDAC cells showed beneficial effects of co-cultured stroma cells, but only under lipid-free serum conditions. To study the metabolic crosstalk between cancer cells and stroma in more detail, we performed an untargeted metabolomic screen of PDAC cells and fibroblasts co-cultured in normoxia and hypoxia, and performed RNA-seq profiling in parallel. We found that stromal cells are metabolically more responsive to co-culture than cancer cells. PDAC cells induce catabolic carbohydrate and protein metabolism in stromal cells, particularly in hypoxia. In contrast, 13C-based metabolic flux assays demonstrated that stromal cells display enhanced anabolic lipid metabolism in co-culture with PDAC cells. Furthermore, de novo synthesized 13C-labeled fatty acids in stromal cells were taken up by PDAC cells. In particular, PDAC cells showed extensive scavenging of lysophospholipids (lyso-PLs) from the culture medium, which was increased in co-culture under hypoxic conditions. These data were confirmed by analyzing portal vein plasma samples isolated from pancreatic cancer patients before and after surgery. In addition, we found metabolites and expression levels of metabolic enzymes from the glycerophospholipid pathway to be enriched in PDAC cells in co-culture and hypoxia. By using fibroblasts, human pancreatic stellate cells and patient-derived cancer-associated fibroblasts (CAFs), we demonstrate direct transfer of lyso-PLs from stromal to PDAC cells via lipid droplets. The transfer of lyso-PLs was abrogated by pharmacological inhibitors of autophagy, or by siRNA-mediated knockdown of autophagy genes in stromal and tumor cells. These data suggest that PDAC cells cause stroma cells to undergo autophagy, and reprogram stroma metabolism to obtain complex lipid species for their metabolic needs in the lipid-starved tumor microenvironment.

Citation Format: Petrus R. De Jong, Sean-Luc Shanahan, Morgan A. Brand, Alejandro D. Campos, Anagha Srirangam, Nikolas Marino, Claudia P. Miller, Olga Zagnitko, Adam D. Richardson, David A. Scott, Brian P. James, Andrew P. Hodges, Ally Perlina, Alexey M. Eroshin, Randall French, Malene Hansen, Sally A. Litherland, Andrew M. Lowy, J. Pablo Arnoletti, Garth Powis. Pancreatic cancer cell growth requires lipids released by tumor-induced stroma autophagy [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 2967. doi:10.1158/1538-7445.AM2017-2967

Modeling of Patient-Derived Xenografts in Colorectal Cancer

Developing realistic preclinical models using clinical samples that mirror complex tumor biology and behavior are vital to advancing cancer research. While cell line cultures have been helpful in generating preclinical data, the genetic divergence between these and corresponding primary tumors has limited clinical translation. Conversely, patient-derived xenografts (PDX) in colorectal cancer are highly representative of the genetic and phenotypic heterogeneity in the original tumor. Coupled with high-throughput analyses and bioinformatics, these PDXs represent robust preclinical tools for biomarkers, therapeutic target, and drug discovery. Successful PDX engraftment is hypothesized to be related to a series of anecdotal variables namely, tissue source, cancer stage, tumor grade, acquisition strategy, time to implantation, exposure to prior systemic therapy, and genomic heterogeneity of tumors. Although these factors at large can influence practices and patterns related to xenotransplantation, their relative significance in determining the success of establishing PDXs is uncertain. Accordingly, we systematically examined the predictive ability of these factors in establishing PDXs using 90 colorectal cancer patient specimens that were subcutaneously implanted into immunodeficient mice. Fifty (56%) PDXs were successfully established. Multivariate analyses showed tissue acquisition strategy [surgery 72.0% (95% confidence interval (CI): 58.2-82.6) vs. biopsy 35% (95% CI: 22.1%-50.6%)] to be the key determinant for successful PDX engraftment. These findings contrast with current empiricism in generating PDXs and can serve to simplify or liberalize PDX modeling protocols. Better understanding the relative impact of these factors on efficiency of PDX formation will allow for pervasive integration of these models in care of colorectal cancer patients. Mol Cancer Ther; 16(7); 1435-42. ©2017 AACR.

Clinically Evaluated Cancer Drugs Inhibiting Redox Signaling

SIGNIFICANCE

There are a number of redox-active anticancer agents currently in development based on the premise that altered redox homeostasis is necessary for cancer cell's survival. Recent Advances: This review focuses on the relatively few agents that target cellular redox homeostasis to have entered clinical trial as anticancer drugs.

CRITICAL ISSUES

The success rate of redox anticancer drugs has been disappointing compared to other classes of anticancer agents. This is due, in part, to our incomplete understanding of the functions of the redox targets in normal and cancer tissues, leading to off-target toxicities and low therapeutic indexes of the drugs. The field also lags behind in the use biomarkers and other means to select patients who are most likely to respond to redox-targeted therapy.

FUTURE DIRECTIONS

If we wish to derive clinical benefit from agents that attack redox targets, then the future will require a more sophisticated understanding of the role of redox targets in cancer and the increased application of personalized medicine principles for their use. Antioxid. Redox Signal. 26, 262-273.

Abstract A10: Redox regulation of the Wnt/β-catenin pathway in colorectal cancer

Colorectal cancer (CRC) is the third most newly diagnosed cancer, and the third most frequent cause of cancer related death in the United States. Thus, there is an urgent unmet need for the development of new therapies for the treatment of CRC. Loss of function mutations in adenomatous polyposis coli (APC), a critical member of the β-catenin destruction complex, lead to elevated protein levels of β-Catenin, and are found in 85% of CRCs, where they are associated with decreased CRC patient survival. Increased levels of β-catenin protein augment the nuclear accumulation of β-catenin where it interacts with transcription factors to induce transcription of target genes promoting cell proliferation, survival, and migration. Currently, there is still no effective therapy targeting aberrant β-catenin transcriptional activity. Here we report on the redox dependency of the Wnt/β-catenin signaling pathway, identified through a forward genetic screen in Drosophila, and identify TxnR1 as a potential target for the inhibition of aberrant β-catenin transcriptional activity through in vivo studies with the APCmin/+ mouse model. Drosophila harboring a mutation in the thioredoxin reductase (txnr1) gene that have a partial lethality phenotype were used in an enhancer/suppressor forward genetic screen. Increased lethality was observed when the txnr1 mutation (Txnr1481) was combined with heterozygous mutations and deletions in dwnt2, while dwnt2 deletion and mutations alone had no effect (on lethality). In addition, β-Catenin mediated transcription, as measured by TOP Flash luciferase assay, was diminished when TxnR1 was silenced by siRNA. To test the translational value of these findings, APCmin/+ mice were treated with PX-12, a human TxnR1 inhibitor, daily by gavage from day 40 to time of death. We observed a dose dependent reduction in the number and size of intestinal polyps by PX-12 treatment, and an increased survival in treated mice. Also, human colorectal cancer cell lines treated with PX-12 displayed attenuated phosphorylation of β-catenin serine residues 552 and 675. These results suggest a conserved mechanism for the redox regulation of the Wnt/β-catenin pathway involving TxnR1; furthermore, inhibition of TxnR1 can inhibit intestinal neoplasia development in an experimental model of CRC.

Citation Format: Alex Campos, Brian James, Petrus De Jong, Garth Powis. Redox regulation of the Wnt/β-catenin pathway in colorectal cancer. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Targeting the Vulnerabilities of Cancer; May 16-19, 2016; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(1_Suppl):Abstract nr A10.

Abstract A25: Pancreatic cancer cells scavenge complex lipids from stroma in the hypoxic tumor microenvironment

Pancreatic ductal adenocarcinoma (PDAC) is non-resectable in 85% of cases and highly resistant to chemotherapy, resulting in a poor 5-year survival (5-7%). Understanding the metabolic vulnerabilities of PDAC in the harsh tumor microenvironment (TME) may lead to novel therapeutic approaches with improved clinical efficacy. The pancreatic TME is characterized by widespread desmoplasia represented by alpha-smooth muscle actin-positive fibroblasts, pancreatic stellate cells and extracellular matrix components, among others. Up to 90% of the pancreatic tumor mass consists of non-neoplastic cells, and high interstitial pressures and poor perfusion both result in severe hypoxia, leading to a more malignant PDAC phenotype. We hypothesized that these conditions lead to specific metabolic constrains in oncogene-driven, rapidly proliferating PDAC cells that experience high levels of stress, in contrast to the surrounding quiescent stromal cells. We used co-culturing of PDAC (MIAPaCa2) and stromal (NIH/3T3) cells in transwell systems as a robust and reproducible model of cell contact-independent interactions in the pancreatic TME. A commercial metabolic profiling platform (Metabolon) and 13C-based flux assays were used to study changes in metabolite levels in both cell types in normoxia or hypoxia (1% O2). We found that hypoxia induced similar metabolic changes in the PDAC and stromal cells, suggesting that hypoxia-regulated metabolic rewiring is independent of cell-type. Interestingly, the metabolic effects of co-culturing were predominantly observed in the stromal compartment, e.g. enhanced glycogenolysis, metabolite changes indicative of gluconeogenesis, and increased dipeptide levels, all reminiscent of a ‘starvation’ phenotype. In contrast, the tumor cells maintained a mixed anabolic and catabolic phenotype, as shown by elevated intracellular levels of essential amino acids and ribonucleotide triphosphates, representative of a ‘feeding’ phenotype. Importantly, a unique dependence on complex lipid species was observed in cancer cells with reciprocal changes in stromal cells. These data suggest that pancreatic cancer cells reprogram stromal cells to ‘feed off’ the metabolic capacity of non-neoplastic cells in the tumor microenvironment, thereby inducing the release of diffusable metabolites to satisfy their specific catabolic needs.

Citation Format: Petrus R. de Jong, Alejandro D. Campos, Sean-Luc Shanahan, Adam Richardson, Garth Powis.{Authors}. Pancreatic cancer cells scavenge complex lipids from stroma in the hypoxic tumor microenvironment. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr A25.

Definition of a Novel Feed-Forward Mechanism for Glycolysis-HIF1α Signaling in Hypoxic Tumors Highlights Aldolase A as a Therapeutic Target

The hypoxia-inducible transcription factor HIF1α drives expression of many glycolytic enzymes. Here, we show that hypoxic glycolysis, in turn, increases HIF1α transcriptional activity and stimulates tumor growth, revealing a novel feed-forward mechanism of glycolysis-HIF1α signaling. Negative regulation of HIF1α by AMPK1 is bypassed in hypoxic cells, due to ATP elevation by increased glycolysis, thereby preventing phosphorylation and inactivation of the HIF1α transcriptional coactivator p300. Notably, of the HIF1α-activated glycolytic enzymes we evaluated by gene silencing, aldolase A (ALDOA) blockade produced the most robust decrease in glycolysis, HIF-1 activity, and cancer cell proliferation. Furthermore, either RNAi-mediated silencing of ALDOA or systemic treatment with a specific small-molecule inhibitor of aldolase A was sufficient to increase overall survival in a xenograft model of metastatic breast cancer. In establishing a novel glycolysis-HIF-1α feed-forward mechanism in hypoxic tumor cells, our results also provide a preclinical rationale to develop aldolase A inhibitors as a generalized strategy to treat intractable hypoxic cancer cells found widely in most solid tumors. Cancer Res; 76(14); 4259-69. ©2016 AACR.

A new HIF-1α/RANTES-driven pathway to hepatocellular carcinoma mediated by germline haploinsufficiency of SART1/HAF in mice

The hypoxia-inducible factor (HIF), HIF-1, is a central regulator of the response to low oxygen or inflammatory stress and plays an essential role in survival and function of immune cells. However, the mechanisms regulating nonhypoxic induction of HIF-1 remain unclear. Here, we assess the impact of germline heterozygosity of a novel, oxygen-independent ubiquitin ligase for HIF-1α: hypoxia-associated factor (HAF; encoded by SART1). SART1(-/-) mice were embryonic lethal, whereas male SART1(+/-) mice spontaneously recapitulated key features of nonalcoholic steatohepatitis (NASH)-driven hepatocellular carcinoma (HCC), including steatosis, fibrosis, and inflammatory cytokine production. Male, but not female, SART1(+/-) mice showed significant up-regulation of HIF-1α in circulating and liver-infiltrating immune cells, but not in hepatocytes, before development of malignancy. Additionally, Kupffer cells derived from male, but not female, SART1(+/-) mice produced increased levels of the HIF-1-dependent chemokine, regulated on activation, normal T-cell expressed and secreted (RANTES), compared to wild type. This was associated with increased liver-neutrophilic infiltration, whereas infiltration of lymphocytes and macrophages were not significantly different. Neutralization of circulating RANTES decreased liver neutrophilic infiltration and attenuated HCC tumor initiation/growth in SART1(+/-) mice.

CONCLUSION

This work establishes a new tumor-suppressor role for HAF in immune cell function by preventing inappropriate HIF-1 activation in male mice and identifies RANTES as a novel therapeutic target for NASH and NASH-driven HCC.

Improving gastric cancer preclinical studies using diverse in vitro and in vivo model systems

BACKGROUND

"Biomarker-driven targeted therapy," the practice of tailoring patients' treatment to the expression/activity levels of disease-specific genes/proteins, remains challenging. For example, while the anti-ERBB2 monoclonal antibody, trastuzumab, was first developed using well-characterized, diverse in vitro breast cancer models (and is now a standard adjuvant therapy for ERBB2-positive breast cancer patients), trastuzumab approval for ERBB2-positive gastric cancer was largely based on preclinical studies of a single cell line, NCI-N87. Ensuing clinical trials revealed only modest patient efficacy, and many ERBB2-positive gastric cancer (GC) patients failed to respond at all (i.e., were inherently recalcitrant), or succumbed to acquired resistance.

METHOD

To assess mechanisms underlying GC insensitivity to ERBB2 therapies, we established a diverse panel of GC cells, differing in ERBB2 expression levels, for comprehensive in vitro and in vivo characterization. For higher throughput assays of ERBB2 DNA and protein levels, we compared the concordance of various laboratory quantification methods, including those of in vitro and in vivo genetic anomalies (FISH and SISH) and xenograft protein expression (Western blot vs. IHC), of both cell and xenograft (tissue-sectioned) microarrays.

RESULTS

The biomarker assessment methods strongly agreed, as did correlation between RNA and protein expression. However, although ERBB2 genomic anomalies showed good in vitro vs. in vivo correlation, we observed striking differences in protein expression between cultured cells and mouse xenografts (even within the same GC cell type). Via our unique pathway analysis, we delineated a signaling network, in addition to specific pathways/biological processes, emanating from the ERBB2 signaling cascade, as a potential useful target of clinical treatment. Integrated analysis of public data from gastric tumors revealed frequent (10 - 20 %) amplification of the genes NFKBIE, PTK2, and PIK3CA, each of which resides in an ERBB2-derived subpathway network.

CONCLUSION

Our comprehensive bioinformatics analyses of highly heterogeneous cancer cells, combined with tumor "omics" profiles, can optimally characterize the expression patterns and activity of specific tumor biomarkers. Subsequent in vitro and in vivo validation, of specific disease biomarkers (using multiple methodologies), can improve prediction of patient stratification according to drug response or nonresponse.

HNF4α is a therapeutic target that links AMPK to WNT signalling in early-stage gastric cancer

BACKGROUND

Worldwide, gastric cancer (GC) is the fourth most common malignancy and the most common cancer in East Asia. Development of targeted therapies for this disease has focused on a few known oncogenes but has had limited effects.

OBJECTIVE

To determine oncogenic mechanisms and novel therapeutic targets specific for GC by identifying commonly dysregulated genes from the tumours of both Asian-Pacific and Caucasian patients.

METHODS

We generated transcriptomic profiles of 22 Caucasian GC tumours and their matched non-cancerous samples and performed an integrative analysis across different GC gene expression datasets. We examined the inhibition of commonly overexpressed oncogenes and their constituent signalling pathways by RNAi and/or pharmacological inhibition.

RESULTS

Hepatocyte nuclear factor-4α (HNF4α) upregulation was a key signalling event in gastric tumours from both Caucasian and Asian patients, and HNF4α antagonism was antineoplastic. Perturbation experiments in GC tumour cell lines and xenograft models further demonstrated that HNF4α is downregulated by AMPKα signalling and the AMPK agonist metformin; blockade of HNF4α activity resulted in cyclin downregulation, cell cycle arrest and tumour growth inhibition. HNF4α also regulated WNT signalling through its target gene WNT5A, a potential prognostic marker of diffuse type gastric tumours.

CONCLUSIONS

Our results indicate that HNF4α is a targetable oncoprotein in GC, is regulated by AMPK signalling through AMPKα and resides upstream of WNT signalling. HNF4α may regulate 'metabolic switch' characteristic of a general malignant phenotype and its target WNT5A has potential prognostic values. The AMPKα-HNF4α-WNT5A signalling cascade represents a potentially targetable pathway for drug development.

Abstract C131: ‘KRAS addiction’ an artifact of 2D culture? Inhibitors of the mut-KRAS NSCLC 3D growth

Introduction: KRAS, the predominant form of mutated RAS (mut-KRAS), is found in ∼25% of patient tumors across many cancer types and plays a critical role in driving tumor growth and resistance to therapy. We identified CNKSR1 (connector enhancer of kinase suppressor of Ras 1) to be critical for mut-KRAS but not wild type (wt)-KRAS signaling and cell proliferation. Its product CNK1 is a multi-domain organizer protein found as part of the Ras membrane signaling nanocluster where it binds to mut-KRas although not to wt-KRas, and is necessary for mut-KRas cell growth and signaling. We have exploited the pleckstrin homology (PH)-domain of CNK1 as a target for drug discovery to inhibit mut-KRas. To understand the role of CNK1 as a regulator of KRas cell growth, evaluation of siKRAS and siCNK1 on 2D and 3D growth were evaluated. We also studied the effects of KRAS cell growth conditions on response to selective inhibitors the PH-domain of CNK1 identified using a computational modeling approach.

Results: Using a panel of twelve NSCLC lines and siRNA knockdown of KRAS we found that the reported growth addiction of some cancer cell lines for mut-KRAS, and the resistance of others, is most likely an artifact of 2D culture. Mut-KRAS NSCLC cell lines showing addiction in 2D growth did not show addiction in 3D anchorage independent growth in agarose, where all cell lines were more sensitive. Wt-KRAS cell lines were largely unaffected by siKRAS knockdown. Additionally, the CNK1 inhibitor PHT-7390 IC50s for 2D growth inhibition of a panel of 8 mut-KRAS NSCLC lines ranged from 0.60 to 100 μM (ave 18.7 μM) yet was found to be considerably more potent in 3D culture with IC50s from 0.03 to 2.99 μM (ave 0.69 μM). The most pronounced difference was seen in H2009 and Calu1 mut-KRAS cells where PHT-7390 IC50s in 2D were >100 μM, while 0.093 and 0.35 μM in 3D. Wt-KRas NSCLC growth inhibition (3 lines) was largely unaffected by PHT-7390 under either condition with average IC50s of 68 and 69 μM in 2D and 3D conditions, respectively. Target engagement in 2D has shown these CNK1 inhibitors block mut-KRAS signaling but not that of wt-KRAS.

Conclusion: Variable enhanced growth dependence on mut-KRAS (“addiction”) is seen in 2D but not 3D. Potent and specific inhibition of mut-KRAS cell line growth by CNK1 PH-domain inhibitors is considerably more robust in 3D culture suggesting a novel approach to inhibit mut-KRAS effect on cancer growth.

Citation Format: D. Lynn Kirkpatrick, Roisin Delaney, Geoff Grandjean, Assael Madrigal, Martin Indarte, Mike Scott, Garth Powis. ‘KRAS addiction’ an artifact of 2D culture? Inhibitors of the mut-KRAS NSCLC 3D growth. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C131.

Abstract A2-29: A PDK1 inhibitors that has antitumor activity in a vemurafenib resistant BRAF(V600E)::NRAS(G12V) melanoma PDX

Phosphatidylinositol 3-kinase/phosphatidylinositide-dependent protein kinase 1 (PDPK1)/Akt signaling is activated in many cancers, and is associated with mutational loss of PTEN function, or activation of Phosphatidylinositide-3-kinase (PI3K). Activation of the PDPK1 signaling pathway contributes to proliferation and survival pathways in tumor cells. In a mouse Braf(V600E)::Pten(-/-) melanoma model genetic inactivation of PDKP1 delays the development of pigmented lesions and melanoma. We have found that the PDPK1 inhibitor PHT-427 has antitumor activity in BRAF(V600E)::NRAS(G12V) melanoma patient derived xenografts (PDX) grown in immune deficient mice.

Pleckstrin homology (PH) domains are 100-120 amino acid domains found in more than 250 human proteins that bind phosphatidylinositide (Ptdlns) lipids in cell membranes. The phosphorylation of Ptdins, and the consequent binding of PH domain containing proteins is found in many signal transduction pathways critical for cell growth, survival, angiogenesis, and metastasis. Though the primary amino acid sequences of PH domains are not highly conserved, PH domains do have a highly conserved tertiary structure. This structural conservation of PH domains combined with the role PH domains play in signal transduction make them promising targets for small molecule inhibitors. PHT-427 was designed to bind PH domains, and experiments show that PHT-427 binds with the highest affinity to the PH domain of PDKP1.

We wanted to test the antitumor activity of PHT-427 in human melanoma PDX models of varying genetic background. About 50% of melanoma tumors are driven by the BRAF(V600E) mutation, and these tumors are effectively targeted with BRAF inhibitors, such as vemurafenib. Unfortunately, these tumors usually develop resistance to vemurafenib, and the disease progresses. Additionally, 40-50% of melanoma tumors do not carry the BRAF(V600E) mutation, indicating the need to target additional pathways in melanoma. We sequenced human PDX samples on the Ion Proton sequencer, using the 409 gene Comprehensive Cancer Panel from Life Technologies. Compared to xenografts, PDXs are closer to the tumor biology of the patient, having a higher degree of molecular subtypes and intratumor heterogeneity, and a mixture of human and mouse stroma. The TMAP alignment program that works with Ion Torrent sequence data cannot handle a combined human-mouse reference genome, we developed a set of scripts we call Graft Extraction Out of REcipient Genome (GEORGE). Sequence reads aligned to the hg19 human reference, and mm10 mouse reference are evaluated by GEORGE and assigned to either the human, or mouse genome. In this project, only human assigned reads were used for variant calling. We sequence 14 melanoma samples, and five samples carried BRAF(V600E). We tested the antitumor activity of PHT-427 in four PDX samples with various BRAF and NRAS mutational statuses. We found that PHT-427 had antitumor activity in a vemurafenib resistant BRAF(V600E)::NRAS(G12V) mutant PDX sample.

Citation Format: Brian P. James, Robert Lemos, Jr., Stacey Bagby, Steven Robinson, William Robinson, John Tentler, S. Gail Eckhardt, D. Lynn Kirkpatrick, Garth Powis. A PDK1 inhibitors that has antitumor activity in a vemurafenib resistant BRAF(V600E)::NRAS(G12V) melanoma PDX. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-29.

Phase II Pilot Study of Vemurafenib in Patients With Metastatic BRAF-Mutated Colorectal Cancer

Purpose

BRAF V600E mutation is seen in 5% to 8% of patients with metastatic colorectal cancer (CRC) and is associated with poor prognosis. Vemurafenib, an oral BRAF V600 inhibitor, has pronounced activity in patients with metastatic melanoma, but its activity in patients with BRAF V600E–positive metastatic CRC was unknown.

Patients and Methods

In this multi-institutional, open-label study, patients with metastatic CRC with BRAF V600 mutations were recruited to an expansion cohort at the previously determined maximum-tolerated dose of 960 mg orally twice a day.

Results

Twenty-one patients were enrolled, of whom 20 had received at least one prior metastatic chemotherapy regimen. Grade 3 toxicities included keratoacanthomas, rash, fatigue, and arthralgia. Of the 21 patients treated, one patient had a confirmed partial response (5%; 95% CI, 1% to 24%) and seven other patients had stable disease by RECIST criteria. Median progression-free survival was 2.1 months. Patterns of concurrent mutations, microsatellite instability status, CpG island methylation status, PTEN loss, EGFR expression, and copy number alterations were not associated with clinical benefit. In contrast to prior expectations, concurrent KRAS and NRAS mutations were detected at low allele frequency in a subset of the patients' tumors (median, 0.21% allele frequency) and were apparent mechanisms of acquired resistance in vemurafenib-sensitive patient-derived xenograft models.

Conclusion

In marked contrast to the results seen in patients with BRAF V600E–mutant melanoma, single-agent vemurafenib did not show meaningful clinical activity in patients with BRAF V600E mutant CRC. Combination strategies are now under development and may be informed by the presence of intratumor heterogeneity of KRAS and NRAS mutations.

Abstract 4448: Identification of a small molecule inhibitor of aldolase A for the targeting of hypoxic cancer cells

Cancer cells are critically dependent on glycolysis. Currently, there is no effective pharmacotherapy that exploits this metabolic vulnerability. We have uncovered a feed forward cycle of anaerobic glycolysis and hypoxia-inducible factor-1 (HIF-1). Glycolysis under hypoxic conditions normally maintains high ATP levels, which is driven by transcriptional activity of HIF-1. Glycolysis inhibition results in a cellular energy crisis, i.e. an increased AMP:ATP ratio, leading to AMPK-mediated phosphorylation of the HIF-1 co-activator p300/CBP. This prevents HIF-1 activity, although HIF-1 protein levels are unchanged, abrogating the feed forward cycle. We identified fructose-1,6-bisphosphate aldolase A (ALDOA) as a top glycolytic enzyme target for inhibiting hypoxic cancer cell glycolysis and HIF-1 activity. Our aim was to identify small molecule inhibitors for ALDOA that may yield compounds for further preclinical development. To this end, a primary high-throughput screen (HTS) was performed with 65,936 compounds using a fluorescence-based NADH oxidation aldolase (cell-free) assay. 640 compounds were further tested in a cherry-pick confirmation screen, from which 112 hits underwent concentration-response curve validation in cell-free assays. From these, 4 hits were further tested in cell-based assays by using colorectal, breast and pancreatic cancer cell lines. A lead compound that showed micromolar potency in inhibiting ALDOA, induced cell death under hypoxic conditions with IC50 values ranging between 2 - 8 μM in the cancer cell lines tested. It also inhibited extracellular flux in a real-time glycolysis assay, inhibited extracellular lactate production under hypoxic conditions as a measure of glycolysis, and blocked hypoxia responsive element (HRE) HIF-1 reporter activity but not HIF-1 protein levels. No effect of the lead compound was observed on mitochondrial respiration. Thus, this compound provides a valuable chemical probe for inhibiting glycolysis in cancer cells. Furthermore, the work provides proof-of-concept that targeting glycolysis with a small molecule inhibitor exerts potent antitumor effects in vitro and is currently being tested in preclinical models as a first-in-class oncological agent.

Citation Format: Petrus R. de Jong, Geoffrey V. Grandjean, Ashwini K. Devkota, Eun Jeong Cho, Kevin N. Dalby, Garth Powis. Identification of a small molecule inhibitor of aldolase A for the targeting of hypoxic cancer cells. [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 4448. doi:10.1158/1538-7445.AM2015-4448

Abstract 2583: Refinement of inhibitors of the KRAS-signaling naocluster protein, CNKSR1, that block oncogenic KRAS signaling and growth

Introduction: KRAS, the predominant form of mutated RAS (mut-KRAS), is found in ∼25% of patient tumors across many cancer types and plays a critical role in driving tumor growth and resistance to therapy. CNKSR1 (connector enhancer of kinase suppressor of Ras 1) a protein associated with KRAS in the RAS membrane signaling nanocluster and we have shown it is critical for mut-KRAS but not wild type (wt)-KRAS signaling and cell proliferation. CNKSR1 is a multi-domain protein with a pleckstrin homology (PH) domain, which we have exploited to discover inhibitors that selectively inhibit mut-KRAS tumor growth. The initial leads identified were found to inhibit mut-KRAS signaling and growth of mut-KRAS isogenic NSCLC cell lines (IC50 ∼ 30 μM) and compound refinement provided PHT-7390 and 7391 (IC50 5 to 10 μM). Importantly, they did not block the growth of wt-KRAS cell lines at concentrations up to 100 μM. In mice the agents had antitumor activity againsta mut-KRAS xenograft model and improved the activity of EGFR inhibitors without observable toxicity, but had poor pharmacokinetic properties.Methods: PHusis has used its in silico computational modeling of the PH-domain of CNK1 to optimize its lead inhibitors to improve potency and pharmacokinetic properties. In silico compound refinement has been paired with surface plasmon resonance spectroscopy (SPR) and in vitro cell line screening to provide the latest panel of highly potent CNK1 inhibitors that are moving toward late preclinical development.

Results: A panel of analogues of PHT-7390 and 7391 were synthesized with the aim of improving potency and pharmacokinetic properties. This structural optimization yielded several analogues with up to 100 fold greater potency than PHT-7390 to mut-KRAS NSCLC lines (IC50 10-100 nM) while retaining the differential in effect against wt-KRAS lines without activity up to 100 μM. Target engagement studies have shown that the agents inhibit mut-KRAS signaling in similar fashion as KRAS knockdown with siRNA, confirming on target effects in cells. Pharmacokinetic properties were also improved and agents have moved to clinical candidate selection. Conclusion: Potent and specific inhibitors of CNK1 PH-domain with improved pharmacokinetics have been identified. These novel PH-domain inhibitors now provide a therapeutic potential for patients with oncogenic KRAS for which there is currently no effective therapy.

Citation Format: D. Lynn Kirkpatrick, Martin Indarte, Mike Scott, Assael Madrigal, Geoffrey Grandjean, Garth Powis. Refinement of inhibitors of the KRAS-signaling naocluster protein, CNKSR1, that block oncogenic KRAS signaling and growth. [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 2583. doi:10.1158/1538-7445.AM2015-2583

Acquired mutations in MAPK signaling pathway following initial pharmacological response in BRAF-mutated metastatic colorectal cancer (mCRC)

629

Background: BRAF V600 mutations are associated with inferior survival and limited responses to standard therapies. Blockade of BRAF by vemurafenib generates reflexive activation of EGFR, whose activity can be overcome by concomitant addition of cetuximab. Early-phase clinical trials have demonstrated objective responses with the combination of vemurafenib and cetuximab in patients with BRAFmutmCRC. Mechanisms of resistance following initial anti-tumor response have not yet been described. Methods: Patient-derived xenograft (PDX) models of BRAFmut mCRC have been established at our institution by subcutaneous implantation of tumor into NSG female mice. Here, two different models of BRAFmut mCRC, one with innate sensitivity to vemurafenib and another with innate resistance, were selected for further study. Mice were given vemurafenib chow (417 mg/kg) and/or intraperitoneal cetuximab (1 mg/kg twice a week). Tumor dimensions were serially measured. Tumor resistance developed after a median of 35 days. Tumor DNA was extracted, and whole exome sequencing was performed and compared to untreated controls. Results: In one model of BRAFmut mCRC, 8 mice treated with vemurafenib demonstrated an initial complete response but later developed resistance despite continued treatment. Exome sequencing of the resistant tumors from 6 of 8 mice revealed novel mutations in EGFR, KRAS, NRAS, and MEK not detected in untreated controls (Table). All mutations are predicted to be damaging in COSMIC. Expansion of tumors with acquired NRAS G13D mutation into another generation of mice showed cross-resistance with the combination of BRAF and EGFR inhibition in vivo. In contrast, another PDX model with innate resistance to vemurafenib did not acquire additional mutations in MAPK oncogenes. Conclusions: Acquired activating mutations in oncogenes critical to MAPK signaling have not been described in BRAFmut mCRC after initial pharmacological response. Such mutations, if present as low-frequency clones prior to treatment, may generate resistance following treatment with BRAF and EGFR inhibitors. [Table: see text]

Hypoxia-induced SUMOylation of E3 ligase HAF determines specific activation of HIF2 in clear-cell renal cell carcinoma

Clear-cell renal cell cancer (CRCC) is initiated typically by loss of the tumor-suppressor VHL, driving constitutive activation of hypoxia-inducible factor-1 (HIF1) and HIF2. However, whereas HIF1 has a tumor-suppressor role, HIF2 plays a distinct role in driving CRCC. In this study, we show that the HIF1α E3 ligase hypoxia-associated factor (HAF) complexes with HIF2α at DNA to promote HIF2-dependent transcription through a mechanism relying upon HAF SUMOylation. HAF SUMOylation was induced by hypoxia, whereas HAF-mediated HIF1α degradation was SUMOylation independent. HAF overexpression in mice increased CRCC growth and metastasis. Clinically, HAF overexpression was associated with poor prognosis. Taken together, our results show that HAF is a specific mediator of HIF2 activation that is critical for CRCC development and morbidity.

A pathway-based approach for identifying biomarkers of tumor progression to trastuzumab-resistant breast cancer

Although trastuzumab is a successful targeted therapy for breast cancer patients with tumors expressing HER2 (ERBB2), many patients eventually progress to drug resistance. Here, we identified subpathways differentially expressed between trastuzumab-resistant vs. -sensitive breast cancer cells, in conjunction with additional transcriptomic preclinical and clinical gene datasets, to rigorously identify overexpressed, resistance-associated genes. From this approach, we identified 32 genes reproducibly upregulated in trastuzumab resistance. 25 genes were upregulated in drug-resistant JIMT-1 cells, which also downregulated HER2 protein by >80% in the presence of trastuzumab. 24 genes were downregulated in trastuzumab-sensitive SKBR3 cells. Trastuzumab sensitivity was restored by siRNA knockdown of these genes in the resistant cells, and overexpression of 5 of the 25 genes was found in at least one of five refractory HER2 + breast cancer. In summary, our rigorous computational approach, followed by experimental validation, significantly implicate ATF4, CHEK2, ENAH, ICOSLG, and RAD51 as potential biomarkers of trastuzumab resistance. These results provide further proof-of-concept of our methodology for successfully identifying potential biomarkers and druggable signal pathways involved in tumor progression to drug resistance.

The effect of disintegrin-metalloproteinase ADAM9 in gastric cancer progression

Advanced gastric cancer is one of the most aggressive gastrointestinal malignancies, and ADAM (A disintegrin and metalloproteinase)-9 is a cell-surface membrane glycoprotein with oncogenic properties that is overexpressed in several cancers. Herein, we investigated the biologic mechanism of ADAM9 in the progression, proliferation, and invasion of gastric cancer. First, we detected ADAM's expression, processing, and protease activity in gastric cancer cells. Protease activity was moderately correlated with ADAM9 protein expression, but was better related to a processed smaller molecular weight (84 kDa) form of ADAM9. Knockdown of ADAM9 or specifically targeted monoclonal antibody (RAV-18) suppressed cancer cell proliferation and invasion in high ADAM9-expressing cells, not in low ADAM9-expressing cells. RAV-18 showed in vivo antitumor activity in a gastric cancer xenograft model. Hypoxia (1% oxygen) induced ADAM9 expression and functional activity in low ADAM9-expressing gastric cancer cells that was inhibited by siRNA knockdown or RAV-18 antibody to levels in normoxic cells. Overall, our studies show that ADAM9 plays an important role in gastric cancer proliferation and invasion, and that while expressed in some gastric cancer cells at high levels that are responsive to functional inhibition and antitumor activity of a catalytic site-directed antibody, other gastric cancer cells have low levels of expression and only when exposed to hypoxia do ADAM9 levels increase and the cells become responsive to ADAM9 antibody inhibition. Therefore, our findings suggest that ADAM9 could be an effective therapeutic target for advanced gastric cancer.

Abstract 1781: Identification of focal adhesion and actin cytoskeleton regulation family genes as druggable target for gastric cancer

Gastric cancer(GC) is the 4th most common malignancy in the world and the 2nd most common cause of cancer related death worldwide (1). The known causes of GC are diet, hygiene, Helicobacter pylori, Epstein-Barr virus and hereditary factors. Other genetic causes of GC are known to be heterogenic, partially due to differences in ethnic/genetic background. Surgical removal of the tumor is the first-line treatment. Targeted therapy agents and chemotherapeutic agents that show survival advantage in other cancer types are being evaluated in GC(2,3), which only target few known oncogenes. Targeted therapy for GC is still an unmet need, and in light of personalized medicine, identifying genes specific to GC is critical for its treatment. From our NGS data, we have discovered protein family members involved in focal adhesion and actin cytoskeleton regulation pathways, which are involved in mitosis and metastasis.

We developed a subpathway network analysis method called PATHOME(unpublished), to identify pathways related to GC. For the first stage, two datasets (84 Korean GC: GSE13861 and 56 Japanese GC:GSE15081)(4,5). Two datasets (25 Korean GC: GSE36968 and 160 Chinese GC:GSE27342)(6,7,8) were used as validation sets. We identified top 10 common pathways. We have then categorized genes within these pathways according their functional category and druggability, either as drug transporter or druggable target. As a result, we identified genes involved in the focal adhesion and regulation of actin cytoskeleton pathways and cell junction, all critical for cell division and metastasis of tumor cells. Genes G1-9 are tight junction genes, and G10-20 are protein family group related to Ras-like GTP-binding protein, G10 - 20. G10, 11 and 12 are ras-like GTPases, and G13-20 are interacting proteins or downstream proteins. We then compared differential expression of these genes between the Asian and Caucasian dataset. G1-9 show co-regulation pattern among the two ethnic group. G9 in particular, is normally expressed in the stomach, and is downregulated (p=0.0045) in GC tumor samples. In contrast, G10 is upregulated in the Korean dataset and is shown to be upregulated in Japanese and Chinese GC sample (public) as well(9,10), but not in our Caucasian dataset(unpublished). The TCGA stomach cancer provisional data via cBioPortal(11) shows that most of the G10 alterations in GC cases are mutations (9% of total cases) with 2 known cases of downregulation. It is interesting that most of the G10 alterations were found in Caucasian patients (11/18 cases).

In our study, we have identified genes that are significant in GC and are druggable targets/drug transporters. It is significant that the pathways we identified are detected in both ethnic groups, with different expression pattern. This finding is critical for personalized treatment and drug development for GC.

Citation Format: Hae Ryung Chang, Seungyoon Nam, Myeong-Cherl Kook, Hee Seo Park, Hae Rim Jung, Youme Gim, Han Liang, Garth Powis, Yon Hui Kim. Identification of focal adhesion and actin cytoskeleton regulation family genes as druggable target for gastric cancer. [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 1781. doi:10.1158/1538-7445.AM2014-1781

Abstract 2671: Targeting the KRAS signaling naocluster protein CNKSR1 provides antitumor activity against mutant KRAS xenografts

KRAS, the predominant form of mutated RAS (mut-KRAS) is found in 25% of patient tumors across many cancer types and plays a critical role in driving tumor growth and resistance to therapy. Its effects are so powerful that it overrides the activity of many molecularly targeted signaling drugs being developed for cancer today such that they cannot be used in patients with mut-KRAS. We have identified genes that when inhibited block the growth of mut-KRAS cancer cells without affecting wild type-KRAS (wt-KRAS) cell growth using a global siRNA screen. A top hit was CNKSR1 (connector enhancer of kinase suppressor of Ras 1), a protein associated with KRAS in the RAS membrane signaling nanocluster. siRNA knockdown of CNKSR1 shows selective inhibition of the growth of mut-KRAS versus wilt type non-small cell lung cancer (NSCLC) cell lines. CNKSR1 is a multidomain protein with a pleckstrin homology (PH)-domain, a 100 to 120 amino acid, highly conserved but low sequence identity 3D superfold. This domain is found in a number of signaling proteins, and is responsible for binding to membrane phosphatidylinositol-3-phosphates (PIP2/3). Over expression of the PH-domain of CNKSR1 in H1373 mut-KRAS NSCLC cells inhibits cell growth suggesting a dominant negative activity, and that the PH-domain of CNKSR1 is necessary for the effects on mut-KRAS activity. PHusis is developing PH-domain inhibitors of signaling proteins through use of its in silico computational modeling platform PhuDock, and has used this approach to identify inhibitors that bind to the PH-domain of CNKSR1. Through rounds of compound refinement we have been optimizing the activity of leads using surface plasmon resonance spectroscopy (SPR), in vitro cell line screening and in vivo xenograft evaluation. Micromolar binders have been improved to nanomolar inhibitors (SPR) that also demonstrate in vitro cytotoxicity. The initial lead PHT-782 (Kd1.8 μM) inhibited mut-KRAS signaling and growth of mut-KRAS isogenic NSCLC cell lines (IC50 ∼30 μM) as effectively as siRNA knockdown of KRAS. Importantly, PHT-782 did not block the growth of wt-KRAS cell lines at concentrations up to 100 μM. In mice PHT-782 exhibited oral bioavailability and had moderate antitumor activity against a mut-KRAS xenograft model without observable toxicity. Refinement has provided PHT-7571 and PHT-7327 with improved PH-domain binding. Additionally, PHT-7327 displays more potent in vivo antitumor activity, both as a single agent in mut-KRAS xenografts and in combination with chemotherapy or EGRF inhibitors. Thus, our studies have shown that the PH-domain of CNKSR1 can be targeted by small molecule inhibitors, selectively blocking mut-KRAS signaling and cell growth, thus creating a novel therapeutic potential for patients with oncogenic KRAS for which there is currently no effective therapy.

Citation Format: Gallen Triana-Balzer, Martin Indarte, Mike Scott, Garth Powis, D. Lynn Kirkpatrick. Targeting the KRAS signaling naocluster protein CNKSR1 provides antitumor activity against mutant KRAS xenografts. [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 2671. doi:10.1158/1538-7445.AM2014-2671

PATHOME: an algorithm for accurately detecting differentially expressed subpathways

The translation of high-throughput gene expression data into biologically meaningful information remains a bottleneck. We developed a novel computational algorithm, PATHOME, for detecting differentially expressed biological pathways. This algorithm employs straightforward statistical tests to evaluate the significance of differential expression patterns along subpathways. Applying it to gene expression data sets of gastric cancer (GC), we compared its performance with those of other leading programs. Based on a literature-driven reference set, PATHOME showed greater consistency in identifying known cancer-related pathways. For the WNT pathway uniquely identified by PATHOME, we validated its involvement in gastric carcinogenesis through experimental perturbation of both cell lines and animal models. We identified HNF4α-WNT5A regulation in the cross-talk between the AMPK metabolic pathway and the WNT signaling pathway, and further identified WNT5A as a potential therapeutic target for GC. We have demonstrated PATHOME to be a powerful tool, with improved sensitivity for identifying disease-related dysregulated pathways.

FXR silencing in human colon cancer by DNA methylation and KRAS signaling

Farnesoid X receptor (FXR) is a bile acid nuclear receptor described through mouse knockout studies as a tumor suppressor for the development of colon adenocarcinomas. This study investigates the regulation of FXR in the development of human colon cancer. We used immunohistochemistry of FXR in normal tissue (n = 238), polyps (n = 32), and adenocarcinomas, staged I-IV (n = 43, 39, 68, and 9), of the colon; RT-quantitative PCR, reverse-phase protein array, and Western blot analysis in 15 colon cancer cell lines; NR1H4 promoter methylation and mRNA expression in colon cancer samples from The Cancer Genome Atlas; DNA methyltransferase inhibition; methyl-DNA immunoprecipitation (MeDIP); bisulfite sequencing; and V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) knockdown assessment to investigate FXR regulation in colon cancer development. Immunohistochemistry and quantitative RT-PCR revealed that expression and function of FXR was reduced in precancerous lesions and silenced in a majority of stage I-IV tumors. FXR expression negatively correlated with phosphatidylinositol-4, 5-bisphosphate 3 kinase signaling and the epithelial-to-mesenchymal transition. The NR1H4 promoter is methylated in ~12% colon cancer The Cancer Genome Atlas samples, and methylation patterns segregate with tumor subtypes. Inhibition of DNA methylation and KRAS silencing both increased FXR expression. FXR expression is decreased early in human colon cancer progression, and both DNA methylation and KRAS signaling may be contributing factors to FXR silencing. FXR potentially suppresses epithelial-to-mesenchymal transition and other oncogenic signaling cascades, and restoration of FXR activity, by blocking silencing mechanisms or increasing residual FXR activity, represents promising therapeutic options for the treatment of colon cancer.

Improved synthesis of 17β-hydroxy-16α-iodo-wortmannin, 17β-hydroxy-16α-iodoPX866, and the [(131)I] analogue as useful PET tracers for PI3-kinase

An improved method for the synthesis of 17β-hydroxy-16α-iodo-wortmannin along with the first synthesis of 17β-hydroxy-16α-iodoPX866 and [(131)I] radiolabeled 17β-hydroxy-16α-[(131)I]iodo-wortmannin, as potential PET tracers for PI3K was also described. The differences between wortmannin and its iodo analogue were compared by covalently docking each structure to L833 in PI3K.

BATTLE-2 program: A biomarker-integrated targeted therapy study in previously treated patients with advanced non-small cell lung cancer (NSCLC)

TPS8118

Background: New strategies incorporating a personalized medicine approach for NSCLC treatment are increasingly explored and were pioneered in the prospective, biomarker-driven clinical program titled Biomarker-integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE-1) (Kim et al Cancer Discov 2011;1:44). Effective therapeutic strategies for mutant KRAS and other biomarkers of resistance in refractory NSCLC remain an unmet medical need. The BATTLE-2 clinical study is using EGFR, PI3K/AKT and MEK inhibitors and is designed to identify biomarkers for optimal patient selection for these therapies, with a long-term goal to significantly improve the survival of NCSLC patients (pts) (ClinicalTrials.gov NCT01248247). Methods: This is a four-arm, open-label, multi-center, biopsy-driven, adaptive randomization, phase II clinical trial in refractory NSCLC pts (failed at least 1 prior line of therapy). After a study-entry tumor biopsy, pts are adaptively randomized, based on KRAS status, to 4 trial arms: erlotinib, erlotinib plus the AKT inhibitor MK-2206, MK-2206 plus the MEK inhibitor selumetinib, and sorafenib. The primary objective is 8-week disease control rate (DCR). Baseline tumor testing includes KRAS and EGFR mutations and EML4/ALK translocation, the latter two being exclusion criteria. The trial is conducted in 2 stages. In Stage 1, 200 evaluable pts are adaptively randomized (AR) based on observed 8-week DCR and KRAS status while predictive biomarkers are being developed. In Stage 2, the AR model is refined to include the most predictive biomarkers tested in Stage 1, with subsequent Stage 2 AR based on the new algorithm, to a total of 400 evaluable pts. Selection of Stage 2 single and/or composite markers (“signatures”) follows a rigorous, internally and externally reviewed statistical analysis. All Stage 1 and 2 randomization biomarker assays are CLIA-certified. 219 pts have been enrolled and 124 pts randomized. 100 pts are evaluable for the 8-week DCR endpoint. Accrual updates, demographics, and further details will be presented at the meeting. Supported by NCI R01CA155196-01A1. Clinical trial information: NCT01248247.

Hypoxia triggers hedgehog-mediated tumor-stromal interactions in pancreatic cancer

Pancreatic cancer is characterized by a desmoplastic reaction that creates a dense fibroinflammatory microenvironment, promoting hypoxia and limiting cancer drug delivery due to decreased blood perfusion. Here, we describe a novel tumor-stroma interaction that may help explain the prevalence of desmoplasia in this cancer. Specifically, we found that activation of hypoxia-inducible factor-1α (HIF-1α) by tumor hypoxia strongly activates secretion of the sonic hedgehog (SHH) ligand by cancer cells, which in turn causes stromal fibroblasts to increase fibrous tissue deposition. In support of this finding, elevated levels of HIF-1α and SHH in pancreatic tumors were determined to be markers of decreased patient survival. Repeated cycles of hypoxia and desmoplasia amplified each other in a feed forward loop that made tumors more aggressive and resistant to therapy. This loop could be blocked by HIF-1α inhibition, which was sufficient to block SHH production and hedgehog signaling. Taken together, our findings suggest that increased HIF-1α produced by hypoxic tumors triggers the desmoplasic reaction in pancreatic cancer, which is then amplified by a feed forward loop involving cycles of decreased blood flow and increased hypoxia. Our findings strengthen the rationale for testing HIF inhibitors and may therefore represent a novel therapeutic option for pancreatic cancer.

Abstract 3836: A 3D high throughput RNA1 screen identifies the TLR4 kinase which alters spheroid architecture: a promising therapeutic strategy for pancreatic cancer

Background: Pancreatic Ductal Adenocarcinoma (PDA) ranks fourth among cancer-related deaths in the United States. The poor prognosis of PDA is due to resistance to current therapies. Contributing to this resistance is the tumor architecture comprising dense desmoplastic stroma, extracellular matrix (ECM), tumor cells and tumor hypoxia. We hypothesized that destabilizing the compact tumor architecture by weakening the interactions between tumor cells alone or tumor cells along with the ECM may result in more effective therapies for PDA.

Methods and Results: Using the pancreatic cell line Panc1, we developed a three dimensional (3D) spheroid model system, that exhibits oxygen gradients and hypoxia that mimics the tumor microenvironment. We used the pancreatic cancer cell line PANC1-HRE that stably expresses HRE-luciferase and detects HIF-1α activation, and a platform comprising a non-matrix nano-structured scaffold, to generate compact spheroids with hypoxic inner cores and HIF-1α activation. A high throughput siRNA screen using the kinome siRNA library and our 3D spheroid modal system identified kinases whose silencing reduced both the level of hypoxia and activity of HIF-1α. The positive control, siRNA against HIF-1α, reduced activity of HIF-1α with no effect on the levels of hypoxia within the spheroids. We identified the kinases Toll-like receptor 4 (TLR4) and its downstream target spleen tyrosine kinase (SYK) as our lead candidates following target validation. Image analysis of spheroids transfected with siRNA against both TLR4 and SYK resulted in the loss of compactness of the spheroids. In addition, these spheroids also demonstrated a significant reduction in the levels of hypoxia determined by the hypoxia probe Lox-1. These findings suggest that the alteration of the spheroid architecture resulted in the reduction in hypoxia. Previous studies have shown that SYK is a direct target of TLR4. Therefore to determine the mechanism through which TLR4 dependent signaling regulates the integrity of the spheroidal architecture we are generating stable cell lines in Panc1 of shRNA targeting TLR4 under an inducible system. We will use our inducible shRNA targeting TLR4 and the two 3D model systems, the hanging drop system (analogous to a primary tumor) and the nanoculture plate system (analogous to the progression of a metastatic loci) to further confirm our findings.

Conclusion: TLR4 mediated signaling regulates the integrity of spheroid architecture. Inhibiting this pathway destabilized the tumor architecture altering the hypoxic state of the spheroid. Our long-term goals are to use known pharmacological inhibitors of TLR4 to study the mechanisms by which this kinase regulates tumor architecture, determine the pre-clinical significance of targeting TLR4 utilizing autochtonous mouse models for PDA and develop TLR4-targeted therapy for PDA.

Citation Format: Geoffrey A. Bartholomeusz, Alex Campos, Geoffrey Grandjean, Garth Powis. A 3D high throughput RNA1 screen identifies the TLR4 kinase which alters spheroid architecture: a promising therapeutic strategy for pancreatic cancer. [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 3836. doi:10.1158/1538-7445.AM2013-3836

Abstract 2076: Inhibiting glycolysis and HIF1α: a novel approach to cancer therapy

Cancer cells satisfy their increased need for energy under conditions of normal oxygen tension by undergoing a high rate of glycolysis followed by lactic acid fermentation, a process known as the Warburg Effect, rather than oxidative phosphorylation as observed in normal cells. Unlike proliferating cancer cells, the internal environment of most solid tumors is hypoxic due to an inadequate or disorganized blood supply. This results in tumors generating ATP through anaerobic respiration, a process many times less efficient than oxidative phosphorylation. The importance of anaerobic glycolysis for cancer cell energy generation makes it an attractive target for inhibiting cancer growth. However, agents currently in use for regulating energy production in tumors are relatively ineffective analogs of glucose or intermediates of the glycolytic pathway.

We performed a high throughput siRNA screen using an siRNA library targeting all known open reading frames of the human genome (Dharmacon Inc.) to identify genes that when inhibited would block hypoxia inducible factor-1 alpha (HIF-1α) transcription factor luciferase reporter activity. A significant number of genes selected and validated were members of the glycolysis pathway. It is known that many glycolysis enzymes are induced by HIF-1α providing a feed forward loop between glycolysis and HIF-1α. We have addressed two questions: (1) what is the biological mechanism by which these two signaling systems regulate one another?; and (2) can specific inhibitors of glycolysis be developed with the added effect of inhibiting HIF-1α? Our mechanistic studies have shown that of the 40 enzymes of glycolysis involving 11 enzymatic steps and various enzyme isoforms, siRNA knockdown of Aldolase A (ALDOA) produces the maximum inhibition of HIF-1α activity. Further work indicated that ALDOA siRNA inhibition of HIF-1α is mediated through AMPK, a sensor of low ATP levels in the cell, since siRNA knockdown of AMPK results in rescue of HIF-1α activity. The effect of ALDOA inhibition is not mediated through a reduction in HIF-1α protein suggesting that, contrary to the canonical AMPK pathway, mTOR and its regulation of translation is not involved. Instead, p300 is phosphorylated by AMPK thus inhibiting its function as a co-activator of HIF-1α.

A structure based drug design approach was employed for lead identification and optimization using the crystal structure of ALDOA (4ALD) and GOLD virtual screening platform. Three compounds have been identified as having effects on the modulation of ALDOA activity in a protein based biochemical assay as well as inhibitory effects on glycolysis itself using the XF96 Analyzer from Seahorse Bioscience. Here, we present an overview of ALDOA target identification, its mechanism as a regulator of HIF-1α activity and virtual drug design methodologies used in the search for novel pharmacological probes which act as dual inhibitors of energy production and the HIF-1α survival pathway.

Citation Format: Geoffrey V. Grandjean, John Kingston, John Kenneth Morrow, Shuxing Zhang, Garth Powis. Inhibiting glycolysis and HIF1α: a novel approach to cancer therapy. [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 2076. doi:10.1158/1538-7445.AM2013-2076

Abstract 3561: Silencing of farnesoid X receptor in human colon cancer by epigenetic mechanisms is associated with cancer progression

Background: Colon cancer is the third leading cause of cancer related deaths in the United States. Epidemiological studies suggest an increase in the intestinal bile-acid load resulting from the consumption of a high-fat diet is a significant risk factor for colon cancer. Bile acids are the endogenous ligands for the farnesoid X receptor (FXR), a ligand-activated transcription factor and member of the nuclear receptor superfamily, and high levels of bile acids can promote colon cancer development. FXR is essential for maintaining bile-acid homeostasis by regulating bile-acid synthesis and transport, preventing the accumulation of intestinal bile acid levels to cancer promoting levels. Previous studies have demonstrated that FXR knockout mice are more susceptible to the development of colon adenocarcinomas, indicating that FXR plays a suppressive role in colon tumor formation. This study investigates the role of FXR in the development of human colon cancer. Methods: Immunohistochemistry was used to label for FXR in normal human colon, colon polyps, and colon adenocarcinomas staged I-IV. SYBR green quantitative PCR and western blot analysis were used to measure expression of FXR and FXR target genes in normal human colon and colon cancers staged I-IV as well as colon cancer cell lines. Reverse phase protein array on colon cancer cell line lysates was used to correlate FXR expression with oncogenic signaling cascades. To test if FXR expression was suppressed by DNA methylation, colon cancer cell lines were treated with a DNA methyltransferase (DNMT) inhibitor and DNMT siRNA and FXR mRNA measured by real-time PCR. Immunoprecipitation with an antibody against 5-methylcytosine (MeDIP) analysis was done in human colon cancer cell lines to determine methylation of NR1H4 (gene encoding FXR) promoter. Results: IHC and qPCR analysis reveals that the expression and function of FXR is markedly reduced early in colon cancer progression, with suppression seen within precancerous lesions. Furthermore, FXR expression in colon cancer cell lines were negatively correlated to oncogenic PI3 kinase signaling cascades and associated with epithelial to mesenchymal transition (EMT). Results suggest DNA methylation as a mechanism of FXR silencing in colon cancer and confirms methylation of the FXR promoter. Conclusion: FXR deficiency in animals indicates FXR serves a tumor suppressive role. Our studies show that FXR is silenced in early in human colon cancer progression possibly by DNA methylation, which could be a cancer promoting event. The overall mechanism of FXR's anti-tumorigenic activity is not fully established but may be due to FXR's role in regulating EMT and bile acid homeostasis. Restoration and enhancement of FXR activity, by blocking DNA methylation or increasing baseline activity of FXR, represents a potential therapeutic option for the treatment of colon cancer.

Citation Format: Ann M. Thomas, Le Zhan, Julie Izzo, Dipen Maru, Imad Shureiqi, Veera Baladandayuthapani, Han Liang, Grace L. Guo, Garth Powis. Silencing of farnesoid X receptor in human colon cancer by epigenetic mechanisms is associated with cancer progression. [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 3561. doi:10.1158/1538-7445.AM2013-3561

Abstract 3233: Modeling evolution of resistance in patient-derived xenografts: resistance to the BRAF inhibitor PLX4720

A major hurdle for targeted cancer therapies is the development of resistance, with many agents showing promising initial results but not providing significant overall survival benefits. To address resistance we need to know the genetic and epigenetic alterations that drive resistance. This knowledge will contribute to modified treatment protocols, new targets, and predictive biomarkers. We are working on a system to model evolution of tumor resistance in a the patient-derived xenograft (PDX) mouse system. Compared to xenografts, PDXs are closer to the tumor biology of the patient, having a higher degree of molecular subtypes and intratumor heterogeneity, and a mixture of human and mouse stroma. In this study, we implanted 1-3mm chunks from a primary colorectal cancer tumor carrying the BRAF V600>E mutation into immunosuppressed NOD/SCID CB.17 mice. Once the tumors were established (100-150mmˆ3 tumor burden), the mice were stratified into two groups, control and fed chow containing the BRAF inhibitor PLX4720, 417 mg/kg (Scientific Diets). The tumors in most of the PDXs in the group fed PLX4720 chow regressed and became very small by day 77. In several cases PDXs that were allowed to develop beyond day 77 became resistant to PLX4720 treatment.

To identify mechanisms of PLX4720 resistance we sequenced DNA and RNA from two resistant PDXs, one untreated control PDX, and a sample of the original patient tumor. We used the Ion AmpliSeq Comprehensive Cancer Panel from Life Technologies to sequence exons from 409 cancer related genes on the Ion Torrent PGM. Additionally, we performed SOLiD 5500 paired-end (50x25 nt) next generation sequencing (NGS) of the whole transcriptome of these samples. Since the stromal component of the PDXs is a mixture of cells of human and mouse origin, and sequence reads of mouse origin could contribute to false positive mutation calls or skew expression analysis of the resistant data, we needed to develop a method for filtering mouse reads out of our sequencing data. To this end, we have developed and applied a read filtering protocol that sorts reads that align to the human genome into three groups, better in human, better in mouse, or ambiguous. 97.7% of the reads from human tissue were defined as better in human with the remaining 2.3% being ambiguous, or better in mouse. PDX derived reads had between 8% and 13% of reads being better in mouse. Only reads defined as better in human were used for expression analysis and SNP calling in this work. In one of the two resistant tumors analyzed this method has identified a candidate resistance mutation, NRAS G13>D. The NRAS mutation is seen in both the RNA-seq and DNA-seq data, and is not seen in the original patient tumor, the control untreated PDX, or in the second resistant tumor. Based on these findings, we feel that PDX provide a powerful model system for examining the evolution of resistance to targeted agents.

Citation Format: Brian P. James, Robert J. Lemos, Feng Tian, Thomas C. Motter, Amin Momin, Nastaran D. Neishaboori, Galina M. Kiriakova, Scott Kopetz, Garth Powis. Modeling evolution of resistance in patient-derived xenografts: resistance to the BRAF inhibitor PLX4720. [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 3233. doi:10.1158/1538-7445.AM2013-3233

Abstract 5534: Metformin increases AMPKα activity by inhibition of AMPKα and cell cycle proliferation in Asian gastric cancer

The LKB1/AMPK signaling pathway has been well elucidated and recent evidence suggests its involvement in cancer cell biology, demonstrating that the reinforcement of the tumor suppressive functions of LKB1/AMPK is a valuable therapeutic strategy for cancers. Interest in metformin as a novel anticancer agent for breast cancer and other solid tumors continue to grow, currently being investigated in several cancer types in both neoadjuvant and metastatic settings. The biological effect of metformin on cancer cells is driven by its ability to activate AMPK through upstream kinase LKB1, tumor suppressor gene in epithelial tissues. Metformin increases intracellular AMP level, which allosterically activates AMPK. We have previously identified the AMPKα as a modulator in gastric cancer (GC) and through experimental evidence. We show the impact of LKB1/AMPK modulation of HNF4α, a dramatic suppression of cancer cell growth.

GC samples were collected and sequenced on SOLiD v 3.0 for both WT-seq and small RNA-seq. Computational analysis showed that 356 out of 18,890 genes were identified as GC related differentially expressed genes in the five-group comparison (normal, tumor stage I, II, III or IV). 28 genes were identified as stage-specific differentially expressed genes, and 13 out of the 28 genes were within the network between HNF4α and HNF1α. In order to test the anti-proliferation activity of metformin in GC cell lines associated with activation of PRKAA1, PRKAA2 and LKB1, and by HNF4α suppression, 4 GC cell lines (NCI-N87, AGS, HS 746T and MKN 45) were treated with metformin. Both PRKAA1/2 showed increased gene expression level when the cells were treated with 10mM of metformin. As for STK11 (LKB1 gene) and HNF4A gene expression level, LKB1 increased and HNF4A decreased with metformin treatment on all four cell lines. Metformin treated NCI-N87 and AGS show that it is involved in cell cycle arrest. Western-blot analysis shows, decreased protein expression of Cyclin A/B and D1 on metformin treated. Lastly, NCI-N87 xenograft study show metformin treated suppression of tumor progression compared to non-treated mouse. During the 28 day treatment of metformin, PRKAA1 and PRKAA2 expression level increased compared to the untreated with. Consistent with in vitro assay, LKB1 level was elevated in the metformin treated tumor compared to the non-treated, and HNF4α level decreased over time in the metformin treated tumor.

Study shows that AMPK is a strong therapeutic tumor suppressor target and that metformin is a potential drug for Asian early gastric cancer patient. In our research in progress, we observe potential relationships between the Wnt pathway and AMPKα in light of WNT druggability with metformin. In conclusion LKB1/AMPK by HNF4α inhibition suggests metformin could be a candidate for gastric cancer treatment, probably in combination with conventional chemotherapy and/or as a maintenance therapy.

Citation Format: Hae Rim Jung, Hae Ryung Chang, Hye-Hyun Seo, Robert Lemos, Hee Seo Park, Han Liang, Garth Powis, Yon Hui Kim. Metformin increases AMPKα activity by inhibition of AMPKα and cell cycle proliferation in Asian gastric cancer. [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 5534. doi:10.1158/1538-7445.AM2013-5534

Resistance to BRAF inhibition in BRAF-mutant colon cancer can be overcome with PI3K inhibition or demethylating agents

PURPOSE

Vemurafenib, a selective inhibitor of BRAF(V600), has shown significant activity in BRAF(V600) melanoma but not in less than 10% of metastatic BRAF(V600) colorectal cancers (CRC), suggesting that studies of the unique hypermethylated phenotype and concurrent oncogenic activation of BRAF(mut) CRC may provide combinatorial strategies.

EXPERIMENTAL DESIGN

We conducted comparative proteomic analysis of BRAF(V600E) melanoma and CRC cell lines, followed by correlation of phosphoinositide 3-kinase (PI3K) pathway activation and sensitivity to the vemurafenib analogue PLX4720. Pharmacologic inhibitors and siRNA were used in combination with PLX4720 to inhibit PI3K and methyltransferase in cell lines and murine models.

RESULTS

Compared with melanoma, CRC lines show higher levels of PI3K/AKT pathway activation. CRC cell lines with mutations in PTEN or PIK3CA were less sensitive to growth inhibition by PLX4720 (P = 0.03), and knockdown of PTEN expression in sensitive CRC cells reduced growth inhibition by the drug. Combined treatment of PLX4720 with PI3K inhibitors caused synergistic growth inhibition in BRAF-mutant CRC cells with both primary and secondary resistance. In addition, methyltransferase inhibition was synergistic with PLX4720 and decreased AKT activation. In vivo, PLX4720 combined with either inhibitors of AKT or methyltransferase showed greater tumor growth inhibition than PLX4720 alone. Clones with acquired resistance to PLX4720 in vitro showed PI3K/AKT activation with EGF receptor (EGFR) or KRAS amplification.

CONCLUSIONS

We show that activation of the PI3K/AKT pathway is a mechanism of both innate and acquired resistance to BRAF inhibitors in BRAF(V600E) CRC and suggest combinatorial approaches to improve outcomes in this poor prognosis subset of patients.