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1.  The novel SMAC mimetic birinapant exhibits potent activity against human melanoma cells 
Purpose
Inhibitor of apoptosis proteins (IAPs) promote cancer cell survival and confer resistance to therapy. We report on the ability of second mitochondria-derived activator of caspases (SMAC) mimetic, birinapant, which acts as antagonist to cIAP1 and cIAP2, to restore the sensitivity to apoptotic stimuli such as tumor necrosis factor (TNF)-α in melanomas
Experimental Design
Seventeen melanoma cell lines, representing five major genetic subgroups of cutaneous melanoma, were treated with birinapant as a single agent or in combination with TNF-α. Effects on cell viability, target inhibition, and initiation of apoptosis were assessed and findings were validated in in 2D, 3D spheroid and in vivo xenograft models.
Results
When birinapant was combined with TNF-α, strong combination activity, i.e. neither compound was effective individually but the combination was highly effective, was observed in twelve out of eighteen cell lines. This response was conserved in spheroid models, whereas in vivo birinapant inhibited tumor growth without adding TNF-α in in vitro resistant cell lines. Birinapant combined with TNF-α inhibited the growth of a melanoma cell line with acquired resistance to BRAF inhibition to the same extent as in the parental cell line.
Conclusions
Birinapant in combination with TNF-α exhibits a strong anti-melanoma effect in vitro. Birinapant as a single agent shows in vivo anti-tumor activity, even if cells are resistant to single agent therapy in vitro. Birinapant in combination with TNF-α is effective in a melanoma cell line with acquired resistance to BRAF inhibitors.
doi:10.1158/1078-0432.CCR-12-2518
PMCID: PMC3618495  PMID: 23403634
birinapant; IAP inhibitor; SMAC mimetic; TNF-α; melanoma
2.  Targeting ER stress–induced autophagy overcomes BRAF inhibitor resistance in melanoma 
The Journal of Clinical Investigation  2014;124(3):1406-1417.
Melanomas that result from mutations in the gene encoding BRAF often become resistant to BRAF inhibition (BRAFi), with multiple mechanisms contributing to resistance. While therapy-induced autophagy promotes resistance to a number of therapies, especially those that target PI3K/mTOR signaling, its role as an adaptive resistance mechanism to BRAFi is not well characterized. Using tumor biopsies from BRAFV600E melanoma patients treated either with BRAFi or with combined BRAF and MEK inhibition, we found that BRAFi-resistant tumors had increased levels of autophagy compared with baseline. Patients with higher levels of therapy-induced autophagy had drastically lower response rates to BRAFi and a shorter duration of progression-free survival. In BRAFV600E melanoma cell lines, BRAFi or BRAF/MEK inhibition induced cytoprotective autophagy, and autophagy inhibition enhanced BRAFi-induced cell death. Shortly after BRAF inhibitor treatment in melanoma cell lines, mutant BRAF bound the ER stress gatekeeper GRP78, which rapidly expanded the ER. Disassociation of GRP78 from the PKR-like ER-kinase (PERK) promoted a PERK-dependent ER stress response that subsequently activated cytoprotective autophagy. Combined BRAF and autophagy inhibition promoted tumor regression in BRAFi-resistant xenografts. These data identify a molecular pathway for drug resistance connecting BRAFi, the ER stress response, and autophagy and provide a rationale for combination approaches targeting this resistance pathway.
doi:10.1172/JCI70454
PMCID: PMC3934165  PMID: 24569374
3.  Development of a novel class of B-RafV600E-selective inhibitors through virtual screening and hierarchical hit optimization 
Organic & biomolecular chemistry  2012;10(36):7402-7417.
Oncogenic mutations in critical nodes of cellular signaling pathways have been associated with tumorigenesis and progression. The B-Raf protein kinase, a key hub in the canonical MAPK signaling cascade, is mutated in a broad range of human cancers and especially in malignant melanoma. The most prevalent B-RafV600E mutant exhibits elevated kinase activity and results in constitutive activation of the MAPK pathway, thus making it a promising drug target for cancer therapy. Herein, we described the development of novel B-RafV600E selective inhibitors via multi-step virtual screening and hierarchical hit optimization. Nine hit compounds with low micromolar IC50 values were identified as B-RafV600E inhibitors through virtual screening. Subsequent scaffold-based analogue searching and medicinal chemistry efforts significantly improved both the inhibitor potency and oncogene selectivity. In particular, compounds 22f and 22q possess nanomolar IC50 values with selectivity for B-RafV600E in vitro and exclusive cytotoxicity against B-RafV600E harboring cancer cells.
doi:10.1039/c2ob26081f
PMCID: PMC3427755  PMID: 22875039
4.  CONTROL OF TUMOR BIOENERGETICS AND SURVIVAL STRESS SIGNALING BY MITOCHONDRIAL HSP90s 
Cancer cell  2012;22(3):331-344.
SUMMARY
Tumors successfully adapt to constantly changing intra- and extra-cellular environments, but the wirings of this process are still largely elusive. Here, we show that Heat Shock Protein 90 (HSP90)-directed protein folding in mitochondria, but not cytosol, maintains energy production in tumor cells. Interference with this process activates a signaling network that involves phosphorylation of nutrient-sensing AMP-activated kinase (AMPK), inhibition of rapamycin-sensitive mTOR complex 1 (mTORC1), induction of autophagy, and expression of an endoplasmic reticulum (ER) unfolded protein response (UPR). This signaling network confers a survival and proliferative advantage to genetically disparate tumors, and correlates with worse outcome in lung cancer patients. Therefore, mitochondrial HSP90s are adaptive regulators of tumor bioenergetics, and tractable targets for cancer therapy.
doi:10.1016/j.ccr.2012.07.015
PMCID: PMC3615709  PMID: 22975376
HSP90; mitochondria; bioenergetics; ER; unfolded protein response; AMPK; autophagy
5.  Paracrine signaling between carcinoma cells and mesenchymal stem cells generates cancer stem cell niche via epithelial-mesenchymal transition 
Cancer discovery  2012;2(9):775-777.
Summary
Li and colleagues present data that cancer cell-derived intereleukin-1 induces prostaglandin E2 and cytokine secretion in mesenchymal stem cells (MSC) to activate β-catenin signaling in the cancer cell. This paracrine signaling between carcinoma cells and MSC leads to the creation of a cancer stem cell niche via epithelial-mesenchymal transition.
doi:10.1158/2159-8290.CD-12-0312
PMCID: PMC3646332  PMID: 22969117
6.  Melanoma-Derived Conditioned Media Efficiently Induce the Differentiation of Monocytes to Macrophages that Display a Highly Invasive Gene Signature 
Pigment cell & melanoma research  2012;25(4):493-505.
Summary
The presence of tumor-associated macrophages (TAMs) in melanomas is correlated with a poor clinical prognosis. However, there is limited information on the characteristics and biological activities of human TAMs in melanomas. In this study, we developed an in vitro method to differentiate human monocytes to macrophages using modified melanoma-conditioned medium (MCM). We demonstrate that factors from MCM-induced macrophages (MCMI-Mϕ) express both M1-Mϕ and M2-Mϕ markers, and inhibit melanoma-specific T cell proliferation. Furthermore, microarray analyses reveal that the majority of genes up-regulated in MCMI-Mϕ are associated with tumor invasion. The most strikingly up-regulated genes are CCL2 and MMP-9. Consistent with this, blockade of both CCL-2 and MMPs diminish MCMI-Mϕ-induced melanoma invasion. Finally, we demonstrate that both MCMI-Mϕ and in vivo TAMs express the pro-invasive, melanoma-associated gene, GPMNB. Our study provides a framework for understanding the mechanisms of crosstalk between TAMs and melanoma cells within the tumor microenvironment.
doi:10.1111/j.1755-148X.2012.01005.x
PMCID: PMC3615702  PMID: 22498258
Melanoma; macrophages; invasion; tumor microenvironment; GPMNB
7.  Identification of a novel family of BRAFV600E inhibitors 
Journal of Medicinal Chemistry  2012;55(11):5220-5230.
The BRAF oncoprotein is mutated in about half of malignant melanomas and other cancers, and a kinase activating single valine to glutamate substitution at residue 600 (BRAFV600E) accounts for over 90% of BRAF-mediated cancers. Several BRAFV600E inhibitors have been developed, although they harbor some liabilities, thus motivating the development of other BRAFV600E inhibitor options. We report here the use of an ELISA based high-throughput screen to identify a family of related quinolol/naphthol compounds that preferentially inhibit BRAFV600E over BRAFWT and other kinases. We also report the X-ray crystal structure of a BRAF/quinolol complex revealing the mode of inhibition, employ structure-based medicinal chemistry efforts to prepare naphthol analogs that inhibit BRAFV600E in vitro with IC50 values in the 80–200 nM under saturating ATP concentrations, and demonstrate that these compounds inhibit MAPK signaling in melanoma cells. Prospects for improving the potency and selectivity of these inhibitors are discussed.
doi:10.1021/jm3004416
PMCID: PMC3383862  PMID: 22537109
8.  Intratumoral Heterogeneity as a Therapy Resistance Mechanism: Role of Melanoma Subpopulations 
Malignant melanoma is an aggressive form of skin cancer whose incidence continues to increase worldwide. Increased exposure to sun, ultraviolet radiation and the use of tanning beds can increase the risk of melanoma. Early detection of melanomas is the key to successful treatment mainly through surgical excision of the primary tumor lesion. But in advanced stage melanomas, once the disease has spread beyond the primary site to distant organs, the tumors are difficult to treat and quickly develop resistance to most available forms of therapy. The advent of molecular and cellular techniques has led to a better characterization of tumor cells revealing the presence of heterogeneous melanoma subpopulations. The discovery of gene mutations and alterations of cell-signaling pathways in melanomas has led to the development of new targeted drugs that show dramatic response rates in patients. Single agent therapies generally target one subpopulation of tumor cells while leaving others unharmed. The surviving subpopulations will have the ability to repopulate the original tumors that can continue to progress. Thus, a rational approach to target multiple subpopulations of tumor cells with a combination of drugs instead of single agent therapy will be necessary for long-lasting inhibition of melanoma lesions. In this context, the recent development of immune checkpoint reagents provides an additional armor that can be used in combination with targeted drugs to expand the presence of melanoma reactive T-cells in circulation to prevent tumor recurrence.
doi:10.1016/B978-0-12-397927-8.00011-7
PMCID: PMC3677516  PMID: 22959031
Melanoma; tumor; heterogeneity; subpopulations; therapy; resistance
9.  GSK3β inhibition blocks melanoma cell/host interactions by downregulating N-cadherin expression and decreasing FAK phosphorylation 
This study addresses the role of glycogen synthase kinase (GSK)-3β signaling in the tumorigenic behavior of melanoma. Immunohistochemical staining revealed GSK3β to be focally expressed in the invasive portions of 12% and 33% of primary and metastatic melanomas, respectively. GSK3 inhibitors and siRNA knockdown of GSK3β were found to inhibit the motile behavior of melanoma cells in scratch wound, 3D collagen implanted spheroid and modified Boyden chamber assays. Functionally, inhibition of GSK3β signaling was found to suppress N-cadherin expression at the mRNA and protein levels and was associated with decreased expression of the transcription factor Slug. Pharmacological and genetic ablation of GSK3β signaling inhibited the adhesion of melanoma cells to both endothelial cells and fibroblasts and prevented transendothelial migration, an effect rescued by the forced overexpression of N-cadherin. A further role for GSK3β signaling in invasion was suggested by the ability of GSK3β inhibitors and siRNA knockdown to block phosphorylation of FAK and increase the size of focal adhesions. In summary, we have demonstrated a previously unreported role for GSK3β in modulating the motile and invasive behavior of melanoma cells through N-cadherin and FAK. These studies suggest the potential therapeutic utility of inhibiting GSK3β in defined subsets of melanoma.
doi:10.1038/jid.2012.237
PMCID: PMC3479306  PMID: 22810307
10.  Cancer Testis Antigens in human melanoma stem cells: expression, distribution and methylation status 
Journal of cellular physiology  2008;215(2):287-291.
Neoplastic populations with stem cell potential have been most recently identified in human cutaneous melanoma, and initially characterized for their phenotypic profile. Being melanoma stem cells (MSC) the most desirable target of therapeutic intervention, we asked whether they express the epigenetically-regulated Cancer Testis Antigens (CTA) on which melanoma immunotherapy is increasingly focusing. Reverse transcription-PCR analyses identified the presence of the large majority of investigated CTA (i.e., MAGE, GAGE, NY-ESO and SSX families) in different MSC populations. MSC expressed MAGE-A proteins as detected by western blot; noteworthy, the distribution of MAGE-A proteins was highly homogeneous within given MSC populations as shown by confocal immunofluorescence. Promoter methylation studies unveiled a homogeneously-demethylated MAGE-A3 promoter that paired MAGE-A3 expression in MSC. Altogether these findings demonstrate that MSC can be efficiently targeted by CTA-directed immunotherapeutic approaches, and suggest that epigenetic patterns most likely drive the expression of CTA in MSC as previously shown for melanoma cells.
doi:10.1002/jcp.21380
PMCID: PMC3624762  PMID: 18205182
cancer stem cells; melanoma; immunotherapy; DNA methylation; cancer testis antigens
11.  PLX4032, a Potent Inhibitor of the B-Raf V600E Oncogene, Selectively Inhibits V600E-positive Melanomas 
Pigment cell & melanoma research  2010;23(6):820-827.
SUMMARY
Targeted intervention of the B-Raf V600E gene product that is prominent in melanoma has been met with modest success. Here, we characterize the pharmacological properties of PLX4032, a next-generation inhibitor with exquisite specificity against the V600E oncogene and striking anti-melanoma activity. PLX4032 induces potent cell cycle arrest, inhibits proliferation, and initiates apoptosis exclusively in V600E-positive cells in a variety of in vitro experimental systems; follow-up xenograft studies demonstrate extreme selectivity and efficacy against melanoma tumors bearing the V600E oncoproduct. The collective data support further exploration of PLX4032 as a candidate drug for patients with metastatic melanoma; accordingly, validation of PLX4032 as a therapeutic tool for melanoma patients is now underway in advanced human (Phase III) clinical trials.
doi:10.1111/j.1755-148X.2010.00763.x
PMCID: PMC3623294  PMID: 20973932
12.  Structure-based design of an organoruthenium Phosphatidyl-Inositol-3-Kinase inhibitor reveals a switch governing lipid kinase potency and selectivity 
ACS chemical biology  2008;3(5):305-316.
Mutations that constitutively activate the PI3K signaling pathway, including alterations in PI3K, PTEN and AKT are found in a variety of human cancers, implicating the PI3K lipid kinase as an attractive target for the development of therapeutic agents to treat cancer and other related diseases. In this study, we report on the combination of a novel organometallic kinase inhibitor scaffold with structure-based design to develop a PI3K inhibitor, called E5E2, with an IC50 potency in the mid-low-nanomolar range and selectivity against a panel of protein kinases. We also show that E5E2 inhibits phospho-AKT in human melanoma cells and leads to growth inhibition. Consistent with a role for the PI3K pathway in tumor cell invasion, E5E2 treatment also inhibits the migration of melanoma cells in a 3D spheroid assay. The structure of the PI3Kγ/E5E2 complex reveals the molecular features that give rise to this potency and selectivity towards lipid kinases with implications for the design of a subsequent generation of PI3K-isoform specific organometallic inhibitors.
doi:10.1021/cb800039y
PMCID: PMC3618672  PMID: 18484710
13.  Direct reprogramming of melanocytes to neural crest stem-like cells by one defined factor 
Stem cells (Dayton, Ohio)  2011;29(11):1752-1762.
Mouse and human somatic cells can either be reprogrammed to a pluripotent state or converted to another lineage with a combination of transcription factors suggesting that lineage commitment is a reversible process. Here we show that only one factor, the active intracellular form of Notch1, is sufficient to convert mature pigmented epidermal-derived melanocytes into functional multipotent neural crest stem-like cells. These induced neural crest stem cells (iNCSCs) proliferate as spheres under stem cell media conditions, re-express neural crest-related genes and differentiate into multiple neural crest derived mesenchymal and neuronal lineages. Moreover, iNCSCs are highly migratory and functional in ovo. These results demonstrate that mature melanocytes can be reprogrammed toward their primitive neural crest cell precursors through the activation of a single stem cell-related pathway. Reprogramming of melanocytes to iNCSCs may provide an alternate source of NCSCs for neuroregenerative applications.
doi:10.1002/stem.740
PMCID: PMC3615703  PMID: 21948558
Notch; melanocytes; neural crest stem cells; reprogramming; dedifferentiation
14.  Beyond ABC: another mechanism of drug resistance in melanoma side population 
It has been shown that a side population (SP), which is characterized by high chemical efflux capacity, is present in human melanoma cell lines. However it was not clear if patients' samples contain the same subpopulation. In this issue, Luo et al. (2012), for the first time, isolated SP cells directly from patients' melanomas. SP cells are resistant to paclitaxel due to the upregulation of ABCB1 and ABCB5. Notably, these cells are also resistant to temozolomide, which is not a substrate of ABC transporters, in an IL-8-dependent manner. This study provides novel clues for understanding how this small, but critical, subpopulation within melanomas is resistant to therapies.
doi:10.1038/jid.2012.220
PMCID: PMC3595155  PMID: 22971921
15.  A modified HSP70 inhibitor shows broad activity as an anticancer agent 
Molecular cancer research : MCR  2013;11(3):219-229.
The stress-induced heat shock protein 70 (HSP70) is an ATP-dependent molecular chaperone that plays a key role in refolding misfolded proteins and promoting cell survival following stress. HSP70 is marginally expressed in non-transformed cells, but is greatly overexpressed in tumor cells. Silencing HSP70 is uniformly cytotoxic to tumor but not normal cells; therefore, there has been great interest in the development of HSP70 inhibitors for cancer therapy. Here we report that the HSP70 inhibitor 2-phenylethynesulfonamide (PES) binds to the substrate-binding domain of HSP70, and requires the C-terminal helical ‘lid’ of this protein (amino acids 573-616) in order to bind. Using molecular modeling and in silico docking, we have identified a candidate binding site for PES in this region of HSP70, and we identify point mutants that fail to interact with PES. A preliminary structure-activity relationship analysis has revealed a derivative of PES, 2-(3-chlorophenyl) ethynesulfonamide (PES-Cl), which shows increased cytotoxicity and ability to inhibit autophagy, along with significantly improved ability to extend the life of mice with pre-B cell lymphoma, compared to the parent compound (p=0.015). Interestingly, we also show that these HSP70 inhibitors impair the activity of the Anaphase Promoting Complex/Cyclosome (APC/C) in cell-free extracts, and induce G2/M arrest and genomic instability in cancer cells. PES-Cl is thus a promising new anti-cancer compound with several notable mechanisms of action.
doi:10.1158/1541-7786.MCR-12-0547-T
PMCID: PMC3606282  PMID: 23303345
Phenylethynesulfonamide; HSP70; HSP72; lymphoma; autophagy; HSP90
16.  The Anti-Melanoma Activity of Dinaciclib, a Cyclin-Dependent Kinase Inhibitor, Is Dependent on p53 Signaling 
PLoS ONE  2013;8(3):e59588.
Although cyclin dependent kinase (CDK)-2 is known to be dispensable for the growth of most tumors, it is thought to be important for the proliferation of melanoma cells, where its expression is controlled by the melanocyte-lineage specific transcription factor MITF. Treatment of a panel of melanoma cells with the CDK inhibitor dinaciclib led to a concentration-dependent inhibition of growth under both 2D adherent and 3D organotypic cell culture conditions. Dinaciclib targeted melanoma cell lines regardless of cdk2 or MITF levels. Inhibition of growth was associated with a rapid induction of G2/M cell arrest and apoptosis. Treatment of human melanoma mouse xenografts with dinaciclib led to tumor regression associated with reduced retinoblastoma protein phosphorylation and Bcl-2 expression. Further mechanistic studies revealed that dinaciclib induces p53 expression whilst simultaneously downregulating the expression of the anti-apoptotic factors Mcl-1 and XIAP. To clarify the role of p53 activation in the dinaciclib-induced cell death, we generated melanoma cell lines in which p53 expression was knocked down using a shRNA lentiviral vector. Knockdown of p53 completely abolished the induction of apoptosis seen following dinaciclib treatment as shown by a lack of annexin-V staining and caspase-3 cleavage. Altogether, these data show that dinaciclib induces apoptosis in a large panel of melanoma cell lines through a mechanism requiring p53 expression.
doi:10.1371/journal.pone.0059588
PMCID: PMC3601112  PMID: 23527225
17.  Stem-like cells and therapy resistance in squamous cell carcinomas 
Cancer stem cells (CSCs) within squamous cell carcinomas (SCCs) are hypothesized to contribute to chemotherapy and radiation resistance and represent potentially useful pharmacologic targets. Hallmarks of the stem cell phenotype that may contribute to therapy resistance of CSCs include quiescence, evasion of apoptosis, resistance to DNA damage, and expression of drug transporter pumps. A variety of CSC populations within SCCs of the head and neck and esophagus have been defined tentatively, based on diverse surface markers and functional assays. Stem-like self-renewal and differentiation capacities of these SCC subpopulations are supported by sphere formation and clonogenicity assays in vitro as well as limiting dilution studies in xenograft models. Early evidence supports a role for SCC CSCs in intrinsic therapy resistance, while detailed mechanisms by which these subpopulations evade treatment remain to be defined. Development of novel SCC therapies will be aided by pursuing such mechanisms as well as refining current definitions for CSCs and clarifying their relevance to hierarchical versus dynamic models of stemness.
doi:10.1016/B978-0-12-397927-8.00008-7
PMCID: PMC3595160  PMID: 22959028
cancer stem cells; drug resistance; squamous cell carcinoma
18.  Resistance to BRAF inhibitors: Unraveling mechanisms and future treatment options 
Cancer research  2011;71(23):7137-7140.
The MAPK pathway has emerged as a central target for melanoma therapy due to its persistent activation in the majority of tumors. Several BRAF inhibitors aimed at curbing MAPK pathway activity are currently in advanced stages of clinical investigation. However, their therapeutic success is limited by the emergence of drug resistance, as responses are transient and tumors eventually recur. Understanding the mechanisms underlying resistance to BRAF inhibitors is essential to develop effective and long-lasting therapies for melanoma patients. Here, we briefly review recent pre-clinical studies providing insight into the molecular mechanisms of resistance to BRAF inhibitors and discuss potential strategies to treat drug resistant melanomas.
doi:10.1158/0008-5472.CAN-11-1243
PMCID: PMC3588168  PMID: 22131348
19.  Isolation and characterization of mouse and human esophageal epithelial cells in 3D organotypic culture 
Nature protocols  2012;7(2):235-246.
This protocol describes the isolation and characterization of mouse and human esophageal epithelial cells and the application of 3D organotypic culture (OTC), a form of tissue engineering. This model system permits the interrogation of mechanisms underlying epithelial-stromal interactions. We provide guidelines for isolating and cultivating several sources of epithelial cells and fibroblasts, as well as genetic manipulation of these cell types, as a prelude to their integration into OTC. The protocol includes a number of important applications, including histology, immunohistochemistry/immunofluorescence, genetic modification of epithelial cells and fibroblasts with retroviral and lentiviral vectors for overexpression of genes or RNA interference strategies, confocal imaging, laser capture microdissection, RNA microarrays of individual cellular compartments and protein-based assays. The OTC (3D) culture protocol takes 15 d to perform.
doi:10.1038/nprot.2011.437
PMCID: PMC3505594  PMID: 22240585
20.  Functional Profiling of Live Melanoma Samples Using a Novel Automated Platform 
PLoS ONE  2012;7(12):e52760.
Aims
This proof-of-concept study was designed to determine if functional, pharmacodynamic profiles relevant to targeted therapy could be derived from live human melanoma samples using a novel automated platform.
Methods
A series of 13 melanoma cell lines was briefly exposed to a BRAF inhibitor (PLX-4720) on a platform employing automated fluidics for sample processing. Levels of the phosphoprotein p-ERK in the mitogen-activated protein kinase (MAPK) pathway from treated and untreated sample aliquots were determined using a bead-based immunoassay. Comparison of these levels provided a determination of the pharmacodynamic effect of the drug on the MAPK pathway. A similar ex vivo analysis was performed on fine needle aspiration (FNA) biopsy samples from four murine xenograft models of metastatic melanoma, as well as 12 FNA samples from patients with metastatic melanoma.
Results
Melanoma cell lines with known sensitivity to BRAF inhibitors displayed marked suppression of the MAPK pathway in this system, while most BRAF inhibitor-resistant cell lines showed intact MAPK pathway activity despite exposure to a BRAF inhibitor (PLX-4720). FNA samples from melanoma xenografts showed comparable ex vivo MAPK activity as their respective cell lines in this system. FNA samples from patients with metastatic melanoma successfully yielded three categories of functional profiles including: MAPK pathway suppression; MAPK pathway reactivation; MAPK pathway stimulation. These profiles correlated with the anticipated MAPK activity, based on the known BRAF mutation status, as well as observed clinical responses to BRAF inhibitor therapy.
Conclusion
Pharmacodynamic information regarding the ex vivo effect of BRAF inhibitors on the MAPK pathway in live human melanoma samples can be reproducibly determined using a novel automated platform. Such information may be useful in preclinical and clinical drug development, as well as predicting response to targeted therapy in individual patients.
doi:10.1371/journal.pone.0052760
PMCID: PMC3532357  PMID: 23285177
21.  Fibroblasts contribute to melanoma tumour growth and drug resistance 
Molecular pharmaceutics  2011;8(6):2039-2049.
The role of tumour-stromal interactions in progression is generally well accepted but their role in initiation or treatment is less well understood. It is now generally agreed that rather than consisting solely of malignant cells, tumours consist of a complex dynamic mixture of cancer cells, host fibroblasts, endothelial cells, and immune cells that interact with each other and micro-environmental factors to drive tumour progression. We are particularly interested in stromal cells (for example fibroblasts) and stromal factors (for example fibronectin) as important players in tumour progression since they have also been implicated in drug resistance. Here we develop an integrated approach to understand the role of such stromal cells and factors in the growth and maintenance of tumours as well as their potential impact on treatment resistance, specifically in application to melanoma. Using a suite of experimental assays we show that melanoma cells can stimulate the recruitment of fibroblasts and activate them, resulting in melanoma cell growth by providing both structural (extra-cellular matrix proteins) and chemical support (growth factors). Motivated by these experimental results we construct a compartment model and use it to investigate the roles of both stromal activation and tumour aggressiveness in melanoma growth and progression. We utilise this model to investigate the role fibroblasts might play in melanoma treatment resistance and the clinically observed flare phenomena that is seen when a patient, who appears resistant to a targeted drug, is removed from that treatment. Our model makes the unexpected prediction that targeted therapies may actually hasten tumour progression once resistance has occurred. If confirmed experimentally, this provocative prediction may bring important new insights into how drug resistance could be managed clinically.
doi:10.1021/mp200421k
PMCID: PMC3235959  PMID: 22067046
22.  A NOTCH3-mediated squamous cell differentiation program limits expansion of EMT competent cells that express the ZEB transcription factors 
Cancer research  2011;71(21):6836-6847.
Zinc finger E-box binding (ZEB) proteins ZEB1 and ZEB2 are transcription factors essential in transforming growth factor (TGF)-β-mediated senescence, epithelial to mesenchymal transition (EMT) and cancer stem cell function. ZEBs are negatively regulated by members of the miR-200 microRNA family, but precisely how tumor cells expressing ZEBs emerge during invasive growth remains unknown. Here we report that NOTCH3-mediated signaling prevents expansion of a unique subset of ZEB-expressing cells. ZEB expression was associated with the lack of cellular capability of undergoing NOTCH3-mediated squamous differentiation in human esophageal cells. Genetic inhibition of the Notch-mediated transcriptional activity by dominant-negative Mastermind-like1 (DNMAML1) prevented squamous differentiation and induction of Notch target genes including NOTCH3. Moreover, DNMAML1 enriched EMT competent cells exhibited robust upregulation of ZEBs, downregulation of the miR-200 family, and enhanced anchorage independent growth and tumor formation in nude mice. RNA interference (RNAi) experiments suggested the involvement of ZEBs in anchorage independent colony formation, invasion and TGF-β-mediated EMT. Invasive growth and impaired squamous differentiation was recapitulated upon Notch inhibition by DNMAML1 in organotypic 3D culture, a form of human tissue engineering. Together, our findings indicate that NOTCH3 is a key factor limiting the expansion of ZEB-expressing cells, providing novel mechanistic insights into the role of Notch signaling in the cell fate regulation and disease progression of squamous esophageal cancers.
doi:10.1158/0008-5472.CAN-11-0846
PMCID: PMC3206139  PMID: 21890822
Notch; EMT; squamous cell differentiation; ZEB1; miR-200
23.  Immunotargeting of tumor subpopulations in melanoma patients 
Oncoimmunology  2012;1(8):1454-1456.
Several melanoma cell subpopulations with tumor-initiating and/or tumor-maintaining properties exist that may contribute to chemoresistance and tumor recurrence after standard therapies. One of these subpopulations expresses a B-cell marker, CD20. In a small pilot trial, we showed that a subset of Stage IV melanoma patients may potentially benefit from an adjuvant treatment using the anti-CD20 antibody rituximab.
doi:10.4161/onci.21357
PMCID: PMC3518536  PMID: 23243627
CD20; adjuvant immunotherapy; melanoma; rituximab; tumor-infiltrating B cells; tumor-initiating subpopulations
24.  From cancer stem cells to tumor maintenance in melanoma 
The utility of different models to identify cancer stem cells continues to be a subject of intense debate. Here, we summarize recent efforts to characterize intra-tumoral heterogeneity of melanoma and delineate key questions for future studies. Within a developing or already established tumor microenvironment, we propose that continuous tumor maintenance is assured by specific subpopulations whose phenotype is not static but instead is dynamically regulated. These small and temporarily distinct subpopulations likely play critical roles in tumor progression. They are important therapeutic targets but only in the context of combination therapies that also eliminate the bulk of the tumor.
doi:10.1038/jid.2011.159
PMCID: PMC3471358  PMID: 21654838
25.  Human breast cancer associated fibroblasts exhibit subtype specific gene expression profiles 
BMC Medical Genomics  2012;5:39.
Background
Breast cancer is a heterogeneous disease for which prognosis and treatment strategies are largely governed by the receptor status (estrogen, progesterone and Her2) of the tumor cells. Gene expression profiling of whole breast tumors further stratifies breast cancer into several molecular subtypes which also co-segregate with the receptor status of the tumor cells. We postulated that cancer associated fibroblasts (CAFs) within the tumor stroma may exhibit subtype specific gene expression profiles and thus contribute to the biology of the disease in a subtype specific manner. Several studies have reported gene expression profile differences between CAFs and normal breast fibroblasts but in none of these studies were the results stratified based on tumor subtypes.
Methods
To address whether gene expression in breast cancer associated fibroblasts varies between breast cancer subtypes, we compared the gene expression profiles of early passage primary CAFs isolated from twenty human breast cancer samples representing three main subtypes; seven ER+, seven triple negative (TNBC) and six Her2+.
Results
We observed significant expression differences between CAFs derived from Her2+ breast cancer and CAFs from TNBC and ER + cancers, particularly in pathways associated with cytoskeleton and integrin signaling. In the case of Her2+ breast cancer, the signaling pathways found to be selectively up regulated in CAFs likely contribute to the enhanced migration of breast cancer cells in transwell assays and may contribute to the unfavorable prognosis of Her2+ breast cancer.
Conclusions
These data demonstrate that in addition to the distinct molecular profiles that characterize the neoplastic cells, CAF gene expression is also differentially regulated in distinct subtypes of breast cancer.
doi:10.1186/1755-8794-5-39
PMCID: PMC3505468  PMID: 22954256

Results 1-25 (70)