Solution pH and oligoamine molecular weight dependence of the transition from monolayer to multilayer adsorption at the air-water interface from sodium dodecyl sulfate/oligoamine mixtures

Neutron reflectivity and surface tension have been used to investigate the solution pH and oligoamine molecular weight dependence of the adsorption of sodium dodecyl sulfate (SDS)/oligoamine mixtures at the air-water interface. For diethylenetriamine, triamine, or triethylenetetramine, tetramine mixed with SDS, there is monolayer adsorption at pH 7 and 10, and multilayer adsorption at pH 3. For the slightly higher molecular weight tetraethylenepentamine, pentamine, and pentaethylenehexamine, hexamine, the adsorption is in the form of a monolayer at pH 3 and multilayers at pH 7 and 10. Hence, there is a pH driven transition from monolayer to multilayer adsorption, which shifts from low pH to higher pH as the oligoamine molecular weight increases from tetramine to pentamine. This results from the relative balance between the electrostatic attraction between the SDS and amine nitrogen group which decreases as the charge density decreases with increasing pH, the ion-dipole interaction between the amine nitrogen and SDS sulfate group which is dominant at higher pH, and the hydrophobic interalkyl chain interaction between bound SDS molecules which changes with oligoamine molecular weight.

Lessons learned from lung cancer genomics: the emerging concept of individualized diagnostics and treatment

The advent of novel therapeutics that specifically target signaling pathways activated by genetic alterations has revolutionized the way patients with lung cancer are treated. Although only few and largely ineffective chemotherapeutic regimens were available 10 years ago, a lung tumor diagnosed today requires extensive pathologic subtyping and diagnosis of genome alterations to afford more effective treatment (eg, in EGFR-mutant adenocarcinoma). This change of paradigm has several profound implications, ranging from preclinical work on the mechanism of action to a novel, more biologically oriented taxonomy and from genome diagnostics to trial design. Here, we have summarized these developments into six conceptual paradigms that illustrate the transition from empirical cancer medicine to mechanistically based individualized oncology.

Kinetics of surfactant desorption at an air-solution interface

The kinetics of re-equilibration of the anionic surfactant sodium dodecylbenzene sulfonate at the air-solution interface have been studied using neutron reflectivity. The experimental arrangement incorporates a novel flow cell in which the subphase can be exchanged (diluted) using a laminar flow while the surface region remains unaltered. The rate of the re-equilibration is relatively slow and occurs over many tens of minutes, which is comparable with the dilution time scale of approximately 10-30 min. A detailed mathematical model, in which the rate of the desorption is determined by transport through a near-surface diffusion layer into a diluted bulk solution below, is developed and provides a good description of the time-dependent adsorption data. A key parameter of the model is the ratio of the depth of the diffusion layer, H(c), to the depth of the fluid, H(f), and we find that this is related to the reduced Péclet number, Pe*, for the system, via H(c)/H(f) = C/Pe*(1/2). Although from a highly idealized experimental arrangement, the results provide an important insight into the "rinse mechanism", which is applicable to a wide variety of domestic and industrial circumstances.

Adsorption of the linear poly(ethyleneimine) precursor poly(2-ethyl-2-oxazoline) and sodium dodecyl sulfate mixtures at the air-water interface: the impact of modification of the poly(ethyleneimine) functionality

The adsorption of the polymer-surfactant mixture of poly(2-ethyl-2-oxazoline)-sodium dodecyl sulfate at the air-water interface has been studied by neutron reflectivity and surface tension. The observed patterns of adsorption more closely resemble those encountered in weakly interacting polymer-surfactant mixtures, rather than the pronounced enhancements in adsorption observed in strongly interacting polymer-surfactant mixtures, such as in the related poly(ethyleneimine)-sodium dodecyl sulfate mixtures. The adsorption was found to be strongly dependent on solution pH, polymer molecular weight, and polymer concentration. At the lower and higher molecular weights studied, there was little enhancement in the sodium dodecyl sulfate adsorption at low sodium dodecyl sulfate concentrations, whereas at the intermediate polymer molecular weights, some enhancement in the adsorption was observed. For the higher-molecular-weight polymers and at increasingly higher polymer concentrations, a significant reduction of the surfactant at the interface compared to pure sodium dodecyl sulfate occurred for sodium dodecyl sulfate concentrations between the critical aggregation concentration and the critical micellar concentration. The results illustrate the important role of modifying the functionality of poly(ethyleneimine) on surface adsorption.

Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing

Lung adenocarcinoma, the most common subtype of non-small cell lung cancer, is responsible for more than 500,000 deaths per year worldwide. Here, we report exome and genome sequences of 183 lung adenocarcinoma tumor/normal DNA pairs. These analyses revealed a mean exonic somatic mutation rate of 12.0 events/megabase and identified the majority of genes previously reported as significantly mutated in lung adenocarcinoma. In addition, we identified statistically recurrent somatic mutations in the splicing factor gene U2AF1 and truncating mutations affecting RBM10 and ARID1A. Analysis of nucleotide context-specific mutation signatures grouped the sample set into distinct clusters that correlated with smoking history and alterations of reported lung adenocarcinoma genes. Whole-genome sequence analysis revealed frequent structural rearrangements, including in-frame exonic alterations within EGFR and SIK2 kinases. The candidate genes identified in this study are attractive targets for biological characterization and therapeutic targeting of lung adenocarcinoma.

Translating the therapeutic potential of AZD4547 in FGFR1-amplified non-small cell lung cancer through the use of patient-derived tumor xenograft models

PURPOSE

To investigate the incidence of FGFR1 amplification in Chinese non-small cell lung cancer (NSCLC) and to preclinically test the hypothesis that the novel, potent, and selective fibroblast growth factor receptor (FGFR) small-molecule inhibitor AZD4547 will deliver potent antitumor activity in NSCLC FGFR1-amplified patient-derived tumor xenograft (PDTX) models.

EXPERIMENTAL DESIGN

A range of assays was used to assess the translational relevance of FGFR1 amplification and AZD4547 treatment including in vitro lung cell line panel screening and pharmacodynamic (PD) analysis, FGFR1 FISH tissue microarray (TMA) analysis of Chinese NSCLC (n = 127), and, importantly, antitumor efficacy testing and PD analysis of lung PDTX models using AZD4547.

RESULTS

The incidence of FGFR1 amplification within Chinese patient NSCLC tumors was 12.5% of squamous origin (6 of 48) and 7% of adenocarcinoma (5 of 76). AZD4547 displayed a highly selective profile across a lung cell line panel, potently inhibiting cell growth only in those lines harboring amplified FGFR1 (GI(50) = 0.003-0.111 μmol/L). AZD4547 induced potent tumor stasis or regressive effects in four of five FGFR1-amplified squamous NSCLC PDTX models. Pharmacodynamic modulation was observed in vivo, and antitumor efficacy correlated well with FGFR1 FISH score and protein expression level.

CONCLUSIONS

This study provides novel epidemiologic data through identification of FGFR1 gene amplification in Chinese NSCLC specimens (particularly squamous) and, importantly, extends the clinical significance of this finding by using multiple FGFR1-amplified squamous lung cancer PDTX models to show tumor stasis or regression effects using a specific FGFR inhibitor (AZD4547). Thus, the translational science presented here provides a strong rationale for investigation of AZD4547 as a therapeutic option for patients with squamous NSCLC tumors harboring amplification of FGFR1.

Differential protein stability and ALK inhibitor sensitivity of EML4-ALK fusion variants

PURPOSE

ALK rearrangement-positive lung cancers can be effectively treated with ALK inhibitors. However, the magnitude and duration of response is heterogeneous. In addition, acquired resistance limits the efficacy of ALK inhibitors, with most upfront resistance mechanisms being unknown.

EXPERIMENTAL DESIGN

By making use of the Ba/F3 cell line model, we analyzed the cytotoxic efficacy of ALK kinase inhibitors as a function of different EML4-ALK fusion variants v1, v2, v3a, and v3b as well as of three artificially designed EML4-ALK deletion constructs and the ALK fusion genes KIF5b-ALK and NPM1-ALK. In addition, the intracellular localization, the sensitivity to HSP90 inhibition and the protein stability of ALK fusion proteins were studied.

RESULTS

Different ALK fusion genes and EML4-ALK variants exhibited differential sensitivity to the structurally diverse ALK kinase inhibitors crizotinib and TAE684. In addition, differential sensitivity correlated with differences in protein stability in EML4-ALK-expressing cells. Furthermore, the sensitivity to HSP90 inhibition also varied depending on the ALK fusion partner but differed from ALK inhibitor sensitivity patterns. Finally, combining inhibitors of ALK and HSP90 resulted in synergistic cytotoxicity.

CONCLUSIONS

Our results might explain some of the heterogeneous responses of ALK-positive tumors to ALK kinase inhibition observed in the clinic. Thus, targeted therapy of ALK-positive lung cancer should take into account the precise ALK genotype. Furthermore, combining ALK and HSP90 inhibitors might enhance tumor shrinkage in EML4-ALK-driven tumors.

Abstract 1682: Uncovering signals of somatic selection through whole exome and whole genome sequencing of lung adenocarcinoma

We have sequenced the exomes of over 100 and the genomes of over 20 lung adenocarcinoma tumor-normal specimen pairs. We performed hybrid capture exome sequencing of nearly 18,000 genes to >100X median per-sample coverage with 76bp paired-end reads. We performed whole genome sequencing achieving 60X median tumor and 20X median normal coverage with 350bp median insert size and 101bp paired-end reads. Our exome analysis yielded over 50,000 substitution and small indel coding events, with a mean somatic mutation rate of 10-11 events / MB. This resulted in over 300 non-synonymous coding events per patient, most of which were presumed to be passenger mutations unrelated to tumorigenesis. This high mutational load required us to develop novel statistical approaches (MutSig, Lawrence et al, in preparation) to identify putative lung adenocarcinoma driver genes under positive somatic selection. We constructed a complex neutral mutation model that considered sequence context and several additional genomic covariates shown to mediate gene to gene inhomogeneities of passenger mutation rates. Identification of significant deviations from this background model allowed us to recover almost all known frequently mutated lung adenocarcinoma genes, including TP53, KRAS, STK11, PIK3CA, EGFR, ERBB2, RB1, SMARCA4, and KEAP1, as well as a host of novel putative driver genes. We applied similar principles to identify pathways and sub-networks of genes undergoing apparent positive selection in lung adenocarcinoma. Whole genome analysis yielded several high-confidence in-frame protein fusion and promoter-gene fusion events enriched in tumor vs normal specimens. We also found large numbers of somatic substitution and indel events in promoters, enhancers, and non-coding DNA elements and identified putative sites of somatic retrotransposition in our whole genome data. Overall, our study eclipses previous large-scale characterization of somatic sequence variation (Refs. 1-3) in lung adenocarcinoma by at least an order of magnitude. Using novel methods adapted to the analysis of high-mutation rate tumor types (lung squamous cell carcinoma, melanoma, colorectal cancer), we are able to recover signals of selection in both known and novel genes and pathways. Our results illuminate novel lung adenocarcinoma tumor biology and provide targets for therapeutic and diagnostic investigation. References 1. Ding et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) vol. 455 (7216) pp. 1069-75 2. Kan et al. Diverse somatic mutation patterns and pathway alterations in human cancers. Nature (2010) vol. 466 (7308) pp. 869-73 3. Lee et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature (2010) vol. 465 (7297) pp. 473-7

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1682. doi:1538-7445.AM2012-1682

ALK mutations conferring differential resistance to structurally diverse ALK inhibitors

PURPOSE

EML4-ALK fusions define a subset of lung cancers that can be effectively treated with anaplastic lymphoma kinase (ALK) inhibitors. Unfortunately, the duration of response is heterogeneous and acquired resistance limits their ultimate efficacy. Thus, a better understanding of resistance mechanisms will help to enhance tumor control in EML4-ALK-positive tumors.

EXPERIMENTAL DESIGN

By applying orthogonal functional mutagenesis screening approaches, we screened for mutations inducing resistance to the aminopyridine PF02341066 (crizotinib) and/or the diaminopyrimidine TAE684.

RESULTS

Here, we show that the resistance mutation, L1196M, as well as other crizotinib resistance mutations (F1174L and G1269S), are highly sensitive to the structurally unrelated ALK inhibitor TAE684. In addition, we identified two novel EML4-ALK resistance mutations (L1198P and D1203N), which unlike previously reported mutations, induced resistance to both ALK inhibitors. An independent resistance screen in ALK-mutant neuroblastoma cells yielded the same L1198P resistance mutation but defined two additional mutations conferring resistance to TAE684 but not to PF02341066.

CONCLUSIONS

Our results show that different ALK resistance mutations as well as different ALK inhibitors impact the therapeutic efficacy in the setting of EML4-ALK fusions and ALK mutations.

Optimization of dosing for EGFR-mutant non-small cell lung cancer with evolutionary cancer modeling

Non-small cell lung cancers (NSCLCs) that harbor mutations within the epidermal growth factor receptor (EGFR) gene are sensitive to the tyrosine kinase inhibitors (TKIs) gefitinib and erlotinib. Unfortunately, all patients treated with these drugs will acquire resistance, most commonly as a result of a secondary mutation within EGFR (T790M). Because both drugs were developed to target wild-type EGFR, we hypothesized that current dosing schedules were not optimized for mutant EGFR or to prevent resistance. To investigate this further, we developed isogenic TKI-sensitive and TKI-resistant pairs of cell lines that mimic the behavior of human tumors. We determined that the drug-sensitive and drug-resistant EGFR-mutant cells exhibited differential growth kinetics, with the drug-resistant cells showing slower growth. We incorporated these data into evolutionary mathematical cancer models with constraints derived from clinical data sets. This modeling predicted alternative therapeutic strategies that could prolong the clinical benefit of TKIs against EGFR-mutant NSCLCs by delaying the development of resistance.

The adsorption and self-assembly of mixtures of alkylbenzene sulfonate isomers and the role of divalent electrolyte

In this paper, the role of the different structural isomers of the anionic surfactant sodium para-dodecyl benzene sulfonate, LAS, on surface adsorption and solution self-assembly has been studied. Using a combination of neutron reflectivity, NR, and small angle neutron scattering, SANS, the effect of mixing an isomer with a short symmetric hydrocarbon chain with one which has an asymmetric hydrocarbon chain on both the equilibrium surface adsorption behavior and the solution microstructure of the mixtures, both in the presence and absence of a divalent cation (Ca(2+)), has been investigated. In the absence of electrolyte, the LAS isomer mixtures form small charged globular micelles throughout the composition range studied. The micelle aggregation number increases with the increase in the asymmetric isomer content, reflecting an increase in the packing efficiency within the micelle. The addition of calcium ions promotes the formation of planar aggregates, as multilamellar vesicles, but only when the symmetric LAS isomer is the major component of the mixture. At a surfactant concentration just above the critical micelle concentration, CMC, and in the absence of electrolyte, the variation in the surface composition is close to the solution composition. Regular solution theory, RST, calculations show that this variation is also close to what is expected for ideal mixing. The addition of Ca(2+) ions induces a different surface behavior, resulting in the formation of multilayer structures at the interface throughout the entire composition range.

Mutations in the DDR2 kinase gene identify a novel therapeutic target in squamous cell lung cancer

While genomically targeted therapies have improved outcomes for patients with lung adenocarcinoma, little is known about the genomic alterations which drive squamous cell lung cancer. Sanger sequencing of the tyrosine kinome identified mutations in the DDR2 kinase gene in 3.8% of squamous cell lung cancers and cell lines. Squamous lung cancer cell lines harboring DDR2 mutations were selectively killed by knock-down of DDR2 by RNAi or by treatment with the multi-targeted kinase inhibitor dasatinib. Tumors established from a DDR2 mutant cell line were sensitive to dasatinib in xenograft models. Expression of mutated DDR2 led to cellular transformation which was blocked by dasatinib. A squamous cell lung cancer patient with a response to dasatinib and erlotinib treatment harbored a DDR2 kinase domain mutation. These data suggest that gain-of-function mutations in DDR2 are important oncogenic events and are amenable to therapy with dasatinib. As dasatinib is already approved for use, these findings could be rapidly translated into clinical trials.

SIGNIFICANCE

DDR2 mutations are present in 4% of lung SCCs, and DDR2 mutations are associated with sensitivity to dasatinib. These findings provide a rationale for designing clinical trials with the FDA-approved drug dasatinib in patients with lung SCCs.

Insights into ALK-driven cancers revealed through development of novel ALK tyrosine kinase inhibitors

Aberrant forms of the anaplastic lymphoma kinase (ALK) have been implicated in the pathogenesis of multiple human cancers, where ALK represents a rational therapeutic target in these settings. In this study, we report the identification and biological characterization of X-376 and X-396, two potent and highly specific ALK small molecule tyrosine kinase inhibitors (TKIs). In Ambit kinome screens, cell growth inhibition studies, and surrogate kinase assays, X-376 and X-396 were more potent inhibitors of ALK but less potent inhibitors of MET compared to PF-02341066 (PF-1066), an ALK/MET dual TKI currently in clinical trials. Both X-376 and X-396 displayed potent antitumor activity in vivo with favorable pharmacokinetic and toxicity profiles. Similar levels of drug sensitivity were displayed by the three most common ALK fusion proteins in lung cancer (EML4-ALK variants E13;A20, E20;A20, and E6b;A20) as well as a KIF5B-ALK fusion protein. Moreover, X-396 could potently inhibit ALK kinases engineered with two point mutations associated with acquired resistance to PF-1066, L1196M, and C1156Y, when engineered into an E13;A20 fusion variant. Finally, X-396 displayed synergistic growth inhibitory activity when combined with the mTOR inhibitor rapamycin. Our findings offer preclinical proof-of-concept for use of these novel agents to improve therapeutic outcomes of patients with mutant ALK-driven malignancies.

Blood-based gene expression signatures in non-small cell lung cancer

PURPOSE

Blood-based surrogate markers would be attractive biomarkers for early detection, diagnosis, prognosis, and prediction of therapeutic outcome in cancer. Disease-associated gene expression signatures in peripheral blood mononuclear cells (PBMC) have been described for several cancer types. However, RNA-stabilized whole blood-based technologies would be clinically more applicable and robust. We evaluated the applicability of whole blood-based gene expression profiling for the detection of non-small cell lung cancer (NSCLC).

EXPERIMENTAL DESIGN

Expression profiles were generated from PAXgene-stabilized blood samples from three independent groups consisting of NSCLC cases and controls (n = 77, 54, and 102), using the Illumina WG6-VS2 system.

RESULTS

Several genes are consistently differentially expressed in whole blood of NSCLC patients and controls. These expression profiles were used to build a diagnostic classifier for NSCLC, which was validated in an independent validation set of NSCLC patients (stages I-IV) and hospital-based controls. The area under the receiver operator curve was calculated to be 0.824 (P < 0.001). In a further independent dataset of stage I NSCLC patients and healthy controls the AUC was 0.977 (P < 0.001). Specificity of the classifier was validated by permutation analysis in both validation cohorts. Genes within the classifier are enriched in immune-associated genes and show specificity for NSCLC.

CONCLUSIONS

Our results show that gene expression profiles of whole blood allow for detection of manifest NSCLC. These results prompt further development of gene expression-based biomarker tests in peripheral blood for the diagnosis and early detection of NSCLC.

Abstract 4977: Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables discovery of a novel C6orf204-PDGFRβ fusion in a patient with T-ALL and eosinophilia

Tyrosine kinase (TK) fusion proteins result from genomic rearrangements that juxtapose TK signaling domains with various upstream partners. Since tumor cells can become dependent upon the resultant constitutive kinase activity for tumorigenesis and survival, TK fusions serve as attractive therapeutic targets. However, identification of TK fusions in cancers has been hindered by experimental techniques that lack sufficient sensitivity and throughput. To overcome these challenges, we developed a screen to systematically identify TK fusions in tumor DNA. This method involves selective capture of regions upstream of GXGXXG kinase motifs where TK fusion breakpoints are likely to occur followed by next generation sequencing and custom computational analysis. This approach was previously validated using cell line DNA (Chmielecki et al, ‘10). Here, we used an improved version of our platform to identify a novel TK fusion using DNA isolated from whole blood of a patient with recurrent precursor T lymphoblastic lymphoma (T-ALL) who presented with new leukocytosis and bone marrow findings compatible with a myeloproliferative neoplasm (MPN) with eosinophilia. Cytogenetic analysis of a bone marrow aspirate prior to treatment for the patient's MPN revealed a karyotype with a t(5;6)(q33-34;q23). At recurrence, a 5q33/PDGFRβ rearrangement with a breakpoint proximal to the MYB locus on chromosome 6 was identified with fluorescence in situ hybridization (FISH). Prior to allogeneic hematopoietic cell transplantation, a brief trial of imatinib confirmed responsiveness of eosinophilia. To identify the exact fusion breakpoint, 3 µg of whole blood genomic DNA was subjected to genomic capture followed by paired-end SOLiD sequencing. Fusion candidates were validated by direct sequencing of PCR products generated with breakpoint spanning primers. Analysis of the recovered sequences identified a fusion involving c6orf204 upstream of the PDGFRβ TK domain. 5’-RACE confirmed expression of c6orf204-PDGFRβ mRNA in the patient's blood cells. Motif analysis of the 5’ c6orf204 sequence present within the fusion revealed a coiled-coil domain, which likely facilitates dimerization of the kinase, as observed in other TK fusions (e.g. BCR-ABL). Interestingly, retrospective FISH studies of the patient's diagnostic lymph node involved by T-ALL also revealed the presence of a PDGFRβ rearrangement. These data suggest that the rearrangement occurred in a multi-potent progenitor cell that gave rise to both the T-ALL and MPN. This finding is analogous to 8p MPNs involving FGFR1, but has not yet been reported with PDGFRβ. Further biochemical analysis of this TK fusion is currently underway, and additional tumor samples are undergoing screening for other novel TK fusions. This work was supported by an SU2C-AACR Innovative Research Grant to WP.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4977. doi:10.1158/1538-7445.AM2011-4977

Abstract LB-263: Novel tumor suppressors and mutationally affected signaling pathways in small-cell lung cancer identified by whole exome sequencing

Small-cell lung cancer (SCLC) is an aggressive lung cancer subtype characterized by early metastasis and a peculiar neuroendocrine phenotype. Unfortunately, SCLC is difficult to sample because these patients are not routinely undergoing surgery. In order to shed light on the biology of this tumor type and to discover novel therapeutic targets, we have conducted whole-exome sequencing of 24 SCLC tumors as well as high-density gene copy number analyses of 64 SCLC specimens. On average we observe a high mutation rate of 7.9±1.0 protein changing mutations per million basepairs and an unusually high C:G&gt;A:T transversion rate that has been associated with excessive smoking. In addition to frequent mutations in TP53 (80%) and RB1(63%), we identified mutations in LRP1B (13/24 samples), a gene that is known to be frequently mutated in lung adenocarcinoma. To our surprise, we found a significant enrichment of neuronal genes (FDR q-value: &lt; 10e-10) suggesting that the neuroendocrine differentiation of SCLC might be primarily driven by mutational events. Other frequently mutated genes encode proteins involved in cell-cell and cell-matrix interactions. This observation might explain the aggressiveness and metastatic capability of SCLC. A systematic analysis of copy number losses and loss of heterozygosity revealed a distinct pattern for novel candidate tumor suppressor genes when integrated with somatic mutations. Performing the pathway analysis on each individual sample clearly showed that SCLC tumors segregate by mutational landscape. Furthermore, the analysis of autopsy-derived tumor specimens revealed that surgically resected tumors are not dissimilar to late-stage SCLC. In summary, we have defined the mutational and genomic landscape of SCLC that may help explaining some of the phenotypic and clinical properties of this fatal tumor type. Our data provides a rich source for future functional analyses of putative tumor suppressor genes and oncogenes as well as for potential novel drug targets.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-263. doi:10.1158/1538-7445.AM2011-LB-263

Abstract 4701: Integrated chemo-genomics approach for the identification of therapeutically amenable targets in small cell lung cancer

Small-cell lung cancer (SCLC) is the third most common lung cancer type and with a median overall survival of only 9.3 month for extended disease patients also one of the deadliest worldwide. While analyses of the genetic landscape of non-small cell lung cancers led to the identification of therapeutically amenable targets such as mutant EGFR or EML4-ALK fusions, the characterization of oncogenic pathways that drive tumorigenesis in SCLC lags behind this development, resulting in a lack of treatment options for SCLC patients. To address this therapeutic need systematically we performed high-resolution gene-copy number (6.0 SNP-arrays) in a cohort of 108 SCLC specimens (n=47 primary samples; n=61 cell lines). This analysis revealed novel recurrent amplifications and deletions that are specifically enriched in SCLC when compared to non-small cell lung cancer specimen. We next annotated the significant genetic lesions found in our SCLC set and linked these with the activity profiles of a library of 270 novel proprietary compounds as well as compounds currently in clinical develop, which were screened in 51 SCLC cell lines. Using an integrated genomics approach we detected genetic predictors for the activity and resistance to known PI3K/AKT-pathway inhibitors as well as novel inhibitors previously not associated with activity in SCLC. Using orthogonal functional assays we validated genetic alterations that predicted cytotoxicity of Pi3-kinase inhibition in SCLC cell lines and we validated compounds that exhibited exquisite cytotoxicity in MYC-amplified tumors. Overall, our data provides the first detailed genetic landscape of small-cell lung cancer with a functional annotation and implies that PI3K/AKT-pathway inhibitors represent therapeutics that warrant further clinical investigation in SCLC patients.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4701. doi:10.1158/1538-7445.AM2011-4701

Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer

Lung cancer remains one of the leading causes of cancer-related death in developed countries. Although lung adenocarcinomas with EGFR mutations or EML4-ALK fusions respond to treatment by epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) inhibition, respectively, squamous cell lung cancer currently lacks therapeutically exploitable genetic alterations. We conducted a systematic search in a set of 232 lung cancer specimens for genetic alterations that were therapeutically amenable and then performed high-resolution gene copy number analyses. We identified frequent and focal fibroblast growth factor receptor 1 (FGFR1) amplification in squamous cell lung cancer (n = 155), but not in other lung cancer subtypes, and, by fluorescence in situ hybridization, confirmed the presence of FGFR1 amplifications in an independent cohort of squamous cell lung cancer samples (22% of cases). Using cell-based screening with the FGFR inhibitor PD173074 in a large (n = 83) panel of lung cancer cell lines, we demonstrated that this compound inhibited growth and induced apoptosis specifically in those lung cancer cells carrying amplified FGFR1. We validated the FGFR1 dependence of FGFR1-amplified cell lines by FGFR1 knockdown and by ectopic expression of an FGFR1-resistant allele (FGFR1(V561M)), which rescued FGFR1-amplified cells from PD173074-mediated cytotoxicity. Finally, we showed that inhibition of FGFR1 with a small molecule led to significant tumor shrinkage in vivo. Thus, focal FGFR1 amplification is common in squamous cell lung cancer and associated with tumor growth and survival, suggesting that FGFR inhibitors may be a viable therapeutic option in this cohort of patients.

Early prediction of nonprogression in advanced non-small-cell lung cancer treated with erlotinib by using [(18)F]fluorodeoxyglucose and [(18)F]fluorothymidine positron emission tomography

PURPOSE

Positron emission tomography (PET) with both 2'-deoxy-2'-[(18)F]fluoro-D-glucose (FDG) and 3'-[(18)F]fluoro-3'-deoxy-L-thymidine (FLT) was evaluated with respect to the accuracy of early prediction of nonprogression following erlotinib therapy, independent from epidermal growth factor receptor (EGFR) mutational status, in patients with previously untreated advanced non-small-cell lung cancer (NSCLC).

PATIENTS AND METHODS

Thirty-four patients with untreated stage IV NSCLC were evaluated in this phase II trial. Changes in FDG and FLT uptake after 1 (early) and 6 (late) weeks of erlotinib treatment were compared with nonprogression measured by computed tomography after 6 weeks of treatment, progression-free survival (PFS), and overall survival (OS).

RESULTS

Changes in FDG uptake after 1 week of therapy predicted nonprogression after 6 weeks of therapy with an area under the receiver operating characteristic curve of 0.75 (P = .02). Furthermore, patients with an early metabolic FDG response (cutoff value: 30% reduction in the peak standardized uptake value) had significantly longer PFS (hazard ratio [HR], 0.23; 95% CI, 0.09 to 0.59; P = .002) and OS (HR, 0.36; 95% CI, 0.13 to 0.96; P = .04). Early FLT response also predicted significantly longer PFS (HR, 0.31; 95% CI, 0.10 to 0.95; P = .04) but not OS and was not predictive for nonprogression after 6 weeks of therapy.

CONCLUSION

Early FDG-PET predicts PFS, OS, and nonprogression after 6 weeks of therapy with erlotinib in unselected, previously untreated patients with advanced NSCLC independent from EGFR mutational status.

Adsorption of polyelectrolyte/surfactant mixtures at the air-water interface: modified poly(ethyleneimine) and sodium dodecyl sulfate

The adsorption of surfactant/polyelectrolyte mixtures of sodium dodecyl sulfate (SDS) and different modified poly(ethyleneimine) (PEI) polyelectrolytes at the air-water interface has been studied using neutron reflectivity and surface tension. Modification of the PEI by the addition of short ethylene oxide (EO) or propylene oxide (PO) groups is shown to have an impact upon the surface adsorption behavior. This is due to a modification of the polymer/surfactant interaction, an increase in the intrinsic surface activity of the modified polyelectrolyte, and changes in the relative importance of surface and solution complex formation. For the polyelectrolyte PEI, there is a marked change in the surface adsorption behavior between the addition of a single EO group and that of the (EO)3 group. The addition of a single EO or PO group to the PEI results in an SDS concentration and solution pH adsorption dependence that is broadly similar in behavior to that of the unmodified PEI/SDS mixture. That is, there is strong surface complexation and adsorption down to low SDS concentrations, and there is evidence of a strong interaction at high pH in addition to the strong electrostatic attraction at low pH. The addition of a larger ethylene oxide group, triethylene oxide (EO)3, results in a surface adsorption behavior that more closely resembles that of a neutral polymer/ionic surfactant mixture, similar to that observed for PEI with a larger ethylene oxide group, notably PEI-(EO)7. In that case, the adsorption of the polymer/surfactant complex is much less pronounced. The adsorption arises predominantly from competition between the polymer and surfactant and indicates a decrease in the polymer/surfactant interaction with increasing pH. That is, increasing the size of the ethylene oxide group induces a transition from a strong surface polymer/surfactant interaction to a weak polymer/surfactant interaction.

Solution self-assembly and adsorption at the air-water interface of the monorhamnose and dirhamnose rhamnolipids and their mixtures

The self-assembly in solution and adsorption at the air-water interface, measured by small-angle neutron scattering, SANS, and neutron reflectivity, NR, of the monorhamnose and dirhamnose rhamnolipids (R1, R2) and their mixtures, are discussed. The production of the deuterium-labeled rhamnolipids (required for the NR studies) from a Pseudomonas aeruginosa culture and their separation into the pure R1 and R2 components is described. At the air-water interface, R1 and R2 exhibit Langmuir-like adsorption isotherms, with saturated area/molecule values of about 60 and 75 Å(2), respectively. In R1/R2 mixtures, there is a strong partitioning of R1 to the surface and R2 competes less favorably because of the steric or packing constraints of the larger R2 dirhamnose headgroup. In dilute solution (<20 mM), R1 and R2 form small globular micelles, L(1), with aggregation numbers of about 50 and 30, respectively. At higher solution concentrations, R1 has a predominantly planar structure, L(α) (unilamellar, ULV, or bilamellar, BLV, vesicles) whereas R2 remains globular, with an aggregation number that increases with increasing surfactant concentration. For R1/R2 mixtures, solutions rich in R2 are predominantly micellar whereas solutions rich in R1 have a more planar structure. At an intermediate composition (60 to 80 mol % R1), there are mixed L(α)/L(1) and L(1)/L(α) regions. However, the higher preferred curvature associated with R2 tends to dominate the mixed R1/R2 microstructure and its associated phase behavior.

Mixing behavior of the biosurfactant, rhamnolipid, with a conventional anionic surfactant, sodium dodecyl benzene sulfonate

The use of small angle neutron scattering, SANS, neutron reflectivity, NR, and surface tension to study the mixing properties of the biosurfactant rhamnolipid with a conventional anionic surfactant, sodium dodecyl 6-benzene sulfonate, LAS, is reported. The monorhamnose rhamnolipid, R1, mixes close to ideally with LAS at the air-water interface, whereas for mixtures of LAS with the dirhamnose rhamnolipid, R2, the LAS strongly partitions to the air-water interface relative to R2, probably because of the steric hindrance of the larger R2 headgroup. These trends in the binary mixtures are also reflected in the ternary R1/R2/LAS mixtures. However, for these ternary mixtures, there is also a pronounced synergy in the total adsorption, which reaches a maximum for a LAS/rhamnolipid mole ratio of about 0.6 and a R1/R2 mol ratio of about 0.5, an effect which is not observed in the binary mixtures. In solution, the R1/LAS mixtures form relatively small globular micelles, L(1), at low surfactant concentrations (<20 mM), more planar structures (lamellar, L(α), unilamellar/multilamellar vesicles, ulv/mlv) are formed at higher surfactant concentrations for R1 and LAS rich compositions, and a large mixed phase (L(α)/L(1) and L(1)/L(α)) region forms at intermediate surfactant compositions. In contrast, for the R2/LAS mixtures, the higher preferred curvature of R2 dominates the phase behavior. The predominant microstructure is in the form of small globular micelles, except for solution compositions rich in LAS (>80 mol % LAS) where more planar structures are formed. For the ternary mixtures, there is an evolution in the resulting phase behavior from one dominated by L(1) (R2 rich) to one dominated by planar structures, L(α), (R1, LAS rich), and which strongly depends upon the LAS/rhamnolipid and R1/R2 mole ratio.