Citations

Abstract Introduction: Cholangiocarcinoma (CCA) is a highly lethal hepatobiliary neoplasm with limited therapeutic options. Thus, new therapeutic strategies are needed to advance our treatment armamentarium for this devastating disease. MicroRNAs represent a new class of endogenous nucleic acids regulating development, cell death, and carcinogenesis. Recent studies have indicated that the miR-106b∼25 cluster, which is upregulated in cancer, has potential antiapoptotic properties. Meanwhile, we have demonstrated that Hedgehog (Hh) signaling is activated in CCA and also has a strong antiapoptotic effect. Based on this information, we posited that Hh signaling may regulate mir-106b∼25 expression. Due to the dependence of CCA on antiapoptotic signals, we conducted a study to determine the role of miR-106b∼25 in CCA apoptosis and unveil its regulatory mechanisms. Experimental procedures: Immortalized benign and malignant human cholangiocyte cell lines were used for the experiments. MicroRNA expression was analyzed using real-time quantitative RT-PCR (qRT-PCR) assays. The effect of the microRNAs was studied using Lipofectamine-based transfection with precursor microRNAs or locked-nucleic acid antagonists (LNAs) to respectively potentiate or decrease microRNAs expression. Functional apoptosis studies employed DAPI staining with fluorescent microscopic analysis of nuclear morphology, or biochemical measurement of caspase-3/7 activity. Western blotting and luciferase assays were conducted to identify potential messenger RNA targets. Results: Expression of miR-106b∼25 was enhanced in malignant vs. benign cholangiocyte cell lines. Treatment with the known antagonist of Hh signaling, cyclopamine, resulted in downregulation of the cluster. Because CCA cells express tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) in vivo, we next examined TRAIL-induced apoptosis in CCA cells. TRAIL-mediated apoptosis was attenuated by transfection with miR-25 and enhanced by LNAs. Computational analysis identified the TRAIL death receptor 4 (DR4) as a potential target of this cluster. Indeed, we observed downregulation of DR4 cellular protein levels during overexpression of miR-106b∼25 and upregulation of DR4 upon cluster inhibition with LNAs. The 3’untranslated region (UTR) of the DR4 mRNA was cloned into a luciferase reporter, and the potential direct regulation of DR4 by miR-106b∼25 examined. Indeed, the regulation of DR4 by miR-106b∼25 was confirmed by this luciferase assay demonstrating a direct inhibitory effect of the miR-106b∼25 polycistron on the DR4 3’UTR. Conclusions: The miR-106b∼25 cluster is overexpressed in malignant cholangiocyte cell lines, likely by a Hh signaling pathway. miR-106b∼25 inhibits apoptosis, at least in part, via downregulation of DR4. LNA targeted inhibition of miR-106b∼25 sensitizes CCA cells to apoptosis and may represent a new therapeutic strategy for this cancer. 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 199. doi:10.1158/1538-7445.AM2011-199

Abstract The pivotal roles of the K-RAS and TGFβ signaling pathways have been well characterized in a number of normal and pathological conditions including human cancer. Hyperactivation of the ERBB/KRAS pathway is known to drive neoplastic transformation, tumorigenesis and metastasis in a large percentage of human cancers while the growth inhibitory actions of TGFβ are critical in preventing cancer. A better understanding of the antagonistic interaction and cross-talk between the K-RAS and TGFβ signaling pathways that control tumorigenesis and metastasis may give rise to novel therapeutic interventions. Our previous work has highlight the importance of SIAH2 in K-RAS-dependent tumorigenesis and metastasis in human cancer. In this study, we showed that SMAD2/3/4 – the essential downstream mediators of TGFβ signaling, are new SIAH2 substrates. SIAH2 physically interacts with, ubiquitinates and degrades SMAD2/3/4 (but not SMAD1 – the downstream mediator of the BMP signaling pathway). The identification of the SIAH2-mediated SMAD2/3/4 modulation/degradation may provide an additional mechanism to explain the well documented, but less understood ERBB/K-RAS and TGFβ antagonism described in normal development, tumorigenesis and metastasis. We propose that the tumor promoting activity of RAS/SIAH2 may be mediated through the degradation of SMAD2/3/4 proteins and thus the relief of TGFβ-dependent growth inhibition in response to ERBB/K-RAS activation. The discovery of the SIAH2-SMAD2/3/4 antagonism downstream of K-RAS and TGFβ signaling pathways may provide a novel mode of antagonistic cross-talk between these two important signaling pathways to explain the growth inhibitory action of the TGFβ pathway and the growth-promoting activity of the K-RAS pathway in the genesis, progression and metastasis of human cancer. Since the substrate specificity of ubiquitin-mediated proteolysis is primarily determined by the E3 ligase, our results provide new insights into the role of altered proteolysis in mediating the context-dependent ERBB/RAS-TGFβ antagonism and cross-talk in human cancers. 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 1980. doi:10.1158/1538-7445.AM2011-1980

Abstract Introduction. Up to now PCNSL incidence in the US was presumed to be increasing in all age groups independent of changes in nosology, new diagnostic techniques, and HIV infection. The intent of our study was, firstly, to extend our prior study of PCNSL incidence in the US (Olson et al, Cancer 2002;95:1504-10) with an additional decade of SEER data; and, secondly, to determine time trends during the HAART era in the US. Methods. PCNSL age-adjusted incidence rates from 1973-2007 were obtained from the nine SEER registries used in the Olson et al. study. Similarly, the same exclusion criteria were used to remove PCNSL most likely associated with HIV (never married males and females; persons of unknown marital status; all cases reported in the San Francisco registry). To assess the accuracy of the criteria in removing HIV associated cases, incidence rates of Kaposi sarcoma (KS) were assessed with and without the use of the same exclusion criteria. Results. The incidence of PCNSL in the general population decreased from 1995 to 2000. Following this decrease, the incidence stabilized and is now beginning to increase in the last 5 years. Stratifying the incidence rate by age group and employing the exclusion criteria, PCNSL incidence has remained stable in the 20-64 year old population, but has steadily increased in the 65+ population. Removing the exclusion criteria did not alter the data for the 65+ population but demonstrated a sharp drop in incidence after 1996 for the 20-64 year old population. Applying the same HIV exclusion criteria the incidence of KS resulted in no appreciable change in incidence rates over the same time frame. Conclusion. The incidence rate of PCNSL is increasing. This increase is driven by a continued increase in incidence among the 65+ population while the incidence for those aged 20-64 has stabilized during the same time frame. An effect of HAART on PCNSL incidence in the US is suggested by the decline in the incidence among the 20-64 year old population without the HIV exclusion criteria. 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 1926. doi:10.1158/1538-7445.AM2011-1926

Abstract Background: Protein kinase C iota (PKCι) is an oncogene that is frequently targeted for tumor-specific gene amplification in human cancers harboring the 3q26 amplicon including Non-Small Cell Lung Carcinoma (NSCLC). PKCι is required for the maintenance of the transformed phenotype of NSCLC cells in vitro and in vivo. In addition, PKCι is critical for lung tumorigenesis in the LSL-K-rasG12D mouse model of NSCLC. Recently, we demonstrated that genetic disruption of Prkcι/λ; in LSL-K-rasG12D mice blocks K-ras-mediated expansion and morphological transformation of bronchioalveolar stem cells (BASCs), the first identifiable step in K-ras-mediated transformation in this model. These results demonstrate that PKCι plays a requisite role in tumor initiation, and suggest that PKCι may serve a similar role in the tumor-initiating activity of lung cancer stem cells. Our current studies aim to identify and characterize the molecular signaling pathway(s) by which PKCι regulates the biology of human lung squamous cell carcinoma (LSCC) tumor initiating cells (TICs) isolated from LSCC cell lines and primary tumors. Methods: Cultures enriched in TICs were established from LSCC lines or primary human LSCC tumors that harbor PRKCI amplification. PKCι expression in TIC cultures was inhibited by lentiviral shRNA, and the effect of PKCι knockdown on their stem-like properties was assessed. Whole genome deep sequencing analysis was performed on mRNA from parental, control TIC and PKCι knockdown TIC cultures in order to identify PKCι-regulated targets and signaling pathways in TICs. Results: LSCC TIC cultures express putative stem cell markers, and exhibit clonal expansion, self-renewal, enhanced anchorage-independent growth and tumorigenic potential in vivo. RNAi-mediated knockdown of PKCι inhibited TIC growth, clonal expansion, transformed growth and tumor initiation. mRNA sequencing revealed that PKCι regulates the expression and function of critical molecules involved in the stem-like phenotype of LSCC TICs. Details of PKCι-mediated signaling in LSCC TICs will be discussed. Conclusions: PKCι is required for maintenance of a highly tumorigenic stem-like population of cells in human LSCC. Given the prevalence of 3q26 amplification in human cancer, PKCι may regulate the biology of TICs in tumor types other than LSCC. Our results provide a rationale for therapeutic targeting of PKCι in LSCC TICs. Citation Format: Verline Justilien, Michael P. Walsh, Syed A. Ali, E. A. Thompson, Alan P. Fields. Protein Kinase C iota is required for the maintenance of a tumor-initiating cell phenotype in lung squamous cell carcinoma. [abstract]. In: Proceedings of the AACR-IASLC Joint Conference on Molecular Origins of Lung Cancer; 2014 Jan 6-9; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2014;20(2Suppl):Abstract nr B02.

Abstract Purpose: The therapeutic potential of PARP inhibitors is predicted to extend beyond BRCA mutant phenotypes to homologous recombination (HR)-deficient cancers. Response of individual ovarian cancers to niraparib was characterized using treatment naïve, patient-derived tumorgraft models and correlated with predicted HR status and gene expression profile. Methods: Utilizing a living tumor bank of patient-derived ovarian xenografts (PDXs), niraparib (MK-4827) was evaluated in five high-grade ovarian cancer tumorgrafts (PDX077, PDX087, PDX039, PDX080 and PDX95) as monotherapy, combination with carboplatin ± paclitaxel and maintenance therapy. Intraperitoneal tumorgrafts were monitored for tumor growth with twice-weekly transabdominal ultrasound imaging. In vivo response to niraparib was correlated to massively parallel sequencing data (BROCA) for HR genes and with each source patient's platinum response. Tumorgrafts were accordingly classified into predicted HR-proficient and HR-deficient phenotypes. PARP1 and poly(ADP-ribose) polymer (pADPr) expression as well as gene expression by DNA microarray were compared between treatment and control tumor replicates, and HR-deficient vs. HR-proficient tumors. Results: PDX077 (verified to harbor a somatic BRCA2 mutation (predicted HR deficient)) and PDX039 without any HR mutations detected by BROCA (predicted HR proficient) both responded to niraparib monotherapy and combination therapy in vivo (p=0.002 and 0.009 for treated vs. control groups, respectively). Significant growth attenuation, but not regression, in response to single agent treatment was demonstrated in PDX080 (CDK12 mutation; predicted HR-deficient; p=0.02 vs. control). In comparison, a BRCA2-mutant model (PDX095) failed to respond to niraparib monotherapy (p=0.97). As predicted, niraparib was not active as a single agent or in combination with chemotherapy in a BRCA wild-type, predicted HR-proficient tumorgraft (PDX087; p=not significant). Niraparib enhanced tumor regression with carboplatin but not with paclitaxel/carboplatin in an HR-deficient tumorgraft (PDX077), and maintenance niraparib therapy was effective in prolonging recurrence-free survival. pADPr inhibition was demonstrated in all niraparib-treated tumorgrafts, while PARP1 degrada-tion was evident in tumorgrafts responsive to single agent niraparib. Differential gene expression was seen in niraparib treated vs. control tumors in HR-deficient tumorgrafts in comparison to HR-proficient tumors at the end of 4 weeks of treatment. Clustering of 6 most/least differentially expressed genes was predictive of response to niraparib. Furthermore, RAD51C and PTEN gene expression were diminished in PDX039 (HR proficient by BROCA; niraparib responsive), suggesting a possible mechanism for its sensitivity to niraparib. Conclusion: Response to niraparib was seen in both BRCA-mutant and BRCA-wildtype xenografts. Thus, BRCA or HR gene mutational status alone was not sufficient to predict response to niraparib. Low RAD51C, PTEN and loss of PARP1 expression following treatment were most characteristic of tumors responding to niraparib. Paclitaxel may be detrimental to the sensitizing effects of PARP inhibition on carboplatin, which may have clinical implications for the incorporation of PARP inhibitors in front-line treatment. Our data are supportive of the phase III study of niraparib as maintenance therapy in patients with platinum-sensitive ovarian cancer. This abstract is also presented as Poster A30. Citation Format: Mariam Al Hilli, S. John Weroha, Marc Becker, Xiaonan Hou, Sean Harrington, Sarah McKinstrey, Kimberly Kalli, Karin Goodman, Keith Wilcoxen, Elizabeth Swisher, Scott Kaufmann, Paul Haluska. In vivo antitumor activity of the PARP inhibitor niraparib (MK-4827) in homologous recombination deficient and proficient ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr PR05.

Abstract Background: Current options to prevent ovarian and breast cancer recurrence are limited. However, signs of anti-tumor immunity are associated with improved survival in patients who have experienced a number of different malignancies. After identifying folate receptor alpha (FR)-derived class II-binding peptides recognized by lymphocytes from patients who previously had breast or ovarian cancer, we developed a multi-peptide vaccine with five peptides, each of which was recognized by more than 25% of the patients. We combined this vaccine with metronomic cyclophosphamide in an attempt to selectively reduce T regulatory cells in the periphery and the tumor microenvironment. Methods: We obtained an Investigational New Drug approval from the Food and Drug Administration to perform a phase I study in 22 patients who were currently in remission from their breast or ovarian cancer. Participants were required to be at least 90 days past any treatment for their disease (other than hormonal treatment, if applicable) and show no current evidence of disease. After 28 days of metronomic cyclophosphamide, six monthly intradermal injections of the vaccine were given. The primary endpoints of the trial are safety and immunogenicity. Results: To date, 15 of 22 patients have enrolled (7 breast and 8 ovarian cancer patients). 4 breast and 2 ovarian cancer patients are available for toxicity evaluation. No serious major adverse events have been observed, with the expected injection site reactions being the primary toxicity experienced by most participants; grade 2 decreased white blood cell counts were observed in 3 patients at completion of cyclophosphamide. Two patients went off study prior to completing all six vaccinations, one for vision changes, and one for disease progression. Immune monitoring is underway, with major assays being ELISAs for high-affinity IgG targeting the FR and FR-peptide specific ELIspots. These data will be presented at the meeting. Conclusions: Metronomic cyclophosphamide followed by intradermal vaccinations with a multi-peptide vaccine targeting the tumor antigen FR appears to be a tolerable regimen at this preliminary point of the study. With the exception of vision changes in one patient, no serious safety concerns have arisen. Pursuit of this strategy in further clinical study will require demonstration of FR-specific immune responses, an acceptable toxicity profile, and demonstration that T regulatory cells are altered in the periphery. Citation Format: Kimberly R. Kalli, Courtney L. Erskine, James W. Krempski, Linda M. Benson, Vera J. Suman, Douglas J. Padley, Allan B. Dietz, Timothy J. Hobday, Amy C. Degnim, Lynn C. Hartmann, Matthew S. Block, Keith L. Knutson. Metronomic cyclophosphamide followed by a multi-peptide folate receptor vaccine for ovarian and breast cancer immunotherapy in the setting of minimal residual disease - a feasibility study. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr A82.

Abstract Our understanding of ovarian cancer is complicated by disease heterogeneity. There are five major histological types, each with alterations in different pathways and distinct clinical outcomes. Even within these histological types there is clinical and molecular heterogeneity. The Ovarian Tumor Tissue Analysis (OTTA) consortium was established to validate prognostic markers for ovarian cancer in a large population of patients to allow stratification by histological type and molecular subtype. OTTA is currently a collaboration among 38 studies and has tissue microarrays (TMAs) from over 8,000 tumors available for immunohistochemical (IHC) analysis. In addition formalin fixed paraffin embedded (FFPE) tissue on slides or cores are available from the majority of OTTA studies for DNA and RNA analysis. Approximatley 60% of the cases are part of the Ovarian Cancer Association Consortium (OCAC) and have genotype data on over 200,000 single nucleotide polymorphisms and extensive epidemiological data. We recently performed IHC analysis of 12 markers using centralised staining and scoring to reduce heterogeneity and improve power to validate biomarkers. We showed that estrogen receptor and progesterone receptor were prognostic markers for endometrioid and high-grade serous carcinomas by performing the first robust subtype-specific analyses of these biomarkers in nearly 3000 patients. In contrast, FOLR1 expression was not associated with survival in 1507 high-grade serous carcinomas. We have shown that FFPE material from OTTA is suitable for RNA expression analysis on high through-put platforms such as the NanoString GX system. Expression analysis of 50 candidate genes in 244 high grade serous ovarian cancer cases has validated prognostic markers identified by The Cancer Genome Atlas (TCGA) project and investigated a series of novel candidate genes. IHC and RNA expression profiling from formalin fixed paraffin embedded (FFPE) tumor tissue is being used to better subclassify the ovarian tumors for further analysis. We would welcome groups with collections of ovarian tumor samples and corrsponding clinical data to join OTTA and participate in ongoing collaborative projects. Citation Format: Susan J. Ramus, Martin Köbel, Weiva Sieh, Michael S. Anglesio, Joshua Millstein, David D. Bowtell, James D. Brenton, Estrid Høgdall, Paul DP Pharoah, Ellen L. Goode, David G. Huntsman. The ovarian tumor tissue analysis (OTTA) consortium. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr A27.

Abstract Background: Mucinous ovarian carcinomas (MC) and mucinous borderline ovarian tumours (MBOT) are associated with ERBB2 amplification and KRAS activating mutations. These events occur in a near-mutually exclusive pattern, and KRAS mutations are more prevalent in MBOTs than MC's whereas ERBB2 amplification is more frequently seen in MCs. Frequencies of mutations in other oncogenes and tumour suppressor genes in MC are not well established though TP53, BRAF, NRAS, and CDKN2A mutations have all been reported. As these carcinomas are commonly chemo-resistant a definitive molecular categorization of this subtype is needed as treatment options are explored. Methods: We undertook review of pathology reports and after exclusion of potential gastric, appendiceal or pancreatic involvement over 100 mucinous ovarian tumours were identified. HPV testing was undertaken to exclude rare metastasis from endocervical primary site. All specimens were assayed for p53 expression via TMA and subject to sequencing of common cancer gene hotspots using Ion-Torrent or Illumina MiSeq. Previously derived data on ERBB2 status was combined in our analysis and, where available, samples showing heterogeneity of ERBB2 amplification and any other Ras-pathway activating mutation were microdissected with components evaluated independently for concurrent hotspot mutations. Results: All samples were consistent with mucinous tumours of ovarian origin and none were HPV positive. We detected mutations in KRAS, BRAF, CDKN2A, TP53, PTEN, PIK3CA as well as presumed somatic/detrimental, variants in APC that have not previously been reported in mucinous tumours. Despite some samples having enriched tumour content, lower than expected allelic frequencies of KRAS activating mutations suggested intra-tumoural heterogeneity. This was consistent with results observed previously with rare ERBB2 amplification coinciding KRAS mutations. Conclusions: The prevalence of Ras-pathway mutations, especially amongst borderline lesions, suggests these mutations are critical for tumour onset. However varying allelic frequencies of KRAS mutations suggest progression to carcinoma is strongly influenced by other molecular features. Citation Format: Michael S. Anglesio, Robertson Mackenzie, Stefan Kommoss, Boris J. Winterhoff, Benjamin Kipp, Jaoquin Garcia, Jesse S. Voss, Kevin Halling, Sarah Kerr, Janine Senz, Winnie Yang, Magnus von Knebel Doeberitz, Elena-Sophie Prigge, Miriam Reuschenbach, Anna V. Tinker, Blake Gilks, Jamie N. Bakkum-Gamez, David G. Huntsman, Jessica N. McAlpine. Defining ovarian mucinous tumors: Cancer genes and heterogeneity. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr A18.

Abstract Glioblastoma multiforme (GBM) is the most common primary brain tumor in adults and is associated with a poor prognosis. Progress in developing effective therapies for this disease is significantly limited by the blood-brain barrier (BBB), which limits the delivery of many anti-cancer agents to infiltrative tumor cells. In addition to physical barriers, such as tight junctions, the efflux proteins bcrp and P-gp in the BBB limit the brain distribution of numerous anti-cancer agents. Palbociclib (PD0332991) is a potent Cdk4/6 inhibitor which has shown remarkable efficacy in treating peripheral (non-brain) tumors. The Cdk4 pathway is dysregulated in approximately 75% of GBM; most commonly, the pathway is hyperactivated through the homozygous deletion of p16 (52%), amplification of Cdk4 (18%), or amplification of Cdk6 (1%). The purpose of this study is to define the role of the efflux transporters P-gp and bcrp in the brain distribution of palbociclib and to examine if an intact BBB limits efficacy. Palbociclib brain distribution studies were performed in FVB wild-type, P-gp knockout (PKO; Mdr1a/b(-/-)), bcrp knockout (BKO; Bcrp1(-/-)), and triple knockout (TKO; Mdr1a/b(-/-)Bcrp1(-/-)) mice after an oral dose (10mg/kg). The concentrations of palbociclib from all distribution studies were determined by a sensitive and specific LC-MS/MS assay. Survival studies were conducted in patient-derived primary GBM xenograft models in athymic nu/nu mice. The brain exposure of palbociclib (AUCbrain-to-AUCplasma ratio) was ∼ 33.5, 3.2, and 150-fold higher as compared to WT mice (WT: .044; PKO: 1.34; BKO: 0.13; TKO: 6.24). Further, the steady-state brain-to-plasma ratio (B/P) of palbociclib after a constant intra-peritoneal infusion of 10 µg/hr for 48hrs was ∼120-fold higher in the TKO mice than the WT mice [WT: (0.21 ± 0.07); PKO: (2.48 ± .13); BKO: (0.43 ± 0.12); TKO: (26.5 ± 5.4) p < 0.0001]. Inhibition of P-gp and bcrp with elacridar (10 mg/kg IP) resulted in a marked increase in palbociclib brain distribution [control B/P (0.06 ± 0.02); elacridar treatment (2.0 ± 1.4)]. For survival studies, palbociclib was dosed at 150 mg/kg/day continuously. Consistent with limited brain penetration, palbociclib did not improve the median survival of an orthotopic GBM xenograft model. In contrast, treatment of GBM22 xenografts grown as flank tumors resulted in profound efficacy with a 70 day prolongation in the time for tumor volume to reach 1000mm3. These data suggest the clinical paradigm of a potent anti-cancer agent (for instance, palbociclib) used in the treatment of peripheral disease is less effective in the treatment of brain tumors due to the BBB and active efflux by P-gp and bcrp. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C81. Citation Format: Karen E. Parrish, Jenny L. Pokorny, Rajendar K. Mittapalli, Katrina Bakken, Jann N. Sarkaria, William F. Elmquist. BBB efflux pump activity limits brain penetration of palbociclib (PD0332991) in glioblastoma. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C81.

Abstract Background: Next-Generation sequencing has revolutionized genomic assessment of cancer and is being increasingly applied in the clinical setting to guide prognostic and therapeutic decision-making. Time to reporting of results, specimen quantity, analyte quality, and ethical-legal-social issues (ELSI) have constrained initial clinical applications to gene panels and whole exome based strategies. Methods: Patients who consented to participate underwent resections, excisional or core biopsies or bone marrow biopsies, followed by fresh frozen tumor/normal nucleic acid extraction, WGS/WES/RNASeq on the Illumina HiSeq2000 or HiSeq2500, bioinformatics analysis and therapeutic target prioritization by a multi-disciplinary Clinical Genomics Board (CGB). All prioritized targets were CLIA validated using Sanger sequencing, RT-qPCR, FISH or IHC as appropriate. Treatment was delivered using on/off-label FDA approved drugs, available clinical trials and single patient INDs. Results: We have enrolled 34 patients with advanced, treatment-refractory cancers [age(yrs): median 59, range 27-91; male/female (62%/38%); ECOG score: 1(92%), 2(4%), 4(4%); tumor type: pancreatic (26%), biliary (24%), multiple myeloma (6%), other (47%): uterine/cervical, NSCLC, mesothelioma, gastric, renal, bladder, testicular, basal cell, melanoma, laryngeal]. Sequencing data is available on 34 patients (WGS/WES/RNASeq [n=23], WGS/RNASeq [n=2], WGS/WES [n=2], WES/RNASeq [n=3] and WGS only [n=4]). The initial 6 patients were evaluated in a non-CLIA pilot phase and 28 in the CLIA enabled phase. Targets of putative therapeutic relevance (total: 44, targets/patient: range 1-4), were prioritized by the CGB in 22 out of 28 patients (79%) for CLIA validation. Time to initial report was 86 days (range 34-143) and time to CLIA validated results 106 days (range 79-152). CLIA validation was achieved in 21 of 22 patients. Genomic, target directed treatment was ultimately instituted in 10 patients [death prior to intended treatment (n=2), death prior to availability of results (n=3), inability to access treatment (n=1) and decision to pursue alternate therapy (n=6)] and preliminary clinical efficacy was noted in 4 patients (2 PR, 2 SD>4 month). Multiple mechanisms of drug access were utilized (on/off label FDA approved drugs [n=8], clinical trial [n=1] and single patient IND [n=1]). Conclusions: Integrated whole genome analysis in a CLIA setting is feasible. Integration of SNV, copy number and transcriptional data may allow for selection of putative driver genes to enhance targeted therapy decisions. Barriers for future broader implementation include need for shorter time to reporting and availability of therapies. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C66. Citation Format: Mitesh Borad. Pilot study of CLIA enabled integrated whole genome (WGS)/exome (WES)/transcriptome (RNAseq) next-gen sequencing to identify therapeutically relevant targets in advanced cancer patients. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C66.