bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract A1-36: The genomics of young lung cancer
Authors: Gitlitz Barbara J. , Morosini Deborah , Sable-Hunt Alicia , Addario Bonnie J. , Oxnard Geoffrey R.
Published: November 2015

Primary lung cancer is increasingly understood as a heterogeneous disease made up of genomically defined subtypes requiring distinct treatment strategies. We hypothesize young age at diagnosis (<40 years) is a clinical characteristic associated with an increased chance for a targetable mutation. Our study will prospectively characterize the somatic and germline genomics of young lung cancer (GYLC). Our goals are to identify a genomically enriched subtype of lung cancer, facilitate delivery of targeted therapy and lay the groundwork for further studies of heritable and environmental lung cancer risk factors. A website allows for virtual consenting so patients can participate remotely and use social media to share our trial.

We have defined 7 genomic alterations of interest, based on the lung cancer mutational consortium (LCMC) (EGFR, KRAS, HER2, BRAF, ALK, ROS1, RET). Subjects will undergo CLIA genomics to ensure that all of these genes have been tested. Those who are wild type will receive additional CLIA genomics using the FoundationOne® Heme panel, with the goal of identifying novel oncogenic drivers. Additional investigational genomics will include blood for germline testing. We believe the prevalence of targetable mutations will be greater in our population as compared to the LCMC and have powered our study to show an increase from 35% to 50%; and an improvement in the use of targeted therapy from 22% to 40%. The trial is currently accruing (NCT02273336). Preliminary results at 20% accrual show over 60% of pts with ALK, ROS1 or EGFR mutations. Further results to be presented at the meeting.

(This trial is facilitated by the Addario Lung Cancer Medical Institute)

Citation Format: Barbara J. Gitlitz, Deborah Morosini, Alicia Sable-Hunt, Bonnie J. Addario, Geoffrey R. Oxnard. The genomics of young lung cancer. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-36.
Abstract A1-52: Identification of drug-sensitive Notch receptor alterations in human breast cancer
Authors: Wang Kai , Zhang Qin , Li Danan , Ching Keith , Zhang Cathy , Zheng Xianxian , Ozeck Mark , Shi Stephanie , Li Xiaorong , Wang Hui , Rejto Paul , Christensen James , Olson Peter
Published: November 2015

While the Notch pathway is reportedly activated in breast cancer, the molecular mechanisms leading to its aberrant activation remain elusive, hampering the optimal development of Notch inhibitors in the clinics. In an effort to identify predictive biomarkers of response to Notch targeted therapies in breast cancer, we used several computational approaches, including novel algorithms for detecting complex structural rearrangements, to analyze next generation sequencing and related omic datasets from The Cancer Genome Atlas (TCGA) breast cancer cohort. We identified simple mutations and complex rearrangements in NOTCH1, NOTCH2 and NOTCH3 that compromised the function of the PEST domain, a negative regulatory domain controlling the duration of active Notch signaling. Focal amplifications of NOTCH2 and NOTCH3 were also observed, as were heterodimerization or extracellular domain alterations, at lower incidence. Mutations and amplifications often activated the Notch pathway as evidenced by increased expression of canonical Notch target genes, and functional mutations were significantly enriched in the triple negative breast cancer (TNBC) subtype. We also sequenced a panel of breast cancer xenograft models and identified models that harbor functionally equivalent PEST domain alterations. These models were significantly more sensitive to a gamma secretase inhibitor (GSI) compared to models without Notch alterations. Gene expression and functional analyses were performed to study the mechanism of activation through mutation and inhibition by GSI. In summary, we demonstrated that Notch pathway is activated via multiple mutational mechanisms primarily involving the PEST domains of NOTCH1, NOTCH2 and NOTCH3. Collectively, approximately 13% of TNBC exhibits a genetic alteration coupled with pathway up-regulation and these alterations may serve as biomarkers to identify patients most likely to respond to Notch inhibitors.

Citation Format: Kai Wang, Qin Zhang, Danan Li, Keith Ching, Cathy Zhang, Xianxian Zheng, Mark Ozeck, Stephanie Shi, Xiaorong Li, Hui Wang, Paul Rejto, James Christensen, Peter Olson. Identification of drug-sensitive Notch receptor alterations in human breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-52.
Abstract A1-55: Combination of a three-microRNA signature and TP53 genotype predicts responses to platinum-based doublet chemotherapy in patients with lung adenocarcinoma
Authors: Shiraishi Kouya , Saito Motonobu , Kohno Takashi
Published: November 2015

Platinum-based doublet, i.e., a combination of a platinum agent and another agent, is a standard regimen to treat non-small cell lung cancer, since molecular target therapy using tyrosine kinase inhibitors is effective only in a subset of patients with tumors with druggable oncogene mutations. Therefore, to identify biomarkers that can discriminate responders who received platinum-based chemotherapy before treatment is important to improve the efficacy of chemotherapy for non-small cell lung cancer. We found that a SNP in TP53 tumor suppressor gene, TP53-Arg72Pro is associated with response to the platinum-based doublet therapy (Shiraishi et al, JCO, 2010). We recently assessed intra-tumor micro (mi)RNA expression as a biomarker for predicting responses to platinum-based chemotherapy in patients with recurrent lung adenocarcinoma. Microarray-based screening of 904 miRNAs followed by quantitative reverse transcription-PCR-based verification in 40 test cohort samples, including 16 (40.0%) responders, was performed to identify miRNAs that are differentially expressed in chemotherapy responders and non-responders. Differential expression was confirmed in a validation cohort (n = 63 samples), including 18 (28.6%) responders. A signature comprising three miRNAs (miR1290, miR196b, and miR135a*) enabled the prediction of a chemotherapeutic response (rather than progression-free and overall survival) with high accuracy in both the test and validation cohorts (82.5% and 77.8%). Examination of the latter was performed using miRNAs extracted from archived formalin-fixed paraffin-embedded tissues. Genotype data for the TP53-Arg72Pro polymorphism, which is associated with responses to platinum-based doublet chemotherapy, were subsequently incorporated into the prediction analysis. Finally, combining this miRNA signature with the TP53-Arg72Pro polymorphism genotype marginally improved the predictive power (Saito et al., Clin. Cancer Res. 2014).

Citation Format: Kouya Shiraishi, Motonobu Saito, Takashi Kohno. Combination of a three-microRNA signature and TP53 genotype predicts responses to platinum-based doublet chemotherapy in patients with lung adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-55.
Abstract A1-59: Multiple mechanisms of MYCN dysregulation in Wilms tumor
Authors: Williams Richard D. , Chagtai Tasnim , Alcaide-German Marisa , Apps John , Wegert Jenny , Popov Sergey , Vujanic Gordan , Tinteren Harm van , Heuvel-Eibrink Marry M. van den , Kool Marcel , Gisselsson David , Graf Norbert , Gessler Manfred , Pritchard-Jones Kathy
Published: November 2015

Background and Purpose: Wilms tumor (WT) is the commonest pediatric renal malignancy. A significant minority of cases have mutations in known genes or recurrent copy number aberrations, but few of these have prognostic value. We have previously observed MYCN copy number gain in WT, an aberration associated with poor outcome in several other childhood cancers. We therefore set out to assess the prognostic significance of MYCN gain in a large WT series, and to explore other mechanisms by which the function of this gene may be dysregulated.

Methods: MYCN copy number was measured in 293 tumours by Multiplex ligation-dependent probe amplification. Whole exome sequencing (Agilent SureSelect V4+UTR/Illumina HiSeq) was carried out on 51 WT tumour/germline pairs. Sanger sequencing was used to confirm variants of interest and to assess an independent panel of 168 WTs. 65 WTs were profiled on Affymetrix SNP arrays (250K Nsp or SNP 6.0), Illumina HumanMethylation450 arrays, and Illumina HumanHT-12 expression arrays, and additional selected tumors on Illumina HumanCytoSNP-12 arrays.

Results: MYCN gain is associated with anaplasia and with poorer relapse-free and overall survival, independent of histology. A somatic p.P44L (c.131C>t) mutation was detected in 3/45 exomes that gave informative data at this position, and in 5/168 additional tumors screened for this variant, an overall frequency of 3.8%. MYCN overexpression in high risk tumors was associated with hypomethylation at specific loci. We observed parallel evolution of genomic copy number gain and point mutation of MYCN in the contralateral tumors of a remarkable bilateral case in which independent contralateral mutations of TP53 also evolved over time. In a second bilateral case, we detected MYCN gain as a germline aberration.

Conclusions: MYCN gain is associated with poor outcome and anaplastic histology in WT. MYCN also appears to be disrupted by other mechanisms in WT, including DNA hypomethylation and a recurrent potential gain of function mutation, P44L. The discovery of a germline aberration suggests that MYCN dysregulation may contribute to tumor predisposition.

Citation Format: Richard D. Williams, Tasnim Chagtai, Marisa Alcaide-German, John Apps, Jenny Wegert, Sergey Popov, Gordan Vujanic, Harm van Tinteren, Marry M. van den Heuvel-Eibrink, Marcel Kool, David Gisselsson, Norbert Graf, Manfred Gessler, Kathy Pritchard-Jones. Multiple mechanisms of MYCN dysregulation in Wilms tumor. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-59.
Abstract A1-63: Characterizing the DNA damage repair defect in HPV-positive oropharyngeal squamous cell carcinoma
Authors: Weaver Alice N. , Cooper Tiffiny S. , Trummell Hoa Q. , Bonner James A. , Rosenthal Eben L. , Yang Eddy S.
Published: November 2015

Although tobacco-associated head and neck cancers (HNCs) are declining in incidence, overall HNC rates are escalating due to increasing prevalence of human papillomavirus (HPV)-associated tumors, especially oropharyngeal squamous cell carcinomas (OPSCCs). Clinically, patients with HPV-associated OPSCCs have improved overall survival and increased response to therapy, especially agents which act by damaging DNA. Based on these observations, we hypothesized that HPV-positive OPSCCs harbor a defect in DNA repair activity and are sensitive to DNA repair-targeted therapy. We evaluated DNA repair activity by immunofluorescent staining for DNA damage-induced formation of DNA repair protein foci. Baseline expression of DNA repair proteins was determined by NanoString nCounter analysis of transcript levels and immunoblotting for protein levels. Therapeutic sensitivity was assessed in vitro using the colony formation assay and in vivo using both cell line-derived xenografts and a patient-derived xenograft. Consistent with our hypothesis, in vitro disease models demonstrated delayed resolution of radiation-induced DNA double strand breaks (DSBs) as assessed by γH2AX foci staining and neutral comet assay. Investigation of the two main DSB repair mechanisms, non-homologous end joining (NHEJ) and homologous recombination (HR), indicated intact activation of both pathways but strikingly diminished recruitment of downstream repair factors DNA-Pk (NHEJ) and BRCA2 (HR) to sites of damage. In addition, protein expression of both DNA-PK and BRCA2 was decreased in HPV-positive compared to HPV-negative HNC cell lines. We next studied susceptibility of HPV-positive OPSCCs to PARP inhibition, a class of anticancer agents which block DNA repair signaling pathways and have proven effective clinically in DNA repair-deficient cancers. In vitro colony formation assays revealed a negative effect on cell survival in HPV-positive but not HPV-negative HNCs treated with the PARP inhibitor veliparib. Importantly, these results were confirmed in vivo in both cell line-derived xenografts and a patient-derived xenograft. In summary, our findings demonstrate for the first time the presence of a significant DNA DSB repair defect in HPV-positive OPSCCs encompassing both NHEJ and HR repair, and suggest therapies targeting DNA repair pathways may help improve therapeutic ratio in this disease.

Citation Format: Alice N. Weaver, Tiffiny S. Cooper, Hoa Q. Trummell, James A. Bonner, Eben L. Rosenthal, Eddy S. Yang. Characterizing the DNA damage repair defect in HPV-positive oropharyngeal squamous cell carcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-63.
Abstract A2-01: SHP-1 is a negative regulator of epithelial-mesenchymal transition in hepatocellular carcinoma
Authors: Fan Li-Ching , Shiau Chung-Wai , Tai Wei-Tien , Hung Man-Hsin , Chu Pei-Yi , Lin Hang , Yu Hui-Chuan , Chen Kuen-Feng
Published: November 2015

Epithelial-to-mesenchymal transition (EMT) is well known to involve in tumor invasion and metastasis. SH2 domain-containing phosphatase 1 (SHP-1) functions as a potent tumor suppressor and also acts as a negative regulator of p-STAT3 (Tyr705) oncogenic signaling. However, little is known about the molecular mechanism(s) through which SHP-1 regulates EMT during hepatocellular carcinoma (HCC) progression. Here, we firstly reported that endogenous SHP-1 protein levels were significantly down-regulated in cells with mesenchymal characteristics and negatively correlated with p-STAT3 (Tyr705) and vimentin but positively correlated with E-cadherin. SHP-1 overexpression abolished TGF-beta-induced p-STAT3 (Tyr705) and EMT, as well inhibited migration and invasion but further rescued by STAT3 overexpression. Constitutively overexpressed SHP-1 tyrosine phosphatase activity by D61A mutated SHP-1 markedly reduced TGF-beta-induced p-STAT3 (Tyr705) and EMT features, but not altered by C453S catalytic dead mutant SHP-1. Consequently, SHP-1 acted as a powerful suppressor in preventing EMT by exerting its activity directly targeted p-STAT3 (Tyr705). Most notably, we discovered a novel SHP-1 agonist SC-43 better than sorafenib to exert more potent anti-EMT effects in vitro as well anti-metastatic growth in vivo. In conclusion, SHP-1 is a potent suppressor of HCC EMT and metastasis, thus, highlighting that SHP-1 may serve as a potential therapeutic target for HCC EMT and metastasis.

Note: This abstract was not presented at the conference.

Citation Format: Li-Ching Fan, Chung-Wai Shiau, Wei-Tien Tai, Man-Hsin Hung, Pei-Yi Chu, Hang Lin, Hui-Chuan Yu, Kuen-Feng Chen. SHP-1 is a negative regulator of epithelial-mesenchymal transition in hepatocellular carcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-01.
Abstract A2-11: PLZF, a tumor suppressor genetically lost in metastatic castration resistant prostate cancer, is a mediator of resistance to androgen deprivation therapy
Authors: Hsieh Chen-Lin , Botta Ginevra , Gao Shuai , Li Tiantian , Allen Eliezer M. Van , Treacy Daniel J. , Cai Changmeng , He Housheng Hansen , Sweeney Christopher J. , Brown Myles , Balk Steven P. , Nelson Peter S. , Garraway Levi A. , Kantoff Philip W.
Published: November 2015

Whole exome sequencing of metastatic castration-resistant prostate cancer (mCRPC) reveal that 5~7% of tumors harbor promyelocytic zinc finger protein (PLZF) homozygous deletions. PLZF is a canonical androgen-regulated tumor suppressor gene whose expression is inhibited by androgen deprivation therapy (ADT). Here, we demonstrate that knockdown of PLZF expression promotes a CRPC and enzalutamide resistant phenotype in prostate cancer cells. Reintroduction of PLZF expression is sufficient to reverse androgen-independent growth mediated by PLZF depletion. PLZF loss enhances CRPC tumor growth in a xenograft model. Bioinformatic analysis of the PLZF cistrome shows that PLZF negatively regulates multiple pathways including the MAPK pathway. Accordingly, our data support an oncogenic program activated by ADT and this acquired mechanism together with the finding of genetic loss in CRPC implicate PLZF inactivation as a mechanism promoting ADT resistance and the CRPC phenotype.

Citation Format: Chen-Lin Hsieh, Ginevra Botta, Shuai Gao, Tiantian Li, Eliezer M. Van Allen, Daniel J. Treacy, Changmeng Cai, Housheng Hansen He, Christopher J. Sweeney, Myles Brown, Steven P. Balk, Peter S. Nelson, Levi A. Garraway, Philip W. Kantoff. PLZF, a tumor suppressor genetically lost in metastatic castration resistant prostate cancer, is a mediator of resistance to androgen deprivation therapy. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-11.
Abstract A2-18: The challenges of using large-scale genomics data to identify novel drivers of lung cancer
Authors: Hudson Andrew M. , Yates Tim , Wirth Chris , Li Yaoyong , Trotter Wendy , Fawdar Shameem , Miller Crispin , Brognard John
Published: November 2015

Lung cancer is one of the major causes of cancer deaths worldwide and only 30% of patients survive the disease for at least one year after diagnosis. Patients are often too frail to receive systemic chemotherapy and there is an urgent need for less toxic, efficacious, targeted therapies. Despite recent efforts with large-scale genomics data we still lack knowledge about driver mutations for the majority of lung cancers.

Increasingly, cancer researchers are using online cancer genomic databases to identify novel targets to investigate. A comparison of two prominent databases from different institutes (CCLE and COSMIC) revealed marked discrepancies in the detection of missense mutations in identical cell lines (57.38% conformity). A major reason for this discrepancy is inadequate sequencing of GC-rich areas. This is a significant issue for lung cancer, with a mutation signature predominantly affecting guanine and cytosine nucleotides and therefore preferring GC-rich regions.

We have therefore focused on GC-rich regions that next-generation-sequencing struggle to cover and discovered over 400 of these regions (cold-spots) in Cancer Consensus and kinase genes alone. We demonstrate how a PAK4 mutation, found in a GC-rich cold-spot in a lung adenocarcinoma cell line, activates the pERK pathway. This suggests that specific targeting of GC-rich regions may be required to uncover further oncogenes and tumour suppressors in lung cancer.

The high mutational burden of lung cancer creates additional challenges in distinguishing driver mutations from a multitude of passenger mutations. One solution is to use siRNA knockdown screens on all genes that are mutated in a cell line and assess cell viability. However we demonstrate that inconsistencies in mutational profiling of cell lines and passaging effects have the potential to influence these types of studies. These limitations also offer new explanations for the discrepancies seen when comparing pharmacogenomics studies.

Citation Format: Andrew M. Hudson, Tim Yates, Chris Wirth, Yaoyong Li, Wendy Trotter, Shameem Fawdar, Crispin Miller, John Brognard. The challenges of using large-scale genomics data to identify novel drivers of lung cancer. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-18.
Abstract A2-22: Mitochondrial dysfunction induces cancer stem-like phenotypes in Hep3B hepatocellular carcinoma cell line
Authors: Han Yu-Seon , Yi Eui-Yeun , Kim Yung-Jin
Published: November 2015

Cancer stem cells (CSCs) are a small population of cancer cells that possess characteristics associated with normal stem cells such as self-renewal and differentiation into multiple cell types. Additionally, CSCs have been reported to relationship on tumor relapse after cancer therapy. Mitochondrial dysfunction (MD) has also been known to be associated with cancer malignancy. In this report, the relation of MD and CSCs were initially investigated using mitochondrial-depleted rho0 cells derived from Hep3B hepatocellular carcinoma cell line. The Hep3B/rho0 cells showed cancer stem-like phenotypes including tumor initiation, tumor malignancy, stem cell-related signaling, chemotherapies and radiotherapy resistance. These results suggest that mitochondrial dysfunction induces cancer stem-like phenotypes. Taken together, mitochondrial dysfunction plays an important role in the acquisition of cancer stem-like phenotypes and could be a novel therapeutic target to cancer therapy.

Citation Format: Yu-Seon Han, Eui-Yeun Yi, Yung-Jin Kim. Mitochondrial dysfunction induces cancer stem-like phenotypes in Hep3B hepatocellular carcinoma cell line. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-22.
Abstract A2-25: Identification of RASA1 as a novel melanoma tumor suppressor gene
Authors: Sung Hyeran , Kanchi Krishna L. , Messina Jane , Lee Ji-Hyun , Kim Youngchul , Ding Li , Wilson Richard K. , Weber Jeffrey S. , Kim Minjung
Published: November 2015

Hyperactivation of the Ras-Raf-Mitogen-activated protein kinase (MAPK) pathway has been commonly observed in melanoma via frequent activating mutations in NRAS and BRAF. Novel mutations in other components of this pathway such as MEK1, MEK2, MAP3K5, and MAP3K9 have been reported recently by high-throughput sequencing efforts. In addition, NF1 (neurofibromatosis type 1), one of the Ras GTPase activating proteins (RasGAPs) that negatively regulate Ras, has been shown to be mutated or suppressed in melanoma. However, importance of other RasGAPs has not been addressed in melanoma.

To obtain a comprehensive view of melanoma genomes, we conducted whole genome sequencing (WGS) of 15 metastatic melanomas and matched normal PBMC genomes from 13 melanoma patients. All melanoma genomes from these 13 patients contained at least one mutation in genes of Ras-Raf-MAPK pathway (MAPK1, MAP3K1, MAP4K2, MAP3K14, NRAS, and BRAF). In addition, we identified two novel, clustered somatic missense mutations (p.Tyr472His and p.Leu481Phe) in RASA1 (RAS p21 protein activator 1, p120RasGAP). In this study, we addressed functional roles of RASA1 in melanoma tumorigenesis. The RNAi-mediated down-regulation of RASA1 promoted, while ectopic expression of wild type RASA1 decreased, anchorage-independent colony formation, tumor growth, and RAS activation. Interestingly, RASA1 Y472H mutant enhanced soft agar colony formation and tumor growth, while RASA1 L481F mutant lost its tumor suppressive activity. Mechanistically, RASA1 required RasGAP activity to suppress colony formation and showed higher activity toward R-Ras (related RAS viral (r-ras) oncogene homolog) isoform among the Ras superfamily of small GTPases. In addition, RASA1 suppressed Ral-A among Ras downstream effectors. Interestingly, RASA1 expression was frequently down-regulated in metastatic melanoma samples (11.4% (4/35) of lymph node metastasis and 3.4% (1/29) of distal metastases) compared to primary melanomas (33.3% (21/63)) and dysplastic nevi (44.1% (15/34)). We also observed significantly shorter overall survival of melanoma patients with BRAF mutations when RASA1 mRNA expression is low. Thus, these data support that RASA1 is a novel melanoma tumor suppressor that is inactivated by suppressed expression or by mutation.

Citation Format: Hyeran Sung, Krishna L. Kanchi, Jane Messina, Ji-Hyun Lee, Youngchul Kim, Li Ding, Richard K. Wilson, Jeffrey S. Weber, Minjung Kim. Identification of RASA1 as a novel melanoma tumor suppressor gene. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-25.
Abstract A2-30: A new fluorescence-based andrographolide exhibits anticancer activity
Authors: Hsu Ya-Hsin , Hsu Yu-Ling , Liu Sheng-Hung , Liao Hsin-Chia , Lee Po-Xuan , Lin Chao-Hsiung , Lo Lee-Chiang , Fu Shu-ling
Published: November 2015

Andrographolide is a lactone diterpenoid compound isolated from the medicinal plant Andrographis paniculata. The anticancer activity of andrographolide has been previously demonstrated both in vitro and in vivo. We recently synthesized an andrographolide derivative, ANDRO-FL, in which a fluorescent chemical structure was covalently conjugated to andrographolide. We found that ANDRO-FL exhibited potent anticancer activity: ANDRO-FL reduced the viability of various types of cancer cells; ANDRO-FL suppressed the migration activity of melanoma cells; ANDRO-FL treatment induced the cleavage of heat shock 90 protein (Hsp90) as well as the downregulation of Hsp90 client oncoproteins such as v-Src and Bcr-abl. Notably, in all aforementioned experiments, ANDRO-FL showed stronger inhibitory effects than andrographolide. The kinetics and distribution of ANDRO-FL in cancer cells were further examined using fluorescence microscopy. The fluorescent signals could be detected within the cells in five minutes after ANDRO-FL treatment and the intensity increased as incubation time increased. Furthermore, the fluorescent signal could be detected in nucleus, cytoplasm, mitochondria, and lysosome. In vitro binding assays demonstrated that ANDRO-FL could covalently bind to several known target proteins of andrographolide, including NF-kB, GST and hnRNP K. In summary, our data indicate that ANDRO-FL is a promising anticancer compound. Moreover, with comparable anticancer profile to andrographolide, Andro-FL can serve an effective tool to further explore the molecular targets underlying the anticancer mechanism of andrographolide. The in vivo anticancer activity of ANDRO-FL is currently under investigation.

Citation Format: Ya-Hsin Hsu, Yu-Ling Hsu, Sheng-Hung Liu, Hsin-Chia Liao, Po-Xuan Lee, Chao-Hsiung Lin, Lee-Chiang Lo, Shu-ling Fu. A new fluorescence-based andrographolide exhibits anticancer activity. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-30.
Abstract A2-31: Chemical proteomics approach reveals a monoacylglycerol lipase-dependent migration suppression of melanoma cells by andrographolide
Authors: Hsu Ya-Hsin , Huang Ting-Yun , Lo Lee-Chiang , Fu Shu-Ling , Lin Chao-Hsiung
Published: November 2015

Andrographolide is the major chemical component of an herbal plant, Andrographis paniculata, and has been reported to exhibit anti-cancer activity. We had previously demonstrated that andrographolide can suppress the migration and invasion of a highly metastatic melanoma cell, B16F10, but the molecular target and regulatory mechanism underlying this phenomenon remain unknown. A chemical proteomics approach using serine hydrolase activity probes and mass spectrometry-based identification was carried out to reveal that monoacylglycerol lipase (MAGL) of lipid metabolism is involved in the andrographolide-mediated suppression of B16F10 cell migration. MAGL has been reported to be elevated in aggressive cancers and associated with tumor metastasis. We observed that the hydrolase activity of MAGL in B16F10 cells was decreased upon andrographolide treatment but not in the poorly metastatic B16F1 cells. In addition, a known MAGL-specific inhibitor (JZL184) was used to demonstrate that suppression of MAGL enzyme activity could reduce B16F10 migration. Notably, overexpression of MAGL in B16F10 cells abrogated the andrographolide-mediated suppression of B16F10 migration, but such overexpression could not rescue the JZL184-mediated suppression. Further analysis showed a downregulation of MAGL mRNA levels in B16F10 cells upon treatment of andrographolide. With the use of an IKK inhibitor (Bay11-7082), the NF-kB signaling pathway is shown to be involved in the andrographolide-mediated suppression of MAGL expression. Taken together, we herein demonstrate that andrographolide suppresses melanoma cell migration via transcriptional downregulation of monoacylglycerol lipase, providing a new anti-cancer mechanism of andrographolide and a basis for further development of potent derivatives.

Citation Format: Ya-Hsin Hsu, Ting-Yun Huang, Lee-Chiang Lo, Shu-Ling Fu, Chao-Hsiung Lin. Chemical proteomics approach reveals a monoacylglycerol lipase-dependent migration suppression of melanoma cells by andrographolide. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-31.
Abstract A2-41: The Amplinome™ Test – A droplet digital PCR (ddPCR) based pan-cancer test to assess gene amplification status in solid tumors
Authors: Wong Amy , Pecson Jennifer , Putcha Girish , Nadauld Lincoln , So Austin P.
Published: November 2015

Gene amplifications constitute >30% of all actionable mutation types present in cancer. However, despite their prevalence and the availability of targeted drug therapies, the development of molecular assays to detect gene amplifications has been limited by technical challenges such as limited DNA quantity and tumor heterogeneity. To address this, we describe the Amplinome™ test, a test that leverages the high precision and accuracy of droplet digital PCR (ddPCR) to determine the amplification status of 12 commonly amplified genes targeted by FDA approved drugs.

Twelve taqman assays were designed to target AURKA, BRAF, CDK4, CDK6, EGFR, ERBB2/HER2, ERBB3/HER3, FGFR1, JAK2, MET, SRC, and VEGFA, and duplexed with the reference gene RNaseP (Epoch, Bothell, WA). Each duplexed assay was then assembled with 2 μL of purified DNA and analyzed via ddPCR (Bio-rad QX-200 ddPCR Platform, Hercules CA). Genes were identified as “amplified” if the observed target:reference ratio was >1.48 (p < 0.005), which adjusts the ASCO-CAP threshold of 2.2 recommended for HER2 amplification for a minimum tumor content of 40%.

The Amplinome test identified 29 of 49 patients having actionable amplifications in at least one of the 12 assayed genes. In contrast, only 6 of 49 patients were identified as having amplifications in these genes through a commercially available sequencing test. An overall concordance rate of 90% (532/588 calls) between the two tests was observed. Discordant calls (56/588) arose from amplifications identified by the Amplinome test but not sequencing (55/56). One discordant call (HER3) was identified as amplified via sequencing, but confirmed to be unamplified via FISH.

The observed 10-fold increase in sensitivity versus a sequencing-based clinical test suggests that the prevalence of actionable amplifications may be significantly underestimated in cancer. This sensitivity, combined with its ability to provide results within an actionable timeframe (<1 week), the underlines the potential value of Amplinome™ test in providing treatment options for oncologists and their patients.

Citation Format: Amy Wong, Jennifer Pecson, Girish Putcha, Lincoln Nadauld, Austin P. So. The Amplinome™ Test – A droplet digital PCR (ddPCR) based pan-cancer test to assess gene amplification status in solid tumors. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-41.
Abstract A2-45: R2: Accessible web-based genomics analysis and visualization platform for biomedical researchers
Authors: Koster Jan , Molenaar Jan J. , Versteeg Rogier
Published: November 2015

In this era of explosive high throughput (HT) genomics data generation, there is a growing need for accessible software solutions that can help unlock biological/clinical characteristics from such data. With the biomedical researcher (with limited or no bioinformatics skills) in mind, we developed a comprehensive web-based system called R2 (http://r2.amc.nl). R2 aids in the analysis and visualization of private/shielded as well as public high throughput data and their associated annotated features.

The R2 platform consists of a database storing both publicly accessible as well as shielded datasets with unified gene annotation, supplemented with a large suite of tools that can be used on these data, and their associated annotation. As such the user experiences the same look & feel throughout the mining process.

In the public section, R2 hosts over 60,000 HT samples. Next to gene expression (microarray and RNA-seq), the platform is also being employed in the integration, analysis and visualization of other data types, such as aCGH, SNP, ChIP, methylation, miRNA, and NGS whole genome sequencing information.

R2 contains an expanding set of interactive analyses which are heavily inter-connected, allowing users to quickly hop from one view (representation of the data) to another. Analyses include, correlation, differential expression, gene sets, gene ontology, transcription factor binding sites, PCA, kmeans, Kaplan Meier scans, signature creation etc. Visualizations include, various gene oriented plots, heatmaps, circos, embedded genome browser, Venn, etc.

Many parts of the R2 platform are publicly accessible through the http://r2.amc.nl portal. The R2 gene expression analysis tools have thus far been used in more than 180 peer-reviewed scientific publications including journals as Nature, Nature Genetics and Cell. R2 also supports restricted / shielded use and is used in many (inter)national collaborative efforts involving unpublished datasets. The webservers have been serving over 900.000 pages over the past 12 months (Nov 2014).

Citation Format: Jan Koster, Jan J. Molenaar, Rogier Versteeg. R2: Accessible web-based genomics analysis and visualization platform for biomedical researchers. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-45.
Abstract A2-46: Melanoma Profiler web tool for integrative genomic analysis of melanoma
Authors: Qaadri Kashef , Stones-Havas Steven , Ammundsen Brett , Trevarton Alexander , Print Cristin
Published: November 2015

Despite ongoing research, metastatic melanoma five-year survival rates remain low and treatment options limited. Researchers can access a rapidly growing amount of molecular and clinical information about melanoma that may be critical to understanding this disease and making clinically relevant treatment decisions. However, this information is becoming difficult to collate and clinically interpret due to its dispersed nature. Presented here is Melanoma Profiler, a new cloud-based web application for clinically relevant metastatic melanoma genomic research. It performs a tumor/normal comparative variant analysis, comparing proband modified genes and pathways to those in a curated set of characterized melanoma tumor samples. To provide clinical decision support, modified genes and pathways are cross-referenced with clinical and molecular data. These data are incorporated from publicly available sources, including: associations between gene expression and patient survival, data concerning drug targets, biomarkers, and druggability as well as past clinical trials. The resultant MelanomaDB cross-reference database integrates data from cutting edge research on a continuous basis. The interface is presented in two tiers: a front-panel summary tier and an evidential detail tier. For the busy clinician, immediately presented in the summary view is a dynamic report clearly highlighting the relevant actionable information, potential drug targets, and a summary of affected genes and pathways. For researchers that wish to dig deeper, they may browse annotated pathway data, and view a comprehensive comparative summary of affected genes in waterfall and heatmap reports. Melanoma Profiler is a free research tool hosted by Biomatters, produced in collaboration with the University of Auckland, New Zealand. A recent Frontiers in Oncology methods article describing the research behind the application can be found at http://bit.ly/1bUilqS. The Melanoma Profiler web application can be found at https://apps.biomatters.com/melanoma-profiler/.

Citation Format: Kashef Qaadri, Steven Stones-Havas, Brett Ammundsen, Alexander Trevarton, Cristin Print. Melanoma Profiler web tool for integrative genomic analysis of melanoma. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-46.
Abstract A2-49: Integrated Omic analysis of lung cancer reveals metabolism proteome signatures with prognostic impact
Authors: Moran Michael F. , Kislinger Thomas , Li Lei , Ignatchenko Vladimir , Wei Yuhong , To Christine , Taylor Paul , Tong Jiefei , Pham Nhu An , Pintilie Melania , Muthuswamy Lakshmi , Shepherd Frances A. , Tsao Ming Sound
Published: November 2015

Cancer results from processes prone to selective pressure and dysregulation acting along the sequence-to-phenotype continuum DNA→RNA→Protein→Disease. An Omics Array integrating DNA gene copy number, mRNA transcriptome, and quantified proteome was assembled into a genetic map representing non-small cell lung carcinoma (NSCLC). Data were collected from patient-matched normal lung, primary tumors, and patient tumor-derived xenograft (PDX) tumors. Dysregulated proteins not previously implicated as cancer drivers were found encoded throughout the genome including but not limited to regions of recurrent DNA amplification/deletion in NSCLC. Unsupervised clustering revealed signatures comprising metabolism proteins particularly highly recapitulated between matched primary and PDX tumors, and which distinguished between the major NSCLC histological subtypes adenocarcinoma (ADC) and squamous cell carcinoma (SCC). Interrogation of The Cancer Genome Atlas (TCGA) revealed sizeable cohorts of NSCLC patients with DNA alterations in genes encoding the metabolism proteome signatures, and accompanied by differences in survival. Similar to the proteome signatures from which they were extrapolated, the gene mutation signatures with prognostic impact discriminated between the lung ADC and SCC subtypes. Serine hydroxymethyltransferase 2 (SHMT2), a key enzyme in serine/glycine and folate-dependent one-carbon metabolism, is upregulated in the proteomes of NSCLC primary and PDX tumours, and is implicated as a driver of recurrent chromosome 12q14.1 amplification in NSCLC. SHMT2, along with other enzymes implicated as anti-folate targets, is also part of a metabolism signature associated with poor outcome in lung ADC. The interrogation of cancer genomes and proteomes for alterations that are related products of selective pressures driving the cancer phenotype may be a general approach to uncover and group together cryptic, polygenic cancer drivers, which might represent new anti-cancer therapeutic targets.

Note: This abstract was not presented at the conference.

Citation Format: Michael F. Moran, Thomas Kislinger, Lei Li, Vladimir Ignatchenko, Yuhong Wei, Christine To, Paul Taylor, Jiefei Tong, Nhu An Pham, Melania Pintilie, Lakshmi Muthuswamy, Frances A. Shepherd, Ming Sound Tsao. Integrated Omic analysis of lung cancer reveals metabolism proteome signatures with prognostic impact. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-49.
Abstract A2-53: Integrative systems analyses reveal addiction of HER2+ breast cancers to ERAD for survival
Authors: Singh Navneet , Joshi Rashika , Komurov Kakajan
Published: November 2015

ERBB2/HER2-positive breast cancers are associated with poor prognosis; and resistance to HER2-targeted therapy is one of the significant clinical challenges. Trastuzumab and lapatinib are two agents that target the HER2 protein in the clinic and constitute the standard of care for HER2+ breast cancers (BCs). However, the clinical benefits of HER2-targeted therapies are limited due to significant de novo (>60%) and acquired resistance (~100%) to these agents during prolonged phases of treatment. No treatment options exist for metastatic HER2+ BCs that have progressed on HER2-targeted therapy. Therefore, targeting of non-oncogenic vulnerabilities is a promising therapeutic approach in tumors that are resistant to oncogene-targeted therapy.

Using an evolutionary selection criterion, we computationally interrogated targetable non-oncogenic vulnerabilities in ERBB2/HER2+ breast cancers, which suffer from a high rate of de novo and acquired resistance to HER2-targeted therapy. We found that the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway is induced in HER2+ breast cancers, partly due to adaptive genomic rearrangements, to counter ER stress caused by increased proteotoxic burden due to heightened HER2/mTOR activity. Genetic and pharmacologic targeting of ERAD lead to irrecoverable ER stress and selectively killed HER2+ breast cancer cells, including those that are resistant to conventional therapy. Cell death due to ERAD inhibition was executed by the IRE1α/JNK pathway, which was suppressed in HER2+ breast cancers due to the activation of JNK phosphatases. Accordingly, inhibiting ERAD in combination with JNK phosphatases synergized in killing HER2+, but not HER2-, breast cancer cells. Our study supports exploiting oncogenic proteotoxicity as a novel therapeutic approach for therapy-refractory breast cancers, and presents an integrated strategy to identify non-oncogenic vulnerabilities in cancers.

Citation Format: Navneet Singh, Rashika Joshi, Kakajan Komurov. Integrative systems analyses reveal addiction of HER2+ breast cancers to ERAD for survival. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-53.
Abstract A2-67: Live cell imaging of ERK reveals unique inhibitor-specific adaptive responses
Authors: Gillies Taryn E. , Distor Kevin , Sànchez Marta Minguet , Pargett Michael , Albeck John
Published: November 2015

Defects in cell-to-cell signaling pathways can result in developmental abnormalities as well as cancer. The Ras/MAPK pathway is a central regulator of gene expression, cellular proliferation, and differentiation that is frequently de-regulated in cancer. While this pathway is a promising target for cancer therapeutics, a major obstacle is the tendency of the pathway to become re-activated via feedback within hours following inhibition. This adaptive response is important because the timing and duration of Ras/MAPK activity are known to determine the resulting cellular response and gene expression pattern. We have developed a new live-cell reporter, EKAR3, that allows ERK activity to be monitored with high temporal precision and resolution of heterogeneous individual cell behavior. To track the detailed pattern of adaptation to Ras/MAPK pathway inhibitors, we imaged over 10,000 individual cells responding to specific inhibitors of EGFR, Raf, MEK, and ERK. ERK activity was immediately reduced upon inhibition, but returned after a period of time ranging from 1-12 hours, depending on the inhibitor and its concentration. Strikingly, different inhibitors were found to induce distinct ERK recovery patterns, ranging from frequent, high-amplitude pulses to extended steady-state activity. We then statistically analyzed the effect of these differential ERK responses on cell behavior to dissect elements of the temporal signal relevant for information transmission in the cell. Our results indicate that, at the level of individual cells, targeted inhibitors induce kinetically distinct adaptive responses, which are likely to determine their effectiveness in controlling different aspects of cellular proliferation, survival, and migration.

Citation Format: Taryn E. Gillies, Kevin Distor, Marta Minguet Sànchez, Michael Pargett, John Albeck. Live cell imaging of ERK reveals unique inhibitor-specific adaptive responses. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-67.
Abstract IA04: Clinical decision support in the era of genome informed cancer medicine
Authors: Levy Mia
Published: November 2015

The emergence of high throughput genomic testing of tumors presents both an opportunity and challenge for use in clinical decision making across the continuum of cancer care. A tsunami of molecular data is now reaching the clinic with variable levels of evidence with respect to clinical validity and clinical utility. Not surprising, a large knowledge gap remains for oncologists who try to apply this new data for clinical decisions at the point of care. In order to address this knowledge gap, we have developed My Cancer Genome (MCG), a publically available website with the mission to curate and disseminate knowledge regarding the clinical significance of genomic alterations in cancer. My cancer genome contains content curated by domain experts on the prognostic and therapeutic implications of genomic alterations in cancers, including experimental therapeutics and active clinical trials. In addition to being publically available via MyCancerGenome.org, the content has also been integrated into a decision support tool for interpretation and reporting of results for tumor next generation sequencing via a commercial partner. Opportunities to scale resources like MCG continue to present opportunities and challenges to the cancer community. Data driven approaches where we learn from the experience of all cancer patients will be needed to help realize the promise of precision cancer medicine.

Citation Format: Mia Levy. Clinical decision support in the era of genome informed cancer medicine. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr IA04.