bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract B30: Src tyrosine kinase inhibitors activate protective, ULK1-dependent autophagy by downregulating oncomir-106-393-cluster expression in non-small cell lung cancer cells
Authors: Rothschild Sacha I. , Gautschi Oliver , Batliner Jasmin , Jost Melanie , Fey Martin F. , Gugger Mathias , Tschan Mario P. 
Published: March 2013

Abstract
Autophagy has been proposed to play a role as cytoprotective mechanism for tumor cell survival under unfavorable conditions and upon anticancer treatment. In lung cancer autophagy is mostly studied as possible resistance mechanism to therapy. There is increasing evidence that protective autophagy occurs upon various types of anti-cancer treatments, including chemo- and radiation therapy. Src tyrosine kinase inhibitors (TKIs) have been shown to inhibit cell migration and invasion in non-small cell lung cancer (NSCLC) cell lines. In clinical trials, however, they show modest activity in combination with chemotherapeutic agents. In the current study we show a marked induction of autophagic activity upon incubation of NSCLC cell lines with Src TKIs as measured by an increased LC3-I to -II conversion, a significant increase in GFP-LC3 dot formation, and a decrease in p62/SQSTM1 protein expression. Increased autophagic activity was found in three NSCLC cell lines (A549, H460, H1299) with two different Src TKIs (saracatinib, dasatinib). Interestingly, the addition of pharmacological autophagy inhibitors such as chloroquine or bafilomycin resulted in cell death in combination with Src TKI treatment. Moreover, we found that Src TKI-induced autophagy is associated with ULK1 expression in all three cell lines investigated. This effect was Src-specific since knocking down endogenous Src using RNAi resulted in a similar induction of ULK1. Using shRNA targeting ULK1 we showed that Src inhibitor induced autophagy is ULK1-dependent. Furthermore, ULK1 is a novel target of microRNA (miR)-106a as shown by ULK1 3′-UTR luciferase experiments and ectopic expression of miR-106a and antimiR-106a in NSCLC cell lines resulting in decreased and increased ULK1 expression upon Src inhibition, respectively. Lastly, in human lung adenocarcinoma compared to matched normal lung tissue (n = 23) miR-106a levels were significantly increased (p&lt;0.0001) whereas ULK1 mRNA expression levels were significantly lower (p&lt;0.0002) in tumor tissue. In conclusion, Src inhibitor-induced protective autophagy might explain their low success in clinical trials. Autophagy induced by Src TKIs depends on ULK1 and combining Src with autophagy inhibitors results in massive cell death as compared to single treatments. Furthermore, downregulation of the ULK1 targeting miR-106a upon Src inhibition allows for the induction of protective autophagy. Combining Src and autophagy inhibitors or Src inhibitors and miR-106a expression may represent attractive treatment options for NSCLC.
Abstract B34: Overcoming resistance to EGFR-Tyrosine Kinase Inhibitor therapy in non-small cell lung cancer
Authors: Sierra Rafael , Chang Anderson , Moffat Jason , Neel Benjamin G. , Tsao Ming-Sound 
Published: March 2013

Abstract
Lung cancer is the leading cause of cancer death in developed countries both for men and women; and the second most common type of cancer diagnosed, with less than 15% of patients surviving beyond 5 years. Since more than 60% of lung adenocarcinomas and more than 90% of lung squamous cell carcinomas express high levels of EGFR mRNA and protein, it has been the focus of efforts to develop new agents that target the EGFR pathway. Clinical trials have demonstrated that patient selection plays a major role for patient response. Patients that present amplification or activating mutations (L878R or exon 19 deletions) of EGFR, have higher response rates. Selection improved response rates from less than 10% to over 60–80%. Despite the promising results, all patients that receive TKI therapy develop resistance to treatment in less than one year. The mechanisms of resistance to EGFR TKi's described so far are those dependant on the overactivation/amplification of other receptor tyrosine kinases (RTK) capable to sustain anti-apoptotic signaling pathways. Our study proposes the use of genome-wide screenings using an 80,000 shRNA library on EGFR resistant cells can identify new genes that mediate the resistance to EGFR targeted therapy and provide the basis for designing new therapeutic approaches to avoid the emergence of resistance. So far, we have generated a shortlist of gene candidates that confer synergistic synthetic lethal interactions with EGFR targeted therapies and that are also highly expressed in resistant cells. We are currently overexpressing candidate genes in sensitive cells searching for those that can confer resistance to EGFR targeted therapies. Our study proposes target genes that can synergize with the current treatments to create new therapeutical strategies that can avoid the acquisition of resistance to targeted therapies. Overall, the information gained from this type of study can be applicable to tumors where ERBB receptor(s) play an important role and targeted therapies are currently used.
Abstract B35: Activation of Putative Compensatory Pathways upon Deletion of Erbb3 in Mutant EGFR-driven Lung Cancer
Authors: Song Xiaoling , Fan Pang-Dian , Guha Udayan , Threadgill David , Varmus Harold , Politi Katerina 
Published: March 2013

Abstract
Lung cancer is the leading cause of cancer-related death in the USA and worldwide. Mutant epidermal growth factor receptor (EGFR)-driven non-small cell lung cancer represents 15% of lung adenocarcinomas. Tumors bearing EGFR mutations are sensitive to treatment with specific tyrosine kinase inhibitors (TKIs) and show radiographic responses in about 70% of cases. However, it is not known why the remaining 30% of the tumors do not respond to these drugs, and patients who initially respond to TKI treatment eventually develop drug resistance on average within a year. These facts underscore the need for a better understanding of the molecular mechanisms that underlie transformation of the lung epithelium by mutant EGFR.
Mutant EGFR-induced signaling is initiated by the formation of EGFR homodimers or heterodimers with other members of the EGFR family (ERBB2, ERBB3 or ERBB4). To investigate the role of EGFR family members in the tumorigenic process driven by mutant EGFR, we used a tetracycline-inducible transgenic model to test the requirement for Erbb3 in mutant EGFR-induced lung tumorigenesis. In this model, deletion of Erbb3 had no effect on tumorigenesis induced by mutant EGFR, suggesting that it is not required to initiate tumorigenesis. Tumors that develop in the absence of Erbb3 remain sensitive to TKIs. Analysis of the biochemical consequences of Erbb3 deletion revealed increased levels of phosphorylation of EGFR and Erbb2 in tumors arising in the absence of Erbb3. Moreover, these tumors show increased activation of the mitogen-activated protein kinase (MAPK) signaling pathway. Together these data suggest that recruitment of compensatory pathways may overcome the need for Erbb3 in tumorigenesis driven by mutant EGFR. Further experiments to test this are ongoing. Knowledge of the role EGFR heterodimerization partners play in mutant EGFR-driven lung cancer can help guide the selection of which EGFR family members to target in the treatment of this disease.
Abstract B7: Use of ponatinib to restrict growth of non-small cell lung cancer (NSCLC) cells overexpressing FGFR1
Authors: Ren Mingqiang , Hong Mei , Wang Suiquan , Cowell John , Hao Zhonglin 
Published: March 2013

Abstract
For advanced stage NSCLC, targeted molecular therapy based on an understanding of the oncogenic driver mutations is emerging as the new front line care replacing chemotherapy where the oncogenic driver mutation is clearly defined e.g EGFR mutation or EML4-ALK translocation. However, the proportion of patients that fall into this category is small and are mostly non-smokers with adeno histology. Identifying new oncogenic drivers in NSCLC is therefore paramount.
In our initial Oncomine database search, we found that FGFRs are overexpressed in various NSCLC tissue specimens. Quantitative real time PCR and Western blot analysis subsequently confirmed overexpression of FGFR1 in about one fourth of NSCLC cell lines analyzed. Among these, H520, H1299 and A549 had significantly higher levels of FGFR1 expression compared to H3122 which carries an EML4-ALK fusion protein. Real time PCR also demonstrated FGFR1 overexpression compared to normal human bronchial epithelial cells transformed by Herpes Papillary Virus E6/E7 (HBE4). Furthermore, as a sign of epithelial to mesenchymal transition, these cells switched from expressing the FGFR1 3b to the 3c form. In a colonogenic assay the growth of cells carrying FGFR1 overexpression/activation is markedly suppressed by ponatinib, a pan FGFR inhibitor as expected. Similarly, ponatinib treatment of NSCLC cell lines using 1 μM concentrations effectively suppressed the phosphorylation level of FGFR1 and its known down-stream targets including pSrc and pPLCγ without significant impact on the total protein expression. Treatment of these cells harboring FGFR1 activation with ponatinib arrests cells at the G1 phase as shown in the flow cytometry analysis. To determine whether the observed effects are specifically due to the suppression of FGFR1 by ponatinib, an shRNA knock down of FGFR1 was performed. Consistently, shFGFR1 significantly inhibited the growth of H520 and H1299 cells, whereas knock-down did not significantly affect the growth of H3122. Similar to ponatinib treatment, shFGFR1 caused more cells to arrest in G1 phase. In a MTT assay, ponatinib synergistically induced growth suppression/killing of H520 cells with cisplatin and paclitaxel. We are currently determining whether ponatinib is effective in inhibiting NSCLC cells derived directly from freshly resected lung cancer specimens.
In conclusion, the FGFR1 pathway is constitutively active in a proportion of NSCLC cell lines and ponatinib is a potent inhibitor of constitutive FGFR1 activation. Ponatinib is potentially useful as a molecularly targeted agent against this portion of NSCLC when used alone or in combination with traditional chemotherapy regimens.
Abstract B8: Targeting p21-activated kinases in human lung cancer
Authors: Ong Christy C. , Jubb Adrian M. , Haverty Peter M. , Zhou Wei , Harris Adrian L. , Belvin Marcia , Friedman Lori S. , Koeppen Hartmut , Hoeflich Klaus P. 
Published: March 2013

Abstract
P21-activated kinases (PAKs) are important mediators of Rac and Cdc42 GTPase function as well as pathways required for Ras-driven tumorigenesis. PAKs have been implicated in signaling by growth factor receptors and morphogenetic processes that control cell polarity, invasion and actin cytoskeleton organization. To better understand the role of PAK1 in lung tumorigenesis, PAK1 genomic copy number and expression were determined for a panel of adenocarcinoma and squamous non-small cell lung cancers (NSCLC) and small cell lung cancers (SCLC). 64% of squamous NSCLC samples were positive for PAK1 expression and 52% of all cases showed staining of moderate (2+) or strong (3+) immunohistochemical intensity in the malignant cells. Nuclear localization of PAK1 was also evident in a significant proportion of squamous NSCLCs. Adjacent normal lung tissue did not express appreciable levels of PAK1. Selective PAK1 inhibition was associated with delayed cell cycle progression in vitro and in vivo. NSCLC cells were profiled using a library of pathway-targeted small molecule inhibitors and several synergistic combination therapies, including combination with antagonists of inhibitor of apoptosis (IAP) proteins, were revealed for PAK1. Dual inhibition of PAK1 and X chromosome-linked IAP (XIAP) efficiently increased effector caspase activation and apoptosis of NSCLC cells. Together, our results provide evidence for dysregulation of PAK1 in NSCLC and a role for PAK1 in cellular survival and proliferation in this indication.
Abstract B9: Cost effectiveness of gene expression profiling for tumor site origin
Authors: Hornberger John , Degtiar Irina , Gutierrez Hialy , Shewade Ashwini , Henner W. David , Becker Shawn , Raab Stephen 
Published: March 2013

Abstract
Background: Gene expression profiling (GEP) reliably supplements traditional clinicopathological information on the tissue of origin (TOO) in metastatic or poorly differentiated cancer. A cost-effectiveness analysis of GEP TOO testing versus usual care was conducted from a third-party payer perspective in the United States.
Methods: A retrospective, observational study examined treatment changes in patients whose physicians had received the GEP TOO test results to help diagnose the tissue-site of their patient's malignancy and to guide appropriate therapy. Changes in planned chemotherapy, surgery, radiation therapy, added blood tests, imaging investigations, and referral to hospice care before and after the GEP TOO test results were recorded. The effect of changes in chemotherapy on survival were based on randomized controlled trials informing appropriate use of chemotherapy cited in National Comprehensive Cancer Network (NCCN) and Up-to-Date guidelines. Drug and administration costs were based on average doses reported in NCCN guidelines. Centers for Medicare and Medicaid Services (CMS) fee schedules were used to obtain other unit costs. Quality-of-life weights were obtained from literature sources. Changes in overall survival, costs, and cost per quality-adjusted life year (QALY) gained were estimated using bootstrap methods.
Results: Use of chemotherapy regimens consistent with guidelines for the final tumor-site diagnosis increased significantly from 42% to 65% (net difference 23%; p&lt; 0.001). Overall survival was projected to increase from 15.9 months to 19.5 months (mean difference 3.6 months, 95%CI [2.0, 5.1]). The average increase in survival adjusted for quality of life was 2.7 months (95%CI [1.4, 3.9]), and average third-party payer costs per patient increased by $10,360 (95% CI [$5,668, $15,053]). The cost per QALY gained was $46,858 (95% CI [$17,995, $75,718]).
Conclusions: GEP TOO testing significantly altered clinical practice patterns for treating metastatic cancer of uncertain primary. It is projected to increase overall survival, QALYs, and costs, resulting in an expected cost per QALY of less than $50,000.
Abstract IA10: Pathology of lung neuroendocrine tumors: In search of evidence for classification
Authors: Linnoila Ilona 
Published: March 2013

Abstract
Neuroendocrine (NE) tumors comprise approximately 25% of all tumors in human lung. As a group they continue to provide challenges at biological, molecular and pathological level for uniform classification. The prototype of NE tumors is the highly aggressive small cell lung cancer (SCLC) that accounts 15% of human lung cancers. For years lung cancers were clinically classified mainly into SCLCs and non-SCLCs (NSCLCs) while it has become evident that lung NE tumors actually form a complex spectrum from SCLC to carcinoid with shifting boundaries. The current WHO classification recognizes SCLC, its variant form combined SCLC, typical and atypical carcinoids as well as large cell NE carcinoma (LCNEC) and its variant form combined large cell carcinoma, the last two cancers under the main NSCLC category of large cell carcinoma. With the exception of the LCNEC, it is expected that the diagnoses will be rendered by routine hematoxylin-eosin stain according the established criteria. Benign entities include diffuse idiopathic pulmonary NE cell hyperplasia which is described in the chapter of preinvasive lesions. Over time there have been several efforts to place lung NE tumors into two to four-tier categories according to their malignant potential (high versus low grade) or degree of differentiation often leaving behind confusing terminology that is later misused. Unlike surgically resected NSCLCs, most NE tumors are frequently diagnosed from biopsies which remains a seldom recognized fact that may create its own biases. The diagnosis that experts most often agree with is SCLC, while distinctions between atypical carcinoid and LCNEC that are in the middle of the spectrum are often disputed. Many molecular studies have also “correctly” classified the endpoints of the NE spectrum while grouping in the middle of it has produced varied results. Moreover, several studies have suggested that NSCLCs with NE features (NSCLC-NEs) is a distinct carcinoma type with worse prognosis than ordinary non-NE NSCLC, while others disagree. Biologically this category is very interesting as NSCLCs and SCLCs are ultimately thought to be derived from the same cell. The regulation of NE differentiation is poorly understood. The proneural achaete-scute homolog 1 (ASCL1), a lineage-dependent oncogene may be a key factor for NE differentiation. On the other hand, it was recently shown that the deletion of the tumor suppressor genes Rb1 and p53 specifically in NE cells, a subpopulation of cells in normal airways, or in alveolar non-NE type2 pneumocytes of mice resulted in SCLCs closely mimicking human disease. These results provide experimental evidence for the close relationship of NE and non-NE epithelial cells in carcinogenesis.
Abstract IA18: Molecular mechanisms regulating synergistic effect of immunotherapy and chemotherapy of cancer
Authors: Gabrilovich Dmitry , Ramakrishnan Rupal , Huang Chun 
Published: March 2013

Abstract
Despite recent advances in the development of new chemotherapeutic drugs and improvements in radiation therapy, conventional cancer therapy often falls short of the goal of controlling tumor progression. Therapeutic cancer vaccines and adoptive T-cell transfer are long considered as very attractive therapeutic options in the treatment of cancer. However, clinical trials of different cancer vaccines performed in recent years demonstrated rather weak clinical efficacy. It has become apparent that therapeutic cancer vaccines given as a single agent may not produce substantial clinical benefits and combination with conventional methods of treatment will be necessary. The use of conventional cancer chemotherapy in combination with cancer vaccines was previously not considered as very attractive due to the potent immunosuppressive effect usually associated with chemotherapy. This paradigm was challenged in recent years by serendipitous observations made in a number of phase I/II clinical trials that reported high rates of objective clinical responses when cancer vaccines were combined with chemotherapy. The paradox is that the types of chemotherapy that are used in lung cancer are known to suppress the immune system. We have recently demonstrated that chemotherapy and cytotoxic T cells (CTL) have a synergistic cytotoxic effect that may be mediated by mannose-6-phosphate receptor (MPR). We have shown that when cancer vaccines or adoptive T-cell transfer are used as a single modality, only limited numbers of T cells are able to penetrate the tumor parenchyma. CTLs exert their cytotoxic effect only against tumor cells that express specific antigen, since it requires a direct cell-cell contact, and release of perforin and granzymes (GrzB). If chemotherapy is administered immediately after immunotherapy, it causes disruption of tumor stroma that allows for better penetration of antigen-specific T cells. Chemotherapy via autophagy causes substantial increase in MPR expression on tumor cells. Small number of activated CTLs interacting with tumor cells expressing tumor antigen can release GrzB that can penetrate into neighboring tumor cells without requirement for cell-cell contact. Therefore large number of tumor cells including those that do not express specific antigen would be susceptible to the effect of CTLs. This may explain substantial enhancement of antitumor effect of combined treatment. It is likely that this effect would not be long-lasting since CTL activity will be eliminated by chemotherapy and the immune suppressive tumor microenvironment. However, it may provide a sufficient window to achieve a significant antitumor effect. Since memory T cells are more resistant to chemotherapy than effector T cells, it is possible that subsequent immunization would be able to boost antitumor immunity and thus provide a longer lasting effect of combined therapy.
Abstract IA2: Network models in oncogene-addicted lung cancer
Authors: Haura Eric B. , Yoshida Takeshi , Fang Bin , Stukalov Alexey , Eschrich Steven , Welsh Eric , Colinge Jacques , Koomen John , Superti-Furga Giulio , Li Jiannong , Rix Uwe , Zhang Guolin , Kim Jae-Young , Bennett Keiryn , Song Lanxi , Chen Ann , Bai Yun 
Published: March 2013

Abstract
Lung cancer is a devastating worldwide disease yet enthusiasm exists for treatment of subsets of the disease with molecularly targeted agents. Mutations in the epidermal growth factor receptor (EGFR) or translocation of echinoderm microtubule associated protein like 4 – anaplastic lymphoma kinase (EML4-ALK) define two unique subsets of lung cancer characterized by sensitivity to tyrosine kinase inhibitors (TKI). Despite striking results with TKI, not all patients respond, the drugs are non-curative, and resistance is universal. Mutations in KRAS also define a group of patients awaiting therapeutic opportunities. We are characterizing signaling networks using tandem affinity purification (TAP) and liquid chromatography-mass spectrometry (LC-MS/MS) to map protein-protein interactions (PPI) and anti-phosphotyrosine immunoprecipitation coupled with LC-MS/MS to map tyrosine phosphorylation. In PC9 cells with mutated EGFR, we characterized a physical EGFR network consisting of 266 proteins by integrating both TAP and pTyr MS data. In H3122 cells harboring EML4-ALK, we identified a PPI network consisting of 113 proteins and using pTyr MS identified changes in tyrosine phosphorylation in 120 proteins (58 decreased, 62 increased) following exposure to ALK tyrosine kinase inhibitor. Functional proteins are being discovered from these networks using siRNA and inhibitor screens. In parallel studies, we have exploited the use of chemical proteomics to discern targets of promiscuous kinase inhibitors and enable optimal combination approaches. In this way, we view network mapping linked to chemical proteomics as one approach to discern novel drug combination studies for in vivo validation and ultimately translation to early phase clinical trials. To translate PPI based mass spectrometry studies to clinic, we are developing in situ assays that identify and quantify PPI using proximal ligation assays (PLA). Pilot studies identify EGFR:Grb2 interactions in formalin fixed human lung cancers. These approaches have the potential to enable ‘network medicine’ by identifying novel combination approaches as well as through identifying subtypes of cancers through network views of cancer.