Only a small fraction of the mammalian genome codes for messenger RNAs destined to be translated into proteins, and it is generally assumed that a large portion of transcribed sequences including introns and several classes of non-coding RNAs (ncRNAs) do not give rise to peptide products. A systematic examination of translation and physiological regulation of ncRNAs has not been conducted. Here, we use computational methods to identify the products of non-canonical translation in mouse neurons by analyzing unannotated transcripts in combination with proteomic data. This study supports the existence of non-canonical translation products from both intragenic and extragenic genomic regions, including peptides derived from anti-sense transcripts and introns. Moreover, the studied novel translation products exhibit temporal regulation similar to that of proteins known to be involved in neuronal activity processes. These observations highlight Correspondence: J.S. (judith.steen@childrens.harvard.edu) or G.K. (gabriel.kreiman@childrens.harvard.edu). 5Current address: Institute for Biochemistry and Molecular Biology Nussallee 11, 53115 Bonn, Germany 6Current address: School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand. 7Current address: Merck Millipore, Im Laternenacker 5, 8200 Schaffhausen, Switzerland 8Current address: Department of Neurobiology, Harvard Medical School †These authors contributed equally Authors contributions: SP: designed and performed the final mass spectrometry and bioinformatics experiments, analyzed the data and wrote the manuscript; MH: developed concept, designed and carried out bioinformatics data analysis, and wrote the manuscript; RC: designed and carried out mass spectrometry validation experiments, molecular biology and biochemistry follow-up experiments, and wrote the manuscript; DW: designed and carried out the quantitative proteomics experiments; RYTC: carried out initial pilot experiments and tested strategies; CD: designed and performed initial neurobiologyexperiments; EH: designed and performed initial neurobiological experiments; HS: contributed to the mass spectrometric experiments and critically evaluated the data; JG: contributed to the conceptual design and critically evaluated the results; GK: developed concept, and supervised the RNA-seq part of the project and wrote the manuscript. JS: developed concept, designed initial experiment, supervised the proteomics part of the project and wrote the manuscript. Accession codes: RNA-seq data is already published (References: 5 and 16). The data can be found on GEO with the code GSE21161 Competing financial interests: The authors declare no competing fiancial interest. HHS Public Access Author manuscript Nat Commun. Author manuscript; available in PMC 2015 May 18. Published in final edited form as: Nat Commun. ; 5: 5429. doi:10.1038/ncomms6429. A uhor M anscript

Introduction: Erlotinib selectively inhibits the EGFR tyrosine kinase activity and consequently the tumour cell growth in patients. The drug is administered orally and being a weak base, its solubility is strongly dependent upon the acidic pH in the gastric fluid. Gastric acid reducing agents (ARAs), such as proton pump inhibitors (PPIs) and H2-receptor antagonists (H2RAs), increase the pH of the stomach (pH > 4) and cause a physicochemical drug-drug interaction. The secretion of H+ is drastically reduced by PPIs due to an irreversible binding to the H/K-ATPase pump. H2RAs have a shorter elimination half-life and competitively inhibit histamine action of H2 receptors, on gastric parietal cells. Our objective was to evaluate the plasma concentrations of erlotinib when given alone or in combination with different groups of ARAs (PPIs and H2RAs) and to simulate the erlotinib plasma concentration using a physiologically based pharmacokinetic (PBPK) model to evaluate possible physicochemical interactions from ARA co-medication. Methods: Three groups of each 8 patients, suffering from pancreatic cancer, received 100 mg erlotinib daily as fixed dose (control group), combined with PPI pantoprazole (PPI group) or combined with H2RA famotidine (H2RA group). Blood samples were collected on day 1 (pre-dose,1,2,3,4,6,8 and 24 hours after administration) and on days 2-7 (pre-dose and 4 hours after administration). Erlotinib samples were stored at -80 °C and were quantified by a HPLC assay. Pharmacokinetic parameters were calculated by a noncompartmental method for extravascular input using WinNonlin 6.0(Phoenix Inc.). The PBPK model was built with the software Gastro Plus™(Simulations Plus Inc.) to simulate plasma concentrations of erlotinib in a population of 25 Caucasian patients. Results: The PBPK model output corresponds well to the mean observed erlotinib plasma concentrations of the control group. The observed Cmax and AUC0-24 of erlotinib on day 1 were consistent with the predicted concentrations by Gastro Plus™(Cmaxobserved=0.78 µg/mL vs. predicted=0.76 µg/ml, AUC0-24observed=10.7 hr*µg/mL vs. predicted=11.8 hr*µg/ml). The mean trough and peak concentrations showed a high inter-patient variability over the whole investigated period in all patient groups. The co-administration of PPIs decreased the erlotinib trough and peak concentrations as well as the AUC0-24 about 50% compared to the control and H2RA group. The mean trough concentration in the PPI group on day 7 was 0.36 µg/mL and therefore below the necessary threshold concentration of 0.5 µg/mL to inhibit the tyrosine kinase activity. On the contrary, the pharmacokinetic parameters of erlotinib did not differ significantly in presence of the H2RAs. The mean trough and peak concentration of erlotinib in the H2RA group on day 7 were 0.671 and 1.78 µg/mL and thus similar to the values of the control group (Ctrough=0.950 µg/mL, Cpeak=1.76 µg/mL). In the H2RA and control group all measured plasma concentrations exceeded the threshold. Conclusion: Co-administration of H2RA drugs instead of PPIs is strongly recommended during erlotinib treatment. H2RAs are given 12 hours before erlotinib administration and therefore show no influence on erlotinib plasma concentrations. PBPK is a useful tool to simulate plasma concentration-time curves of a drug and model possible interactions based on patient observations, physicochemical properties and drug classifications.

Dr Horlait et al. [1.Horlait M. Leys M. De Greve J. Van Belle S. Integrating communication as a core skill in the global curriculum for medical oncology.Ann Oncol. 2017; Abstract Full Text Full Text PDF PubMed Scopus (2) Google Scholar] claim that the topic ‘communication’ has not been given the position in the 2016 Edition of the Global Curriculum (GC) that it deserves. We are pleased to read that the authors did a comparative analysis between the three editions of the GC [2.Dittrich C. Kosty M. Jezdic S. et al.ESMO/ASCO Recommendations for a Global Curriculum (GC) in Medical Oncology ― Edition 2016.Ann Oncol. 2016; 27: 1378-1381Abstract Full Text Full Text PDF PubMed Scopus (26) Google Scholar, 3.Dittrich C. Kosty M. Jezdic S. et al.ESMO/ASCO Recommendations for a Global Curriculum in Medical Oncology – Edition 2016.ESMO Open. 2016; 1: 1-96Abstract Full Text Full Text PDF Scopus (55) Google Scholar]. The conclusion that ‘clinical and treatment aspects of cancer care are the focal point of all three versions’ certainly reassures all contributors that they have done their job. What else should be the focus of such recommendations for medical oncology? If Horlait et al. have dared to take a slightly deeper look into the GC or at least at its Table of Contents they could easily have found that 8 out of 12 (67%) sections of the GC are not dedicated to clinical and treatment aspects of cancer care—as reproached—but to various important general aspects [3.Dittrich C. Kosty M. Jezdic S. et al.ESMO/ASCO Recommendations for a Global Curriculum in Medical Oncology – Edition 2016.ESMO Open. 2016; 1: 1-96Abstract Full Text Full Text PDF Scopus (55) Google Scholar]. Horlait et al. obviously missed the opportunity to carefully compare to what extent the content and position of ‘communication’ in the GC has evolved since its original appearance. Whereas in the original publication in 2004, only a short paragraph of about 50 words subordinated under ‘palliative care and end-of-life care’ was reserved for this topic and, in the GC Update 2010, a chapter of its own of about 40 words dealt with communication, we have dedicated substantially more attention and space to it in the 2016 Edition of the GC [3.Dittrich C. Kosty M. Jezdic S. et al.ESMO/ASCO Recommendations for a Global Curriculum in Medical Oncology – Edition 2016.ESMO Open. 2016; 1: 1-96Abstract Full Text Full Text PDF Scopus (55) Google Scholar]. The topic has been worked out by three independent experts nominated by ESMO and ASCO to equilibrate, therewith potential differences with regard to culturally sensitive contents relevant in communication. We even dedicated an entire section of one complete page to ‘communication’ with detailed learning objectives and have subcategorised the most pertinent items with regard to the outcome requirements. We are proud to learn that ESMO/ASCO Recommendations are applied in Flanders. The cited research on medical oncology trainees in Flanders which have revealed that ‘there is a need to upgrade the quality of communication skills of future oncologists’ dates from a time when the GC was not available, and the criticised ‘communication’ section of the GC Edition 2016 can, therefore, not be linked to the actual training situation in Flanders. In addition, this report is not available but only submitted for publication. We certainly fully respect the spirit of Flanders (Belgium) seeking for particularity in the field of communication and beyond. However, we would like to refer to the fact that 47 national oncology societies have endorsed the entire 2016 Edition of the GC [3.Dittrich C. Kosty M. Jezdic S. et al.ESMO/ASCO Recommendations for a Global Curriculum in Medical Oncology – Edition 2016.ESMO Open. 2016; 1: 1-96Abstract Full Text Full Text PDF Scopus (55) Google Scholar]. Finally, it was of utmost importance to find a reasonable equilibrium among the unlimited details of all the necessary fields with impact on the training in medical oncology. It should also be remembered that training has to focus on core components of communication in order not to succumb to fragmentation [4.Stiefel F. Bourquin C. Communication in oncology: now we train – but how well?.Ann Oncol. 2016; 27: 1660-1663Abstract Full Text Full Text PDF PubMed Scopus (31) Google Scholar]. We welcome constructive criticism and recommendations for future updates of the GC which aims to contribute to ameliorate the fast moving field of medical oncology. None declared.

Introduction: Erlotinib selectively inhibits the intracellular phosphorylation of human EGFR-Type 1, expressed on the cell surface of normal and cancer cells, thus preventing the signal transduction and resulting in an inhibition of angiogenesis which prevents proliferation, invasion and migration of tumor cells. To date only few data have been reported about the plasma disposition of erlotinib during long time administration. We report the monitoring of erlotinib plasma concentration in 14 patients when given daily 100 mg together with other various drugs up to 60 weeks. The objective was to assess the steady-state pharmacokinetics and Ctrough of erlotinib over a long time period and to evaluate variability of plasma concentrations when combined with other drugs. Methods: 14 patients suffering from pancreatic cancer received erlotinib at a daily flat dose of 100 mg p.o. and were monitored over a prolonged time period up to 60 weeks. Whole blood samples were collected on day 1 (pre dose, 1, 2, 3, 4, 6, 8 and 24 hours after administration), on days 2-8 (pre dose and 4 hours after administration) and once weekly in the morning before next erlotinib administration. Erlotinib samples were stored at -80o C and were quantified by a sensitive and selective isocratic reversed phase HPLC assay at the end of this investigation. Pharmacokinetic parameters on day 1 and from days 2 to 8 were calculated by a noncompartmental method for extravascular input using WinNonlin 6.0 (Phoenix Inc. USA) Results: The plasma concentrations parameters of erlotinib on day 1, on days 2-8 and on all weeks are listed in the Table 1. We observed a difference in Ctrough with patients having proton-pump inhibitors (PPIs) co-medicated and those without co-medication. Our analyses showed that the Ctrough of the 6 patients, who received erlotinib in combination with PPIs, pantoprazole or esomeprazole, dropped below the recommended concentration threshold of 0.5 µg/ml which is necessary to inhibit the tyrosine kinase (TK). Conclusion: Erlotinib did not accumulate in the blood, even when given up to 60 weeks. Co-administration of a PPI is strictly prohibited in order to achieve therapeutic plasma concentrations above threshold. Our results give evidence for a physical-chemical drug interaction between erlotinib and PPIs. Solubility of erlotinib observed is decreased by a change of gastric pH-value in the stomach. We strongly recommend therapeutic drug monitoring of erlotinib when combined with PPIs in order to ensure that the needed Ctrough concentration of 0.5 µg/ml for TK inhibition is exceeded.

Less than 2% of mammalian genomes code for messenger RNAs which are translated into proteins. A much larger part of the genome is transcribed into a variety of species 1-3, many of which are generally classified as “non-coding” RNAs4-9. However, no systematic examination of translation from these species has been reported. At the same time,~ 80% of peptides from high-throughput massspectrometry experiments do not match sequences in annotated databases12, suggesting that many potentially un-annotated translation products exist. Here, computational methods were used to identify and create a database of transcripts from a quantitative high-throughput total RNA sequencing dataset. Proteomics data from this experimental context were then searched against this database to investigate whether putative non-coding transcripts are translated into protein products. While thousands of peptide spectrum …

The European Society for Medical Oncology (ESMO) and the European Organisation for Research and Treatment of Cancer (EORTC) welcome the adoption of the Clinical Trials Regulation (CTR) by the European Union (EU) as a clear signal that the EU supports research while fully respecting patients' rights and safeguards. The CTR is a step in the right direction to correct years of serious challenges faced by researchers when performing clinical trials. However, there are still many unresolved issues that may yet take research efforts down the wrong path. In this editorial, the pros and cons of several major features of the Regulation are analysed from the standpoint of academia and are outlined in a systematic way, thereby recognising the achievements of the CTR, emphasizing ongoing or newly created challenges, and offering proposals for solutions. The European CTR [1.The European Parliament and the Council of the European Union Regulation (EU) No 536/2014 of the European Parliament and of the Council of 16 April 2014 on clinical trials on medicinal products for human use, and repealing Directive 2001/20/EC.. 2014; L158 (OJ EU): 1-76Google Scholar] was adopted by the Council of the EU and the European Parliament and published in the official journal of the EU on 27 May 2014. It is currently in the early stages of implementation and is likely to become applicable in 2016. It repeals Directive 2001/20/EC, which resulted in loss of competitiveness for European trialists and a reduction in trials of up to 25% since 2007 [2.Hartmann M. Impact assessment of the European Clinical Trials Directive: a longitudinal, prospective observational study analysing patterns and trends in clinical drug trial applications submitted since 2001 to regulatory agencies in six EU countries.Trials. 2012; 13: 53Crossref PubMed Scopus (40) Google Scholar, 3.Hearn J. Sullivan R. The impact of the “clinical trials” directive on the cost and conduct of non-commercial cancer trials in the UK.Eur J Cancer. 2007; 43: 8-13Abstract Full Text Full Text PDF PubMed Scopus (66) Google Scholar] due to, among other reasons, an excess of bureaucratic requirements which were especially challenging for non-commercial cancer clinical trials. The CTR harmonises the rules for setting up and conducting clinical trials. It offers the use of a single, free-of-charge online portal, administered by the European Medicines Agency (EMA), as an exclusive platform for stakeholder interaction in the clinical trial process, mainly for submission and maintenance of clinical trial applications and authorisations within the EU. The CTR will not take effect until the portal is fully operational, i.e. not before June 2016. We envisage three essential challenges. First, the portal must be as user-friendly as possible and take into account different types of users. Secondly, the portal should facilitate the work of investigators running academic trials who rarely have robust administrative support yet will now be encouraged to submit all information simultaneously. Information submitted should be kept to the strict minimum; otherwise, it will delay submission even longer than current practice because initiating sites need time to collect all documents especially for international trials. Thirdly, the assessment process requires a strict workflow procedure and tight timelines, and should support stakeholders with appropriate automatic reminders and deadline warning programmed into the system. A user-friendly portal that takes into consideration the needs of all possible stakeholders is key, especially for academia. EORTC is one of the academic partners in the EMA Multi-stakeholder Working Group and is dedicated to providing input in order to make the portal as user-friendly as possible. The CTR also introduces a new category of studies: the ‘low-intervention clinical trial’ with simplified, risk-proportional monitoring and safety reporting as estimated by the trial sponsor. This should present major savings on costs and a more adequate procedure for many, while also avoiding the often daunting bureaucratic minutiae of prescriptive detail. The concept of a low-intervention clinical trial has been watered down with the removal of simplified assessment procedures. A minimised variant, the central monitoring, i.e. automatic data check using statistical properties of the collected data, that has been shown to be an efficient (superior and cheap) substitute to on-site monitoring, should be considered as alternative. In addition, we invite EU Member States to consider providing at least insurance coverage equal to the coverage for standard treatment as part of the national implementation process. Transparency of clinical trial data is a key issue for regulators and governments, and EMA is confronted therewith while holding two from each other independent positions. Transparency was described by the then EMA's Executive Director, Guido Rasi, as an essential element to ‘rebuild trust and confidence in the whole system’ [4.European Medicines Agency. Access to clinical-trial data and transparency: Workshop report. www.ema.europa.eu/docs/en_GB/document_library/Report/2012/12/WC500135841.pdf (21 July 2013, date last accessed).Google Scholar]. In principle, since 2012, EMA has been willing to share full raw datasets, including individual patient data once anonymised. This ‘Policy 0070’ applies to data of clinical trials that are part of the marketing authorisation (MA) applications for medicines that have been or will be authorised by EMA beyond the scope of the CTR, e.g. trials that are conducted outside of the EU, but submitted to EMA for MA in Europe. Whether this will apply also for trials registered via the EU portal based on the CTR may depend on the result of a recent public consultation of the concerned stakeholders by EMA. At first glance, EMA has to be applauded for removing the previous restrictions that allowed post-registration access only to redacted data in a non-downloadable format. EMA's new open Policy 0070 allows the user to download and print clinical study reports (CSRs) that holds true exclusively for EMA's action outside of the CTR frame (www.ema.europa.eu/ema/index.jsp?curl=pages/news_and_events/news/2014/10/news_detail_002181.jsp&mid=WC0b01ac058004d5c1). But, for the preponderant situation where EMA will execute the CTR, there are challenges to overcome as information can still be categorised as commercially confidential information and the process of accessing individual patient data has not yet been solved. In addition, based on the CTR, only summaries of clinical results data, but not raw data will be made publicly available. EMA's execution of the greatly applauded transparency measures taken so far is critical, because they only apply to non-EU Member States applications which are not subject to the CTR and EU law. EMA's transparency measures should not be undermined by pressure from the pharmaceutical industry, justified on grounds stated as ‘practising commercially confidential information, in particular through taking into account the status of the marketing authorisation for medicinal product, unless there is an overriding public interest in this closure’, when EMA deals within the CTR-based frame applicable to EU Member States (www.pharmatimes.com/article/14-04-08/AbbVie_strikes_compromise_with_EMA_on_data_disclosure.aspx). A balanced approach is needed to deal with the juxtaposed topics of transparency of clinical trials and the ongoing discussion on data protection. The EU General Data Protection Regulation (GDPR) should exclusively protect patient confidentiality to the extent this is needed without jeopardising patients' right to transparency of the results of clinical research. We are convinced that researchers know how to responsibly deal with and access raw data for independent re-analysis of clinical trial results. EMA should put in place safeguards to guarantee that the re-analyses of strictly de-identified personal data will be carried out exclusively in accordance with the highest scientific ethical standards. This would avoid the criticism that data of clinical trials are presented in a biased manner. Transparency of clinical trial data is of global value. The fact that some pioneer researchers in the pharmaceutical industry have recognised this and are allowing access to de-identified patient data should be a good basis to accept the importance of this concept [5.Nisen P. Rockhold F. Access to patient-level data from GlaxoSmithKline clinical trials.N Engl J Med. 2013; 369: 475-478Crossref PubMed Scopus (101) Google Scholar]. We urge the European Parliament, the European Commission and the European Council to make sure that the new EU GDPR does not abolish the progress achieved in the field of transparency. The inclusion of the all-important principle of ‘one-time consent’ in the CTR is a critical milestone in the medical research community because access to patient data and tissue beyond the end and the scope of a trial is essential for successful medical research. The acceptance by a patient that data generated within a specific trial may be used for further investigations outside that trial—with adequate and monitored protection of privacy and all patient rights—represents a unique and important achievement [6.The European Parliament and the Council of the European Union. Regulation (EU) No 536/2014 of the European Parliament and of the Council of 16 April 2014 on clinical trials on medicinal products for human use, and repealing Directive 2001/20/EC. OJ EU 2014; L158: 30, Article 28.2.Google Scholar]. This is arguably the greatest sign of respect and self-determination towards patients, many of whom decide to participate in clinical trials for more than personal gain. For them, one-time consent means they can continue to contribute to research by ‘donating’ their data to research even beyond the scope and the end of a specific trial. This will hasten advances in research because trial databases are a precious source of information, and serve the ultimate goal of providing better treatments without incurring any risk to the patients. According to the CTR, ‘scientific research making use of the data outside the protocol of the clinical trial shall be conducted in accordance with the applicable law on data protection’ [6.The European Parliament and the Council of the European Union. Regulation (EU) No 536/2014 of the European Parliament and of the Council of 16 April 2014 on clinical trials on medicinal products for human use, and repealing Directive 2001/20/EC. OJ EU 2014; L158: 30, Article 28.2.Google Scholar]. However, the European Parliament's Resolution Amendment 191 to Article 81 on the EU GDPR insists on specific patient consent for every use of patient data and tissue that would neutralise the concept of a one-time consent, and severely hinder research in Europe [7.European Commission European Commission. Proposal for a Regulation of the European Parliament and of the Council on the protection of individuals with regard to the processing of personal data and on the free movement of such data (General Data Protection Regulation) COM (2012) 11 final. 2012Google Scholar]. We have to make sure that the new EU GDPR may allow the option of the one-time consent also under the perspective of privacy and that the degree to which national countries may derogate is minimised to avoid discrepancies in rules across the EU, with obvious limitations to collaborative research [8.Casali P.G. Risks of the new EU Data protection regulation: an ESMO position paper endorsed by the European oncology community.Ann Oncol. 2014; 25: 1458-1461Abstract Full Text Full Text PDF PubMed Scopus (24) Google Scholar]. The CTR imposes, though without clearly stipulating it, a coordination process between national authorities and ethical committees (ECs). Currently in most countries, ECs do not—or rarely—communicate with competent national authorities. In some countries, this communication is additionally cumbersome because of the high number of ECs involved in the evaluation of research. National authorities and ECs will require close interaction if unnecessary delay is to be avoided, and the number of ECs will have to be limited to be able to comply with deadlines. It is imperative to assure meaningful communication between all stakeholders if real success is to be achieved and which can only be regulated through the national implementation of the Regulation. EU Member States have the right to ‘opt-out’ from the clinical trial in case they do not agree on the research proposed. This prevents some Member States from ‘vetoing’ a trial accepted by the others. There is still the possibility of a clinical trial being refused in some European Member States, yet accepted in others. This means that individual countries may decline to participate in a trial even if it has already been accepted by other countries. It is hoped that this opt-out option will become less commonly used as European regulations at the national level become more homogenous. The CTR suggests patient involvement in clinical trials. The CTR does not go far enough on patient involvement in clinical trials and only suggests that patients be members of the ECs. Cancer patients clearly have a high degree of interest in participating in the design and decision making of clinical trials. They should be given the opportunity to become involved with a subject that will frame how research on their disease needs to be conducted, and how the data gained from studying their data and tissue is to be used. While patient involvement can be determined at the national level, a comprehensive definition is required ESMO will work with EORTC on the issues above, especially through the EORTC-ESMO European Clinical Cancer Research Forum which brings together EU collaborative research groups and which met for the first time in October 2014. One goal of the group will be to provide recommendations to guide Ministries of Health (or Ministries of Justice for issues related to data protection) in implementing the CTR in a harmonised fashion across all Member States on topics such as insurance or ECs. In addition, EORTC will work closely with EU institutions and conduct workshops with focus groups on specific topics and ESMO will gather feedback from its members and national oncology societies to submit it to the EU Clinical Trials Advisory Group that is responsible for answering questions and monitoring implementation of the CTR. Another key task for ESMO will be providing education to ESMO members on how to run clinical trials according to the CTR that is, how to use the new EMA clinical trials portal, paperwork requirements and administrative regulations, a harmonised wording of patient informed consent forms, collaboration with ECs, etc. We hope that our united efforts will result in a consensus for a common position on clinical trials throughout Europe. The CTR represents one of the most important changes in the field of clinical trials in the last decade. Although still very much a work in progress, it is an opportunity to facilitate clinical cancer research in Europe and reduce some of the burdens that have proven so costly in the past. We welcome all readers' thoughts on this topic and are eager to promote debate, especially within national oncology societies. We particularly need that support to assure that this new beginning is not hampered by the new EU GDPR, whose text is currently under revision and absolutely needs to safeguard the future of public health research by allowing a derogation from consent for epidemiological population-based registries, and by including the concept of a broad, but withdrawable one-time consent from patients for use of their data and biobank tissues for future public research as well as in clinical trials. We are concerned whether the specific changes to the Regulation as advocated by the cancer community will prompt the European authorities to adequately address this issue. The authors thank Gracemarie Bricalli, and Tanya Kenny from the ESMO Head Office, as well as Malvika Vyas of Rohde Public Policy, for their valuable contribution. The authors have declared no conflicts of interest.

Only a small fraction of the mammalian genome codes for messenger RNAs destined to be translated into proteins, and it is generally assumed that a large portion of transcribed sequences--including introns and several classes of noncoding RNAs (ncRNAs)--do not give rise to peptide products. A systematic examination of translation and physiological regulation of ncRNAs has not been conducted. Here we use computational methods to identify the products of non-canonical translation in mouse neurons by analysing unannotated transcripts in combination with proteomic data. This study supports the existence of non-canonical translation products from both intragenic and extragenic genomic regions, including peptides derived from antisense transcripts and introns. Moreover, the studied novel translation products exhibit temporal regulation similar to that of proteins known to be involved in neuronal activity processes. These observations highlight a potentially large and complex set of biologically regulated translational events from transcripts formerly thought to lack coding potential.

BACKGROUNDWe conducted a phase I trial of gemcitabine (gem) with concurrent radiotherapy in patients with muscle-invasive bladder cancer (BC) ineligible for surgery or cisplatin or refusing organ loss.PATIENTS AND METHODSPatients with urothelial cancer, cT2-T4, cN0-1, M0, ineligible for surgery due to local tumor extension, PS, age or co-morbidities or who refused surgery were included. After maximal transurethral resection, the treatment schedule included: twice-weekly i.v. infusion of gem [dose levels (DL) 1-6: 20, 27, 30, 33, 50 and 40 mg/m(2), respectively] for 30 min and concurrent radiotherapy (RT) to the bladder with 55.5 Gy. The primary end point was to determine the maximum-tolerated dose (MTD) and the dose recommended (RD) for further studies of this gem schedule. The secondary end point was late toxicity. The MTD was defined by dose-limiting toxicity (DLT) in 2 or more of 6 patients, discontinuation of RT and/or gem for >1 week in 2 or more of 6 patients due to grade (G) 3/4 acute and/or late toxicity in more than 2 of 18 patients.RESULTSThirty-five of 44 patients were assessable for toxicity and thus the primary end point. DLTs occurred in two of five patients at dose level 5: one G3 alanine aminotransferase elevation and one G3 fatigue. The MTD, therefore, was 50 mg/m(2) gem twice weekly. At DL 6 with 40 mg/m(2), the RD was established: only one of six patients developed G3 fatigue and diarrhea. Late toxicity was rare and of low grade (only G1-2). The 2-year locoregional failure rate was 32% (9/28); 10 of 28 patients (38%) were alive with an intact bladder and no evidence of recurrent disease, 9 patients developed distant metastases and 6 died of their disease.CONCLUSIONSGemcitabine in combination with RT is well tolerated in BC patients ineligible for surgery and/or cisplatin. The RD of gemcitabine for subsequent trials is 40 mg/m(2) twice weekly with concurrent radiation.

Aim: UMPC represents an unmet therapeutic need. Maximum tolerated dose (MTD), PK, safety, and doses recommended for phase II (RPIID) of CEB were determined, and the prognostic potential of CTCs was assessed. (EudraCT 2008-004444-36).Methods: A 3 + 3 design was used with stepwise dose escalation (DE) starting with C until reaching MTD followed by DE of E and B of one step each. C, E, and metabolites were measured with HPLC. CTCs were determined by anti-EpCAM immunomagnetic enrichment technology.Results: 30 out of 35 pts (15 f, 15 m) aged 63.9 + /-8.4 yrs, with ECOG status 0 (77%) or 1 (23%) and unresectable (N = 1)/metastatic disease (N = 29) were evaluable for MTD. C (mg/m2 bid) was started with 500 (dose level (DL) 1; N = 7), escalated to 650 (DL2; N = 6), 800 (DL3; N = 8), and reached MTD with 900 (DL4; N = 8). At DL5 (N = 3), C 800 was combined with E, escalated from 100 to 150mg po d. At DL6 (N = 3), C and E dosages were kept, B was escalated from 5 to 10mg/kg q 2wks. Whereas DLTs in form of diarrhea (N = 2), erythema, herpes, rectal bleeding, and hand-foot syndrome (N = 1 each) were found during DE of C in DL1 (1 pt), DL2 (1 pt), DL3 (1 pt), and DL4 (3 pts), no further DLT was observed with the DE of E and B. Overall, 264 cycles were applied. Extensive PK could not verify modulation of E by C. Due to the different modes of activation and metabolization of C and E, a PK interaction seems not to be probable. High inter-individual variability of PKs was detected. The most severe G3/4 toxicities per pt were: hand-foot syndrome (16.7%), diarrhea, hyperbilirubinemia, rash/acne (10% each), myocardial infarction, paronychia, cheilitis, anemia (3.3% each). 2 pts (7%) reached PR, 17 pts (61%) had stable disease. PFS was median 3.6 mos (1.3-19.2), OS was median 6.8 mos (1.8-34.0+). No CTC (CTC-) was detected in 13 pts, 1-4 CTCs (CTC+) in 11 pts. PFS in CTC- was median 9.6 mos (95%CI 5.2, 13.9), in CTC+ median 2.8 mos (95%CI 1.4, 4.2); this difference revealed a trend (p = 0.079; Breslow).Conclusions: RPIID is C 800mg/m2 bid, E 150mg po d and B 10mg/kg q 2wks. CEB can be applied safely and has demonstrated clinical activity.Disclosure: C. Dittrich: received honoraria from Roche Austria; the research institute directed by CD received unrestricted research grants from Roche Austria; G. Nirnberger: received honoraria / consultation fees from Roche Austria; M. Czejka: The working group directed by MC received grants/research support from Roche Austria; K. Geissler: The research institute directed by KG received grants/research support from Roche Austria. All other authors have declared no conflicts of interest.

Background: The presence of CTC in metastatic BC is associated with an impaired prognosis. Recent data show a reduced disease-free survival and increased risk of death in the presence of CTC in EBC. Therefore, patients with persisting CTC after (neo)adjuvant chemotherapy might benefit from additional systemic treatment. Recent data have reinforced the hypothesis that trastuzumab can eliminate tumor cells by antibody dependent cell cytotoxicity (ADCC) or other immune mechanisms. Preclinical data have provided evidence that the benefit of trastuzumab may be associated with targeting cancer stem cells in a HER2 independent model (Ithimakin et al Cancer Res 2013). Trastuzumab eliminated CTC, irrespective of the HER2 status of the primary tumor and of CTC and this was associated with reduced relapses(Georgoulias et al Ann Oncol 2012). Trial Design: Treat CTC trial is a multicenter European randomized phase II trial, sponsored by the EORTC and run under the BIG umbrella. It will assess the efficacy of trastuzumab in eliminating persisting CTC after the completion of (neo)adjuvant chemotherapy and surgery in patients with HER-2-negative EBC. Eligible patients will be randomized in a 1:1 ratio to either 6 cycles of trastuzumab or observation. Patients’ peripheral blood will be tested again for CTC after 18 weeks. Main Eligibility criteria: - Adequately excised HER2-negative EBC - Evidence of CTC detection using the CellSearch technology after completion of (neo)adjuvant chemotherapy - Completion of adjuvant chemotherapy for node-positive disease or neoadjuvant chemotherapy with residual invasive disease in breast or lymph nodes (no complete pathological response) - Histological Grade > 1 and primary tumor size > 1 cm Specific aims: The primaryobjective of the trial is to evaluate whether trastuzumab decreases the detection rate of CTC in patients with HER2-negative EBC by comparing the trastuzumab treated arm to the observation arm. Furthermore, clinical outcomes as measured by Recurrence Free Interval (RFI), Invasive Disease Free Survival (IDFS), Disease Free Survival (DFS) and Overall Survival (OS)) between the trastuzumab and observation arms will be compared. Present accrual and target accrual: Treat CTC started patient screening in April 2013 in Belgium. It is estimated that 2175 women will be registered to include 174 patients eligible for randomization. Accrual is expected to be completed in 2 years. Methods: The primary test will be a one-sided test to compare the trastuzumab arm to the observation arm for the CTC detection rate at week 18 (superiority test). The comparison for the primary endpoint will be performed on the intention-to-treat population using a one-sided test with overall a of 0.1. The odds ratio and its confidence interval will be estimated using a logistic regression model. The comparison of RFI, IDFS, DFS and OS will be done using a two-sided test in a proportional hazards model for cause specific hazard, adjusted for the stratification factors. Perspectives: Given the prognostic relevance of CTC in BC, the Treat CTC trial will be the first multicenter, randomized trial in which CTC are used to guide treatment decisions in EBC. The results of this trial will help to clarify the clinical utility of CTCs in early disease. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr OT1-3-02.

Erlotinib is an oral epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor approved for the treatment of non-small cell lung cancer and when combined with gemcitabine for pancreatic cancer. Dose reduction of erlotinib in patients with severe hepatic impairment has been established. We present the case of a male patient suffering from an adenocarcinoma of the pancreas with metastases in the liver and lung, whose disease progression led to highly elevated bilirubin levels of >14 mg/dl accompanied by icterus and pruritus. Despite the known contraindication, the patient agreed to be treated with 150 mg erlotinib p.o. per day. We performed therapeutic drug monitoring of erlotinib on day 1 after the first ingestion of erlotinib and then over a period of 19 days. One-compartment pharmacokinetics on day 1 were calculated, and, based on these data, a pharmacokinetic simulation for the following 19 days was run. On day 1 after the first erlotinib ingestion, plasma concentrations were identical to those described in the literature. On the following days, erlotinib plasma concentrations remained at a similar order of magnitude after daily ingestion. Compared with published data, OSI420 plasma concentrations were clearly higher from day 1 to 16. Due to disease progression, the last intake of erlotinib was on day 16, but plasma concentrations of the drug and metabolite increased excessively thereafter. The data give evidence that total bilirubin levels up to 14 mg/dl do not necessarily cause elevated plasma concentrations of erlotinib when given in doses of 150 mg per day.

Background: PEM and ERL have been approved as second-line monotherapy for locally advanced or metastatic NSCLC. The combination of PEM + ERL showed synergistic activity in preclinical studies. This multicenter, randomized, open-label study assessed the efficacy and safety of PEM + ERL vs. PEM.

BI 2536, a novel Polo-like kinase 1 inhibitor, was assessed in patients with unresectable advanced exocrine adenocarcinoma of the pancreas. The study employed a two-stage design. Randomised first-line patients received BI 2536 200 mg on day 1 (n=43) or 60 mg on days 1–3 (n=43) every 21 days. Recruitment of second-line patients was planned for a second stage dependent on an interim analysis demonstrating ⩾2 responses in the first 18 evaluable patients following 12 weeks of treatment and/or tumour control ⩾12 weeks in 5 patients per schedule. Primary end point was objective response rate (ORR). By independent review, ORR was 2.3% (all partial) and 24.4% had stable disease as confirmed best response. The second stage was not initiated. Median overall and progression-free survivals were 149 (95% confidence interval (CI), 91–307) and 46 days (95% CI, 44–56). Most common drug-related adverse events were neutropenia (37.2%), leukopenia (29.1%), fatigue (29.1%) and nausea (22.1%); most common grade 3/4-related events were neutropenia (36.0%), leukopenia (27.9%) and thrombocytopenia (8.1%). Given the low ORR and poor survival, further development of BI 2536 monotherapy is not warranted in this population.