FCT PhD Programme Medicines and Pharmaceutical Innovation (i3du)

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1 FCT PhD Programme Medicines and Pharmaceutical Innovation (i3du) Course BIOMARKERS AND ASSAY DEVELOPMENT February 6-10, 2017 Faculty of Pharmacy Amphitheatre B Universidade de Lisboa, Portugal The FCT PhD Programme in Medicines and Pharmaceutical Innovation (i3du; trains students in target discovery, drug design, preclinical development, and drug safety, bridging the translational gap from discoveries on disease targets and mechanisms into novel diagnostic and therapeutic agents. The i3du Programme offers a training course on Biomarkers and Assay Development that will be held at the Research Institute for Medicines (imed.ulisboa), Faculty of Pharmacy, Universidade de Lisboa, in Lisbon, 6-10 Februray This course is designed to cover principles and applications of biomarkers and assay development, from identification to validation, to impact in drug discovery, and disease diagnosis and prognosis. We welcome the participation of external academic and scientific community members. Registration ( is free but mandatory. Organizing committee at imed.ulisboa/ff Cecília Rodrigues (Coordinator) Adelaide Fernandes Elsa Rodrigues Paula Leandro Rui Castro Rui Moreira Susana Solá 1

2 Course outline Biomarkers are now an integral part of the drug discovery and development process, acting as indicators of mechanism of action, efficacy, safety and disease progression, as well as assisting in diagnosis, and patient selection and design of clinical trials. Biomarkers also offer the potential to inform treatment decisions and bring personalized medicine into clinical practice. In early stage drug discovery, biomarkers are used to validate in vitro target modulation. As projects progress, biomarker assays are developed for pharmacokinetic/pharmacodynamic (PK/PD) models, profiling molecules prior to testing in disease models as initial proof of concept. PK/PD models can also assist in dose-to-man scaling predictions for use in clinical trials. The biomarker assays developed during the in vitro discovery phases are frequently used as efficacy or toxicity endpoints in the clinic. Clinical trials, particularly in oncology, are frequently designed around these biomarkers, in addition to biomarkers of disease progression. In contrast, less evidence exists to recommend the use of any biomarker of pathological processes in neurodegenerative diseases, opening the door for conducting future disease progression biomarker studies. Goals and Learning Outcomes Understand the development of both efficacy and translational biomarker assays in cell lines, primary cells and tissues; Explore formats ranging from nucleic acids, protein markers and signaling pathways to cellular phenotypic changes; Apply on-target cellular readouts to support medicinal chemistry optimization projects; Use a range of assays for pharmacodynamic models to determine dosing regimens, and in disease models to correlate target coverage with diseasemodifying effects, including functional readouts showing inhibition of target function. Programme The course is divided into a balanced blend of lectures on theoretical, practical and laboratory case-based discussions presented during a dedicated course with limited attendance. The training programme has specific slots allocated to seminars and workshops, including informal discussions with lecturers. Early discovery requires broad expertise in biomarker identification and assay development across many therapeutic areas. We will focus on oncology, central nervous system, and metabolic diseases and address the development of quantitative assays in primary or immortalized cells, stem cells or induced pluripotent stem cells, or disease tissue that can be used as pharmacodynamic or disease models. Ultimately, these models will act as efficacy and translational markers from the in vivo phase to the clinic. A broad range of endpoints can be employed to support biomarker selection, including genomic, proteomic, phosphoprotein and epigenetic markers. Assay technologies will be discussed. 2

3 6th February h00 Welcome address Cecilia Rodrigues Genetic Biomarkers Organizers: Elsa Rodrigues, Susana Solá (imed.ulisboa) 17h00 DNA and aging: early target discover Miguel Godinho Instituto Gulbenkian Ciência, Oeiras Genomic approaches to metabolic diseases Inês Barroso Welcome Trust Sanger Institute, UK Drug discovery and personalized medicine Luka Clarke BioISI, Faculdade de Ciências, Universidade de Lisboa i3du PhD Students ONLY Imaging tools in biomarker discovery Liana Silva End of day 7th February 2017 Genetic Biomarkers Organizers: Rui Castro, Susana Solá (imed.ulisboa) mirnas and long noncoding RNAs Francisco Enguita imm, Universidade de Lisboa RNA biology in health and disease Manuel Santos ibimed, Universidade de Aveiro Aveiro, Portugal 3

4 17h00 mirna potential for personalised medicine Rui Castro Personalized medicine in cancer Pedro Borralho Novartis, Portugal End of day 8th February 2017 Proteomic Biomarkers Organizers: Paula Leandro, Adelaide Fernandes (imed.ulisboa) From early candidate discovery to a panel of validated protein biomarkers Adelaide Fernandes Glycobiology in cancer Celso Reis i3s Instituto de Investigação e Inovação em Saúde, Universidade do Porto Porto, Portugal Protein biomarker detection from bench to bedside Goreti Sales BIOMARK, Instituto Superior de Engenharia Porto, Portugal Biotechnology & Biomarkers João Pedro Conde INESC Microssistemas e Nanotecnologias, IST, Universidade de Lisboa Sofia Corte-Real Technophage, 4

5 9th February 2017 Metabolomic Biomarkers Organizers: Paula Leandro, Rui Moreira (imed.ulisboa) Metabolomics in drug discovery and development Matilde Marques CQE, IST Lisboa, Portugal Metabolomics in preclinical and clinical drug development Margarida Silva NMR metabolomics in disease Luís Gafeira Gonçalves ITQB, Universidade Nova de Lisboa Oeiras, Portugal i3du 1 st Year PhD Students ONLY How to write a research project? Cecilia Rodrigues Group discussions Elsa Rodrigues, Susana Solá, Paula Leandro 16h30 End of day 10th February 2017 Biomarker Assays Organizers: Cecilia Rodrigues, Rui Moreira (imed.ulisboa) Chemical probes for biomarker discovery Rui Moreira Lisboa, Portugal 5

6 Cell assays to support medicinal chemistry Cecilia Rodrigues Lisboa, Portugal Disease models for drug discovery Jorge Oliveira REQUIMTE/LAQV, Faculdade de Farmácia, Uiversidade do Porto Porto, Portugal Research Project: group discussions Cecília Rodrigues, Elsa Rodrigues, Susana Solá, Paula Leandro (room A.3.4. and A.3.8.) 6

7 Assessment (i3du 1 st Year PhD students ONLY) Assessment of the course consists in the preparation and submission of a research project, characters long (including spaces). Students are grouped to build multidisciplinary teams. Each group works throughout the week on a research project that should reflect the topic of the course, including methodologies and strategies to solve an innovative research question. The project is expected to adhere to the following general structure: a) Title; b) Conceptual hurdle and innovative idea to be tested; c) Plan and methods: d) Relevance of the project (scientific and social impact). The students will select a broad topic of research and are expected to propose a specific project. This project will be evaluated according to the following criteria and weight: a) Novelty and relevance (30%); b) approach to the problem (30%); c) multidisciplinarity of the research plan (40%). Students will attend a workshop on How to write a research project. Specific slots are allocated in the course programme for group discussions, which will take place in prebooked rooms. 7