French version

MASTER of Oncology 3.0 : omics studies to personalized medicine

Master of Precision Oncology : omics studies to personalized medicine aims to review oncology fundamentals owing to allowing access to the three specialties of Master 2.

Nora MOUMJID

Head of Master of Precision Oncology

nora.moumjid@univ-lyon1.fr

Pierre SAINTIGNY

Head of Master of Precision Oncology

pierre.saintigny@lyon.unicancer.fr

Claire BARDEL

Head of Master of Precision Oncology

claire.bardel-danjean@univ-lyon1

→ First semester teaching unit (30 ECTS)

Omics Technologies and big data in Oncology - 6 ECTS

This teaching unit is articulated around 3 modules of about 20 hours each :

Module 1 « Focus on genomics » : In this module, the main types of methods for identifying genome variations (point mutations and structural variations) will be presented with particular emphasis on massively parallel sequencing technologies and their application in oncology.
Module 2 « Omics diversity »: in this module, the different omics technologies outside genomics (transcriptomics, epigenomics, proteomics and metabolomics), the data they produce, the bioinformatics stages of pre-treatment of the data and their applications in oncology will be treated.
Module 3 « Methods of omics data analysis »: In this module, students will learn how to use the R software to manipulate, analyze and visualize omic data from bioinformatic pre-treatment steps.

✉ Responsible for teachung unit : Claire BARDEL (claire.bardel@univ-lyon1.fr)

Jonathan LOPEZ (jonathan.lopez@chu-lyon.fr)

⊕ Time distribution : 43h Lecture | 4h DG | 13h Laboratory

❝❞ Languages : English (or French)

✎ Evaluation Methods : Written final exam (50 %) + Oral presentation (30%) + practical work evaluation (20%)

Impact of precision oncology on medical practices and ethics - 6 ECTS

The objective of this teaching unit is to enable students (interns and students in biology) to forge a reflexive and critical approach to current developments in precision medicine, particularly in relation to the modifications induced for clinicians as in the organization of hospital structures, and with the ethical and societal issues that this new direction of oncology research raises.

It will thus be necessary to address epistemological themes (in particular the question of whether we are facing a paradigm shift), the reconfiguration of translational research (design of targeted therapies, reorganization of clinical trials). , the sociology of health (especially in the context of the modification of health professions and their articulation at the hospital) and ethics (patient trajectories, understanding of what is a risk factor, impact lifestyle habits, etc.).

This is to ensure that students are able to become aware of the actors involved in the research / clinical interface upstream of the constitution of research projects, and that they can subsequently collaborate so effective and ethical, taking into account the impacts induced in the different fields of health.

✉ Responsible for teaching unit: Julie HENRY (Julie.HENRY@lyon.unicancer.fr)

Marc BILLAUD (Marc.BILLAUD@lyon.unicancer.fr)

⊕ Time distribution : 34h Lecture | 10h DG

❝❞ Languages : French. Courses material in english

✎ Evaluation Methods : Oral (100%) | Validation: elaboration of a group file (internal + students in biology), on a point of translational research integrating its possible impact on the medical practice and the ethical stakes it raises.

PS: Oral presentation in interdisciplinary group (research and medical practice) of a work on the scientific, epistemological, societal and ethical issues of a project or a practice at the interface between research and clinical.

Economic analysis of OMICS and personalized medicine - 6 ECTS

1. Omics and personalized medicine

- State of play and prospects from a socio-economic point of view: Course 4h00

- Economic evaluation of personalized medicine in oncology:
- Initiation to methods: 6h00 class + 3h00 ED

- Presentation and case analysis: 6:00 ED

Work in learning lab: 6h practical work: critical analysis in group of omics in a given pathology (melanoma, breast cancer etc.) based on a documentary research in session (3h00 practival work) then presentation (3h00 practical work)

2. Big data and personalized medicine

- State of play and analysis from a socio-economic point of view: Course 4h00

- Big data and economic analysis: case study: 6:00 ED

Work in learning lab: 6h TP on analysis in group of the economic stakes of big data in a given pathology based on a documentary research in session (3h00 TP) then presentation (3h00 TP)

✉ Responsible for teaching unit: Nora MOUJID (nora.moumjid@univ-lyon1.fr)

⊕ Time distribution : 14h Lecture | 15h DG | 12h Laboratory

❝❞ Languages : French

✎ Evaluation Methods : Written exam 50% + Practical work : 50% (group work)

Bibliography and research projet writing - 6 ECTS

During this EU, students will:

- Conduct a bibliographic search related to their internship topic
- Learn how to use this bibliographic work to write a research project / a briefing note according to the type of internship done by the student

After a first course presenting the expectations for this project and the methods of writing this type of document, students will work on their project independently. TD sessions are scheduled regularly to track project progress.

✉ Responsible for teaching unit: Pierre SANTIGNY (pierre.saintigny@lyon.unicancer.fr)

Nora MOUJID (nora.moumjid@univ-lyon1.fr)

⊕ Time distribution : 1h30 Lecture | 10h DG

❝❞ Languages : English

✎ Evaluation Methods : Project-type report research to obtain funding (100%)

Anglais pour la communication professionnelle niveau 2 - 3 ECTS

Teaching unit which favors scientific English, training in oral expression, the layout of a symposium poster, etc.

✉ Responsible for the teaching unit : Joann PIGAT (joann.pigat@univ-lyon1.fr )

⊕ Time distribution : 30h DG

❝❞ Languages : English

✎ Evaluation methods: continuous monitoring (100%)

OPTIONAL TEACHING UNIT - 3 ECTS
Choose 1 teaching unit :

Focused destruction of cancer - 3 ECTS

✉ Responsible for teaching unit: Frédéric PADILLA ( frederic.pad@gmail.com)

Michel RIVOIRE (michel.rivoire@lyon.unicancer.fr)

⊕ Time distribution : 20 h Lecture | 5h DG

❝❞ Languages : French. Courses material in english

✎ Evaluation methods : Written final exam (100%)

Immunology & Cancer - 3 ECTS

This teaching unit builds on students' basic immunology knowledge to develop fundamental research concepts in immunology that have applications in clinical and pharmaceutical research in the field of oncology. The topics will be:

anti-tumor immune response and its manipulation

Action mechanisms of carcinogens of infectious origin; the "multi-hit-multi-step" or step progression of cancerization; the antigenic profile of the tumor cells; molecular analysis of the tumor microenvironment; Functional alterations of immune system cells infiltrating tumors

Immune system cancers

Panorama and specificity within cancers; analysis of the immune response after immunotherapy; tumor escape mechanisms; monoclonal antibodies in cancer immunotherapy; Hematopoietic stem cell transplantation as a model for immunotherapy

the protection of patients immunosuppressed by treatments or following an infection.

Cytokine action mechanisms capable of restoring immune functions during chemo or radiotherapy; concept of secondary cancer and state of research on the parameters useful for monitoring the occurrence of an infection or cancer on models of studies relating to organ or blood donation, patients infected by HIV or HCV, to patients immunosuppressed by treatment following a transplant or primary cancer.

✉ Responsible for teaching unit : Christine DELPRAT (christine.delprat@univ-lyon1.fr)

⊕ Time distribution : 18h lecture

❝❞ Languages : English

✎ Evaluation methods : Courses : final written exam (50%) + oral presentation (50%)

Innovation et intellectual properties- 3 ECTS

The speakers all have IP expertise and come from the academic world of research, the National Institute of Industrial Property (INPI) and "industrial property advice" firms.

The teaching consists of six courses:

- CM 1 Inaugural conference on the intellectual property (1 hour).

- CM 2 Patents A to Z (4 hours).

- CM 3 Worldwide Patent Databases (2 hours).

- CM 4 Patent infringement and litigation (3 hours).

- CM 5 Counterfeiting (2 hours).

-CM 6 Experience feedback on IP (2 hours).

The courses are reinforced by two sessions of TD, in computer room, to carry out a concrete work around the searchable databases in network (Internet):

- TD 1 Online access to patents (2 hours).

- TD 2 Patent case study (2 hours).

✉ Responsible for teaching unit: Marc LE BORGNE (marc.le-borgne@univ-lyon1.fr)

⊕ Time distribution : 14h CM | 4h TD

❝❞ Languages : French

✎ Evaluation Methods : Final written exam

Introduction to molecular bioinformatics- 3 ECTS

Description not specified

✉ Responsible for teaching unit: Celine BROCHIER (Celine.brochier@univ-lyon1.fr)

Arnaud MARY (arnaud.mary@univ-lyon1.fr)

⊕ Time distribution : 20 h Lecture | 5h DG

❝❞ Languages : Not specified

✎ Evaluation Methods : Not specified

Oncology- 3 ECTS

✉ Responsible for teaching unit: Not specified

⊕ Time distribution : Not specified

❝❞ Languages : Not specified

✎ Evaluation Methods : Not specified

Methods and ethics practices in health domain - 3 ECTS

Between the current legislation, the codes of ethics, the recommendations of good practice and the certifications issued by the High Authority of Health (HAH), we can have the impression that the field of practices of care is already well marked and we could no longer see what place it could remain for ethical questioning. And yet, once these elements of different statuses (more or less binding) are posited, everything remains to be done from an ethical point of view, in the sense that what it would be most adjusted in a given situation remains unresolved, and where these regulations themselves require constant re-interrogation. The challenge of this course is to draw the contours, the modalities and the conditions for an ethical reflection that takes into account this general context while taking root in everyday practices.

Objectives: to acquire reflexive tools to discern and think about ethical questions in concrete situations; Being able to mediate between a conceptual approach and clinical cases, and understand how reflexion feeds back from the field; Analyze the underlying issues and make accurate use of terms commonly used in contemporary health debates.

✉ Responsible for teaching unit: Julie HENRY (Julie.HENRY@lyon.unicancer.fr)

⊕ Time distribution : 20 h Lecture

❝❞ Languages : Not specified

✎ Evaluation Methods : Oral (100%) | Elaboration, oral presentation and discussion of an ethical reflection based on a clinical case or a question of health currently in question.

Medicals practices : between research and clinic- 3 ECTS

The objective of this teaching unit is to give students an idea of what can be today (with the joint evolution of therapeutic innovations, medical practices, the involvement of the patient in his care and patient associations on steering committees, societal demands, etc.) to be an oncologist in connection with active research or to be a researcher in a health center. It consists of a series of interventions by researchers and clinicians in the form of feedback and experience sharing on what their professional practice is at the interface between research and clinical, with various profiles: clinicians from different groups, more or less involved in clinical trials; oncologist engaged in supportive care; researcher in translational research and / or prevention; fundamental researcher on how research objects are defined, etc. This is to make students aware of the interference between research, clinical, patient perspective and social representations in order to lead them to subsequently establish effective collaborations upstream projects.

✉ Responsible for teaching unit: Isabelle RAY-COQUARD

Thomas BACHELOT

⊕ Time distribution : 20 h Lecture

❝❞ Languages : French

✎ Evaluation Methods : Oral (100%) | Oral presentation of the results of a study conducted with clinicians involved in research or researchers working closely with the clinic, in order to bring out new themes.

PS: Oral presentation of medical, ethical and societal issues raised by a project or practice at the interface between research and clinical.

Notes: - 4 half-days on schedule, at ENS Lyon, Fridays - very difficult to validate remotely, without having taken the courses.

Pharmaceutical industries strategy and medical technologies(IAE)- 3 ECTS

Not specified

✉ Responsible for teaching unit: Not specified

⊕ Time distribution : 46h Lecture

❝❞ Languages : Not specified

✎ Evaluation Methods : Not specified

Systems Biology - 3 ECTS

Systemic biology aims to answer biological questions by integrating wet experiments into iterative cycles with computer modeling, simulation and theory. This is essentially an interdisciplinary approach. The objective of this teachning unit will be to provide the basics needed to adopt this approach, and a rough view of the field. It is intended to be accessible to any student in biology, with a strong desire to explore more formal approaches (mainly mathematics and computer science)

The following topics will be addressed

A general introduction to systemic biology

- Good practices in systemic biology

- Large-scale omic data to dynamic modeling

- What is a mathematical model?

- An introduction to the theory of dynamic systems

- Gene networks

- Metabolic networks

- Multi-scale modeling

- Information contained in noise: biological phenomena seen as distributions.

All courses will be illustrated with practical examples from recent literature.

✉ Responsible for teaching unit: Olivier Grandrillon (olivier.gandrillon@ens-lyon.fr)

⊕ Time distribution : 18h DG

❝❞ Languages : English

✎ Evaluation Methods : Report of personal reflexion (100%)

Tissue and cell engineering + mémoire complémentaire- 3 ECTS
  Lecture part
A) Phenotypic and Mechanical characterization of cells and tissues – force, adhesion and motility studies - microsystems for cell culture, diagnosis, drug screening… : 8 hours
B) Biomaterials and scaffolds able to finely tune various cell responses : 6 hours

  Practical part
C) Basics of Image Analysis
-3 theoretical courses with examples on a free software Image J -3 courses for developing a project in tandem : tracking endothelial cells on patterned surfaces.

✉ Responsible for teaching unit :   Jean-Paul RIEU (jean-paul.rieu@univ-lyon1.fr)

  ⊕ Time distribution: 10h Lecture

❝❞ Languages : English

✎ Evaluation methods : Lecture : Bibliographic assay (50%) + Projet Report (50%)

→ Second semester teaching units (30 ECTS)

Academic research internship or company internship - 24 ECTS
The Apogée code for internship agreements is: IPH2264M.

Internships will be offered to students in all the topics covered in the M2 course in connection with the omics and personalized medicine. A multidisciplinary co-supervision will be strongly encouraged with, for example a co-supervision between a clinician or researcher in oncology (Center Léon Bérard / Cancer Research Center of Lyon, CHU Lyon, International Center for Research in Cancer, ...) and bioinformatics / biostatistics teams such as the Bioinformatics-Gilles Thomas Synergie Lyon Cancer platform or the human and social sciences of the different structures. Students will be able to attend molecular, organ-specific, multi-disciplinary meetings at the Forum of Data Mining, different CRCL / CLB seminars depending on the nature of the project.

OPTIONAL TEACHING UNIT- 3 ECTS
Choose 1 teaching unit :

Aging and Cell Death - 3 ECTS

Biology of cell death: necrosis, necroptosis, apoptosis and autophagy and their relationship to aging Cellular senescence: molecular mechanisms of control and escaping. Cellular aging and damage to molecules: reactive oxygen species, proteins, nucleic acids Cellular aging and metabolism: theories of caloric restriction, metabolic signalling pathways Physiopathology of aging: organisms longevity, aging diseases and neurodegenerative diseases

✉ Responsible for teaching unit : Carole KRETZ (Carole.Kretz@univ-lyon1.fr)

⊕ Time distribution : 13h Lecture | 5h DG

❝❞ Languages : English and French

✎ Evaluation methods : Oral presentation (75%) | continuous monitoring (25%)

Level 1 animal experimentation accreditation (CPUAFS) - 3 ECTS

This training will take place at the veterinary school of Lyon (VetAgro Sup campus - Marcy l'étoile) The goal is to allow students who wish to validate the Level 1 animal experimentation by continuing the study of animal models started in the first year of master of oncology.

Spontaneous models in experimental oncology: oncogenesis, specificities related to the domestic animal, specificities of the clinical veterinary oncology framework, ethical regulation, design and implementation of pre-clinical and clinical tests in animals, animal samples and tumor banks and quality system.

✉ Responsible for teaching unit : Delphine GREZEL (delphine.greze@vetagro-sup.fr)

⊕ Time distribution : 15h Lecture |15 h DG

❝❞ Languages : French

✎ Evaluation methods : Written final exam (100%)

Drug Delivery + additional memory- 3 ECTS

The objective of this course is to introduce students to the use of nanotechnology for the development of new types of contrast agents and drugs that specifically target cancer cells for diagnostic and therapy purposes (theranostics).

The course is divided into four parts:

1- General introduction, principle and hopes,
2- How to design nanoparticles for imaging, vectorization and drug delivery?
3- Medical imaging.
4- Vectorization and therapy.

✉ Responsible for teaching unit : Charlotte Rivière (charlotte.riviere@lpmcn.univ-lyon1.fr)

⊕ Time distribution: 10h DG

❝❞ Languages : English

✎ Evaluation methods : Mid-term evaluation and oral presentation of scientific publication

Health economy and cancer - 3 ECTS
Different topics will be covered: Health Systems (HMS), Health Expenditure (NM) Health Expenditure Control, Health Care Supply (NM and HMS), Health Professionals (NM), Health Institutions (HMS), and an introduction to the medico-economic evaluation

✉ Responsible for teaching unit : Nora MOUMJID (nora.moumjid@univ-lyon1.fr)

Carole Siani (carole.siani@univ-lyon1.fr)

and Hans‐Martin SPATH (Hans-Martin.Spath@adm.univ-lyon1.fr)

⊕ Time distribution : 24h Lecture | 6h DG

❝❞ Languages : French

✎ Evaluation methods : Final written exam - Courses (66.67%) | Oral presentation - Practical Work (33.33%)
- Metastasis, Migration et EMT- 3 ECTS
Acquisition of the most recent concepts of the metastatic dissemination process, knowledge of colonization mechanisms at molecular and cellular levels, early detection method, notion of niche and dormancy and targeted therapies
✉ Responsible for teaching unit : Chantal Diaz (chantal.diaz@univ-lyon1.fr)

⊕ Time distribution : 20h Lecture | 10h DG

❝❞ Languages : French

✎ Evaluation methods : Lecture : written exam (100%)

MADP : Methods for proteomics data analysis- 3 ECTS

Description not specified

✉ Responsible for teaching unit: Sophie AYCIRIEX (sophie.ayciriex@univ-lyon1.fr)

⊕ Time distribution : 16h Lecture | 10h DG | 4h Laboratory

❝❞ Languages : Not specified

✎ Evaluation Methods : Not specified

Think cancer in the light of the patient himself - 3 ECTS

Bring humanities and social sciences into the scientific training as a complement. Put into action the national guidelines of the CNIB. Contribute to a perspective of the Descartes epistemology from which science comes to understand its strengths and limitations

✉ Responsible for teaching unit : Romain PARENT (romain.parent@inserm.fr)

⊕ Time distribution : 25 h DG

❝❞ Languages : French

✎ Evaluation methods : Dissertation (10 pages) deadline : june

Targeted therrapies and smal molecules- 3 ECTS

The aim of the teaching unit is to gain knowledge on the "small molecule" side of kinase inhibitors (ATP-competitive, allosteric modulators, inhibitors of protein-protein interactions).

The curriculum is articulated around seven interventions:

- CM 1 Conference in the field of kinase inhibitors (1 hour) "Targeting cancer with small molecule kinase inhibitors"

- CM 2 "Design and Kinase Inhibitor Chemistry" (3 hours)

- CM 3 Structure-Based Drug Design (2 hours)

- CM 4 Ligand-Based Drug Design (2 hours)

- CM 5 Physicochemical properties and ADMET parameters of kinase inhibitors (2 hours)

- CM 6 Specificities and mechanisms of action of kinase inhibitors (2 hours)

- CM 7 Vectorization of kinase inhibitors (2 hours)

The courses are complemented by two TD sessions:

- TD 1 Case Study 1 (2 hours)

- TD 2 Case Study 2 (2 hours)

✉ Responsible for teaching unit: Marc LE BORGNE (marc.le-borgne@univ-lyon1.fr)

⊕ Time distribution : 18h lecture

❝❞ Languages : Not specified

✎ Evaluation Methods : Not specified