Experimental Oncology

6 EC

Semester 1, period 1

5234EXPO6Y

Owner Master Biomedical Sciences
Coordinator R.L. Beijersbergen PhD
Part of Master Biomedical Sciences, track Oncology,

Course manual 2023/2024

Course content

The master course experimental oncology deals with the main themes of basic cancer research and treatment, the implications of groundbreaking new research for diagnosis and treatment of cancer, and the clinical implementation. Teachers are fundamental researchers and clinicians involved in the development and implementation of state-of-the-art cancer therapies. Topics include e.g. molecular cancer diagnostics, the hallmarks of cancer, mechanisms of drug resistance, immunotherapy of cancer. The course evolves around four major themes; hormone regulated cancers, DNA damage and genomic instability, targeted therapy and resistance and immunology and immunotherapy. Lectures covering different fields of research and treatment provide background and reference.  The different topics will be dealt with in lectures, workshops and assignments (essay with pitch presentation,  a group assignment with presentation and a research proposal with pitch).

Recommended  prior knowledge
Solid, advanced knowledge in the areas of cell biology and genetics (eg. courses Celbiologie (6 EC), Moleculaire Biologie/Biochemie (T) (6 EC), Anatomie en Ontwikkelingsbiologie (12 EC), Medische Biochemie en Pathofysiologie (12 EC)).

Study materials

Literature

  • The biology of cancer by R.A. Weinberg (2nd edition). 

Syllabus

  • electronic copies of Handouts

Objectives

  • Aim of the course Experimental Oncology is to provide insight into the molecular basis of normal and tumor cell behaviour 
  • to provide insight into the development of new methods for cancer diagnosis and therapy.
  • To review and discuss the historical context and evidence for novel targeted cancer therapies
  • To review, analyse and discuss the up-to-date status of the field in relation to an outstanding research question in oncology
  • The ability to define, describe and discuss a research proposal related to an oncology related question

Teaching methods

  • Lecture
  • Presentation/symposium
  • Self-study
  • wiring a research proposal
  • Supervision/feedback meeting
  • Working independently on e.g. a project or thesis

Lectures provide the general background and the current standing of the respective clinical or research field. They also introduce the latest developments and insights in the respective research area. lectures given by experts in the respective research field.

There will be 3 workshops each around a specific theme. Students will get assignments schie will be discussed within the group.

There are 2 "interview the teacher" sessions in which the students prepare questions based on information provided by the teacher to get familiar with the research field, the current concepts and discuss open questions. 

The students have to write an essay on the historical development of a targeted drug in clinical use and present their findings in a pitch presentation.

The students have to address an outstanding question in oncology in a small group. They have to investigate recent findings, implications, shortcomings and future research for this question in relation to technological developments. The group presents the findings  in a presentation.

Each student has to independently write a research proposal on a research topic  captured during the course. They will have to define the research question and discuss its relevance, generate a hypothesis, discuss the experimental approach to test the hypothesis and discuss the potential outcomes. Each student will present the research proposal in a pitch presentation followed by a short discussion. 

During the course introductions and workshops are provided for the different assignments in the course. The students will provide feedback to their peers and will receive feedback on the different steps in the assignments. 

 

Learning activities

Activity

Number of hours
lectures 36
workshops 12
preparation 47
presentations 18
feedback 10
Self Study 45
 Totaal 6 EC a 28 h 168

 

Attendance

Requirements of the programme concerning attendance (OER-B):

  1. Attendance during practical components exercises is mandatory.

Additional requirements for this course:

presence at lectures and  workshops  is mandatory

Completion of assignments, written and presentations is mandatory

Absence needs to be communicated with the course coordinator

Assessment

Item and weight Details

Final grade

1 (25%)

assigment 1

Bonus

1 (25%)

assignment 2

Mandatory

1 (25%)

assignment 3

Mandatory

1 (25%)

assignment 4

Mandatory

0.5 (12%)

assignment 2 pitch

Mandatory

0.5 (12%)

assignment 4 pitch

Mandatory

The final grade is the average of  assignment 2 (25%), pitch assignment 2 (12.5%),  assignment 3 (25%), assignment 4 (25%), pitch assignment 4 (12.5%). The scores for assignment 1 are bonus points adding 0.25 point (0 to 4 bonus points possible) to assignment  2.

The final grade has to be higher than a 5.5 to pass the course. 

If a deadline for an assignment is not met, that part will  be graded zero ( 0)

 

 

Inspection of assessed work

Contact the course coordinator to make an appointment for inspection.

The students can only request an appointment for inspection after all the grades are in and the final score has been calculated and communicated with the students.

Assignments

assignment 1 individual

  • exercise in writing a short essay about the history and development of a target therapeutic

    Peer review of short essay

    both assignments are graded 0-1-2

assignment 2 individual

  • written essay about the history and development of a target therapeutic graded 0-10

assignment 2 individual

  • Short presentations  about the history and development of a target therapeutic graded 0-10

assignment 3 group

  • presentation about an outstanding question in oncology related to new technologies graded 0-10

research proposal individual

  • written research proposal on oncology related subject/problem graded 0-10

research proposal individual

  • presentation research proposal on oncology related subject/problem graded 0-10

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

COURSE ON EXPERIMENTAL ONCOLOGY  
Date   October 2 to October 27, 2023  
Location   room Z4 in NKI   
WEEK 1      
DATE / TIME   SUBJECT TEACHER
MONDAY  2/Oct    
10.45-11.10   START COURSE-pick up acces pass and coffee/tea in room Z4
11.10 - 12.00   Introduction course Roderick Beijersbergen
12.10 - 13.00   Introduction assignment 1 and 2 Roderick Beijersbergen
lunch break      
13.30 - 14.20   Advanced early cancer diagnostics Beatriz Carvalho
14.30 - 15.20   Advanced early cancer diagnostics Beatriz Carvalho
       
    Self-study preparation lecture Clinical trials paper @ Surfdrive
    preparation assigment 1  
       
DATE / TIME   SUBJECT TEACHER
TUESDAY 3/Oct    
9.00 - 9.50   Survival data analysis Roderick Beijersbergen
10.00 - 10.50   Survival data analysis Roderick Beijersbergen
coffee break      
11.10 - 12.00   The study of mouse models for cancer Jos Jonkers
12.10 - 13.00   The study of mouse models for cancer Jos Jonkers
lunch break   1 hour break - please read paper Soesan  
14.00-14.50   Clinical trials Marcel Soesan
15.00-15.45   Clinical trials   Marcel Soesan
    preparation assigment 1  
 24.00    deadline hand-in assigment 1  
DATE / TIME   SUBJECT TEACHER
WEDNESDAY 4/Oct    
9.00 - 9.50   Workshop Hormone Regulated Cancers Andre Bergman
10.00 - 10.50     Wilbert Zwart
coffee break      
11.10 - 12.00     Hugo Horlings
12.10 - 13.00      
lunch break      
13.30 - 16.00   feedback and discussion assigment 1 Roderick Beijersbergen
       
       
       
DATE / TIME   SUBJECT TEACHER
THURSDAY 5/Oct    
    preparation assignment 2 @ home  
       
       
       
       
       
       
       
       
24.00   deadline hand-in slides for pitch presentation assigment 2  
DATE / TIME   SUBJECT TEACHER
FRIDAY 6/Oct    
9.00 - 9.50   pitch presentations assigment 2 Roderick Beijersbergen
10.00 - 10.50      
coffee break      
11.10 - 12.00   pitch presentations assigment 2  
12.10 - 13.00      
lunch break      
13.30 - 14.20   pitch presentations assigment 2  
14.30 - 15.20      
 SUNDAY  8/Oct    
24.00   deadline hand-in assigment 2  
WEEK 2      
DATE / TIME   SUBJECT TEACHER
MONDAY  9/Oct    
9.00 - 9.50   Next generation sequencing Arno Velds
10.00 - 10.50   Next generation sequencing Roderick Beijersbergen
coffee break      
11.10 - 12.00   Introduction assignment 3 Roderick Beijersbergen
12.10 - 13.00   Introduction research proposal Roderick Beijersbergen
lunch break      
13.30 - 15.00   preparation assigment 3 in groups
       
       
       
DATE / TIME   SUBJECT TEACHER
TUESDAY 10/Oct    
9.00 - 9.50   DDT and TLS Heinz Jacbobs
10.00 - 10.50   DDT and TLS Heinz Jacbobs
coffee break      
11.10 - 12.00   Aneuploidy and CIN  Jonne Raaijmakers
12.10 - 13.00   Aneuploidy and CIN  Jonne Raaijmakers
       
    Preparation interview the teacher: Benjamin Rowland  
       
       
       
DATE / TIME   SUBJECT TEACHER
WEDNESDAY 11/Oct    
9.00 - 9.50   Interview the teacher: Benjamin Rowland  
10.00 - 10.50   Shaping the genome in interphase and mitosis  
coffee break      
11.10 - 12.00   feedback and discussion assigment 3 Roderick Beijersbergen
12.10 - 13.00   feedback and discussion assigment 3 Roderick Beijersbergen
lunch break      
13.30 - 15.00   preparation assigment 3  in groups
    and research proposal   
       
       
DATE / TIME   SUBJECT TEACHER
THURSDAY 12/Oct    
9.00 - 9.50   Epigenetics and Gene Regulation Elzo de Wit
10.00 - 10.50   Epigenetics and Cancer Fred van Leeuwen group
coffee break      
11.10 - 12.00   Epigenetics Interactive Session Elzo de Wit &
12.10 - 13.00   Epigenetics Interactive Session Fred van Leeuwen group
lunch break      
13.30 - 14.20   How to write a research proposal Roderick Beijersbergen
14.30 - 15.20   How to write a research proposal Roderick Beijersbergen
       
       
DATE / TIME   SUBJECT TEACHER
FRIDAY 13/Oct    
    preparation assignment 3 and research proposal @ home  
       
WEEK 3      
DATE / TIME   SUBJECT TEACHER
MONDAY  16/Oct    
9.00 - 9.50   Cancer genomics Lodewyk Wessels
10.00 - 10.50   Cancer genomics Lodewyk Wessels
coffee break      
11.10 - 12.00   Targeted Therapy Roderick Beijersbergen
12.10 - 13.00   Targeted Therapy Roderick Beijersbergen
lunch break      
13.30 - 15.00   preparation assignment 3  in groups
    and research proposal  
       
       
DATE / TIME   SUBJECT TEACHER
TUESDAY 17/Oct    
9.00 - 9.50   Workshop: Functional genomic screening  
10.00 - 10.50     Nicolaas Boon
coffee break     Roderick Beijersbergen
11.10 - 12.00     Johan Kuiken
12.10 - 13.00      
       
Z4 not available after 3 PM      
       
       
       
DATE / TIME   SUBJECT TEACHER
WEDNESDAY 18/Oct    
9.00 - 9.50   TBA  
10.00 - 10.50   TBA  
       
11.10 - 12.00   TBA  
12.10 - 13.00   TBA  
lunch break      
13.30 - 15.00   preparation assignment 3 in groups
    and research proposal  
       
       
DATE / TIME   SUBJECT TEACHER
THURSDAY 19/Oct    
9.00 - 9.50   RNA translation and the ribosome Wiliam Faller group
10.00 - 10.50   RNA translation and the ribosome William Faller group
coffee break      
11.10 - 12.00   mRNA translation and Reuven Agami group 
12.10 - 13.00   cancer immunotherapy Reuven Agami group 
lunch break      
13.30 - 15.00   preparation assignment 3 in groups
    and research proposal  
       
 24.00    deadline hand-in slides presentation assignment 3  
DATE / TIME   SUBJECT TEACHER
FRIDAY 20/Oct    
9.00 - 9.50   presentations assigment 3 Roderick Beijersbergen
10.00 - 10.50      
coffee break      
11.10 - 12.00   presentations assigment 3  
12.10 - 13.00      
lunch break      
13.30 - 14.20   presentations assigment 3  
14.30 - 15.20      
       
Week 4      
       
       
DATE / TIME   SUBJECT TEACHER
MONDAY  23/Oct    
9.00-9.50   Feedback and discussion research proposal Roderick Beijersbergen
10.00-10.50   Feedback and discussion research proposal Roderick Beijersbergen
coffee break      
11.10 - 12.00   Protein structure and drug design Titia Sixma
12.10 - 13.00   Protein structure and drug design Titia Sixma
       
Z4   preparation research proposal  
    preparation Interview Rene Bernards 24/10  
       
       
DATE / TIME   SUBJECT TEACHER
TUESDAY 24/Oct    
9.00 - 9.50    Immunology and Immunotherapy Leila Akari
10.00 - 10.50    Immunology and Immunotherapy Leila akari
coffee break      
11.10 - 12.00   Interview the teacher: Rene Bernards Rene Bernards
12.10 - 13.00   Novel strategies for targeted therapy  Rene Bernards
       
Z4   preparation research proposal  
       
       
       
DATE / TIME   SUBJECT TEACHER
WEDNESDAY 25/Oct    
9.00 - 9.50   Telomeres, DNA damage and cancer Jacqueline Jacobs
10.00 - 10.50   Telomeres DNA damage and Cancer Jacqueline Jacobs
coffee break      
11.10 - 12.00   TCR and Neoantigens Wouter Scheper
12.10 - 13.00   TCR and Neoantigens Wouter Scheper
       
Z4   preparation research proposal  
       
       
       
DATE / TIME   SUBJECT TEACHER
THURSDAY 26/Oct    
9.00 - 9.50   CART-T therapy Maria Themeli AUMC
10.00 - 10.50   CART-T therapy Maria Themeli AUMC
coffee break      
11.10 - 12.00   Immuno-therapy resistance Daniel Peeper
12.10 - 13.00   Immuno-therapy resistance Daniel Peeper
       
Z4   preparation research proposal and pitch presentation  
       
       
 24.00    deadline hand-in slides for proposal pitch  
DATE / TIME   SUBJECT TEACHER
FRIDAY 27/Oct    
9.00 - 9.50   proposal pitches Roderick Beijersbergen
10.00 - 10.50      
coffee break      
11.10 - 12.00   proposal pitches  
12.10 - 13.00      
lunch break      
13.30 - 14.20   proposal pitches  
14.30 - 15.20      
15.30 - 16.20   Evaluation and Borrel  
       
Sunday 29/oct    
24.00   deadline hand-in research proposal  

 

Timetable

The schedule for this course is published on DataNose.

Additional information

Course will be held at the NKI-AVL, Plesmanlaan 121, Amsterdam
For information, contact mw. Patty Lagerweij (p.lagerweij@nki.nl)

Homepage NKI-AVL: http://www.nki.nl

Contact information

Coordinator

  • R.L. Beijersbergen PhD