Molecular Oncology

Course manual 2025/2026

Course content

The course Molecular Oncology centers on one of the most common tumor types: colorectal cancer. The course covers the important molecular signalling pathways involved, and the steps through which colon cancer arises - from a small polyp to a metastasised malignant cancer. We will explain how the advent of detailed molecular analysis methods has helped us to understand most of the underlying (epi)genetic changes and the molecular pathways involved. In the course, students will learn how mutations, large chromosomal defects, epigenetic regulation, and other molecular events impacts on tumor biology. These lectures on molecular data and analyses are made interactive in several interactive bioinformatics sessions.

A second important topic of the course is the role of heterogeneity within tumours. A growing number of tumors are now known to consist of cells with two or more different phenotypes. The different phenotypes vary in molecular pathways, the ability to divide and resistance to therapy. It is becoming increasingly clear that the different types of tumour cells closely resemble various stages of the development of the tissue from which the tumour originated. The consequences of this heterogeneity as well as the mechanisms that govern it will be discussed. Specifically, the role of stem cells and cancer stem cells in colon cancer is discussed.

Heterogeneity also exists between tumors, and during the course, we will explain how these differences manifest, and the mechanisms that are involved. Parallels between intra- and intertumor heterogeneity are discussed.  How the different levels of heterogeneity and cancer cell phenotypes affect therapy response will be discussed. New drugs that specifically inhibit cancer pathways and epigenetic processes are also explained.

In several journal club sessions, students will present and discuss seminal research papers covering the topics lectured during the course.

Study materials

Literature

• Molecular Biology of the Cell | Alberts et al., 7th edition

• OPTIONAL: The Biology of Cancer | Robert A Weinberg, 2nd edition or newer

Software

• r2.amc.nl

Other

• Scientific publications (will be shared in the course)

Objectives

• To understand and describe key molecular pathways in cancer.
• Understand the molecular analyses used in cancer research, such as whole genome sequencing, bulk and single cell RNA-Seq, ChIP sequencing.
• Apply basic bioinformatic analyses using the above data types.
• Understand the fundamental causes of intratumor heterogeneity and its role in therapy resistance.
• Understand intertumor heterogeneity and its clinical consequences.
• Explain how drugs act on mutated proteins and cellular states.
• Independently present and discuss a published research article in English.

Teaching methods

• Lecture
• Computer lab session/practical training
• Presentation/symposium

The Lectures are given in person at the AMC, and also recorded for later reference. They will prepare the students for the exam. 

The practical course is also on site (presence mandatory) and will teach basic bioinformatics skills. These connect to the lectures given and are required to fully understand the molecular events that drive cancer. 

The Literature Presentations (presence mandatory) will teach students how to critically interpret literature, to explain the study to their peers, and to discuss these papers. Presenters are graded. Papers will be announced and shared shortly. The aim of these presentations is two-fold: you will learn to present scientific content to a group of peers, and you are required to understand a scientific paper well enough to present it and answer questions about it. 

Learning activities

Attendance

Additional requirements for this course:

Attendance with Literature Presentations (Referaten) and the R2 practical bioinformatics course is mandatory.  These cannot be done online. Absence should be discussed with the coordinator. 

Assessment

The exam is a written test, aligning with the learning goals stated with the lectures. 

Inspection of assessed work

On demand; students should contact the coordinator. 

Assignments

The graded parts of the course are the exam that the students study for and are prepared for in the lectures. 

The students also prepare, and perform literature presentations. This is graded and presence is mandatory. 

The bioinformatics course is done in collaborations in small groups and will familiarize the students with basic gene expression analysis. This part is not graded but presence is mandatory. 

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

Additional information

After taking the test and having received your grades, it is possible to review your test an scoring upon request. 

Processed student feedback

In response to the 2024 evaluations and comments from the OC, the following changes were implemented:

• Two new clinical lectures have been added this year; one from a surgical perspective, and one by a medical oncologist.
• It will be ensured that the learning objectives for each lecture are well defined beforehand, revisited during the lecture, and revisited again at the end.
• The OC proposed integrating workshops into the curriculum to encourage students to actively engage with the material and develop collaboration skills. Since the schedule is already set, we will instead link the computer lab sessions to the lectures, such as mentioning during gene expression lectures that these analyses will be covered in the lab.
• Albert's Biology of the Cell is the book to accompany the course and content will be referenced. 

Previous year's changes:

• During or directly after the lectures, formative testing will be done. Also, a test exam will be made available on Canvas. 
• The R2 bioinformatics practical course has been made more interactive between students, to boost collaborative skills.
• Test questions will made more more clear. 

Contact information

Coordinator

• M.F. Bijlsma

m.f.bijlsma@amsterdamumc.nl
(please do not use my uva.nl email address)
Adore/RDC ZH3J079
020-4448099

Staff

• dr. J.J.B. Koster
• dr. L. Hoyng
• dr. K.J. Lenos
• dr. N.L. Leveille
• prof.dr. J.P. Medema
• dr. S Van Hooff
• M. v.d. Vlugt
• J. Tuynman
• T. Buffart