Notes from all the lectures of the Oncogenesis course. With extended explanations rather than only points. Short summary of content at the beginning of every topic and generally take-home messages at the end of the topics. I added some notes of what I think is important for the exam.
Cancer Biology- Exam 6 portion of final 2024/2025 (100% verified)
Cancer Biology: Exam #1 2024/2025 (100% verified)
Biology of Cancer 2024/2025 (100% verified)
All for this textbook (23)
Written for
Vrije Universiteit Amsterdam (VU)
Oncology
M_OONC03 (ONCOGENESIS)
All documents for this subject (1)
Seller
Follow
Maitetxu
Reviews received
Content preview
ONCOGENESIS
By Maite Erguin
Course coordinators: Ruud Brakenhoff, Rob Wolthuis & Gerben
Vader
Master’s in Oncology. 2022-2023
Vrije Universiteit Amsterdam
,CONTENT:
1. CELL SIGNALING AND CANCER GENES Marcel Spaargaren ....................................................... 5
Signal transduction .................................................................................................................... 5
Oncogenes ................................................................................................................................. 7
Tumor suppressor genes (TSG) ................................................................................................. 8
2. HALLMARKS OF CANCER Jos Poell........................................................................................... 10
3. CELL CYCLE CONTROL Rob Wolthuis ....................................................................................... 12
Problem 1: Replicate each chromosome ................................................................................ 12
Problem 2: Equal distribution of each chromosome over two daughter cells ....................... 13
Key molecules of the cell cycle ................................................................................................ 14
Cell cycle and cancer therapy .................................................................................................. 16
4. CHROMOSOMAL INSTABILITY AND ANEUPLOIDY IN CANCER Gerben Vader ......................... 17
Aneuploidy definition .............................................................................................................. 17
Chromosomal instability (CIN) ................................................................................................ 17
Effects on cell physiology ........................................................................................................ 18
CIN and aneuploidy in oncogenesis ........................................................................................ 18
5. MASSIVELY PARALLEL SEQUENCING (MPS): DNA METHODS. Daoud Sie ............................... 19
Steps in NGS ............................................................................................................................ 19
Grooming................................................................................................................................. 20
Find mutations through alignment to genome ....................................................................... 20
Find aberrations in copy number ............................................................................................ 21
Tissue storage by FFPE ............................................................................................................ 21
Targeted (re)sequencing ......................................................................................................... 21
Different sequencing machines............................................................................................... 21
6. p53 PATHWAY Job de Lange ................................................................................................... 22
Regulation of p53 in normal cells ............................................................................................ 22
Tumor suppression by P53 ...................................................................................................... 22
Tumors with wildtype P53 ...................................................................................................... 23
Tumors with mutant P53 ........................................................................................................ 25
7. CANCER GENOMICS Ruud Brakenhoff .................................................................................... 26
Oncogene activation ............................................................................................................... 26
Types of DNA changes ............................................................................................................. 27
8. PROGRESSION MODELS IN CANCER Ruud Brakenhoff ............................................................ 29
Genetic model for colorectal carcinogenesis .......................................................................... 29
Head and neck squamous cell carcinoma (HNSCC):................................................................ 30
9. TGF-β SIGNALING AND CANCER Luuk Hawnkels ..................................................................... 32
Physiological roles of TGF- β: .................................................................................................. 33
Mutations in TGF-β pathway in cancer ................................................................................... 33
Epithelial cells and cancer-associated fibroblasts (CAFs) ........................................................ 34
Endothelial cells ...................................................................................................................... 34
Therapy targeting angiogenesis .............................................................................................. 35
10. THE WNT SIGNALLING CANCER PATHWAY Wim de Lau ....................................................... 36
Role of WNT in development .................................................................................................. 36
Transduction of Wnt ............................................................................................................... 36
WNT pathway in cancer .......................................................................................................... 37
11. MASSIVELY PARALLEL SEQUENCIGN (MPS): RNA METHODS Peter Henneman.................... 38
Microarrays for transcript profiling......................................................................................... 38
RNA-seq ................................................................................................................................... 39
1
, DNA vs RNA NGS data ............................................................................................................. 40
Single-cell RNA sequencing (scRNA-seq) ................................................................................. 41
12. REGULATED PROTEIN SYNTHESIS IN CANCER William Faller ................................................ 42
Initiation .................................................................................................................................. 42
Elongation ............................................................................................................................... 43
The ribosome .......................................................................................................................... 43
13. NON-CODING RNAs IN CANCER Nicolas Leveille ................................................................... 44
miRNA discovery ..................................................................................................................... 45
miRNA biogenesis.................................................................................................................... 46
Experimental prediction of miRNA target sites ...................................................................... 46
miRNAs in cancer .................................................................................................................... 47
Long non-coding RNA (lncRNA) ............................................................................................... 48
14. APPLICATION OF MPS IN CANCER RESEARCH Jan Molenaar ................................................ 49
Neuroblastoma........................................................................................................................ 49
Patient X .................................................................................................................................. 51
15. INTRATUMORAL HETEROGENEITY/SINGLE CELL Hugo Snippert ........................................... 52
Patient organoids and drug response ..................................................................................... 52
Tumor evolution ...................................................................................................................... 53
16. GENOME EDITING BY CRISPR CAS Rob Wolthuis .................................................................. 54
CRISPR/Cas9 mechanism ......................................................................................................... 54
Gene editing ............................................................................................................................ 55
Reducing off-target effects ..................................................................................................... 55
Base editing: CRISPR without DNA breaks .............................................................................. 56
Prime editing method ............................................................................................................. 56
Other uses for CRISPRs ............................................................................................................ 56
17. EPIGENETIC ALTERATIONS IN CANCER Fred van Leeuwen ................................................... 57
Epigenetics .............................................................................................................................. 57
DNA methylation ..................................................................................................................... 57
Epigenetics in cancer development ........................................................................................ 59
Epigenome and transcription factor maps .............................................................................. 59
H3K79 methylation by DOT1L ................................................................................................. 59
18. METABOLIC CHANGES IN CANCER Bas Teusink .................................................................... 60
Impact on glucose and amino acid metabolism...................................................................... 60
The Warburg effect ................................................................................................................. 61
19. CELL DEATH MECHANISMS AND AUTOPHAGY Saskia Cillessen ............................................ 62
Apoptosis ................................................................................................................................. 63
Autophagy ............................................................................................................................... 64
Necrosis ................................................................................................................................... 66
20. IN VITRO MODELS Angelina Huseinovic ................................................................................ 66
Cell lines .................................................................................................................................. 67
Cell culture method types ....................................................................................................... 68
DNA/RNA transfection ............................................................................................................ 68
Functional assays..................................................................................................................... 69
21. MOLECULAR CARCINOGENESIS OF BREAST CANCER Wesseling ........................................... 70
Developmental process ........................................................................................................... 70
Breast cancer initiation ........................................................................................................... 70
Ductal carcinoma in situ (DCIS) ............................................................................................... 71
2
, 22. HIGH THROUGHPUT LOSS OF FUNCTION (LOH) SCREENS IN MAMMALIAN CELLS René
Bernards ...................................................................................................................................... 72
Approaches to loss function genetic screens .......................................................................... 72
Uses of loss of function screens in oncology .......................................................................... 72
23. HEMATO-ONCOGENESIS J Cloos ........................................................................................... 74
Diagnostic ................................................................................................................................ 75
Lymphoma ............................................................................................................................... 75
Multiple myeloma ................................................................................................................... 75
Leukemia ................................................................................................................................. 76
24. CANCER GENETICS Quinten Waisfisz..................................................................................... 77
Linkage analysis ....................................................................................................................... 77
Association studies .................................................................................................................. 78
25. CANCER STEM CELLS Louis Vermeulen ................................................................................. 78
Stem cells ................................................................................................................................ 78
Cancer stem cells ..................................................................................................................... 79
26. MECHANISMS OF VIRUS-MEDIATED CELL TRANSFORMATION Renske Steenbergen .......... 80
Retroviruses ............................................................................................................................ 80
DNA viruses ............................................................................................................................. 81
How do viruses cause cancer .................................................................................................. 82
27. HPV-MEDIATED CERVICAL CARCINOGENESIS AND IMPLICATIONS THEREOF Renske
Steenbergen ................................................................................................................................ 82
Human Papillomavirus (HPV) .................................................................................................. 82
Cervical cancer ........................................................................................................................ 83
Prevention ............................................................................................................................... 84
28. HPV AND NON-CERVICAL CANCERS Ruud Brakenhoff .......................................................... 84
Detection ................................................................................................................................. 84
Penile cancer ........................................................................................................................... 85
Lung cancer ............................................................................................................................. 85
Head and neck squamous cell carcinoma (HNSCC) ................................................................. 86
29. MOUSE MODELS I + II Jonkers ............................................................................................... 86
Importance of mouse models for cancer ................................................................................ 86
How to make transgenic and knockout mice .......................................................................... 87
How can we model sporadic cancer in mice ........................................................................... 88
How to find genotype-phenotype correlations ...................................................................... 89
How to identify novel cancer genes ........................................................................................ 89
How to test anticancer strategies in mice ............................................................................... 89
30. ROLE OF EBV IN HUMAN CANCER Michiel Pegtel ................................................................. 90
B cells....................................................................................................................................... 90
Dual tropism ............................................................................................................................ 90
EBV diagnosis .......................................................................................................................... 90
Genes modulating B cell physiology driving cancer ................................................................ 91
31. PRECURSOR LESIONS OF THE LUNG Hans Daniels ................................................................ 92
Lung cancer ............................................................................................................................. 92
Central airway lesions ............................................................................................................. 93
Parenchymal lesions ................................................................................................................ 93
32. HEREDITARY CANCER AND GENETIC COUNSELING Charlotte Dommering........................... 93
Colorectal cancer..................................................................................................................... 93
Lynch syndrome ...................................................................................................................... 94
3
The benefits of buying summaries with Stuvia:
Guaranteed quality through customer reviews
Stuvia customers have reviewed more than 700,000 summaries. This how you know that you are buying the best documents.
Quick and easy check-out
You can quickly pay through credit card or Stuvia-credit for the summaries. There is no membership needed.
Focus on what matters
Your fellow students write the study notes themselves, which is why the documents are always reliable and up-to-date. This ensures you quickly get to the core!
Frequently asked questions
What do I get when I buy this document?
You get a PDF, available immediately after your purchase. The purchased document is accessible anytime, anywhere and indefinitely through your profile.
Satisfaction guarantee: how does it work?
Our satisfaction guarantee ensures that you always find a study document that suits you well. You fill out a form, and our customer service team takes care of the rest.
Who am I buying these notes from?
Stuvia is a marketplace, so you are not buying this document from us, but from seller Maitetxu. Stuvia facilitates payment to the seller.
Will I be stuck with a subscription?
No, you only buy these notes for $15.44. You're not tied to anything after your purchase.
