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
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
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