Index
Pathology of primary skin tumors ........................................................................................................... 2
Neoplasia ............................................................................................................................................. 2
Skin cancer............................................................................................................................................... 4
Clinical pathology .................................................................................................................................... 5
Different skin tumors .............................................................................................................................. 8
Basal cell carcinoma (BCC) .................................................................................................................. 9
Squamous cell carcinoma (SCC) .......................................................................................................... 9
Melanocytic tumors .......................................................................................................................... 10
Common Nevi (moedervlek) ............................................................................................................. 13
Spitz nevus ......................................................................................................................................... 13
Malignant melanocytic tumors: MELANOMA ................................................................................... 15
Lentigo maligna (melanoma)............................................................................................................. 17
Langerhans cell histiocytosis (LCH)................................................................................................ 20
Merkel cell carcinoma (MCC) ........................................................................................................ 21
Gene mutations in tumors .................................................................................................................... 23
Detection of chromosomal aberrations, translocations and CNV ........................................................ 28
Copy number alterations:.................................................................................................................. 29
Detection aberrations hematological.................................................................................................... 32
Molecular pathology: lymphoma diagnostics, clonality assessment .................................................... 35
Pathophysiology of Cervical Cancer ...................................................................................................... 38
Artificial intelligence .............................................................................................................................. 51
Basics ................................................................................................................................................. 51
The Urinary system................................................................................................................................ 56
Basis ................................................................................................................................................... 56
Nephropathology: kidney diseases ................................................................................................... 66
Kidney diseases ..................................................................................................................................... 70
Nephrotic diseases ............................................................................................................................ 70
Minimal change disease ................................................................................................................ 70
Focal and segmental glomerulosclerosis....................................................................................... 70
Membranous glomerulopathy ...................................................................................................... 71
Nephritic syndrome ........................................................................................................................... 71
Immune complexes formation ...................................................................................................... 71
ANCA disease ................................................................................................................................. 72
Anti GBM disease .......................................................................................................................... 72
,Pathology of primary skin tumors
Neoplasia
- Geneticallly driven growth of cells
- Tumor: formation of a mass, which can grow die to inflammation. It can be neoplastic or
non-neoplastic. A large scar can also be a tumor
- Neoplasia: new growth of cells, which is always genetically driven
- Neoplasm can be benign or malignant. Not always forms a mass (e.g. it can also be blood-
bound in e.g. leukemia)
- Neoplasia examples: warts, moles, nevus. They are benign genetically driven lesions.
- Neoplasia is driven by genetic alterations such as mutations, structural chromosomal
alterations (translocation or gene fusion), copy number variations (losses or gains of parts or
whole chromosomes), viral transformation (viral DNA gets incorporated into the cell).
Dutch: Benign: goedaardig, Malignant: kwaadaardig
- Malignant: mitosis in tissue and infiltration in other tissues and can go to lymph nodes and
other organs. Cells of malignant tissue do not look like the precursor cells.
Benign tumor ≠ premalignant
,3 types of genetic alterations
1. Mutations (small) (=Mutation = a nucleotide
change in DNA)
• Activation of oncogenes
• loss of function/expression of tumor
suppressor genes
Substitution: when a nucleotide is replaced by another
nucleotide, resulting in the substitution of the amino acid and then change sequence.
Insertion: of one or more nucleotides, which leads t o out-of-frame mutations. This changes the
sequence of the protein. Then an inactivated or ineffective protein is created.
Deletion: one of a few nucleotides are deleted, this leads to an out-of-frame mutations and thus a
non-sense sequence.
2. Copy number variations (large)
Losses or gains of whole chromosomes or part of chromosomes.
• loss of tumor suppressor genes
3. Chromosomal translocations
• expression or activation of oncogenes
3 types of genes can be involved in oncogenesis (oncogenesis only occurs when the genes affected
are involved in oncogenesis). Genes involved in the formation of cancer:
1. (proto)oncogenes: main function is to promote cell proliferation and survival. When a
mutation or amplification occurs, it leads to a gain of function, activations or over expression.
This promotes more cell proliferation and survival.
2. Tumor suppressor genes: main function is to inhibit cell proliferation and induction of
apoptosis. When there is a mutation in these genes, this will lead to inactivation or loss of
function of the tumor suppressor gene, this then leads to the loss of induction of apoptosis
and loss of inhibition of cell proliferation.
3. Mutation/ mismatch repair genes (DNA repair genes): main function is to repair DNA
replication errors. When there is a mutation in the genes, this will lead to loos of function
and results in an accumulation of DNA errors.
Mutations can be somatic or germ-line:
, - Somatic mutations: acquired during life, present only in certain
cells of the body and they are dependent on the cause of the
mutation. E.g. UV induced TP53 mutations in epithelial cells of
the skin. Mutations due to smoking mostly only affect epithelial
cells of the lung, mutations occur later in life and are only
present in one place of the body.
- Germ-line mutations: hereditary, congenital, present in all cells
of the body. They are already present in the fertilized egg and
are disturbed to all cells of the body.
Benign neoplasia’s usually have simple genetic alterations:
- Most common nevi (moles) have only one mutation > 60% BRAF, 20% NRAS
- Spitz nevi (non-pigmented moles in children) only have one chromosomal translocation in
one of the oncogenes: ALK, ROS of NTRK translocation.
The development of cancer is a multistep process
Cancer occurs when there are several mutations (at least 6) in different
genes controlling cell growth, differentiation and death.
1. autonomous cell proliferation: growth
2. new vessels formation: growth (new vessels for oxygen and nutrition)
3. loss of programmed cell death (apoptosis): growth, survival
4. loss of differentiation: loss of function
5. loss of cell contact inhibition: invasion
6. growth into and out of vessels: metastasis (genes need to be hit for
cancer to occur). The tumour that can grow out and metastasize usually
have all the different mutations
Clonal evolution model: every time a new mutation in one the cells, there is a clone of this cell within
the tumour. This clone will have a proliferation or survival advantage over the rest of tumour. Every
time there is a new mutation, this mutation will have an advantage over the rest of the cells
Skin cancer
- Skin cancer is the most common primary location of cancer.
- When warts start to look different + invade, but still look like the epidermis: SCC
- BRAF mutation = melanoma
- Incidence skin cancer is rising fast (= epidemic). This can be because:
o The skin is the largest organ
o Aging of the population
o Lifelong exposure to UV light
Pathology of primary skin tumors ........................................................................................................... 2
Neoplasia ............................................................................................................................................. 2
Skin cancer............................................................................................................................................... 4
Clinical pathology .................................................................................................................................... 5
Different skin tumors .............................................................................................................................. 8
Basal cell carcinoma (BCC) .................................................................................................................. 9
Squamous cell carcinoma (SCC) .......................................................................................................... 9
Melanocytic tumors .......................................................................................................................... 10
Common Nevi (moedervlek) ............................................................................................................. 13
Spitz nevus ......................................................................................................................................... 13
Malignant melanocytic tumors: MELANOMA ................................................................................... 15
Lentigo maligna (melanoma)............................................................................................................. 17
Langerhans cell histiocytosis (LCH)................................................................................................ 20
Merkel cell carcinoma (MCC) ........................................................................................................ 21
Gene mutations in tumors .................................................................................................................... 23
Detection of chromosomal aberrations, translocations and CNV ........................................................ 28
Copy number alterations:.................................................................................................................. 29
Detection aberrations hematological.................................................................................................... 32
Molecular pathology: lymphoma diagnostics, clonality assessment .................................................... 35
Pathophysiology of Cervical Cancer ...................................................................................................... 38
Artificial intelligence .............................................................................................................................. 51
Basics ................................................................................................................................................. 51
The Urinary system................................................................................................................................ 56
Basis ................................................................................................................................................... 56
Nephropathology: kidney diseases ................................................................................................... 66
Kidney diseases ..................................................................................................................................... 70
Nephrotic diseases ............................................................................................................................ 70
Minimal change disease ................................................................................................................ 70
Focal and segmental glomerulosclerosis....................................................................................... 70
Membranous glomerulopathy ...................................................................................................... 71
Nephritic syndrome ........................................................................................................................... 71
Immune complexes formation ...................................................................................................... 71
ANCA disease ................................................................................................................................. 72
Anti GBM disease .......................................................................................................................... 72
,Pathology of primary skin tumors
Neoplasia
- Geneticallly driven growth of cells
- Tumor: formation of a mass, which can grow die to inflammation. It can be neoplastic or
non-neoplastic. A large scar can also be a tumor
- Neoplasia: new growth of cells, which is always genetically driven
- Neoplasm can be benign or malignant. Not always forms a mass (e.g. it can also be blood-
bound in e.g. leukemia)
- Neoplasia examples: warts, moles, nevus. They are benign genetically driven lesions.
- Neoplasia is driven by genetic alterations such as mutations, structural chromosomal
alterations (translocation or gene fusion), copy number variations (losses or gains of parts or
whole chromosomes), viral transformation (viral DNA gets incorporated into the cell).
Dutch: Benign: goedaardig, Malignant: kwaadaardig
- Malignant: mitosis in tissue and infiltration in other tissues and can go to lymph nodes and
other organs. Cells of malignant tissue do not look like the precursor cells.
Benign tumor ≠ premalignant
,3 types of genetic alterations
1. Mutations (small) (=Mutation = a nucleotide
change in DNA)
• Activation of oncogenes
• loss of function/expression of tumor
suppressor genes
Substitution: when a nucleotide is replaced by another
nucleotide, resulting in the substitution of the amino acid and then change sequence.
Insertion: of one or more nucleotides, which leads t o out-of-frame mutations. This changes the
sequence of the protein. Then an inactivated or ineffective protein is created.
Deletion: one of a few nucleotides are deleted, this leads to an out-of-frame mutations and thus a
non-sense sequence.
2. Copy number variations (large)
Losses or gains of whole chromosomes or part of chromosomes.
• loss of tumor suppressor genes
3. Chromosomal translocations
• expression or activation of oncogenes
3 types of genes can be involved in oncogenesis (oncogenesis only occurs when the genes affected
are involved in oncogenesis). Genes involved in the formation of cancer:
1. (proto)oncogenes: main function is to promote cell proliferation and survival. When a
mutation or amplification occurs, it leads to a gain of function, activations or over expression.
This promotes more cell proliferation and survival.
2. Tumor suppressor genes: main function is to inhibit cell proliferation and induction of
apoptosis. When there is a mutation in these genes, this will lead to inactivation or loss of
function of the tumor suppressor gene, this then leads to the loss of induction of apoptosis
and loss of inhibition of cell proliferation.
3. Mutation/ mismatch repair genes (DNA repair genes): main function is to repair DNA
replication errors. When there is a mutation in the genes, this will lead to loos of function
and results in an accumulation of DNA errors.
Mutations can be somatic or germ-line:
, - Somatic mutations: acquired during life, present only in certain
cells of the body and they are dependent on the cause of the
mutation. E.g. UV induced TP53 mutations in epithelial cells of
the skin. Mutations due to smoking mostly only affect epithelial
cells of the lung, mutations occur later in life and are only
present in one place of the body.
- Germ-line mutations: hereditary, congenital, present in all cells
of the body. They are already present in the fertilized egg and
are disturbed to all cells of the body.
Benign neoplasia’s usually have simple genetic alterations:
- Most common nevi (moles) have only one mutation > 60% BRAF, 20% NRAS
- Spitz nevi (non-pigmented moles in children) only have one chromosomal translocation in
one of the oncogenes: ALK, ROS of NTRK translocation.
The development of cancer is a multistep process
Cancer occurs when there are several mutations (at least 6) in different
genes controlling cell growth, differentiation and death.
1. autonomous cell proliferation: growth
2. new vessels formation: growth (new vessels for oxygen and nutrition)
3. loss of programmed cell death (apoptosis): growth, survival
4. loss of differentiation: loss of function
5. loss of cell contact inhibition: invasion
6. growth into and out of vessels: metastasis (genes need to be hit for
cancer to occur). The tumour that can grow out and metastasize usually
have all the different mutations
Clonal evolution model: every time a new mutation in one the cells, there is a clone of this cell within
the tumour. This clone will have a proliferation or survival advantage over the rest of tumour. Every
time there is a new mutation, this mutation will have an advantage over the rest of the cells
Skin cancer
- Skin cancer is the most common primary location of cancer.
- When warts start to look different + invade, but still look like the epidermis: SCC
- BRAF mutation = melanoma
- Incidence skin cancer is rising fast (= epidemic). This can be because:
o The skin is the largest organ
o Aging of the population
o Lifelong exposure to UV light
