Theme 1A – Cancer biology and genetics
SSA
SSA-01: Hereditary colorectal cancer
1. The lifetime risk of developing colorectal cancer is 1 in 23 for men and 1 in 26 for
women.
2. A family history of CRC is indeed a significant risk factor for the disease. The closer
relatives affected, the higher the risk. Some families may have hereditary syndromes
(Lynch syndrome or familial adenomatous polyposis (FAP)), which significantly
increase the risk of CRC. Statistically, around 20-30% of CRC cases are associated with
a family history of the disease.
3. Most CRC cases are sporadic, meaning they occur without a strong genetic
predisposition. However, there are some hereditary syndromes associated with high-
penetrant genetic mutations that significantly increase the risk. They account for 5%
of CRC cases. These syndromes include:
a. Lynch syndrome (hereditary non-polyposis colorectal cancer, HNPCC). Most
common. It is caused by mutations in DNA mismatch repair genes (MLH1,
MSH2, MSH6, PMS2).
b. Familial adenomatous polyposis (FAP). This is a rare, high-penetrant,
autosomal dominant syndrome caused by mutations in the APC gene. It leads
to numerous polyps and if not treated, virtually guarantees the development
of CRC.
c. MUTYH-Associated polyposis (MAP). Recessive. Mutations in MUTYH gene.
4. The clinical genetics department investigates the different forms of hereditary CRC via
genetic testing, pathology assistance (assessment of tumor tissue) and molecular
analysis.
5. Absent staining of MLH1 protein can indicate the potential presence of Lynch
syndrome. In most cases in the general population, however, absence of MLH1
staining is not due to Lynch syndrome but due to “sporadic hypermethylation”.
Sporadic hypermethylation of the MLH1 gene promoter (= epigenetic alteration)
leads to the inactivation of the MLH1 gene, resulting in the loss of expression of
MLH1 protein. It occurs because of changes in DNA methylation patterns in the
tumor.
6. Surveillance protocols in case a mutation is found:
a. Lynch syndrome:
i. Colonoscopy. Starting in early 20s, then every 1-2 years. Goal is to
detect/remove polyps.
ii. Endometrial cancer screening (biopsy).
b. FAP:
i. Colonoscopy. Goal is to detect/remove polyps.
ii. Prophylactic surgery (removal of the colon) (when patient is in late
teens or early 20s).
iii. Endoscopy (upper GI tract).
c. MAP:
i. Colonoscopy. Goal is to detect/remove polyps.
ii. Surgery considerations.
7. If the family fulfills the criteria for familial CRC (= FCC, also Late-Onset Familial
Clustering CRC), the advice is:
, a. Surveillance and screening. Initial screening at 40 or 10 years before the
youngest affected relative’s diagnosis.
b. Frequency of screening every 5 years.
c. Lifestyle factors physical activity, a balanced diet, avoid smoking/alcohol.
d. Genetic counseling.
8. The underlying cause of CRC could be influenced by genetic and environmental
factors. Some families have higher genetic predisposition, while others may be more
affected by lifestyle factors or sporadic mutations.
9. Types of mutations almost always linked to tumor predisposition:
a. Germline mutations in tumor suppressor genes (leading to loss-of-function).
b. DNA mismatch repair (MMR) gene mutations, such as MLH1, MSH2, MSH6
and PMS2.
c. BRCA1 and BRCA2 mutations. Breast and ovarian cancer.
Types of mutations with uncertain links to tumor predisposition:
d. Common somatic mutations (e.g., KRAS mutation in pancreatic cancer).
e. Variants of uncertain significance (VUS), meaning it is unclear whether they
increase cancer risk.
f. Polygenic risk factors. Instead of a single, high-penetrance mutation,
polygenic risk factors involve multiple common, low-risk genetic variants that,
when combined, contribute to a person’s overall cancer risk.
10. Psychological mechanisms to not get genetically tested:
a. Fear and anxiety.
b. Denial.
c. Stigma and discrimination (employment, insurance, social relationships).
d. Lack of information.
e. Psychological burden.
f. Autonomy and control.
SSA-02: Cancer and the genome
Nevoid basal cell carcinoma syndrome (NBCCCS) is an autosomal dominant disorder
characterized by multiple basal cell skin cancers. Other common signs include jaw cysts, pits
on the palms of the hands/soles of feet, calcium deposits in the brain, developmental
disability and skeletal changes. The PTCH gene (“patched”), responsible for the disorder, is on
chromosome 9. The PTCH gene encodes a protein involved in the Hedgehog signaling
pathway, which regulates cell growth and development. In the absence of functional PTCH,
the pathway can become dysregulated, leading to uncontrolled cell growth and tumor
development, including basal cell carcinomas.
Molecular analysis of tumor and non-tumor DNA from an affected individual reveals the
presence of a heterozygous mutation in the PTCH gene, but loss of the functional allele in the
tumor.
1. PTCH is thus a tumor-suppressor gene because loss of function leads to malignant
transformation. Also, this case demonstrates the ‘two-hit’ hypothesis. The first hit is
inherited (this is the heterozygous mutation found in the blood), is present in all cells
and predisposes the patient to the development of tumor. The second hit is a somatic
(acquired mutation) of the functional allele, which leads to loss of function.
2. The disorder is inherited from the father, so the allele lost in the tumor would be
inherited from the mother.
,Highly specific chromosome translocations have been shown to be responsible for the onset
of certain types of lymphomas and leukemias since they result in the activation of a
particular oncogene. Examples include translocations between chromosomes 8 and 14 in
patients with Burkitt's lymphoma and between chromosomes 9 and 22 in patients with
chronic myelogenous leukemia (CML).
3. Two ways by which a chromosome translocation can activate a proto-oncogene:
a. Excess production. Translocations can lead to proto-oncogenes being placed
under the control of stronger regulatory elements, leading to increased
expression. This is the case in CML.
b. Novel protein production (due to gene fusion). Often in translocation, a
segment of one chromosome (including proto-oncogene), becomes fused
with a segment of another chromosome (including regulatory elements)
hybrid gene created with altered activity, leading to uncontrolled cell growth.
This is the case in Burkitt’s lymphoma (involving MYC proto-oncogene).
4. Translocation may inactivate tumor suppressor genes by breaking it into two inactive
parts.
TP53 plays a central role in the induction of apoptosis and in the regulation of the cell cycle.
Other tumor suppressor genes such as RB and CDKN2A also have roles in cell cycle control.
The tumors occurring in patients with a mutation in RB (retinoblastoma, osteosarcoma) or
CDKN2A (melanoma) are quite specific, whereas mutated TP53 is associated with many types
of tumors. This is because:
TP53 is a broad TSG, whereas RB and CDKN2A primarily regulate the G1 phase of the
cell cycle and thus have a more limited set of function.
The genes have different expression patterns across different tissues. RB is relevant in
the retina (retinoblastoma) and bone (osteosarcoma), and CDKN2A primarily controls
the cell cycle for melanocytes.
o Also, these tissues have different cell division rates.
TP53 is an averagely sized gene and does not become more frequently mutated than
comparable sized genes. Although more than 50% of tumors contain mutations in the TP53
gene, disruption of the p53 pathway is found in over 90% of all tumors. An example of an
alternative route leading to p53 dysfunction is the over-expression of the MDM2 gene, which
is involved in the degradation of p53 protein after completion of repair.
Disruption of the p53 pathway is so important for cancer development due to its role in
maintaining genomic integrity and regulating cell behavior. Reasons why the p53 pathway is
important:
- Cell cycle regulation (if there’s damage cell cycle arrest).
- Apoptosis induction.
- DNA repair (it can activate genes involved in DNA repair).
- Senescence (cells lose the ability to divide).
- Tumor suppression (it is a potent TSG).
- Chemoresistance (dysfunctional p53 often resistant to chemo- and radiotherapy).
DNA damages are chemical modifications of the bases (e.g., DNA adducts) or phosphate
backbone (double strand breaks). When unrepaired DNA polymerases will not recognize
, damaged DNA bases as natural substrates and may incorporate an incorrect nucleotide
opposite the DNA lesion during replication. After a second round of replication a final
alteration (=mutation) in the DNA sequence is formed that is present on both DNA strands as
complementary bases.
Mammalian cells exhibit a preference for repairing DNA damage in actively transcribed genes
(= transcription-coupled repair, TCR). TCR focuses on DNA damage in the transcribed strand
of genes; it recognizes and repairs specific lesions that block transcription. The preference for
active genes is because by first repairing that part of DNA that is needed for the production
of new mRNAs and thus for new proteins, a cell increases its chances to survive.
Organization of TCR:
(1) Detection of transcription-blocking lesions (adducts, thymine dimers, or other
structural abnormalities that interfere with RNA polymerase).
(2) RNA polymerase stalling ( accumulation).
(3) Recruitment of TCR factors (CSA and CSB). They bind to stalled RNA polymerase.
(4) Initiation of repair. NER (nucleotide excision repair) proteins come in.
(5) Restoration of transcription. RNA polymerase resumes transcription.
When cytosine (C) undergoes deamination, it is converted into uracil (U) (naturally found in
RNA). If unrepaired, this will lead to a point mutation known as C-to-T, because DNA
polymerase will recognize the uracil as if it were thymine, leading to the incorporation of
adenine (A) opposite the uracil. This mismatch will result in a C-to-T mutation. They are
relatively common.
The various repair systems are quite effective in repairing the following damages:
- one that depurinates DNA
- one that produces single strand nicks into the backbone.
- one that causes thymidine dimers.
These damages affect the nucleotide sequence of only one of the DNA strands, allowing their
error-free repair by making use of the genetic information from the other complementary
undamaged strand.
In the case that two DNA strands are covalently linked (interstrand-crosslink, ICL), error-free
repair is dependent on the presence of a homologous molecule (the sister chromatid at the
end of S-phase or in the G2-phase of the cell cycle). ICL are absolute blocks for DNA
replication and transcription, demanding their repair for replication (and thus cell division)
can proceed, providing an explanation for the also very strong toxicity of crosslinking agents.
NHEJ
NHEJ is a DNA repair pathway that repairs ds-breaks. DNA ligase IV is a key enzyme in this
pathway. It functions by sealing the broken ends of DNA strands back together. If you have a
homozygous mutation in the DNA ligase IV gene, you have impaired ability to repair double
strand breaks.
Xeroderma Pigmentosum (XP)
XP = inherited condition characterized by sensitivity to UV rays from sunlight. The condition
mostly affects the eyes and areas of skin exposed to sun. The nervous system may also
SSA
SSA-01: Hereditary colorectal cancer
1. The lifetime risk of developing colorectal cancer is 1 in 23 for men and 1 in 26 for
women.
2. A family history of CRC is indeed a significant risk factor for the disease. The closer
relatives affected, the higher the risk. Some families may have hereditary syndromes
(Lynch syndrome or familial adenomatous polyposis (FAP)), which significantly
increase the risk of CRC. Statistically, around 20-30% of CRC cases are associated with
a family history of the disease.
3. Most CRC cases are sporadic, meaning they occur without a strong genetic
predisposition. However, there are some hereditary syndromes associated with high-
penetrant genetic mutations that significantly increase the risk. They account for 5%
of CRC cases. These syndromes include:
a. Lynch syndrome (hereditary non-polyposis colorectal cancer, HNPCC). Most
common. It is caused by mutations in DNA mismatch repair genes (MLH1,
MSH2, MSH6, PMS2).
b. Familial adenomatous polyposis (FAP). This is a rare, high-penetrant,
autosomal dominant syndrome caused by mutations in the APC gene. It leads
to numerous polyps and if not treated, virtually guarantees the development
of CRC.
c. MUTYH-Associated polyposis (MAP). Recessive. Mutations in MUTYH gene.
4. The clinical genetics department investigates the different forms of hereditary CRC via
genetic testing, pathology assistance (assessment of tumor tissue) and molecular
analysis.
5. Absent staining of MLH1 protein can indicate the potential presence of Lynch
syndrome. In most cases in the general population, however, absence of MLH1
staining is not due to Lynch syndrome but due to “sporadic hypermethylation”.
Sporadic hypermethylation of the MLH1 gene promoter (= epigenetic alteration)
leads to the inactivation of the MLH1 gene, resulting in the loss of expression of
MLH1 protein. It occurs because of changes in DNA methylation patterns in the
tumor.
6. Surveillance protocols in case a mutation is found:
a. Lynch syndrome:
i. Colonoscopy. Starting in early 20s, then every 1-2 years. Goal is to
detect/remove polyps.
ii. Endometrial cancer screening (biopsy).
b. FAP:
i. Colonoscopy. Goal is to detect/remove polyps.
ii. Prophylactic surgery (removal of the colon) (when patient is in late
teens or early 20s).
iii. Endoscopy (upper GI tract).
c. MAP:
i. Colonoscopy. Goal is to detect/remove polyps.
ii. Surgery considerations.
7. If the family fulfills the criteria for familial CRC (= FCC, also Late-Onset Familial
Clustering CRC), the advice is:
, a. Surveillance and screening. Initial screening at 40 or 10 years before the
youngest affected relative’s diagnosis.
b. Frequency of screening every 5 years.
c. Lifestyle factors physical activity, a balanced diet, avoid smoking/alcohol.
d. Genetic counseling.
8. The underlying cause of CRC could be influenced by genetic and environmental
factors. Some families have higher genetic predisposition, while others may be more
affected by lifestyle factors or sporadic mutations.
9. Types of mutations almost always linked to tumor predisposition:
a. Germline mutations in tumor suppressor genes (leading to loss-of-function).
b. DNA mismatch repair (MMR) gene mutations, such as MLH1, MSH2, MSH6
and PMS2.
c. BRCA1 and BRCA2 mutations. Breast and ovarian cancer.
Types of mutations with uncertain links to tumor predisposition:
d. Common somatic mutations (e.g., KRAS mutation in pancreatic cancer).
e. Variants of uncertain significance (VUS), meaning it is unclear whether they
increase cancer risk.
f. Polygenic risk factors. Instead of a single, high-penetrance mutation,
polygenic risk factors involve multiple common, low-risk genetic variants that,
when combined, contribute to a person’s overall cancer risk.
10. Psychological mechanisms to not get genetically tested:
a. Fear and anxiety.
b. Denial.
c. Stigma and discrimination (employment, insurance, social relationships).
d. Lack of information.
e. Psychological burden.
f. Autonomy and control.
SSA-02: Cancer and the genome
Nevoid basal cell carcinoma syndrome (NBCCCS) is an autosomal dominant disorder
characterized by multiple basal cell skin cancers. Other common signs include jaw cysts, pits
on the palms of the hands/soles of feet, calcium deposits in the brain, developmental
disability and skeletal changes. The PTCH gene (“patched”), responsible for the disorder, is on
chromosome 9. The PTCH gene encodes a protein involved in the Hedgehog signaling
pathway, which regulates cell growth and development. In the absence of functional PTCH,
the pathway can become dysregulated, leading to uncontrolled cell growth and tumor
development, including basal cell carcinomas.
Molecular analysis of tumor and non-tumor DNA from an affected individual reveals the
presence of a heterozygous mutation in the PTCH gene, but loss of the functional allele in the
tumor.
1. PTCH is thus a tumor-suppressor gene because loss of function leads to malignant
transformation. Also, this case demonstrates the ‘two-hit’ hypothesis. The first hit is
inherited (this is the heterozygous mutation found in the blood), is present in all cells
and predisposes the patient to the development of tumor. The second hit is a somatic
(acquired mutation) of the functional allele, which leads to loss of function.
2. The disorder is inherited from the father, so the allele lost in the tumor would be
inherited from the mother.
,Highly specific chromosome translocations have been shown to be responsible for the onset
of certain types of lymphomas and leukemias since they result in the activation of a
particular oncogene. Examples include translocations between chromosomes 8 and 14 in
patients with Burkitt's lymphoma and between chromosomes 9 and 22 in patients with
chronic myelogenous leukemia (CML).
3. Two ways by which a chromosome translocation can activate a proto-oncogene:
a. Excess production. Translocations can lead to proto-oncogenes being placed
under the control of stronger regulatory elements, leading to increased
expression. This is the case in CML.
b. Novel protein production (due to gene fusion). Often in translocation, a
segment of one chromosome (including proto-oncogene), becomes fused
with a segment of another chromosome (including regulatory elements)
hybrid gene created with altered activity, leading to uncontrolled cell growth.
This is the case in Burkitt’s lymphoma (involving MYC proto-oncogene).
4. Translocation may inactivate tumor suppressor genes by breaking it into two inactive
parts.
TP53 plays a central role in the induction of apoptosis and in the regulation of the cell cycle.
Other tumor suppressor genes such as RB and CDKN2A also have roles in cell cycle control.
The tumors occurring in patients with a mutation in RB (retinoblastoma, osteosarcoma) or
CDKN2A (melanoma) are quite specific, whereas mutated TP53 is associated with many types
of tumors. This is because:
TP53 is a broad TSG, whereas RB and CDKN2A primarily regulate the G1 phase of the
cell cycle and thus have a more limited set of function.
The genes have different expression patterns across different tissues. RB is relevant in
the retina (retinoblastoma) and bone (osteosarcoma), and CDKN2A primarily controls
the cell cycle for melanocytes.
o Also, these tissues have different cell division rates.
TP53 is an averagely sized gene and does not become more frequently mutated than
comparable sized genes. Although more than 50% of tumors contain mutations in the TP53
gene, disruption of the p53 pathway is found in over 90% of all tumors. An example of an
alternative route leading to p53 dysfunction is the over-expression of the MDM2 gene, which
is involved in the degradation of p53 protein after completion of repair.
Disruption of the p53 pathway is so important for cancer development due to its role in
maintaining genomic integrity and regulating cell behavior. Reasons why the p53 pathway is
important:
- Cell cycle regulation (if there’s damage cell cycle arrest).
- Apoptosis induction.
- DNA repair (it can activate genes involved in DNA repair).
- Senescence (cells lose the ability to divide).
- Tumor suppression (it is a potent TSG).
- Chemoresistance (dysfunctional p53 often resistant to chemo- and radiotherapy).
DNA damages are chemical modifications of the bases (e.g., DNA adducts) or phosphate
backbone (double strand breaks). When unrepaired DNA polymerases will not recognize
, damaged DNA bases as natural substrates and may incorporate an incorrect nucleotide
opposite the DNA lesion during replication. After a second round of replication a final
alteration (=mutation) in the DNA sequence is formed that is present on both DNA strands as
complementary bases.
Mammalian cells exhibit a preference for repairing DNA damage in actively transcribed genes
(= transcription-coupled repair, TCR). TCR focuses on DNA damage in the transcribed strand
of genes; it recognizes and repairs specific lesions that block transcription. The preference for
active genes is because by first repairing that part of DNA that is needed for the production
of new mRNAs and thus for new proteins, a cell increases its chances to survive.
Organization of TCR:
(1) Detection of transcription-blocking lesions (adducts, thymine dimers, or other
structural abnormalities that interfere with RNA polymerase).
(2) RNA polymerase stalling ( accumulation).
(3) Recruitment of TCR factors (CSA and CSB). They bind to stalled RNA polymerase.
(4) Initiation of repair. NER (nucleotide excision repair) proteins come in.
(5) Restoration of transcription. RNA polymerase resumes transcription.
When cytosine (C) undergoes deamination, it is converted into uracil (U) (naturally found in
RNA). If unrepaired, this will lead to a point mutation known as C-to-T, because DNA
polymerase will recognize the uracil as if it were thymine, leading to the incorporation of
adenine (A) opposite the uracil. This mismatch will result in a C-to-T mutation. They are
relatively common.
The various repair systems are quite effective in repairing the following damages:
- one that depurinates DNA
- one that produces single strand nicks into the backbone.
- one that causes thymidine dimers.
These damages affect the nucleotide sequence of only one of the DNA strands, allowing their
error-free repair by making use of the genetic information from the other complementary
undamaged strand.
In the case that two DNA strands are covalently linked (interstrand-crosslink, ICL), error-free
repair is dependent on the presence of a homologous molecule (the sister chromatid at the
end of S-phase or in the G2-phase of the cell cycle). ICL are absolute blocks for DNA
replication and transcription, demanding their repair for replication (and thus cell division)
can proceed, providing an explanation for the also very strong toxicity of crosslinking agents.
NHEJ
NHEJ is a DNA repair pathway that repairs ds-breaks. DNA ligase IV is a key enzyme in this
pathway. It functions by sealing the broken ends of DNA strands back together. If you have a
homozygous mutation in the DNA ligase IV gene, you have impaired ability to repair double
strand breaks.
Xeroderma Pigmentosum (XP)
XP = inherited condition characterized by sensitivity to UV rays from sunlight. The condition
mostly affects the eyes and areas of skin exposed to sun. The nervous system may also
