Cancer

Question 1

Importance of genetic testing in breast cancer management

Answer 1

1. Risk assessment; genetic testing can identify individuals with an increased risk of developing breast cancer, allowing for proactive screening and early detection.
2. Treatment planning; the results of genetic testing can inform treatment decision such as the choice of chemotherapy or targeted therapies
3. Family planning: Genetic testing can help families understand the risk of passing on breast cancer mutations to future generations

Question 2

Why do somatic genetic testing: identifying tumours-specific mutation

Answer 2

1. Tumour profiling: Somatic testing provides insight into the genetic makeup of a specific tumour, identifying mutations that might drive its growth and development.
2. Targeted therapies; the identification of specific mutation allows for the selection of targeted therapies that are more likely to be effective against the tumour
3. Prognosis assessment: the genetic profile of a tumour can be used to predict its aggressiveness and likely response to treatment,aiding in personalised prognosis.

Question 3

Advantage and limitations of each testing method

Answer 3

Advantage: can identify specific mutations driving tumour, growth, leading to targeted therapies and personalised treatment strategies
Limitations: limited to the specific tumour being analysed, might not reflect mutations in other tumours.

Question 4

Advantages and limitations of germline testing

Answer 4

Advantage :Identifies inherited genetic predisposition to breast cancer, allowing for early intervention and preventive measure
Limitation: not always informative for all individuals scan lead to anxiety or unnecessary intervention in some case.

Question 5

Clinical implications of somatic and germline findings

Answer 5

Combining both somatic and germline testing results provides a comprehensive understanding of the genetic landscape of breast cancer, allowing for more precise and effective management

Question 6

Personalised treatment strategies based on genetic test result

Answer 6

1. Targeted therapies: genetic testing can identify patients who may benefit from specific targeted therapies that target the mutated genes driving their tumour growth.
2. Chemotherapy optimisation : genetic testing can guide the selection of chemotherapy drugs that are more likely to be effective and have fewer side effective and have fewer side effects for a particular patient.
3. Risk reduction strategies: for individual with inherited mutations, personalised risk-reduction strategies may include enhanced screening risk-reducing medications or even prophylactic surgery

Question 7

Compare between benign vs malignant tumour

Answer 7

1. Grow locally/cannot spread - capable of invading neighbouring tissue and blood vessels to spread.
2. Encapsulated (surrounded by a protective “sac” - Non-encapsulated
3. Slow growing - Rapidly growing
4. Similar in appearance to the cell of origin- dissimilar in appearance to the cell of origin
5. Less likely to recur after surgical removal - More likely to recur after surgically removal

Question 8

What can cause cells to become cancerous

Answer 8

1. Genetic changes
2. Abnormal cell division
3. Epigenetic changes
4. Proliferation vs apoptosis changes
5. Cellular changes

Question 9

Define proto-oncogenes

Answer 9

1. Genes that Promote cell growth and mitosis
2. Mutations cause proto-oncogenes to become oncogenes

Question 10

Define tumour suppressor genes

Answer 10

1. Discourages cell growth
2. Temporarily halt cell division to carry out DNA repair

Question 11

DNA repair genes

Answer 11

1. Codes for enzymes involved in repairing mutated DNA

Question 12

Oncogenes role in inherited cancers

Answer 12

1. Inherit germline muation (genetic predisposition)
2. Dominant inheritance pattern on pedigree analysis
3. Example MEN type 2
4. Most cancer - causing mutations involving oncogenes are acquired through chromosomal rearrangement or gene duplication

Question 13

Define knudsons two hit hypothesis

Answer 13

Knudson’s two-hit hypothesis explains how cancer can develop due to mutations in tumor suppressor genes. It proposes that both alleles of a tumor suppressor gene must be inactivated for cancer to arise. The “first hit” is usually a germline mutation (inherited) or a random mutation, while the “second hit” occurs later in life, often due to environmental factors or additional mutations.

This hypothesis is particularly important in hereditary cancers, such as retinoblastoma, where individuals inherit one defective gene copy and only need one more mutation to initiate cancer.

Question 14

Characterise sporadic cancer

Answer 14

1. Increasing age
2. Occurrence of cancer in an individual not related to other cancers in a family
3. No known inherited component in cancer aetiology

Question 15

Characterise Inherited cancer

Answer 15

1. Get cancer at Younger ages
   2.Clustering of related cancer within a family
2. Bilateral cancers
3. Rare cancers

Question 16

What is the best way to identify individuals at risk of inherited cancer syndromes

Answer 16

1. Young age at diagnosis
2. Multiple cases of close relatives with early -onset cancer (disease specific)
3. Bilateral disease in paired organs
4. Apparent Mendelian patterns of inheritance
5. Rare cancers (e.g male breast cancers)
6. Ancestry from a high risk population

Question 17

What technical considerations are there when testing for inherited cancers

Answer 17

1. Traditional methods are slow and expensive but very accurate
2. Which genes are included in the panel?
3. What is their “actionability”?
4. What is the coverage of the panel?
5. Is Sanger sequencing used to confirm mutations ?
6. Is MLPA performed to detect large deletions / duplications

Question 18

What do we have to consider about ethnicity when testing for inherited cancer

Answer 18

1. Is the patient from a high risk ancestry
2. Is there a founder mutation to test for
3. What is the pick up rate of the founder mutation testing .

Question 19

What do we have to consider about family history when testing for inherited cancer

Answer 19

1. Has testing been performed previously ?
2. Is there a known mutation in the family
3. Which test would be most appropriate.

Question 20

What is a liquid biopsy

Answer 20

Liquid biopsies are less-invasive tests that detect cancer-related genetic material, such as cell free tumor DNA (cftDNA)

Question 21

Logistical & technical limitations (& Solutions) of liquid biopsy

Answer 21

1. limited access to LB in community hospitals outside clinical protocols , excessive cost of assay & lack of ctDNA analysis technology in house
   1.1 Solution- centralisation referral cancer centre’s + standardised preanalytical conditions (protocol). Use ctDNA tests as companion diagnostic to access treatment
2. Numerous available ctDNA assays have highly variable technical features in terms of sensitivity, specificity, & targets, without available direct comparisons.
   2.1 simplification and standardised sample acquisition . Standardisation quality check pipeline.

Question 22

List the biological limitations of liquid biopsies

Answer 22

1. Non-shedding carcinoma
2. Clonal haematopoiesis
3. Lack of commonly accepted cut-off to define ctDNA molecular findings
4. Finding multiple genetic changes at the same time
5. RNA unstable

Question 23

Explain the limitation of LB, non-shedding carcinoma and give solutions.

Answer 23

Limitation- decrease DNA shedding into blood stream 20% of with increased risk of false negative results
Solution- Initial assessment and monitoring should not rely only on ctDNA but include ctDNA among other standard staging and diagnostic methods.

Question 24

Explain the limitation of LB, clonal haematopoiesis and the solution to this

Answer 24

1. Limitation- presence of circulating DNA mutations in cancer- related genes in Peripheral blood cells derived from non cancerous clones from the bone marrow, leading to potential false positive results
   Solution -Paired peripheral blood cells sequencing whenever ctDNA detects mutations at low allele frequency. Paired sequencing of both one solid tumour biopsy/surgery sample and ctDNA to identify specific trunk mutations

Question 25

Explain the limitation of LB, lack of commonly accepted cut-off to determine ctDNA positivity, and the solution.

Answer 25

Limitation- There is no universally accepted threshold or cut-off for what constitutes a significant ctDNA finding. This makes it difficult to standardize the interpretation of results across different patients and clinical settings. The amount of ctDNA in the bloodstream can vary greatly, even within the same type of cancer, and without a clear cut-off, clinicians may struggle to decide when a ctDNA finding is clinically meaningful.
Solution- the identification of specific cut-offs shared by different methodologies would be warranted

Question 26

Explain the limitation of LB, lack of approved targeted treatment based on ctDNA molecular findings, and give thee solution

Answer 26

Limitation- despite the opportunity to identify specific CRC molecular alterations, currently there are no approved treatment options based on ctDNA findings.
Solution- clinical trials to guide targeted treatments based on interventional ctDNA molecular results are warranted.

Question 27

Explain the limitation of LB, concomitant identification of several genetic alterations, give a solution

Answer 27

Limitation - Liquid biopsies often detect multiple genetic alterations in ctDNA, some of which may not be directly relevant to the cancer being investigated. This complexity can make it difficult to interpret which mutations are driving the cancer’s behavior and which are incidental or non-actionable. The presence of multiple alterations can also complicate decisions on targeted therapy, especially when conflicting mutations are identified.

Solutions- providing comprehensive report might help clinicians in results interpretation toward improving clinical decision

Question 28

Explain the limitation of LB, RNA unstable, give solution

Answer 28

Limitation- RNA, particularly circulating RNA (e.g., miRNA or mRNA), is inherently unstable and prone to rapid degradation in blood samples. This instability makes it difficult to obtain reliable and reproducible results from RNA-based liquid biopsies. Special handling and storage conditions are required to preserve RNA integrity, and even then, the results may not be as consistent as those obtained from DNA-based analyses.
Solution- improve technique make more robust

Question 29

Explain tumour heterogeneity

Answer 29

Tumor heterogeneity refers to the genetic, molecular, and cellular differences that exist within and between tumors in the same patient. This variation can occur at two levels:

Inter-tumor heterogeneity: Differences between tumors in different patients or even between primary tumors and metastases in the same patient.
Intra-tumor heterogeneity: Variability within a single tumor, where different regions of the tumor have distinct genetic mutations, cell types, or drug sensitivities.

Question 30

How does tumor heterogeneity affect cancer treatment (just read through)

Answer 30

Impact on Cancer Testing:
Biopsy Limitations: A traditional tissue biopsy typically samples a small portion of the tumor, which may not fully represent the diversity within the tumor. This can result in missing key mutations or variations that exist in other parts of the tumor or in metastases, leading to incomplete or inaccurate diagnosis.
Treatment Resistance: Due to heterogeneity, some tumor cells may be more resistant to treatment. Even if the test identifies a targetable mutation, other parts of the tumor might not respond to the therapy, causing treatment failure or relapse.
Evolution of Tumor Over Time: Tumors evolve as they grow and spread. A single test might not capture this dynamic process, and treatment based on an earlier sample may become ineffective as new mutations arise in different parts of the tumor.

Question 31

Explain how PARP inhibitors work

Answer 31

PARP inhibitors work by targeting a specific DNA repair pathway in cancer cells, exploiting a concept called synthetic lethality. PARP (poly ADP-ribose polymerase) is an enzyme that helps repair single-strand DNA breaks through the base excision repair pathway. Here’s how PARP inhibitors function:

Blocking PARP Function: PARP inhibitors prevent the PARP enzyme from repairing single-strand DNA breaks. Normally, PARP binds to damaged DNA and recruits other proteins to fix the break.
Accumulation of DNA Damage: When PARP is inhibited, the single-strand breaks cannot be repaired, leading to the formation of more dangerous double-strand breaks during DNA replication.
Exploiting Deficient DNA Repair: In normal cells, double-strand breaks can be repaired by a pathway called homologous recombination repair (HRR), which relies on proteins like BRCA1 and BRCA2. However, cancer cells with mutations in BRCA1/BRCA2 or other genes involved in HRR are already deficient in repairing double-strand breaks.
Cell Death in Cancer Cells: In these HRR-deficient cancer cells, the inhibition of PARP leads to the accumulation of unrepaired DNA damage, ultimately causing cell death. Normal cells, which have intact homologous recombination repair, are less affected by PARP inhibitors.

Question 32

Explain how PARP inhibitors work

Answer 32

PARP inhibitors work by targeting a specific DNA repair pathway in cancer cells, exploiting a concept called synthetic lethality. PARP (poly ADP-ribose polymerase) is an enzyme that helps repair single-strand DNA breaks through the base excision repair pathway. Here’s how PARP inhibitors function:

Blocking PARP Function: PARP inhibitors prevent the PARP enzyme from repairing single-strand DNA breaks. Normally, PARP binds to damaged DNA and recruits other proteins to fix the break.
Accumulation of DNA Damage: When PARP is inhibited, the single-strand breaks cannot be repaired, leading to the formation of more dangerous double-strand breaks during DNA replication.
Exploiting Deficient DNA Repair: In normal cells, double-strand breaks can be repaired by a pathway called homologous recombination repair (HRR), which relies on proteins like BRCA1 and BRCA2. However, cancer cells with mutations in BRCA1/BRCA2 or other genes involved in HRR are already deficient in repairing double-strand breaks.
Cell Death in Cancer Cells: In these HRR-deficient cancer cells, the inhibition of PARP leads to the accumulation of unrepaired DNA damage, ultimately causing cell death. Normal cells, which have intact homologous recombination repair, are less affected by PARP inhibitors. This is called synthetic lethality.

Question 33

Clinical utility of genetic testing for familial cancer

Answer 33

1. Carrier testing in families
2. Regular screening in gene carriers
3. Prophylactic surgery
4. Prophylactic drugs

Question 34

Potential clinical utility of GWAS for sporadic cancer

Answer 34

1. New drug targets
2. Stratify disease subtypes:
   - different disease outcomes
   -different drug
   -early detection : liquid biopsy

Question 35

Questions to ask on how we might apply genetic testing for cancer in an African setting

Answer 35

1. How to identify people at risk.? To we have the protocols or infrastructure in place especially in rural areas
2. Is there Access to and funding for genetic tests ?
3. To we have enough trained genetic counsellors
   Do we have a plan of action for mutation carriers or people at high risk ?
4. We need to develop PRS for African population
5. How to prioritise population screening ? FH or PRS ???

Question 36

PARP inhibitors have shown efficacy in what cases.

Answer 36

1. Patients with tumour with mutations in Other homologous repair genes (HR deficient) eg. CHEK2, RAD51C
2. CANCERS not breast cancer but caused by mutated BRACA so.. prostate and ovarian

Question 37

Advantage of liquid biopsy

Answer 37

Early detection of tumour as it can be done when patient is asymptomatic.

Question 38

Characterise DNA methylation changes in cancer and how you would create therapies.

Answer 38

1. Gene promoter CpG islands aquire abnormal hypermethylation resulting in transcriptional silencing
2. Observed at tumour suppressor genes and DNA repair genes
3. Therapy: therapy that inhibits DNA methyltransferase resulting in reverse hypermethylated DNA leading to transcriptional reactivation of tumour suppressor genes

Question 39

Histone acetylation changes in cancer and therapies for cancer.

Answer 39

1. Acetylation regulates biology crucial to cancer, they are critical co-activators for oncogenic and lineage -specific transcription factors
2. Therapies: histone acetyltransferase inhibitors that inhibit histone and non histone acetylation leading to closed chromatin of oncogenes, inhibiting ontogenetic expression programs stopping the driving of tumour growth.

Question 40

Clinical application of epigenetic drug: Monotherapy

Answer 40

1. Drive tumor growth, arrest, differentiation, and cell death
2. Target cancer-specific gene expression programs
3. Synthetic lethality opportunities with mutated Epigenetic enzyme complexes

Question 41

Clinical application of epigenetic drug: combinations

Answer 41

1. Enhance the activity and durability of clinically approved drugs
2. Combinations synergies with chemo and targeted therapies
3. Targeted Epigenetically - driven drug resistant state

Question 42

Clinical application of epigenetic drug: Immuno-oncology

Answer 42

1. Improve patient response to immune checkpoint inhibitors
2. Prime immune system for checkpoint therapies
3. Reactive antigenicity of “cold tumours’’
4. Sustains anti-tumour T-cell response