Biol3108 Revision Questions

Describe the key mechanism(s) for cellular transformation of chicken, mouse and/or human cells by RNA tumour viruses

Discuss the broader implications of the discovery that human genomes contained cellular counterparts of viral oncogenes (protooncogenes).

There are various methods of detection and analysis of genome instability. Explain one of these methods and what it measures. What are the implications for cancer diagnosis and treatment?

Avian Leukemia Virus (ALV) induces leukaemia by inserting in the promoter of:

• TP53

• Myc

• Ras

• Src

Myc

Anaplasia means:

• A well differentiated tumour

• A benign lesion

• A slow growing tumour

• A poorly differentiated tumour

A poorly differentiated tumour

Chromosome segments copied many times and fused head-to-tail in long arrays form:

• Double minutes

• Homologous deletions

• Double chromatids

• Homogenously stained regions

Homogenously stained regions

Patient X was diagnosed with breast cancer. What antibody stain would you use to aid diagnosis and direct treatment?

• HER2 antibody

• P21 antibody

• Myc antibody

• Ras antibody

HER2 antibody

Which of these characteristics is a unique feature of malignant neoplasms?

• Fast growth

• Metastasis

• Increased nuclear-cytoplasmic ratio

• Abnormal mitosis

Metastasis

What are the cellular mechanisms that prevent genomic instability?

DNA repair pathways

Telomere maintenance

Centrosome maintenance

What is the difference between DNA Pol I & III?

DNA Pol I:

• Synthesises short stretches of DNA

• Only in the lagging strand

• 5’ to 3’ polymerase activity

• 5’ to 3’ endonuclease activity (proof-reading function)

• 3’ to 5’ endonuclease activity (proof-reading function)

• Is slow

DNA Pol III:

• Main Pol used in replication, synthesis of new DNA strand

• Works on both the leading and lagging strands

• Has 5’ to 3’ polymerase activity

• 3’ to 5’ exonuclease activity

• Synthesises long stretches of DNA

• Very fast

What are the mechanisms of DNA repair? Describe their mechanisms.

Nucleotide excision repair

Base excision repair 

Mismatch repair

What are the double stranded DNA repair mechanisms? Describe their mechanisms.

Homologous recombination

Nonhomologous end joining

What is needed to protect chromosome ends?

Telomeres

Why do telomeres shorten with each cell division?

Why is there a D-loop formed at the telomere?

What are telomeres made of?

Repetitive DNA sequences

Do cells have active telomerase?

How does telomerase function?

What is chromatin? What molecules form it? What is its function?

Do chromatin remodeling complexes need energy sources?

How do chromatin remodeling complexes influence chromatin compaction

WHat activities do chromatin remodeling complexes perform within chromatin? Give examples.

Are chromatin remodeling complexes involved in replication?

Yes, chromatin remodelling complexes are involved in DNA replication. They facilitate the process by modulating nucleosome position and composition, which helps replication enzymes access DNA, disassemble nucleosomes ahead of the replication fork, and assemble new chromatin after replication

What do histone post-translational modification do?

Give examples of heterochromatin/euchromatin modifications

Give examples of facultative heterochromatin formation. Which post translational modifications? Which protein complexes are involved?

The most likely epigenetic modification of oncogenes in cancer is:

• Histone methylation

• DNA hypermethylation

• Histone acetylation

• DNA acetylation

Histone acetylation

A CpG island:

• Is a region of DNA with less than 50 base pairs

• Has a GC content higher than 50%

• Is rarely seen in prostate cancer

• Is frequently acetylates

HAs a GC content higher than 50%

Faults in which DNA repair pathways can induce chromosomal translocations?

• MMR and BER

• HR and NHEJ

• HR and MMR

• NER and BER

HR and NHEJ

DNA is coiled around:

• Chromatin to form nucleosomes

• Genes to form nucleosomes 

• Protein to form nucleosomes 

• Chromosomes to form nucleosomes

Protein to form nucleosomes

Which method is not regularly used to detect and analyse genome instability?

• Single cell sequencing

• Karyotyping

• Fluorescence in situ hybridisation (FISH)

• Bisulfite sequencing

Bisulfite sequencing

Inhibitory phosphorylation of Cyclin B occurs via:

• CAK

• Wee1

• Chk1

• Cdc25

Wee1

Which statement about pRb is most correct?

• pRb is a potent oncogene

• pRb binds Bcl2 to promote apoptosis

• pRb binds the E2F transcription factor to prevent S phase

• pRb binds the transcription factor E2F to stimulate S phase

pRb binds the E2F transcription factor to prevent S phase

p21, the protein activated by p53 after DNA damage is:

• A ubiquitin ligase

• a CDK inhibitor

• A phosphatase

• A MDM2 inhibitor

a CDK inhibitor

Spindle checkpoint defects can result in:

• Chromosome bridges

• Telomere lengthening

• G1 phase

• DNA replication

Chromosome bridges

BH3 mimetics such as venetoclax kill cancer cells by:

• Inhibiting Myc

• Inhibiting MDM2

• Inhibiting Bcl-2

• Inhibiting p27

Inhibiting Bcl-2

Which of the following is not a direct cause of oncogenesis in humans:

• HTLV-1

• Merkel Cell Polyomavirus

• Human Immunodeficiency Virus

• Epstein-Barr Virus

Human Immunodeficiency Virus

Childhood malaria contributes to development of EBV related lymphomas in which of the following ways:

• Impairment of host immunity following malaria infection

• Increased susceptibility to EBV infection following malaria infection

• Increased genomic instability following malaria infection

• Increased lymphocyte production in response to malaria infection

Increased genomic instability following malaria infection

Which of the following is not a factor in the contribution of HIV infection to viral oncogenesis in humans:

• Impairment of host immunity following HIV infection

• Increased dissemination of malignant cells following HIV infection

• Increased susceptibility to infection with oncogenic viruses following HIV
  infection

• Increased inflammatory factors following HIV infection

Increased dissemination of malignant cells following HIV infection

Describe examples where viral modulation of host pathways contributes to oncogenesis.

Describe the cancers associated with EBV. What factors might contribute to the regional variation in the cancers caused by this virus?

As cells age Telomeres:

• Shorten

• Lengthen

• Replicate

• Fuse

Shorten

Ectopic expression of which protein induces a cellular senescence phenotype?

• pRb

• CycD

• Myc

• p16 (INK4A)

p16(INK4A)

Multiple molecular changes are required for cancer initiation and progression.

What was the tumour type that suggested cancer evolves over a long time?

What sequence of cellular and genetic changes are associated with evolution of this cancer?

What is clonal evolution? Discuss in context with acquired chemotherapy resistance.

Discuss the evidence for the “mutator phenotype” and whether it might be a necessary step for tumourigenesis.

Describe the key principles of stem cell fate regulation within the stem cell compartment.
Why do you think an understanding of the stem cell-niche interaction might be important for improving cancer treatment?

Although cancer cell dissemination can start early during tumour progression, most cells leaving a tumour fail to colonise distant organs and instead succumb to various stresses.” What are these stresses?

Eliminated once entering the blood stream due to sheer stress within microvessels, cell-death induced by loss of attachment to a substrate (anoikis), and lysis by natural killer cells.
Stresses encountered following extravasation into the host tissue, including reduced bioavailability of nutrients, oxidative stress, and immune attack by tissue resident
immune cells (i.e. tissue resident macrophages and natural killer cells). Bone-marrow derived, and peripheral immune cells are also recruited to eliminate the newly seeded
metastases. The host tissue is a hostile place!

A large array of gene expression changes is required to promote metastasis. Do these changes occur in the primary tumour or once the disseminated cancer cell has seeded a distant tissue?

Both. Gene expression changes in the primary tumour prime the cells for metastasis, while other gene expression changes develop in the host tissue to allow the cells to adapt to the new environment.

New mutations are not required to promote metastasis. What evidence exists to support this claim?

The mutation patterns and overall mutational burden are almost indistinguishable between primary and metastatic cancers. However certain clones with particular genetic
alterations will dominate in metastatic lesions, which can be explained by the monoclonal metastasis model as described in L17 (slide 17)

After the primary tumour is removed by surgical resection, the patient may develop clinically detectable metastases years later. How is this possible if circulating tumour cells are eliminated from the blood stream after 24 hours?

Micrometastases which form before the removal of the primary tumour, can enter proliferative quiescence before colonising the tissue as a macrometastases.

Alternatively, a macrometastases may fail to grow to a clinically detectable size due to factors in the host stroma or insufficient vascularisation.
Evidence of metastatic dormancy – reported cases of organ transplant recipients who have developed metastases after receiving organs from donors who had been deemed cured of melanoma

On page 37, under the subheading Developing therapies for micro- and macrometastases the authors make the statement “While targeting the early steps of tumour invasion and survival in the circulation are, in our opinion, unlikely to be effective at preventing or treating metastasis, targeting micrometastatic cells could prevent metastasis”. Why do you think the authors have drawn this conclusion?

Patients presenting with stage IV cancer have overt metastatic disease and therefore interfering with further seeding is likely to be futile in halting disease progression.
In patients that do not present with clinical mets, the primary tumour is usually surgically excised prior to treatment with systemic or targeted therapies, thereby quickly eliminating the source of circulating tumour cells. Patients that develop distant recurrence following primary tumour removal, indicates that micrometastases had formed prior to surgery.

EMT-inducing transcription factors:

• Are specific to cancer

• Have non-overlapping functions in activating/repressing gene expression

• Can induce the expression of other EMT transcription factors

• Can act in isolation to execute the entire EMT program

Can induce the expression of other EMT transcription factors

Local invasion does not involve:

• Disruption of extracellular matrix (ECM) by proteases

• An increase in cell motility

• An ability to undergo epithelial to mesenchymal transition (EMT)

• Avoiding interaction with surrounding stromal cells

Avoiding interaction with surrounding stromal cells

Metastasis requires:

• A cell with the primary tumour acquiring new mutation, which favours the metastatic process

• The ability of a cell to maintain a mesenchymal phenotype at the site of seeding

• Clonal selection of pre-existing mutations present in the primary tumour

• A complete epithelial to mesenchymal transition to occur

Clonal selection of pre-existing mutations present in the primary tumour

Which statement about the actin cytoskeleton is correct?

• Filopodia and lamellipodia are actin-based structures, but invadopodia are not

• Rho GTPases remodel the actin cytoskeleton by activating actin-binding proteins

• The only function of the actin cytoskeleton is to help cells move

• Filopodia are composed of branched actin filaments

Rho GTPases remodel the actin cytoskeleton by activating actin-binding proteins

Epithelial to mesenchymal transition is commonly associated with:

• A static actin cytoskeleton

• The induction of E-cadherin expression

• The acquisition of stemness

• The formation of invadopodia in neoplastic cells which secrete MMPs

The acquisition of stemness

List two cell types of the immune system that can kill
cancer cells by the secretion of cytotoxic granules,
and the mechanism of action. What are the
implications for cancer treatment?

A patient has a mysterious B cell cancer. This patient also carries genetic deficiencies such that their B cells do not generate antibodies and their NK cells are defective in antibody-dependent cell-mediated cytotoxicity. Discuss TWO immunotherapies and evaluate their efficacy in the context of this patient’s genetics.

Which one of the following cell types secretes antibodies?

• B cells

• Macrophages

• Dendritic cells

• T cells

B cells

Which of the following statements about immunotherapy is correct?

• CAR-T cell therapy targets immune checkpoint proteins.

• Immunotherapy is used as frequently as chemotherapy

• Immunotherapy is affordable for all cancer patients

• Immunotherapies can induce innate and adaptive immune responses

Immunotherapies can induce innate and adaptive immune responses

Which of the following statements does NOT support the idea that the immune system monitors and eliminates cancer cells?

• Mice injected with live tumour cells develop tumours whereas mice injected with dead tumour cells do not develop tumours

• Humans whose tumours have high levels of tumour-infiltrating lymphocytes survive longer than those whose tumours have low levels of tumour-infiltrating lymphocytes

• Mice lacking perforin have an elevated incidence of spontaneous tumours compared to control mice expressing perforin

• Immunocompromised patients experience a higher incidence of cancers

Mice injected with live tumour cells develop tumours whereas mice injected with dead tumour cells don’t develop tumours

Which statement about innate immunity is most correct?

• Innate immunity provides rapid and early responses

• Innate immunity generates immunological memory that can prevent re-infection by the same microorganism

• Innate immunity is triggered by the generation of antigen-specific effector cells with high specificity

• T helper cells are a type of innate immune cells

Innate immunity provides and early responses

Which of the following statements about CAR-T cells is most correct?

• Cytokine release syndrome is a side effect of CAR-T cell therapy

• CAR-T cell therapy is standard care for all breast cancer patients

• Resistance to CAR-T cell therapy never develops

• CAR-T cells require co-stimulation by dendritic cells

Cytokine release syndrome is a side effect off CAR-T cell therapy

The drug discovery and pre-clinical testing phases of a therapeutic designed to
be used to treat cancer is performed to:
A: Evaluate how well the therapy acts on the molecular target/process
B: Refine a large list of molecules down to a handful (‘hit to lead’)
C: Identify whether the therapy has the desired effect in animal models of cancer
D: All of the above

D

Targeted therapies are designed to:
A: Remove or reduce the amount of tumour tissue
B: Target specific proteins/molecular interactions in cancer cells to block/modify their activity
C: Kill cancer cells and the surrounding stromal cells
D: Activate the immune system to kill cancer cells

B

You are in charge of a team of cancer therapeutics researchers in a small biotech
company, and you have been given the task of developing a new drug.
The target you are required to develop the drug for is a highly novel receptor tyrosine
kinase called NOVR.

NOVR is:
• Structurally similar to the Epidermal Growth Factor Receptor (EGFR)
• Activated after stimulation with a ligand (NOV ligand)
• Located in the cell membrane (N-terminus is located extracellularly)
• Activated after ligand stimulation, where the intracellular tyrosine kinase domain
becomes phosphorylated which leads to MAPK pathway activation
Genomic analysis of tumours isolated from breast cancer patients shows that NOVR
expression is highly upregulated, however, the gene itself is not found to be
mutated in breast tumours

Given what we know about NOVR, which approach do you think is the most appropriate
for drug development?
A: Rational drug discovery
B: High-throughput screening

A

You are a junior group leader who has an interest in identifying a novel small molecule therapeutic which will lead to the activation of double-stranded DNA breaks (DSBs) in cancer cells, as a means to induce cytotoxicity and cancer cell death.

A hard-working PhD student in the lab has developed a phenotypic assay which is able to measure the amount of DSBs in cancer cells.

Which approach do you think may be the most appropriate for drug development?
A: Rational drug discovery
B: High-throughput screening

B

Targeted therapies are designed to:

• debulk tumour tissue

• kill all cells

• activate B cells

• target specific proteins

Target specific proteins

What is the target of the treatment successfully used in melonoma?

• B-RAF

• AKT

• Rb

• MYC

B- RAF

Clinical trials designed to test a small number of human volunteers/patients to identify a safe dose of the drug, route of administration and how the drug affects the body are:

• Phase II

• Phase IV

• Phase III

• Phase I

Phase I

Which situation might require a rational drug screen approach?

• The aim is to test whether approved therapeutics can be repurposed for other diseases

• Molecular target is unknown

• Multiple pathways need to be targeted

• Knowledge of lead compound mechanism of action is required from the start

Knowledge of lead compound mechanism of action is required from the start

Which treatment can most readily be used for precision medicine?

• Tyrosine kinase inhibitors

• Chemotherapy

• Surgery

• Hormone therapy

Tyrosine Kinase Inhibitors

Why is the lymphatic system important for cancer cell invasion?

How do Tissue Inhibitors of Metalloproteinase (TIMPs) impact angiogenesis in normal cells and how they are dysregulated in cancer?

What are the changes that occur in tumour-associated vasculature and how do they contribute to tumour progression?

Loss of function mutations in which of the following genes has been linked to anti-PD-1 resistance?

• B2M

• KRAS

• EGFR

• KMT2D

B2M

Which one of the following is a T-cell inhibitory receptor?

• LAG-3

• CD28

• OX40

• PD-L1

LAG-3

What tumour characteristic can indicate a favourable response to anti-PD-1 therapy?

• Large tumour size

• High mutational burden

• Presence of tumour associated macrophages

• T cell exhaustion phenotype

High mutational burden

Which event might prevent a T-cell from effectively responding to a tumour antigen?

• Increase in granzyme production

• Loss of PD-1 expression

• Physical association with the tumour cell

• Upregulation of CTLA-4

Upregulation of CTLA-4

Which of the following statements about anti PD-1 therapy is most correct?

• Immune related side effects are more common with anti-PD-1 therapy than anti-CTLA-4 therapy

• DNA mismatch repair proficient tumours are more likely to respond to anti-PD-1 therapy than tumours with DNA mismatch repair deficiency

• The tumour mutational burden is negatively correlated with the objective response rate in patients treated with anti-PD-1 therapy

• PD-L1 immunohistochemistry is performed routinely in metastatic lung squamous cell carcinoma

PD-L1 immunohistochemistry is performed routinely in metastatic lung squamous cell carcinoma