Genetics 4

Question 1

Ultimately, what is cancer caused by

Answer 1

Cancer is driven by an accumulation of genetic changes that lead to altered levels of transcription or aberrant gene transcripts. If a mutation makes one cell divide faster than others, it has a selective advantage over the other cells in the body, natural end-point of evolution in the body.

Question 2

What is the difference between mis-sense and nonsense mutations in terms of the protein produced

Answer 2

Mis-sense- abnormal protein

Nonsense- truncated protein

Question 3

What are the hallmarks of malignant tumours

Answer 3

Originally, 6 were described:

Dysregulated growth
Autologous pro-growth signalling
Insensitive to anti-growth signalling
Evasion of apoptosis
Limitless replication
Sustained angiogenesis
Invasion/metastasis
More recently, 4 more have been added:
Dysregulation of energy metabolism
Promotion of inflammation
Genome instability and mutation
Evasion  of immune system

Question 4

What is the central cause of cancer

Answer 4

Genome instability

Question 5

What are the types of disordered growth

Answer 5

Insensitivity to anti-growth signals
Autonomy of growth signals
Sustained angiogenesis

Question 6

What are the types of disordered death

Answer 6

Resistance to apoptosis

Limitless replicative potential

Question 7

What are the types of disordered behaviour

Answer 7

Metastasis
Inflammation
Evasion of immune system
Dysregulation of metabolism

Question 8

How is cancer a polyclonal disease

Answer 8

On tumour is made up of different cells each with different genotypes due to the presence of new mutations. This is why cancers are common. The driver mutation greatly increases the rate at which other mutations occur. This is because the driver mutation gives the cell a growth advantage, and will be able to generate mutant offspring faster, each with a higher risk of acquiring a new mutation. This is accelerated by multilevel selection between the different cells in the tumour.
Rate of mutations is also increased by genome instability.

Question 9

What is meant by the driver mutation and why is it important to determine

Answer 9

The first mutation that appears which leads to the development of a tumour.
Important:
Understand how the disease develops
Diagnose more accurately
Devise targeted therapy
Monitor response to therapy

Question 10

What are the great challenges in understanding tumorigenesis

Answer 10

To distinguish between driver mutations, which are causally implicated in the development of cancer and passenger mutations which are incidental and arise from the driver mutation

Question 11

What are the two different genes in which driver mutations occur

Answer 11

Tumour suppressor genes

Oncogenes

Question 12

What is tumorigenesis driven by

Answer 12

Activation of oncogenes

Homozygous inactivation of TS genes

Question 13

What is the role of proto-oncogenes

Answer 13

Proto-oncogenes
Promote growth and proliferation 
Growth factors
Transcription factors
Tyrosine kinases ( GAIN OF FUNCTION)

Question 14

What is the role of tumour-suppressor genes

Answer 14

Tumour suppressors
Regulating cell division
DNA damage checkpoints
(damage=no division)
Apoptosis
DNA repair
Loss of function

Question 15

Consequences of mutated tumour suppressor gene

Answer 15

Faulty growth inhibitor protein which can no longer carry out its function

Question 16

Describe Knudson’s two hit hypothesis

Answer 16

The founder cell of the tumour needs to suffer ‘two hits’- which may be simple mutations or any other genetic change. In familial versions of cancer, one hit is already inherited, hence only one more hit is required. The familial susceptibility is inherited as a dominant trait, but the cellular phenotype that allows the cell to form a tumour is recessive, hence two hits are required.

Question 17

What are the characteristics of hit 1 and hit 2

Answer 17

Hit 1 reduces transcript/protein level but is insufficient to cause a phenotypic effect- often a point mutation

Requires inactivation of second allele (hit 2) causing total loss of transcription  malignant potential- often deletion

Question 18

How do we detect familial loss of heterogeneity

Answer 18

Genetic markers in which the patient happens to be heterozygous will only show a single allele in the tumour

Question 19

How do we detect sporadic loss of heterogeneity

Answer 19

SNP array.

SNPs are common, hence loss of SNPs indicates large scale deletion.

Question 20

Characteristics of oncogenes

Answer 20

No gene is inherently an oncogene (correctly called proto-oncogenes)
Activated oncogenes “over-ride” apoptosis
Damaged cells survive and proliferate
Signalling cascades/mitogenic pathways

Question 21

Describe the inherited predisposition of ovarian and breast cancer

Answer 21

2-4% of breast cancer cases are caused by germline mutation of BRCA1 or BRCA2

60% risk of developing breast cancer by age of 90

Earlier average age of onset

Increased risk of ovarian cancer

BRCA2 mutations also predispose to breast cancer in men

Question 22

Wat is the role of BRCA

Answer 22

TSGs
DNA repair genes
homologous recombination
Mutation  impaired DNA repair

Question 23

What types of mutations can occur in BRCA

Answer 23

Many hundreds of different mutations – unlike say CF or SCD. Point mutations, small frameshifts, exon deletions/insertions, whole gene deletions…PRIVATE MUTATIONS.

Question 24

Describe the Inherited predisposition to colorectal cancer

Answer 24

Familial adenomatous polyposis (FAP)
Lynch syndrome (HNPCC)
Peutz-Jegher syndrome
Gardner syndrome

Question 25

What is FAP

Answer 25

>1% of all colorectal cancers | Virtually 100% lifetime risk of cancer

Question 26

Describe patient management of cancers

Answer 26

Positive family history: Manchester criteria- breast Amsterdam criteria- Colon Genetic screening ``` Positive Surveillance Prophylactic Sx Chemoprevention Family work-up ```

Question 27

Causes of breast cancer

Answer 27

2-4% of Breast Cancer patients have BRCA mutations 10-20% of cases have some evidence of family history with no BRCA mutation Possible monogenes?? ~80% have no family history Likely polygenic

Question 28

Describe the penetrance of rare and common allele variants

Answer 28

Rare variants- high penetrance- high risk | Common variants- low penetrance- low risk

Question 29

How can we explore the causes of polygenic cancers

Answer 29

``` Genome Wide Association Studies (GWAS) Linked SNPs SNP fishing” for linked SNPs Large patient cohorts studied Identifies possible candidate genes/genomic regions Can identify genes or pathways of interest NOT usually causal – not functional Often very small individual effect ``` Transcriptome Chips/mRNA array Differentially expressed transcripts Compares expression profile of malignant vs. normal tissues Large patient cohorts studied Identifies possible candidate genes Can identify genes or pathways of interest Are they causal – or effect of dysregulation? Usually functional – but might not be first event

Question 30

Describe the analysis of the Kallikrein locus | in looking for polygenic risk factors

Answer 30

Serine-protease genes Dysregulated in breast, prostate & ovarian cancer and other malignancies mRNA chip work: KLK14 upregulated in malignant vs. normal breast tissue Can we find the cause of upregulation? Could this be a risk factor for sporadic Breast Cancer Cause rather than effect?

Question 31

Describe the role of translocations in cancer

Answer 31

If two intragenic regions fuse, new genes with potentially oncogenic properties can arise- fusion product formed between two genes originally on two different chromosomes

Question 32

Why is knowledge is most extensive in haematological malignancies

Answer 32

knowledge is most extensive in haematological malignancies (leukaemias and lymphomas) for 2 main reasons Generally leukaemic genomes are more stable than those of solid tumours – therefore easier to pinpoint pathogenetic changes driving disease Relative ease of performing cytogenetics on haematopoeic circulating cells

Question 33

What are the two types of leukaemia

Answer 33

Chronic- Lymphocytic and myeloid | Acute- myeloid and lymphoblastic

Question 34

Describe chronic myeloid leukaemia

Answer 34

clonal myeloproliferative disorder  overproduction of mature granulocytes 1 to 2 cases per 100,000 15% of all adult leukaemias Disease of middle age/elderly ``` Three phases: o Chronic (benign) o Accelerated (ominous) o Blast crisis (acute leukaemic, invariably fatal) ```

Question 35

What is the Philadelphia chromosome

Answer 35

Philadelphia chromosome in >90% t(9,22) BCR-ABL1 fusion protein  NO Philadelphia chromosome = bad

Question 36

Why is the Philadelphia chromosome important in CML

Answer 36

BCR-ABL1 fusion - the molecular hallmark of CML Codes for tyrosine kinase Fusion proteins provide ideal chemotherapeutic targets Imatinib blocks the ATP binding site of BCR-ABL1 But…20-30% patients on imatinib lose their response and require a second line TKI therefore monitoring is important for disease management

Question 37

Which technique is more sensitive to monitoring response to treatment

Answer 37

Microscopic techniques are useful at diagnosis but only biochemical monitoring of the BCR-ABL1 gene transcript by RT-qPCR provides the requires sensitivity for early detection of disease relapse

Question 38

Why do we need to quantify residual disease in CML

Answer 38

Response over first 3-12 months accurately defines long-term response to TKI and helps guide clinical management Absence of cytogenetic response by 12 months or >10% RT-qPCR at 3 months  change of therapy Loss of RT-qPCR negativity is an indicator of an emerging therapy resistant clone and imminent relapse  change of therapy

Question 39

What is AML

Answer 39

Divided into FAB M0-7 FAB M3 – medical emergency – DIC and haemorrhage (acute promyelocytic form)  FAB M5 – gum infiltration ± lymphadenopathy, hepatomegaly, splenomegaly

Question 40

Causes of AML

Answer 40

Abnormal accumulation of immature granulocytes called promyelocytes FUSION GENE: retinoic acid receptor alpha (RARα) on chr 17 and PML on chr 15 t(15;17)(q22;q12)

Question 41

What are RAR alphas

Answer 41

Nuclear receptor bound by retinoic acid Regulator of DNA transcription PML-RARα protein binds too strongly to DNA – blocks transcription and differentiation of granulocytes all trans retinoic acid (ATRA) therapy - dissociates co-repressors allowing normal transcription & differentiation ATRA does not kill cells Continuous therapy needed as residual stem cells remain Like CML, APML is monitored by cytogenetics and/or FISH and/or RQ-PCR

Question 42

Characterisations of each translocation in cancer

Answer 42

t(8,14)- cMYC-IgH - Burkitt’s lymphoma t(9;22) - BCR-ABL - Philadelphia, CML t(15;17) - RARA-PML - APML t(11;22) - FLI1-EWS - Ewings sarcoma

Question 43

What is pharmacogenomics

Answer 43

Pharmacogenomics is the branch of pharmacology which deals with the influence of genetic variation on drug response

Question 44

Describe the role of pharmacogenomics in cancer

Answer 44

Increasingly useful in planning chemotherapy Identify which patients are most likely to respond to certain cancer drugs Assay presence/absence of particular somatic mutations KRAS test with cetuximab for colorectal cancer KRAS mutation = less likelihood of response EGFR test with gefitinib for non-small cell lung cancer EGFR mutation = greater likelihood of response BCR-ABL1 “T315I” test with dasatinib for CML BCR-ABL1 T315I mutation = unlikely to respond