Genetics and Epigenetics 1 - C Hogan

Question 1

What are germline mutations?

(1 mark)

Answer 1

Detectable variation within germ cells. Mutations in these cells are the only mutations that can be passed on to offspring

Question 2

What is haploinsufficiency?

(1 mark)

Answer 2

Normal copy of gene still present but abnormal copy prevails

Question 3

What is SV40 large T-antigen?

(2 mark)

Answer 3

• Hexamer protein dominant acting oncoprotein derived from the polymavirus SV40
• TAg able to produce malignant transformation in various cell types

Question 4

Are transformed cancer cells immortal?

(1 mark)

Answer 4

Yes x

Question 5

What can be seen if you express RaV12/ Raf CAAX in cells in vivo?

(3 marks)

Answer 5

• Find cells form clumps of cells showing continuous growth
• No dependency factors
• Loss of contact inhibition - cells grow on top of each other
• Trigger tumourogenesis

Question 6

Give an example of an inherited germline mutation.

(1 marks)

Answer 6

Broca gene or RB gene

Question 7

What are mutagens?

(1 marks)

Answer 7

• External factors that create DNA damage and can cause tumours e.g. smoking, radiation etc.

Question 8

What are sporadic somatic mutations?

(2 marks)

Answer 8

• Random mutation in germline that only affects individuals and can’t pass onto offspring
• May trigger activation of oncogenes, loss of TS genes and inefficient DNA repair pathways

Question 9

What are driver gene mutations?

(1 marks)

Answer 9

Directly/ indirectly confers a selective growth or survival advantage to the cell

Question 10

What are passenger gene mutations?

(1 marks)

Answer 10

No direct or indirect advantage - neutral impact on phenotype

Question 11

What are somatic mutations?

(1 mark)

Answer 11

Mutations that occur in non-germ cells

Question 12

What are oncogenes?

(1 mark)

Answer 12

Gene that when mutated increases selective growth advantage to the cell e.g Ras activation pathway

Question 13

What are tumour suppressor genes?

(1 mark)

Answer 13

Gene that when inactivated by mutation increases selective growth advantage of the cell - most mutated gene in cancer = p53

Question 14

Give a few examples of some common cancer mutations.

(1 mark)

Answer 14

Rb, PTEN, APC

Question 15

What are epigenetic mutations?

(2 marks)

Answer 15

• Mutations that cahnge gene expression/ chromatin without changing DNA sequence
• stable and heritable change in gene expression

Question 16

What does an epigenetic deregulator in cancer do?

(2 marks)

Answer 16

• De-regulation of gene expression
• Shut down of tumour suppressor genes
• Activation of oncogenes

Question 17

What is an epigenetic modulator?

(1 mark)

Answer 17

• Gene activates/ represses machinery e.g. APC

Question 18

What is an epigenetic mediator?

(1 mark)

Answer 18

• Genes regulated by epigenetic modifier e.g. DNMT3A, TET2

Question 19

What is an epigenetic modifier?

(1 mark)

Answer 19

• Gene thats mutated or not that modifies DNA methylation or chromatin structure or its interpretation in cancer. Increases pluripotency or survival. e.g. SOX2

Question 20

What do you need to do to tumour stem cells to avoid relapse?

(1 mark)

Answer 20

Need to KO - their ablity to shift between different cell states is quite plastic due to changes in epigenetics

Question 21

What process of epigenetics increases progenitor status in cancer cells?

(1 mark)

Answer 21

• Deregulation
• Epigenetic modifiers can use stem cells to become more metastatic

Question 22

What is the purpose of DNA methylation?

(1 mark)

Answer 22

• Function is to silence genes - key to imprinting somatic cells silences inactive genes - ones inactive in adulthood are silenced

Question 23

Basic outline of how DNA methylation occurs

(3 marks)

Answer 23

• Cytosine and adenine reisdue od DNA can be methylated
• Methyl group covalently attached to CG-rich dinucleotide sequence (DNMTs)
• CG rich regions aka CpG islands normally sites for transcription initiation

Question 24

What are CpG islands (CGIs)?

(2 marks)

Answer 24

• Small regions of genomic DNA
• Most mamalian promoters arre CGIs
• CGIs are not methylated
• Gene repression occurs via polycomb comlpexes - allow for more palstic control than DNA methylation
• Life long methylatio at CGIs e.g. x-chromosome inactivation

Question 25

What are the phases of DNA methylation?

(3 marks)

Answer 25

• De novo methylation (DNMTs)
  
  • ​Covalently add methyl groups to CpG rich sequences - DNMT 3a and 3b
  • DNMT3c in rodents (male)
  • DNMT3L stimulates DNMT3a and 3b activity
• Maintenance
  
  • ​Covalently add methyl groups to hemimethylated DNA
  • DNMT1 (also needs UHRF1)
  • Restores methylation patterns after DNA replication
• DNMT2 methylates tRNAs

Question 26

Why is removal of methyl groups important and what does it require?

(2 marks)

Answer 26

• Passive demethylationn - in absence of maintenance DNMT activity
• Active de methylation requires TET oxidases

Question 27

What do methyl binding domain proteins do?

(2 marks)

Answer 27

• Bind to and interpret methylated CG-rich sequences to alter chromatin
• Co-ordinate crosstalk between methylation, histone modification and chromatin organization

Question 28

How does transcriptional silencing occur with MBD2?

(1 mark)

Answer 28

• MBD2 recruits NuRD complex to induce histone deacetylation and chromatin compaction

Question 29

Which DNA methylation genes are frequently mutated in cancer?

(1 mark)

Answer 29

DNMT3 and TET genes

Question 30

Which sort of enzymes are key targets by therapeutic drugs?

(2 marks)

Answer 30

• Histone modifying enzymes
• BRD4 part of transcriptional elongation pathway - critical for expression of key tumour promoting oncogenes i.e. MYC

Question 31

What sort of therapy do drug tolerant cancer cells tend to respond to?

(1 mark)

Answer 31

HDACi therapy combined with KDM depletion as this ablates teh surivival mechanism

(KDM = potassium depletion)

Question 32

Give a few examples of epigenetic modifier mutations and what cancers they occur in.

(3 marks)

Answer 32

• TET2 mutation in myelomonocytic leukaiemia - mouse models show increased self renewal and myeloproliferation in context of impaired erythroid differentiation
• H3K36 methyltransferase mutations in haematological and solid tumours -
• SETD2 mutation worsen progression in renal cell carcoma

Question 33

How do myofibroblasts support maintenance of CSC states in the colon?

(1 mark)

Answer 33

Produce hepatocyte growth factor to locally support CSCs - shows epigenetic mediator important for CSC state and tumour progression

Question 34

What does a mutation in epigenetic modulator p53 cause?

(1 mark)

Answer 34

Gain of function mutation inducing histone modifying enzymes MILL1/2 & MDZ causing genome wide incerase in histonee H3K9 deacetylation and H3K4 trimethylation

Question 35

How can a mutation in modulators affect DNA and histone methylation?

(2 marks)

Answer 35

Cause a production of oncometabollites that inhibit α-ketoglutarate-dependent epigenetic modifiers i.e. TET hydroxylases and histone lysine demethylases