Genetics and Epigenetics 1 - C Hogan Flashcards
What are germline mutations?
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Detectable variation within germ cells. Mutations in these cells are the only mutations that can be passed on to offspring
What is haploinsufficiency?
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Normal copy of gene still present but abnormal copy prevails
What is SV40 large T-antigen?
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- Hexamer protein dominant acting oncoprotein derived from the polymavirus SV40
- TAg able to produce malignant transformation in various cell types
Are transformed cancer cells immortal?
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Yes x
What can be seen if you express RaV12/ Raf CAAX in cells in vivo?
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- 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
Give an example of an inherited germline mutation.
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Broca gene or RB gene
What are mutagens?
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- External factors that create DNA damage and can cause tumours e.g. smoking, radiation etc.
What are sporadic somatic mutations?
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- 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
What are driver gene mutations?
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Directly/ indirectly confers a selective growth or survival advantage to the cell
What are passenger gene mutations?
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No direct or indirect advantage - neutral impact on phenotype
What are somatic mutations?
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Mutations that occur in non-germ cells
What are oncogenes?
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Gene that when mutated increases selective growth advantage to the cell e.g Ras activation pathway
What are tumour suppressor genes?
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Gene that when inactivated by mutation increases selective growth advantage of the cell - most mutated gene in cancer = p53
Give a few examples of some common cancer mutations.
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Rb, PTEN, APC
What are epigenetic mutations?
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- Mutations that cahnge gene expression/ chromatin without changing DNA sequence
- stable and heritable change in gene expression
What does an epigenetic deregulator in cancer do?
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- De-regulation of gene expression
- Shut down of tumour suppressor genes
- Activation of oncogenes
What is an epigenetic modulator?
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- Gene activates/ represses machinery e.g. APC
What is an epigenetic mediator?
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- Genes regulated by epigenetic modifier e.g. DNMT3A, TET2
What is an epigenetic modifier?
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- Gene thats mutated or not that modifies DNA methylation or chromatin structure or its interpretation in cancer. Increases pluripotency or survival. e.g. SOX2
What do you need to do to tumour stem cells to avoid relapse?
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Need to KO - their ablity to shift between different cell states is quite plastic due to changes in epigenetics
What process of epigenetics increases progenitor status in cancer cells?
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- Deregulation
- Epigenetic modifiers can use stem cells to become more metastatic
What is the purpose of DNA methylation?
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- Function is to silence genes - key to imprinting somatic cells silences inactive genes - ones inactive in adulthood are silenced
Basic outline of how DNA methylation occurs
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- 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
What are CpG islands (CGIs)?
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- 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
What are the phases of DNA methylation?
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-
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
Why is removal of methyl groups important and what does it require?
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- Passive demethylationn - in absence of maintenance DNMT activity
- Active de methylation requires TET oxidases
What do methyl binding domain proteins do?
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- Bind to and interpret methylated CG-rich sequences to alter chromatin
- Co-ordinate crosstalk between methylation, histone modification and chromatin organization
How does transcriptional silencing occur with MBD2?
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- MBD2 recruits NuRD complex to induce histone deacetylation and chromatin compaction
Which DNA methylation genes are frequently mutated in cancer?
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DNMT3 and TET genes
Which sort of enzymes are key targets by therapeutic drugs?
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- Histone modifying enzymes
- BRD4 part of transcriptional elongation pathway - critical for expression of key tumour promoting oncogenes i.e. MYC
What sort of therapy do drug tolerant cancer cells tend to respond to?
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HDACi therapy combined with KDM depletion as this ablates teh surivival mechanism
(KDM = potassium depletion)
Give a few examples of epigenetic modifier mutations and what cancers they occur in.
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- 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
How do myofibroblasts support maintenance of CSC states in the colon?
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Produce hepatocyte growth factor to locally support CSCs - shows epigenetic mediator important for CSC state and tumour progression
What does a mutation in epigenetic modulator p53 cause?
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Gain of function mutation inducing histone modifying enzymes MILL1/2 & MDZ causing genome wide incerase in histonee H3K9 deacetylation and H3K4 trimethylation
How can a mutation in modulators affect DNA and histone methylation?
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Cause a production of oncometabollites that inhibit α-ketoglutarate-dependent epigenetic modifiers i.e. TET hydroxylases and histone lysine demethylases
