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L2- Genetic drivers of cancer - Coggle Diagram
L2- Genetic drivers of cancer
Genetic drivers of cancer
Cancers develop through multiple genetic & epigenetic changes
Multistep process reflecting stochastic genetic & epigenetic changes in key cancer genes (oncogenes & tumour suppressors)
Changes in key genes confer “hallmark” capabilities & are selected – driver events
Accumulation of changes in key genes can take decades
Genome sequencing found hundreds of mutns per cell in normal oesophageal epithelium of ~20yr olds & >2000 mutns per cell in 72yr old with no sign of cancer
Mutn frequency in oesophageal cancer is ~10-fold higher than in normal oesophagus – can reflect loss of protective mechanisms such as DNA repair machinery, as well as selection for advantageous mutations
Oncogenic activation - cancer development involves elevated activity of oncogenes
Pnt mutns in coding sequence can alter activity e.g. pnt mutns lock Ras in GTP-bound active form, resulting in constitutive signals (down MAPK) that promote development of colon cancer
Chromosomal rearrangements can introduce aberrant control elements causing abnormal expression e.g. in Burkitts lympoma, an Ig enhancer becomes positioned near MYC gene, raising its expression in B cells
Elevated expression can result from changes to upstream regulators e.g. MYC gene is induced in colon cancers by beta catenin, following loss of APC
Chromosomal amplifications can increase copy number & hence expression levels e.g. MYC gene is frequently amplified in breast cancers
Amplifications can be extrachromosomal
Inactivation of tumour suppressors - cancer development involves reduced tumour suppressor activity
Tumour suppressor genes are often silenced by epigenetic regulation e.g. MMR genes are frequently silenced by DNA methylation in colon cancer
Chromosomal rearrangements can delete part or all of a tumour suppressor gene
e.g. APC gene is commonly deleted in colon cancers
Point mutations in coding sequence can alter activity
e.g. point mutns in p53 are common in many cancer types
Tumour suppressor p53
p53 is commonly mutated
deleted/mutated in 50% human cancers (highest freq of any known gene)
e.g. p53 gene mutated in 90% of oesophageal cancers
In normal oesphagus from organ donors, 5-35% of epithelial cells have p53 mutations
Most p53 mtns arise somatically, but germ-line mutns occur in some cancer-rpone families e..g Li-Fraumeni syndrome
Most p53 mutns are misense substitutions - deletions are less common than for other tumour suppressor genes. Missense mutns may confer oncogenic activity.
Background
p53 is a txn factor - N-terminal txn actn domains, central DNA-binding domain, & C-terminal tertamerisation & regulatory domains
binds DNA as tertamer made from pair of dimers
Target genes: csk inhibitor p21 (to arrest cell cycle) & death gene Bax (to induce apoptosis)
Txn actn domain stimulates txn by binding & recruiting TFIID & histone acetyltransferases (HATs) e.g. p300
Dominant negative effect of mutnt p53
mutnt p53 -> oncogenic effects through more than one mechanism
In heterozygous cells, mutant p53 can have dominant negative effects, where mutnt p53 binds and inactivates WT p5 as have both WT and mutnt molecules
As p53 binds DNA as tetramer = inclusion of mutnt monomers compromises DNA binding & function of teratmer
GOF by mutnt p53
Some missense p53 mutnt display activities not shown by WT p53
E.g. Some oncogenic p53 mutnts can bind txn factor ETS2 & induce its target genes e.g. MLL1- WT p53 does not interact with ETS2 of ETS2 targets.
Inducrion of MLL1 == important for oncogenic acitivry of p53 GOF mutnts - results in abberant txn patterns through epigentic activity
Restoring function 2 mutnt p53
GOF alters its conformation & drugs have been developed to try and restore conformation & hence WT function to p53 with missense mutns
APR246 binds mutnt p53 & restores ability to induce apoptosis (by changing its conformation) in cancer cell lines & mouse models
Multiple clinical trials - either as a monotherapy or in combination wit other drugs.
In a phase III mutlicentre randomised trial, patienrs with myelodysplastic syndrome treated with APR264 combined with standard treatment of azacytidine - remission rate of 22% was boosted to 33% by APR246..
Myelodysplastic syndrome = rare cancer of blood stem cells. Have insufficient normal blood. Affects old people predominantly.
Arsenic trioxide is a drug used by traditional Chinese medics to treat promyelocytic leukaemia.
Recently found to bind to many p53 mutnts, stabilise structure & restore activity
clinical trials testing the efficacy of arsenic trioxide in multiple cancer types.
Introducing WT-p53 to cancer cells
2003: head & neck cancer treated in China using adenovirus vector to express WT p53 - first FDA-approved gene therapy for cancer
Virus disabled to prevent propagation & patient recieves 5 injections into tumour in 3 day intervals
Not used outside China
A lipid-based nanoparticle delivering exogenous DNA carrying WTp53 gene is in phase II trials in USA to treat pancreatic cancer
Unlike viruses, low immunogenicity & can be carried throughout body in the bloodstream - inclusion of an antibody fragment can sometimes be used to target nanoparticle to specific cell type(s) e.g. cancer cells
Technology to deliver mRNA developed rapidly during SARS-CoV-2 pandemic & considered great potential 4 cancer therapeutics
MDM2
= Ubiquitin ligase that controls p53 level by polyubiquitination, causing proteasomal deggradation
Gene bound & activated by p53- causes its won destruction/ negative feedback loop
Prevents excessive accumulation of p53 & allows return to basal p53 levels once inducing stimuli are removed - negative feedback loop
MDM2 is essential because p53 can active apoptosis - MDM2 knockout mice die in utero die to p53 induced cell death
mutnt p53 accumulates to higher levels that WT p53 bc MDM2 not induced by mutnt. MDM2 lost binding activity so doesn't bind to MDM2 so no negative feedback loop.
Target for Anti-cancer drugs
Nutlin drugs = prevent p53 degradation by MDM2
Several nutlin derivatives been in clinical trials
Trials 4 various cancer types found increased p53 & p21 expression, confirming nutlin acts as intended
Trials = suspended bc patients suffered adverse side effects esp. nausea & haematological toxicity
Many other MDM2 inhibitory drugs are still in clinical trials
Regulation & activation of p53
Many PTMs regulate p53
Many kinases regulate p53
E.g. ATM kinase phosphorylates p53 on Ser 15 in response to DNA damage - inhibits MDM2 binding & stabilised p53 - allows p53 to accumulate & induce apoptosis or cell cycle arrest until DNA repaired
Other kinases phosphorylate other p53 residues, with various effects that depend on context
Considerable redundancy - if you lose one kinase another kinase may have a different effect
Multiple stresses activate p53
p53 probably evolved as a coordinator of stress responses
Different stresses trigger different types of response, in terms of PTM & target genes- extremely context-dependent
PTMS afford flexibility & allow responses to be tailored to a stimulus
Best studied is response to DNA damage- but is most important?
Apoptosis in response to DNA damage may not be reqrd for tumour supp. by p53, at least in mouse models
Tumour suppression by p53
ARF is required 4 tumour suppression by p53
Experiments to show: experiments carried out with mice injected with an oncogenic chemical. WT mice used in this way die after 12 weeks. All died of cancer by 24 weeks. p53 super mice had better survival rates.
p53super mice have an extra copy of p53 gene & show reduced cancer incidence
Tested effed of deleting gene ARF. Treating ARFnull mice with durg, died very quickly and having extra copy of p53 provided no signifcant benefit. So can conclude, benefit of p53 requires presence of ARF.
How?
Hotly debated. Best characterised p53 responses = cell cycle arrest & apoptosis. However, p53 mutn found that induces cell cycle arrest & apoptosis, but fails to suppress tumorigenesis - implies other pathways can substitute
Oncogenic stress can cause p53 to induce senesence in some contexts -until recently, senescence was considered tumour-suppressive, inhibiting proliferation of cells at risk of oncogenic activation
However, now senescent cells considered an emerging hallmark of cancer, promoting an inflammatory microenvironment that can stimulate tumourigenesis
Intial tumour suppressive benefit of arresting proliferation may be followed by tumourigenic effects through chronic inflammation
p53 can also suppress angiogenesis, migration & metastasis
Relative improtance of difference effects depends on context
Oncogenic GOF p53 mutnts can have the opposite effect to wtP53 on many of the same activities. These activities are acheived by controlling transcription of batteries of genes. Which genes are regulated depends on cell type & type of stress - induction of several protective pathways may provide failsafe protection.
ARF
1 of 3 tumour supp genes in 35kb locus that is often deleted in tumours e.g. melanoma. (bad design to have tumour suppressor genes in close proximity bc a deletion can take out all 3 at once.)
ARF & INK4a share same 2nd & 3rd exons, but these are translated in alternative reading frames to give polypeptides with no sequence similarity.
ARF & INK4a have seperate promoters & 1st exons
INK4a and INK4b genes encode p16 & p15 inhibitors of cyclin D-dependent cdk4 & 6.
Binds MDM2, inhibits its ubiquitin ligase activity & sequesters it in the nucleolus (affects ARFs localisation)
INK4a and INK4b genes encode p16 & p15 inhibitors of cyclin D-dependent cdk4 & cdk6
ARF promoter has EZF sites & is induced by oncogenic signals e.g. sustained activation of EZF after RB inactivation
ARF triggers a p53 response
ARF also has p53-independent functions, including inhibition of ribosome biogenesis