Genomic Basis of Cancer Predisposition Flashcards
How frequent are Cancer Predisposition Genes with germline mutations?
Rare
Cancer predisposition genes confer
high or moderate risks of cancer (> 2 fold relative risks)
What is the penetrance of Cancer Predisposition Genes?
At least 5% of individuals with the relevant mutations develop cancer
Majority of mutations in cancer predisposition genes result in what?
Loss of function within cell
What percentage of cancers are due to cancer predisposition genes with germline mutations?
What is this equivalent to?
Why can this be considered an underestimate?
3%
More than 300,000 cancers per year worldwide
Not all genes have been identified.
The contribution of predisposition genes with germline mutations to individual cancers is highly variable.
What are some examples?
Germline mutations in RB1 frequent in retinoblastoma
Adult cancers:
15% of ovarian cancers
20% of medullary thyroid cancers
30% of phaeochromocytomas
What is Retinoblastoma?
Rare childhood cancer
60% cases sporadic (unilateral)
40% cases inherited (bilateral, younger onset)
What mutated gene causes Retinoblastoma?
RB1
What is the first tumour suppressor gene cloned?
How is this inherited and with what percentage penetrance?
RB1- Binds and inactivates the
E2F (repressing transcription of genes required for S phase)
Autosomal dominant inheritance with 90% penetrance.
What is the first way in which the majority of cancer predisposition genes been discovered?
What is used in conjunction with this?
Using this technique what genes were discovered?
- Linkage analysis allows tracking of disease associated genomic markers in families (59 genes identified this way).
Microsatellites are a class of genetic polymorphism commonly used for mapping, linkage analysis and to trace inheritance patterns.
BRCA1, BRCA2 discovered with this method
What is the second method by which cancer predisposition genes may be discovered?
When is this technique unsuccessful and successful?
What genes were discovered using this method?
Candidate-based strategies
Less successful particularly those that are somatically mutated in cancers (only 12 identified this way).
More success if look at candidate genes that function in similar pathways to known cancer predisposition genes.
eg BRIP, PALB2
mutations confer a 2-3 fold increased risk of breast cancer
Next generation sequencing allows genome wide mutational analysis but is unsuccessful in the discovery of candidate predisposition genes
True or false
False
It is successful
Describe the inheritance patterns for cancer predisposition genes
Most are autosomal dominant
28 autosomal recessive
4 X-linked
1 Y-linked
Bi- allelic mutations often cause a more severe phenotype
–e.g. biallelic BRCA2, PALB2, MLH1 mutation carriers have a high risk of childhood cancer, whereas monoallelic mutation carriers have an increased risk of adult cancers.
What are the mechanisms of action for cancer predisposition genes?
Most are tumour suppressor genes ie mutations cause loss of function and behave like classic tumour suppressor genes
Some also have dominant loss of function mechanisms (haplo-insufficiency) ie gene needs both alleles to be functional in order to express the wild type.
Gain-of-function mutations – generally encode kinases and become constitutively activated by the cancer predisposing mutation.
For many genes the phenotype and the cancer risk is modified by other genetic and non genetic factors
What is an example of a heritable gain of function cancer predisposition gene? What are the molecular mechanisms?
What does this predispose an individual to?
RET
Modifying variants that are not oncogenic alone but can increase oncogenicity in combination with other mutations.
Point mutations at specific sites lead to constitutive activation, either by promoting dimerization or by altering conformation and favouring kinase activity.
Multiple endocrine neoplasia type 2
Some cancer genes predispose carriers to specific histological subtypes of a cancer.
What are examples?
BRCA1 is particularly associated with triple-negative breast cancer and serous ovarian cancer
CDH1 is particularly associated with lobular breast cancer and diffuse gastric cancer
Can some cancer genes predispose carriers to multiple cancers?
Yes
What is the most common syndrome associated with colorectal cancer?
Familial adenomatous polyposis (FAP)
What is Familial adenomatous polyposis (FAP) caused by?
What is it characterised by?
Mutation in APC gene
1000s polyps throughout colon
The inheritance pattern of Familial adenomatous polyposis (FAP) is…
Is there an exception to this?
autosomal dominant
Yes, 30% de novo mutation rate. Therefore germline mutations can occur de novo thus some patients with such cpgs may not have a strong family history of cancer
What can influence the phenotype in Familial adenomatous polyposis (FAP)?
Site of the mutation
What is the most common of the inherited colon cancer susceptibility syndromes?
What is the mean age of diagnosis?
What other cancers is this associated with?
Lynch Syndrome
47
Endometrial cancer is the most common, occurring in up to 70% of women who are gene carriers.
Ovarian, gastric, small bowel, renal pelvis, ureter, pancreatic, and brain cancers
Lynch Syndrome caused by a mutation in what gene?
DNA mismatch repair (MMR) gene
Describe DNA mismatch repair (MMR) genes
MLH-1, MSH-2, MSH-6
MMR system recognizes base-pair mismatches that occur during DNA replication and repairs them.
DNA mismatches commonly occur in repetitive sequences called microsatellites.
Loss of MMR leads to ‘microsatellite instability’, and an increased rate of mutation
What are high risk mutations in breast cancer?
What do they confer?
What do they account for?
BRCA1, BRCA2, TP53, PTEN
A 10-20 fold increased risk of breast cancer
Account for large breast cancer families (few families with 2 or 3 cases of breast cancer), account for only approx 20% of familial breast cancer
What are moderate risk mutations in breast cancer?
What do they confer?
CHEK2, ATM, BRIP, PALB2
Confer a 2-3 fold increased risk of breast cancer
In what fashion are BRCA1 and BRCA2 mutations inherited?
An autosomal dominant fashion, but act recessively on the cellular level as tumor suppressor genes involved in double-stranded DNA (dsDNA) break repair
Mutations and rearrangements or deletions in BRCA1 and BRCA2 explain what percentage of familial breast cancers?
15%
BRCA1-associated breast cancer is more often…
oestrogen- receptor (ER) negative
Why is it more difficult to identify a cohort of women at high risk of BRCA2 that must undergo screening?
BRCA2-associated breast cancers have the same distribution of cancer subtypes as found sporadically.
Why are risks associated with Breast Cancer predisposition genes complex?
- A specific mutation can confer different risks of developing a particular cancer in different contexts- Although most protein truncating mutations in BRCA2 result in nonsense mediated RNA decay mutations in the centre of the gene have higher risk of ovarian compared to breast cancer
- Genetic & non genetic modifying factors
- Risk is higher if mutations occurs in a carrier with strong family history (80% vs 45% lifetime risk)
What are the clinical applications of genetics in cancer?
- Influence treatment
breast cancer patients with BRCA1 & 2 mutations respond to platinum-based chemotherapies & PARP inhibitors
Cancer patients with lynch syndrome /
BRCA1 & 2 mutations have high mutational load and more stromal-infiltrating immune cells - may respond well to immunotherapy
- Screening and prevention
Provide information about cancer risks to relatives.
If identified can offer screening or risk-reducing measures
- Screening – colonoscopy for colorectal cancer, MRI +/- mammograms for breast cancer
- risk-reducing surgery – mastectomy for BRCA1 & 2 carriers, removal of colon in APC carriers, removal of stomach in CDH1 carriers
CHEK2 and PALB2 are examples of what?
Genes with moderate penetrance mutations
CHEK2*1100delC carriers is found in…
controls (0.5%),
in patients with breast cancer (1.3%)
in patients with breast cancer from familial studies (3.0%)
The odds ratio for developing CHEK2*1100delC is higher for those who are oestrogen positive
True or false
True
What is a partner and localizer of BRCA2
PALB2
Similar frequency to that seen among patients with BRCA2 mutations, 74% with what mutated gene are estrogen receptor positive?
PALB2
Risk of breast cancer arising due to a PALB2 mutation is higher for those with a family history
True or false
True
Moderate-penetrance mutations have been estimated to be responsible for less than 3% of familial breast cancer
What does this imply and mean in relation to recent technologies?
The low overall contribution to hereditary breast cancer implies that widespread testing is unlikely to be cost- effective.
HOWEVER using next gen sequencing panels these genes can be sequenced relatively easily at little extra cost
Breast Cancer has a significant genetic component - If you have a first degree relative with breast cancer you are 1.8 times more likely to develop breast cancer compared to general population
But high & moderate risk mutations collectively account for only approx
30% of familial breast cancer
Similar for other complex disease
What accounts for the missing heritability?
Single nucleotide polymorphisms
Consequence of a SNP within coding region of gene
1.Nothing
e.g.CGG & CGA code for same amino acid
(Arg)
- Change in amino acid e.g. GGA (Gly) to GAA (Glu) MAY have biological consequences
- Premature stop codon
e.g (TAG/TAA/TGA) protein significantly
changed = mutation
Many SNPs occur in non–coding regions of the genome
What is susceptibility to a complex genetic inheritance conferred by?
What is needed to confer a range of susceptibilities in the population?
A large number polymorphisms within genes, each conferring a small risk
Combine all polymorphisms
How is complex genetic inheritance best studied?
Using association studies (case- control studies) rather than family linkage studies
Candidate gene approach
» requires prior knowledge
» Screening of DNA repair pathway identified inactivating mutations in 4 genes:CHEK2, ATM, BRIP, PALB2 (moderate penetrance)
Genome Wide Association Study (GWAS)
» Doesn’t rely on current knowledge
There are 10 million SNPs in the human genome and many of these SNPs are inherited together or ‘tag’ each other.
Why is this advantageous?
Can examine by analysing 500,000 tag SNPs.
All can analysed on a single microarray
Allows us to perform Genome Wide Association Studies (GWAS) rather
than candidate gene association studies
How many independent common variants associated with breast- cancer risk have been identified?
These variants typically have minor allele frequencies higher than…
All confer risks that are less than…
Almost all these polymorphisms occur in…
Similarly for other solid tumours such as…
313
1%
1.5 times as high as those in the general population
noncoding sequences
colorectal cancer, ovarian cancer etc
Single SNPs not useful for risk prediction
What is of clinical value instead?
Combined score based on genotypes of a large number of loci can have predictive value (polygenic risk score) e.g
In UK, 56 of 10 million women carry two copies of the low-risk allele for each SNP - Relative risk of breast cancer of 0.43 equivalent to a 4.2% lifetime risk (compared with a population average of 9.4%)
In UK, 7 of 10 million women carry two copies of the risk allele for each SNP - have a the relative risk of breast cancer of 2.7 equivalent to a 23% lifetime risk
Including BC-associated SNPs in risk assessment can provide more accurate risk prediction than family history alone. (Genetics in Medicine 2016 doi:10.1038/gim.2016.43)
What are the benefits of accurately assessing risk?
Can personalise screening for those most at risk
Better than a screening programme based on age alone.
Also detect cancers in younger women.
Enable us to offer chemoprevention to those who are most likely to benefit.
In those with absolute risk with high risk germ-line mutations, what is also inherited?
Low risk predisposition SNPs
What is an example of the use of a polygenic risk score in breast cancer?
Using a PRS of 94 breast-cancer- and 18 ovarian-cancer-modifying SNPs B
BRCA1-mutation carriers:
90th percentile of the PRS have an absolute risk of 75% of developing breast cancer by age 80
10th percentile have a risk of 56%
BRCA2-mutation carriers:
ovarian cancer risk is 19% by age 80 for women at the 90th percentile of the PRS
those at the 10th percentile have a risk of 6%.
How can the polygenic risk score be of clinical use?
May alter the uptake or timing of prophylactic surgery and other clinical interventions.
Personalized prediction in BRCA1- and BRCA2-mutation carriers should also include information on reproductive and family history, mammographic density, lifestyle, and environmental factors, and the position of the mutation
Why is Risk Reduction currently relatively crude?
such as prophylactic surgeries. This is effective but have significant morbidity
Confer significant long-term morbidity and can generate medical and psychological sequelae.
What tool has been used in precision cancer prevention strategies?
Multigene panel testing has identified families affected by unexpected mutations in high-penetrance genes
e.g., colon cancer patients with BRCA1 /2 mutations and breast cancer patients with Lynch syndrome),
What is a caveat of precision cancer prevention strategies?
What is needed?
Spectrum of cancer risk conferred wider and more complicated
Prevention strategies rely on the assumption that all carriers are at uniformly high cancer risks, resulting in many healthy mutation carriers being recommended to undergo prophylactic radical risk- reducing surgery.
Need to understand how lifestyle, environment and rare and common germline changes influence risk of specific malignancies so can offer more precise interventions for reducing cancer risk.
How have mouse models been used to improve the effectiveness of cancer prevention strategies?
Mouse model of Lynch syndrome demonstrated that the short chain fatty acid butyrate generated by gut microbiota from complex carbohydrates, can act as an oncometabolite by promoting the proliferation of cancer- initiated intestinal epithelial cells (Belcheva et al., 2014).
Altering the gut microbiome or reducing dietary carbohydrate lowers intestinal carcinogenesis in MMR-deficient mice (but not MMR-proficient mice).
COX-2 inhibitors can reduce intestinal adenoma burden
In APCMin/+ mice, a model of familial adenomatous polyposis COX-2 inhibitors induce alterations in the gut microbiome reducing intestinal crypt stem cell proliferation and adenoma formation (Montrose et al., 2016).
Suggest that there are extrinsic factors (antibiotic, diet, or microbial reprogramming), which could theoretically be exploited to facilitate cancer prevention.
How can cancer be prevented through chemo prevention?
- NSAIDs in Lynch Syndrome
- Tamoxifen reduces contralateral breast cancer in BRCA1 carriers
- Denosumab used to treat osteoporosis and bone metastasis – potent inhibitor of RANK L (important in development of basal like breast cancers which are common in BRCA1). Trial investigating if denosumab can reduce risk of developing triple negative breast cancer/basal breast cancer in those who are known to have a BRCA1 mutation
Why is pancreatic cancer often lethal?
No effective prevention, early detection, or therapy,
Why might performing multigene germline testing on all newly diagnosed pancreatic cancer may very well be the most effective approach for identifying high-risk families.
What might also help?
Recent data suggest >15% of individuals with pancreatic cancer have germline mutations in cancer predisposition genes ( BRCA1, BRCA2, PALB2, the MMR genes, ATM, CDKN2A, TP53)
Imaging people with high-penetrance mutations maybe help detect it early so treatable
Why is Precision Oncology needed?
Previously cancer patient treatment based on evidence from large clinical trials
Cancers are unique
Patients are unique
Targeted Therapies for Breast Cancer historically based on the expression of what receptors?
Hormone receptors
- Oestrogen Receptor (ER)
- Progesterone Receptor (PR)
Her2 ( erbB2) receptor
Receptors associated with breast cancer are prognostic
True or false
True
What is an example of a receptor associated with breast cancer that is predictive?
Oestrogen Receptor (ER) predictive of response to oestrogen blockers: Tamoxifen Aromatase Inhibitors
What is Trastuzumab (Herceptin) ?
First humanised monoclonal antibody
for the treatment of breast cancer
Targets HER2 oncoprotein
High affinity and specificity
95% human, 5% murine
- decreased potential for immunogenicity
- increased potential for recruiting
immune-effector mechanisms
What does personalised breast cancer care include?
Gene expression profiling to predict benefit of chemotherapy
High-throughput tumor DNA sequencing to identify actionable mutations
- Help select correct patients for new therapeutic interventions eg PIK3CA mutations.
- Her2 missense mutations – respond to tyrosine kinase inhibitors eg neratinib
- ESR1 mutations predicts resistance to endocrine treatment
Liquid biopsy samples to produce near real time snapshots of tumour mutational profiles.
What is the Oncotype DX test?
A 21 gene assay test with 16 outcome related genes and 5 references genes
How do levels of gene expression detected by the Oncotype Dx test conclude determine Recurrence Score?
Higher expression levels of
“favorable” genes = ↓ recurrence score
Higher expression levels of
“unfavorable” genes = ↑ RS
Cutoff points chosen based on Results of NSABP trial B-20
A risk score is calculated from 0 -100
Once PIK3CA mutation validated what is the clinical impact?
Eligible for a number of clinical trials with PIK3CA targeted drugs
As lower mutational burden, unlikely that any immunotherapy trials will be of benefit
Patient does not have a high-risk inherited breast cancer gene mutation
