Cancer Genetics 2 Flashcards
What are the mutational processes in cancer genomics
Intrinsic mutational processes - each division inevitably results in some mistakes
Environmental and lifestyle exposures
Mutator phenotype - the more it divides due to driver mutations, the more mutations it picks up
Chemotherapy - selective for resistance
What are the mutational types in cancer genomics
Passenger mutations - mutations acquired that do not impact the function of the cell
Driver mutations - mutations that drives growth and division, escaping cell cycle mechanisms
Genetic instability which influences the gathering of more passenger and driver mutations
Chemotherapy resistance mutation
What is the genomic equivalent of predisposed and acquired mutations
Constitutional (germline) mutations
Somatic mutations - tumour specific
What is a tumour specific mutation
Tumour specific mutation = genetic variation which is present in the whole genome sequencing of the tumour but NOT the germline is considered somatically acquired
How can you identify tumour specific mutations
Need to WGS two whole genomes - to find what mutations were acquired after birth
Germline genome
Tumour genome
Where do you get germline DNA to test for tumour specific mutations
For solid tumours germline (lung, breast, ovarian) = lymphocytic DNA (blood sample)
For haematological malignancies the tumour sample is from blood and germline will be another tissue
For example fibrocytic DNA from a skin biopsy
What is a circos plot
This forms a ring of circles, each ring giving different pieces of information as seen below
What does a circos plot identify
Mutations to be sorted into passenger and driver mutations according to the gene they’re in
Tumour mutational burden
The number of somatically acquired mutations present in cancer DNA
Mutational signature
A pattern of mutation types which can give clues to the underlying mutagenic processes at work in the cancer cells
What is a mutational signature
A pattern of mutation types which can give clues to the underlying mutagenic processes at work in the cancer cells
What is a tumour mutational burden
The number of somatically acquired mutations present in cancer DNA
What are the classes of cancer genes
Oncogenes (accelerator on)
Tumour suppressor genes (cutting the brake cables)
Need to lose both copies for oncogenesis
DNA repair genes (not mending the car) – most of these are also classed as tumour suppressor gene
What are the potential tests for somatic mutations
Single driver mutations
Gene panels
Whole genome sequencing - pricy as you need to sequence two genomes (germline and somatic)
Childhood cancer
Haematological malignancies
Certain metastatic cancers
What are some examples of driver genes
Single driver mutation
BRAF V600E – Oncogene
Gene panel
Rb1 – Tumour suppressor gene
BRCA1 or BRCA2 – Tumour suppressor gene/DNA repair gene
MLH1 – Tumour suppressor gene/DNA repair gene
What is the pathogenic pathway of the BRAF V600E mutation
BRAF V600E – Oncogene
Over activation of RAS-MAPK pathway
BRAF inhibitor therapies can be given
What is the pathogenic pathway of RB1 mutations
Rb1 – Tumour suppressor gene
Control of cell cycle, prevents activation of replication
Thus failure = replication
What is the pathogenic pathway of BRCA1/2 mutations
BRCA1 or BRCA2 – Tumour suppressor gene/DNA repair gene
Failure of homologous recombination - can’t do HDR
Damaged chromosomes/ds-breaks/replication forks not repaired
What is the pathogenic pathway of MLH1 mutations
MLH1 – Tumour suppressor gene/DNA repair gene
Can have epigenetic suppression: (hyper)methylation of promotor region
Failure of mismatch repair
What are passenger mutations
Don’t in theory contribute to oncogenesis
However, high mutational burden may lead to a more unstable mutagenic phenotype
Sometimes it may be hard to tell if a variant in a cancer gene is a driver mutation or is actually a benign variant not impacting on the function of the gene
Why should you undertake germline testing after identifying a driver mutation
If we only undertake driver mutation testing or large panel sequencing without paired germline we do not know if a variant is somatic only or may also be present in the germline
If it was in germline it can affect relatives, so it may be needed to offer germline testing
When do you offer a germline test
If the somatic mutation is a Class 4/5 (likely pathogenic) variant in a known cancer susceptibility gene
VAF >30% (variant allele frequency - how many reads has the variant been seen in)
Each cancer biopsy may have different driver mutations, but if it is in 50% then it suggests that most cells have it as it was the original germline genome
Need to consider difference between on-tumour and off-tumour findings
Mutations not usually found in that type of cancer e.g. BRCA mutation in LUNG cancer
What happens if you cannot find a driver mutation
We don’t always find a driver mutation
We don’t know the driver mutations for every cancer type
Cancer genomes can have huge numbers of mutations
We can look at other information from the cancer genome to help guide management
What is tumour mutational burden
Tumour mutational burden - number of specific types of mutations that have been somatically acquired and found in tumour DNA
Refers to the number of SNP or the overall mutational burden
High mutational burden = genome is very different to germline, and looks different to normal cells
What treatments are effective against tumours with high mutational burden
Immunotherapy agents have been shown to have clinical efficacy in tumours with high mutational burden
Help immune system see that these cells are so different
What may be a cause of high mutational burden
A high mutational burden can be caused by failure of DNA repair pathways and often occurs with mismatch repair deficiency or proof-reading polymerase deficiency
What are immunotherapies
Normally, activated lymphocytes/T-cells would recognise these cells with high mutational burden
However, PDL-1 hides these abnormal tumour cells from the immune system
Immunotherapies act against the PDL-1 pathway allowing T-cells to recognise the cancer cells
This can be a therapeutic strategy across cancers with high mutational burden
What is mutational profiling
Identification of mutational signatures to infer the underlying cause of a cancer
What are some examples of DNA mutagens
Different causes of DNA mutagens cause different types of mutations
Internal - reactive oxygen species, ineffective DNA repair mechanisms
External - UV light, ionising radiation, cigarette smoke, chemical consumptions
What are mutagenic processes
Each of our cells is subject to multiple mutagenic processes
The exposure to a mutagenic process can be of differing lengths
What do the mutational signatures show in relation to mutagenic processes
Each cell will contain a “pattern” of mutations which reflect the
Type of mutagenic process
Length of the exposure to the mutagenic process
How do you measure the type of mutation
SNP - measuring number of SNP and the context
What is the base preceding and subsequent to the SNP - does an SNP associate with a specific triplet
There are only 6 different types of base substitutions
C>A and G>T, C>G and G>C, T>A and A>T, T>G and A>C
You find that in a group of patients that HER2+ve breast cancer was due to a C>T change, this was found on a heatmap this more likely occurs when a G follows what may this mean
Occurs in CpG pairs
The process of mutation may be involved in methylation
What is non-negative matrix factorisation
Mathematic calculation measuring the proportion of occurrence of each feature
E.g. most people have eyes taking up 10% of their face
OR… cancers have X% of Y mutation = signature
What is mutational signature 7
The major mutation type is C>T
Commonly occurs when C or T is preceding the SNP
Showing predominance of TC>TT and CC>CT mutation
Associated with cancers in which UV light exposure is a known risk factor
What tumour types present with signature 7
Melanoma
Skin cancer
Cancers of the lip
Oral squamous cancers
All associated with UV light exposure risk
Why does UV light cause TC>TT / CC>CT mutations in signature 7
UV light mutates DNA in a specific way causing dinucleotide mutations at dipyrimidines (C and T’s)
Additionally, Signature 7 exhibits a strong transcriptional strand-bias indicating that mutations occur at pyrimidines by formation of pyrimidine-pyrimidine photodimers
These mutations are being repaired by transcription-coupled nucleotide excision repair
If a circos plot has many internal lines indicating structural rearrangements is this likely to be a germline or somatic mutation
Germline
This indicates many ds-breaks which leads to more rearrangement due to loss of homologous recombination - showing signature 3
In what cancers is homologous recombination deficiency - signature 3 - found
Elevated numbers of large (longer than 3bp) insertions and deletions
Found in breast, ovarian and pancreatic cancers
What are potential treatments for breast cancer caused by germline mutations
Treated with various drugs and platinum chemotherapy - carboplatin, as well as paclitaxel, bevacizumab
Surgery was performed
Platinum-sensitive on each occasion
Generates interstrand cross-links stopping replication
Requires intact HR pathways to repair, but this is lost thus the tumour cells die
BRCA1 + BRCA2-deficient cells therefore highly sensitive to platinum chemotherapy
Why are BRCA1/2 mutations sensitive to platinum therapy
Generates interstrand cross-links stopping replication
Requires intact HR pathways to repair, but this is lost thus the tumour cells die
If BRCA1/2 loss = loss of HDR pathways, how do these cells survive
Poly-ADP-ribose polymerase (PARP) - enzyme critical to DNA single strand break repair via BER pathway
Activated by DNA damage + recruits proteins to site of damage to create a repair complex
PARP inhibitors stop this thus used to treat BRCA1/2 cancers to stop all cell repair
What do PARP inhivitors do
PARP Inhibitors - prevents repair, and stops tumour cells from dividing (synthetic lethality)
Offer individualised treatment for ovarian cancer in women with germline BRCA mutations/tumours with somatic loss of BRCA
What are DNA repair deficiencies
Accumulation of DNA damage and activation of cellular signalling
Mismatch repair - short insertions and deletion
POLE/POLD1 - point mutations
C>A in context of TCT
Homologous recombination - larger indels
Aneuploidy - CNV’s - gene dosage effects
What are the immunosuppressive effects of DNA repair deficiencies
Increased neoantigens = MHC I presentation = T cell activation
Cytosolic DNA = STING pathway = Type I IFN response
STING agonists may be used to treat this
Upregulation of PDL-1
Anti-PD1/PD-L1 agents can be used
Which cancers are related to mismatch repair deficiency
Colorectal cancers
What genes are involved in mismatch repair
MLH1, MSH2, MSH6, PMS2 and EPCAM
How can you test for mismatch repair deficiency
MSI (microsatellite instability)/MMR (mismatch repair) IHC – loss of MSH2 and MSH6
WGS
What may be seen in a circos plot showing mismatch repair deficiency
Signature 6 - sign of mismatch repair deficiency (MMR)
Circos plots have thick bars = many SNP’s = high mutational burden
What drug can be used to target DNA repair/mismatch repair deficiencies
Anti-PD1/PD-L1 agents can be used, pembroluzimab
What are endocrine tumour syndromes
Genetic predisposition to developing tumours effecting the endocrine glands
Includes both endocrine and non-endocrine tumours too
‘Benign’ and/or malignant
Benign tumours can be a cause of morbidity via the symptoms they cause
Hormone secreting/non-secretory
What are the symptoms of endocrine tumour syndromes
Overproduction of hormones
Mass effect of tumour - pressing on adjacent structures
What are multiple endocrine neoplasia syndromes
Presence of tumours involving two or more endocrine glands in one individual
Autosomal dominant
Challenging to diagnose, and classification can be confusing
MEN1
MEN2 - MEN2A, MEN2B (aka MEN3), FMTC
MEN4
What does the MEN1 gene do
MEN1 is a tumour suppressor gene due to inactivating mutations in MEN1 gene
Protein product of MEN1 is Menin which is involved in the regulation of transcription
It mediates between transcription factors and histone modifiers to facilitate transcription
Loss can disrupt downstream signalling pathways involved in regulation of cell growth and proliferation
What does loss of MEN1 gene lead to
Loss can disrupt downstream signalling pathways involved in regulation of cell growth and proliferation
How penetrant is MEN1
Highly penetrant - 50% by age 20 years, 95% by age 40 years
Variable expressivity even within families
What systems are affected by MEN1 mutations
Parathyroid - hyperplasia thus hyperparathyroidism
Pituitary - pituitary adenomas
Pancreas - duodeno-pancreatic neuroendocrine tumours (DP-NETS)
What are the parathyroid glands
Four parathyroid glands sitting posterior of the thyroid gland, important in regulating blood calcium
Parathyroid hormone signals bones to release calcium, signals kidneys to prevent release of calcium and increase vitamin D and signals intestines to absorb more calcium
Multiglandular involvement
Turned off via negative feedback - increased calcium
How is the parathyroid hormones deactivated
Turned off via negative feedback (increased calcium)
How are parathyroid adenomas tested
Uptake of radioisotope
What is hyperparathyroidism
Constant hormone secretion > Hypercalcaemia
What symptoms occur as a result of hyperparathyroidism
Hyperparathyroidism = constant hormone secretion
Hypercalcaemia Bones (fracture), stones (kidney), groans (constipation) and psychic moans (confusion/depression)’
Occurs in 95% individuals with MEN1
Only 1-2% of all hyperparathyroidism is due to MEN1, consider if onset <45 years
Does hypo or hyperparathyroidism affect individuals with MEN1
Occurs in 95% individuals with MEN1
Only 1-2% of all hyperparathyroidism is due to MEN1, consider if onset <45 years
How is hyperparathyroidism treated
Parathyroidectomy
What are the three types of anterior pituitary adenomas
Prolactinomas (60%)
Somatotrophinomas (20%)
Corticotrophinomas and non-functioning tumours (<15%)
What are the symptoms of pituitary adenomas
Disrupt hormone secretion
Prolactinoma
Secretes prolactin = galactorrhoea + amenorrhoea
Somatotrophinoma
Secretes growth hormone = gigantism (all bones, children)/acromegaly (limb and face bones, adults)
Corticotrophinoma
Secretes ACTH > cortisol = Cushing’s disease
Mass effect
Headaches
Compression of the optic chiasm (‘2’ on diagram)
Bitemporal hemianopia (‘tunnel vision’)
What is a mass effect and what is it caused by
Pituitary adenoma
Headaches
Compression of the optic chiasm (‘2’ on diagram)
Bitemporal hemianopia (‘tunnel vision’)
What are pancreatic tumours
Tumours of gastro-entero-pancreatic tract (stomach, duodenum, pancreas, and intestinal tract)
What are the types of pancreatic tumours
Gastrinoma - duodenal, metastatic potential, peptic ulcer disease
Insulinomas - hypoglycaemia
Glucagonoma - hyperglycaemia, anorexia, glossitis, anaemia, diarrhoea, venous thrombosis, rash
VIPoma - diarrhoea
Non-secreting tumours
What are the suveillance options for individuals with MEN1
Predictive genetic testing from age 10
Surveillance (identify disease at asymptomatic/early stage)
From age 10 - predictive testing, annual pituitary hormones, gastric hormones, Ca, PTH
From age 16 - abdominal imaging (3-yearly), MRI brain (3-yearly)
What is MEN2
Autosomal dominant, all caused by inactivating mutations in the RET proto-oncogene
Highly penetrant
Prevalence 1/30,000
What genes cause MEN2
MEN2A (60-90%)
Familial Medullary Thyroid cancer (FMTC) (5-35%)
FMTC likely same as MEN2A but with reduced penetrance of hyperparathyroidism and phaeo
MEN2B (5%)
What symptoms occur as a result of MEN2A
Medullary thyroid cancer (90-95%)
Early adulthood onset
Parathyroid hyperplasia (20-30%)
Phaeochromocytoma (20-30%) - tumours of the adrenal medulla, can be benign
Often bilateral
What are the symptoms of familial medullary thyroid cancer
Medullary thyroid cancer - middle age
No other features
How can you tell MEN2A and familial medullary thyroid cancer apart
FMTC = only medullary thyroid cancer, middle age not early and no other symptoms
What are the symptoms of MEN2B
Medullary thyroid cancer - up to 100%
Early childhood onset
Phaeochromocytomas (50%)
Mucosal neuromas of the lips and tongue - bumps and lumps
Marfanoid habitus - similar characteristics of Marfan syndrome
Tall, skinny, long arm span
Medullated corneal nerve fibres
Intestinal ganglioneuromatosis
If you had a patient who was tall, skinny and had long arm span, what could this mean
Marfan
MEN2B
Which is more severe MEN2A or MEN2B
MEN2B
What is medullary thyroid cancer
Associated with C cell hyperplasia
These are calcitonin producing cells
May see ↑ calcitonin
Often multifocal or bilateral
Symptoms:
Neck mass or pain
Diarrhoea
Metastasizes early
What are the surveillance options for MEN2A/B FMTC and medullary thyroid cancer
Offer predictive testing in childhood
Risk-reducing thyroidectomy
Timing of surgery according to ATA Risk classification of pathogenic variant
Level D – highest risk (1st year of life)
Level A – lowest risk (can delay beyond 5 years)
Yearly surveillance
Clinical assessment
Calcitonin and calcium levels
Metadrenalines (plasma/urine) - measuring of hormones
Ultrasound of neck (unless post-thyroidectomy)
What are the yearly surveillance options for MEN2A/B FMTC and medullary thyroid cancer
Clinical assessment
Calcitonin and calcium levels
Metadrenalines (plasma/urine) - measuring of hormones
Ultrasound of neck (unless post-thyroidectomy)
What is a phaeochromocytoma
Tumour of adrenal gland
These are organs which sit above the kidneys
What is a tumour of adrenal gland called
Phaeochromocytoma
What is a paraganglioma
Tumour of nerve cells
May be called ‘extra-adrenal phaeos’
What is a tumour of the nerve cells called
Paragangliomas
May be called ‘extra-adrenal phaeos’
Where are the adrenal medulla and ganglia of sympathetic nervous system derived from
Adrenal medulla and ganglia of sympathetic nervous system are both neural crest derivatives
What do the adrenal medulla and ganglia of sympathetic nervous system do
Synthesise and secrete catecholamines (adrenaline, noradrenaline)
What does a pheochromocytoma secrete
Catecholamine
What are the symptoms of pheochromocytoma
Episodic symptoms – headaches, sweating, palpitations, tremor, hypertension & arrhythmias
Can be life-threatening
What are paragangliomas derived from and where are they found
Rare tumours derived from neural tissues
From within autonomic nervous system
Sympathetic NS often retroperitoneal
Parasympathetic NS often adjacent to aortic arch, neck, skull base
May be hormone secreting (catecholamines) or cause mass effect
What are genetic causes of phaeochromocytoma
RET gene -MEN2A/MEN2B
SDHB/D/A/C SDHAF2 MAX TMEM127 Familial paraganglioma
VHL
NF1
What is familial phaeochromocytoma and paraganglioma syndrome (PPGL) caused by
SDHB, SDHD, SDHA, SDHAF2, MAX, TMEM127
SDHB risk of malignancy +/- renal cancer
Autosomal dominant
What is the unique genetic feature of PPGL
Parent of origin effect in SDHD, SDHAF2 and MAX
Disease only seen after PATERNAL transmission
What are the screening options for PPGL
Age to commence screening varies per gene
Clinical evaluation
Biochemistry (urine/plasma metadrenalines)
Imaging of neck, thorax, abdomen 2-5 yearly
What is another name for familial isolated pituitary adenomas
Pituitary adenoma predisposition
What are the causes of familial isolated pituitary adenomas
Mutations in aryl hydrocarbon receptor interacting protein (AIP) gene
Autosomal dominant
What tumours are found as a result of familial isolated pituitary adenomas
Variability in tumour type within different family members
Often macroadenomas (>10mm)
Type of pituitary adenoma impacts the hormone involved thus the symptoms
There may also be a mass effect and cause deficiencies of other pituitary hormones
What are the different types of pituitary adenoma
Prolactinoma
Secretes prolactin = galactorrhoea + amenorrhoea
Somatotrophinoma
Secretes growth hormone = gigantism (all bones, children)/acromegaly (limb and face bones, adults)
Corticotrophinoma
Secretes ACTH > cortisol = Cushing’s disease
Somatomammotropinoma - growth homrone and proclactin
Nonfunctioning - none
Thyrotropinoma - TSH > hyperthyroidism
What are the management and surveillance options with endocrine tumour syndromes
Medical therapy e.g., somatostatin analogues, growth hormone receptor antagonists, dopamine agonists
Surgery, +/- radiotherapy
Surveillance
Annual clinical assessment
Annual pituitary function tests
Pituitary imaging
What is Von Hippel Lindau Syndrome caused by
Autosomal dominant Highly penetrant (age-dependent, 98% penetrance by age 60) , with mean diagnosis at 25 years Variability in phenotype within families
Caused by inactivating mutations in VHL tumour suppressor gene
What is the inheritance pattern of Von Hippel Lindau Syndrome
Autosomal dominant Highly penetrant (age-dependent, 98% penetrance by age 60) , with mean diagnosis at 25 years Variability in phenotype within families
What are the tumours associated with Von Hippel Lindau Syndrome (VHL)
Wide range of tumours, most commonly retinal angiomas and cerebellar haemangioblastomas
Cysts in kidneys, pancreas and epididymis
Suspect if >1 VHL associated tumour or family history
What is the normal and abnormal function of VHL
VHL protein complex ubiquitylates α-subunits of HIF transcription factors = target for proteolysis
Absence of VHL protein complex causes stabilisation of HIF α- subunits
As they don’t undergo proteolysis HIF transcription factors activate downstream growth factors including VEGF
What are the surveillance options for VHL
From age 5 - annual ophthalmology
From age 8 - annual metanephrines (plasma/24h urinary)
From age 16
Annual clinical neurological examination and MRI/US abdomen
MRI brain every 1-3 years, MRI spine if neurological symptoms or signs
Annual audiological questionnaire
