Session 6 Flashcards
What is the most common cancer in women in the UK?
Breast cancer (30% of new cancer in females) and lifetime risk of 1 in 8
What factors would prompt higher suspicion of hereditary breast cancer?
What models can be used to assess likelihood of BRCA1/BRCA2?
Early onset, two or more breast primaries, breast and ovarian in a single patient, fhx of Breast and ovarian cancers, Ashkenasi Jewish population, male breast cancer
BRCAPRO, Myriad II and BOADICEA
What is triple negative breast cancer?
Lack of estrogen or progesterone receptors and also reduced or lack of HER2 expression
What two genes are most common cause of AD hereditary breast cancer?
What percentage of HBOC cases do they account for?
What is lifetime cancer risk?
BRCA1 and BRCA2
66% and 34% respectively
BRCA1 - of 46-87% for BC, 39-63% for ovarian cancer, 0.95% for male cancer
BRCA2 - 38-84% for BC, 16.5-27% for ovarian cancer, 20% for prostate cancer, 8.9% for male BC
What is BRCA1?
What is its function?
Tumour suppressor gene on chromosome 17 encodes BReast CAncer gene 1
Forms complexes with BARD1 for ubiquiton ligase function.
Interacts with proteins involved in controlling cell cycle. LoF BRCA1 variants cause defects in DNA repair, defects in transcription, abnormal centrosome duplication, defective G2/M cell cycle checkpoint regulation, impaired spindle checkpoint, and chromosome damage.
What is BRCA2?
What is its function?
Tumour suppressor gene on chromosome 13 encodes BReast CAncer gene 2
Interacts with RAD51 to mediate Homologous recombination DNA repair - particularly important during DNA synthesis in late G1 and S phase
What types of variants are observed in BRCA1/BRCA2?
Loss of function - mainly nonsense and frameshift. Also missense and structural (up to 10%)
What are three Ashkenazi Jewish founder variants and what is carrier frequency?
c.68_69delAG and c.5266dupC in BRCA1 and c.5946delT in BRCA2
1 in 40 people
How can BRCA1/2 status be used in guiding treatment?
Most are HER-2 negative so anti-HER2 treatments not advised
High percentage of BRCA2 are are oestrogen receptor (OR)-positive so can be treated with an oestrogen antagonist (e.g. Tamoxifen) - reduces risk by up to 50%
Use of PARP inhibitors - PARP-1 (poly-(ADP ribose) polymerase-1 enzyme repairs single-strand DNA breaks by base-excision repair. In BRCA1 and BRCA2 null cells, double-strand breaks cannot be repaired and thus PARP inhibition leads to apoptosis
Which other inherited cancer syndromes have an association with increased risk of Breast cancer?
Li-Fraumeni syndrome - TP53
Peutz-Jeghers syndrome - STK11
Cowden Syndrome - PTEN
Lobular breast cancer - CDH1
Neurofibromatosis type I – NF1
Ataxia telangiectasia - ATM
Li-Fraumeni syndrome type 2 - CHEK2 (one specific variant)
What third gene is now considered to be most common cause of AR hereditary breast cancer?
PALB2
What is a carcinoma?
What are the common subtypes?
Cancer that develops from epithelial cells
Adenocarcinoma - Glandular origin
Hepatocellular - form of adenocarcinoma seen in liver
Renal Cell
Squamous Cell - Squamous cell in the skin/lining of the digestive tract
Where do Renal Cell Carcinomas arise?
What are the two main types?
What are the symptoms?
the proximal tubular epithelium
clear cell and papillary renal cell carcinoma
haematuria (blood in the urine), loin pain, malaise, anorexia, weight loss, pyrexia, anaemia and hypertension
What are two most common genetic alteration in clear cell carcinoma?
What other genetic syndromes are associated with clear cell carcinoma?
Chromosome 3p deletion and inactivation of the VHL suppressor gene (Von Hippel-Lindau syndrome)
Birt-Hogg-Dubé syndrome, Tuberous sclerosis complex, Hereditary Paraganglioma, BAP1 Tumour Predisposition Syndrome
What is Von Hippel-Lindau syndrome?
Autosomal dominant Loss of Function variants in the VHL tumour suppressor chromosome 3. Involved in HIF regulation- which causes cell division and blood vessels formation in low oxygen.
Malignant RCC
Haemangioblastomas
Phaeochromocytomas
Renal cysts
What is Tuberous sclerosis complex?
Autosomal Dominant LoF variants in TSC1 (Chr 9) or TSC2 (Chr 16)
Numerous noncancerous (benign) tumours in multiple tissues (including kidneys). Variable severity but also causes dev delay
What is Hereditary Paraganglioma?
What is interesting about the inheritance?
Autosomal Dominant loss of function variants in subunits of the succinate dehydrogenase complex (which is involved in the Krebs cycle)
Noncancerous (benign) tumours in paraganglia = paraganglioma, AKA pheochromocytoma in the adrenal glands. Increased risk of RCC.
SDHAF2 and SDHD only paternally inherited
What is BAP1 Tumour Predisposition Syndrome?
BAP1 encodes BRCA associated protein 1 a tumour suppressor with a role in deubiquitination
Associated with multiple cancers - including Clear cell renal carcinoma
Why are chromosome 3 balanced translocations associated with clear RCC?
Can result in loss of 3p - which encodes multiple RCC gene = VHL, PBRM1, BAP1 and SETD2
What are Squamous Cell Carcinomas?
In which cancer are they common?
Cancer arising from squamous cells in the outer layer of skin and in the mucous membranes
Head and neck squamous cell carcinoma (HNSCC)
Lung cancer
What is Head and neck squamous cell carcinoma (HNSCC)?
What genes are most commonly associated?
Type of Squamous cell carcinoma which can occur in multiple sites across mouth, nose and throat - presenting with ulcers, unusual bleeding or pain, sinus congestion, sore throat, earache, pain when swallowing or difficulty swallowing, a hoarse voice, difficulty breathing, or enlarged lymph nodes.
CDKN2A, FAT1, HRAS, NOTCH1, PIK3CA, PTEN, TP53
What are the major risk factors for Hepatocellular Carcinomas?
Chronic hepatitis B virus (HBV) infection, chronic hepatitis C virus (HCV) infection, prolonged dietary aflatoxin exposure, alcoholic cirrhosis, and cirrhosis due to other causes
What is difference between Hepatoblastomas and Hepatocellular Carcinomas?
Hepatoblastomas arise from undifferentiated hepatocytes in children under 3
Hepatocellular Carcinomas arises from hepatocytes but is more common as you get older and associated with cirrhosis
What is the main oncogenic pathway in Hepatocellular Carcinomas? Which genes are involved?
Wnt/β-catenin pathway - CTNNB1, AXN1, TP53, CDKN2A
What are the stages of the cell cycle? And what happens?
G0 - resting phase and not actively dividing
G1 - Growth phase - Each chromosome exists as a single double stranded helix - at no point is DNA synthesised in this phase.
At the G1 checkpoint - the restriction point - the cell is committed to division and moves into the S phase.
S phase - DNA synthesis replicates the genetic material. Each chromosome now consists of two sister chromatids.
G2 phase - Cell continues to grow. The G2 checkpoint ensures enough cytoplasmic materials necessary for mitosis and cytokinesis.
M phase - The cell stops growing. Nuclear division (mitosis) followed by a cell division (cytokinesis). The Metaphase checkpoint in the middle of mitosis ensures that the cell is ready to complete cell division.
What complex/proteins control passage through cell cycle control checkpoints?
How?
Cyclins and Cyclin-dependent kinases (CDKs)
CDKs are catalytic and phosphorylates proteins to orchestrate entry into the next phase. They are always constitutively expressed but no active without a cyclin synthesised at each specific stage
What is the first cell cycle checkpoint?
What factors are assessed?
What happens to pass this checkpoint?
G1 checkpoint
DNA integrity, molecular signals, nutrients, cell size. Stimulation by mitogens and can be blocked by anti-proliferative cytokines.
Cell growth enables CDK4-cyclin D formation, phosphorylation of retinoblastoma protein, relieves inhibition of E2F transcription factor, Cyclin E now expressed and binds to CDK2. G1-S phase transition
What is the second cell cycle checkpoint?
What happens to pass this checkpoint?
G2 checkpoint
CDK1 is activated by phosphorylation and de-phosphorylation of specific amino acid residues by Cyclin-Activating Kinase (CAK) and the wee1 protein. CDK1-cyclin B formation (aka MPF). Allows G2-M phase transition
What is the final cell cycle checkpoint?
What factors are assessed?
What happens to pass this checkpoint?
M checkpoint
Assembly at metaphase plate and correct sister chromatids attachment to spindle microtubules
Anaphase-promoting complex (APC) activated, Degrades cyclin B = MPF disassembly, Relieves inhibition of ‘separase’ (a cysteine protease) = spindle cut, Sister chromatid separation = anaphase entry
How can dysregulation of Cyclins and enzymes called CDKs effect cell cycle progression and cancer?
Overexpression of cyclin D1 - gene amplification or translocation and Ras and PI3 kinase signalling pathways
Inactivation of Cyclin-dependent kinase inhibitors - e.g. phosphorylation by the oncogene AKT causes re-localisation of Kinase Inhibitory Protein to cytoplasm and AKT overexpression is observed in breast cancers.
What is an oncogene? How can they arise?
Oncogenes typically encode cell proliferation and apoptosis controlling proteins and arise from proto-oncogene
- Point mutations, deletions, or insertions that lead to a hyperactive gene product
- Point mutations, deletions, or insertions in the promoter region of a proto-oncogene that lead to increased transcription
- Gene amplification events leading to extra chromosomal copies of a proto-oncogene
- Chromosomal translocation events that relocate a proto-oncogene to a new chromosomal site that leads to higher expression
- Chromosomal translocations that lead to a fusion between a proto-oncogene and a second gene, which produces a fusion protein with oncogenic activity
What is a tumour suppressor gene?
Activate anti-proliferative and pro-apoptotic pathways and thus protect cells against cancer
What is TP53?
What are three key roles of TP53?
Tumour suppressor gene which encodes p53 - a 53kDa potent transcription factor known as the guardian of the genome
1) Stops the cell cycle at the G1 and G2 checkpoint by triggering production of CDK inhibitor (CKI) proteins to allow time for DNA repair (e.g. GADD45 and p21 which inhibit CDK2/cyclin E and block passage through G2 checkpoint)
2) activate DNA repair enzymes
3) triggering programmed cell death (expression of pro-apoptotic proteins such as BAX and PUMA)
How are levels of p53 regulated in normal cells?
Expression triggered by genotoxic stresses (e.g. radiation)
Negative feedback loop regulates levels - p53 induces the expression of MDM2 gene, murine double minute 2 protein which is a ubiquitin ligase, which in turn promotes the degradation of p53
How often is TP53 involved in cancer?
The most common mutated gene
~50% of tumours have mutated form of TP53
17% exhibit MDM2 gene amplification and increased p53 degradation
What are the mechanisms of p53 inactivation?
1) variants in DNA binding domain = loss of transcription factor role
2) Deletion of carboxyl-terminal domain = inability to form functional tetramers
3) Duplications of MDM2 = increased p53 degradation
4) Viral infection = Viral oncogenes bind an inactivate p53 (or cause degradation)
5) Deletion of p14ARF = failure to inhibit MDM2 causes increased degradation of p53
6) Mislocalisation of p53 = loss of p53 function in nucleus
What two genes are encoded by CDKN2A?
How are they involved in cell cycle control?
CDKN2A encoded by Exons 1α, 2 and 3
p14ARF encoded by Exons 1β, 2 and 3
CDKN2A - inhibits kinase which inactivate RB1. Loss of CDKN2A leads to loss of RB1 function and inappropriate cell cycling.
p14ARF - mediates G1 arrest by destabilising MDM2. Loss of p14ARF p14ARF causes increased degradation of p53 and loss of cell cycle control
What are the possible therapeutic targets for MDM2-p53 pathway?
Blocking MDM2 expression
Inhibiting MDM2-p53 binding
Stopping the E3 ubiquitin ligase activity of MDM2
What are the detection approaches for Circulating tumour cells?
Protein expression-based technologies
Physical Property-based
Functional Assays
What are the two types of Protein expression-based technologies?
Give an example of each
Positive enrichment - capture using markers on CTCs e.g. EPCAM cell surface marker on circulating epithelial tumour cells but not blood cells
Negative enrichment - capture and removal using markers on leukocytes e.g. removal of CD45+ leukocyte
What process complicated Protein expression-based technologies for CTCs?
How can this be addressed?
Epithelial to mesenchymal transition (EMT) of carcinoma cells
Positive enrichment - plastin 3 is not downregulated by CTC during EMT and not expressed in blood cells
Negative enrichment - magnetic field or bi specific antibodies against antigens on leukocytes and erythrocytes that induce the formation of large multicellular rosettes which can be removed by centrifugation
Give two examples Physical Property-based technologies for Circulating tumour cells detection
Filtration and chip for size but CTCs can be of various sizes so require complex approaches (e.g. dielectrophoresis )
What is the only CTC detection method which is FD approved?
CellSearch for Breast, prostate and colorectal cancer. Immunocytochemistry (ICC) for a combination of markers
Give two examples Functional Assays for Circulating tumour cells detection
What do both methods require first?
EPISPOT assay, which detects specific proteins secreted during the in vitro culture of CTCs
Invasion assay that examines the ability of CTCs to digest a fluorescently labelled cell adhesion matrix
isolation of CTCs by another method prior to functional testing
What are the two most common forms of CNS tumours?
Gliomas and meningiomas
What grades/types of CNS tumours?
Why complex?
Grade 1 and 2 tumours are low grade, slow growing, relatively contained and unlikely to spread to other parts of the brain.
Grade 3 and 4 tumours are high grade, fast growing and can be referred to as ‘malignant’ or ‘cancerous’ growths. They cannot usually be treated by surgery alone, but often require other treatments, such as radiotherapy and/or chemotherapy.
Even low grade (sometimes called benign) have significant morbidity and mortality due to space occupation in brain
What are the key groups of CNS tumours?
Tumours of neuroepithelial tissue – astrocytomas, oligodendrogliomas.
Tumours of the sellar region – pituitary ademonas,
craniopharyngiomas.
Embryonal tumours – medulloblastomas.
Lymphomas – primary CNS lymphoma.
Germ cell tumours – germinoma, teratoma.
Tumours of the meninges – meningiomas.
Metastatic tumours – any primary site, but most commonly bronchial or breast tumours.
(Tumours of the nerve sheath – schwannoma, neurofibromas (N.B. peripheral nervous system)) a
What are the CNS major glial types? And what are their main functions?
astrocytes - cuffs around individual synapses, control of blood-brain barrier; regulate brain neurotransmitters, control potassium levels in the extracellular space, and CNS development.
oligodendrocytes - formation of myelin sheath around nerve fibres
What are Medulloblastoma?
Grade IV invasive embryonal CNS tumour - embryonal tumours form in embryonic cells that remain in the brain after birth
What is the common cytogenetic abnormality in Medulloblastoma?
17p loss and 17q gain - usually isochromosome 17q
Seen in up to 50% of tumours
What are the four sub groups of Medulloblastoma?
WNT - CTNNB1 variants (B-catenin) cause increase WNT signalling. Loss of chromosome 6 only cytogenetic (almost always in children). 10% of medulloblastomas , equal sex distribution, children over 4 and adolescents, rarely metastasise and excellent prognosis
SHH- Variants increasing Sonic hedgehog signalling. loss of chromosome 9q (PTCH1) and and 10q (SUFU) most common cytogenetic. 30% of medulloblastomas
Group 3 - male predominance. Worst prognosis. no clear driver but MYC amplification commonly seen. 25% of medulloblastoma
Group 4 - male predominance. no clear driver. Most metastatic. 35%–40% of all medulloblastoma
What are the most common type of brain neoplasms? Give two examples
CNS gliomas
Oligodendroglioma and Glioblastoma
What are the common genetic findings in Oligodendroglioma?
How are they useful?
Loss of 1p and 19q – in up to 80% of cases
Mutations in IDH1/IDH2 - 2-hydroxyglutarate which supresses histone lysine demethylases and leads to hypermethylation
Loss of 1p and 19q distinguish oligodendroglioma from diffuse astrocytoma and predicts increased chemosensitivity and better prognosis
What are the common genetic findings in Glioblastoma?
Gain of 7p - EGFR gene
9p loss - CDKN2A gene
10q loss - PTEN gene
13q deletion - RB gene
Amplification of MDM2 frequently seen
Inactivation of NF1, TP53, IDH1/2
What are the two genetic profiles seen in Glioblastoma?
Type 1 = TP53 inactivation (usually in secondary tumours). MDM2 amplification or CDKN2A silencing (both result in deregulation of the TP53 pathway), IDH1 mutation.
Type 2 = EGFR amplification/overexpression (usually in de novo tumours). PTEN is mutated in about 30% of cases.
Which variants in Glioblastoma are associated with an improved prognosis?
IDH1
What epigenetic finding in Glioblastoma is prognostic and why?
MGMT gene hypermethylation - this reduces cells ability to repair DNA following exposure to alkylating agents.
Alkylating drugs therefore useful therapy and patients show better progression free survival
Which cancer syndromes have a high CNS tumour burden?
Neurofibromatoses
TSC
Li-Fraumeni
VHL
What percentage of of Colorectal cancer (CRC) is associated with an established familial genetic syndrome?
15%
Which is most common familial genetic syndrome causing CRC?
Lynch syndrome - Hereditary Non-Polyposis Colorectal Cancer (HNPCC)
Germline variants in which genes are a cause of Lynch syndrome?
MLH1, MSH2, MSH6, PMS2 and EPCAM
Which Lynch genes have a later age of onset and more reduced penetrance?
MSH6 and especially PMS2
What is the mutational mechanism for EPCAM in Lynch syndrome?
deletions in the 3’ end of EPCAM gene, upstream of MSH2, creates EPCAM-MSH2 fusion transcripts resulting in epigenetic hypermethylation of the MSH2 promoter and loss of MSH2 expression
What tumour testing is recommended prior to germline testing in suspected Lynch cases?
Immunohistochemistry - presence or absence of MLH1, MSH2, MSH6 and PMS2
Microsatellite instability - measures length of quasi-monomorphic mononucleotide markers which have size shifts between normal and tumour in MMR deficient
MLH1 promoter methylation - common in sporadic cancers
BRAF V600E somatic testing
Which Lynch genes demonstarte concurrent loss on IHC? Why?
MSH2 and MSH6
MLH1 and PMS2
They form heterodimers in the MMR pathway
What loss of staining IHC patterns are observed in Lynch and what is underlying cause for each?
Loss of MSH2 and MSH6 = MSH2 LoF
Loss of MLH1 and PMS2 = MLH1 LoF (variant or promoter hypermethylation)
Isolated loss of either MSH6 or PMS2 = respective LoF variants
When is MSI testing indicated?
What are the three possible outcomes of MSI?
Normal IHC - may indicate not Lynch or a missense in one of the genes which would produce non-functional but immunoreactive protein
1) Tumours with two or more altered mononucleotide markers are high-level MSI (MSI-H). Increased risk that the tumour is due to a MMR gene defect
2) Microsatellite stable (MSS). Not supportive of a MMR gene defect
3) If only one marker shows instability, this is not considered sufficient to be classed as instability associated with LS but may be of significance and warrant further investigation.
When would MLH1 promoter methylation studies be undertaken?
What does MLH1 promoter methylation indicate?
Cases with loss of MLH1 and PMS2
More associated with sporadic cancers. And do not need to be tested for germline variants
Why is BRAF V600E testing on tumour tissue useful?
Associated with MLH1 methylation, and together indicate sporadic cancer
Useful screening method to avoid MMR germline testing (but 1% of Lynch patients have in tumour - therefore use in combi with MLH1 promoter methylation)
Which MMR gene is complicated for Germline testing? Why?
PMS2 has pseuodgene PMS2CL which makes sequencing 3’ difficult for NGS (may require long range and then nested)
What type of EPCAM variants do seen in Lynch?
What are the phenotypic differences?
Deletions of different sizes:
- Large deletions of the entire gene spanning into MYH2 - loss of MYH2 start
- Smaller deletions remove EPCAM termination codon and 3’UTR and cause transcriptional read-though from EPCAM into MSH2 and subsequent MSH2 promoter hyper methylation and gene silencing
Methylation causing variants are associated with a cancer phenotype restricted to the GI tract - less severe overall
What are the MMR dimers in the MMr complex and what are their functions?
Which subunits are dominant ?
MSH2 (dom)-MSH6 (MutSα) dimer preferentially repairs single base mismatch or mononucleotide repeats
The MSH2 (dom)-MSH3 dimer (MutSβ) preferentially recognises larger loop out errors such as dinucleotide repeats.
MLH1 (dom)-PMS2/PMS1/MLH3 dimer recruited to MSH2 dimer and recruits an exonuclease
How does the MMR complex know which strand to excise ?
Parent strand will have methylated A in nearby GATC sequence and will cut other strand
What syndrome is caused by germline bi-allelic MMR LoF variants?
mismatch repair cancer syndrome (MMRCS) - rare childhood cancer predisposition syndrome
What cancers are most commonly associated with Lynch?
Colon, endometrial, stomach, pancreas, prostate, ovarian, bladder
What is the most common polyposis syndrome?
How is it characterised?
FAMILIAL ADENOMATOUS POLYPOSIS (FAP)
Hundreds to thousands of adenomatous colonic polyps during the second decade of life. Almost 100% risk of CRC without colectomy
What are the extracolonic manifestations of FAP?
Fundic gland polyps in stomach
Desmoid tumours
Congenital hypertrophy of retinal pigment epithelium (CHRPE)
What is the underlying genetic cause of FAP?
Adenomatous polyposis coli (APC) is a tumour supressor which regulates the phosphorylation of β-catenin, which marks it for destruction by the proteasome
Loss of APC leads to accumulation of β-catenin to activate transcription factors resulting in changes the proliferation and differentiation state of cells (e.g. c-myc)
Outline the genotype-phenotype correlation seen with APC variants
Mutation cluster region (codons 1284 and 1580) – most severe - develop highest number of polyps and highest risk of CRC at younger age
Mutation in 5’ or 3’ regions, or exon 9 may develop attenuated FAP
Missense variants associated with less severe disease
Why do variants in APC 5’ and 3’ regions, and exon 9 cause AFAP?
5’ - truncating mutations in the first couple of exons can escape NMD by undergoing translational initiation upstream
3’ - APC has a large final exon (>2000 aa), many nonsense mutations in this region escape NMD = partially functioning proteins with varying extents of loss of the C-terminus, resulting in AFAP
Exon 9 - there is an alternatively spliced isoform of exon 9 lacks 100 amino acids. This isoform is present in normal tissues. If the mutated codon is within this region, it will absent from some transcripts, resulting in a milder phenotype.
What other syndromes are associated with APC variants?
Gardner syndrome - FAP with extracolonic manifestations of osteomas, and soft tissue tumours
Turcot syndrome - colorectal neoplasia and brain tumours
Which other polyposis syndrome presents similar to AFAP?
What is the cause?
MUTYH-associated polyposis
Germline bi-allelic MUTYH variants
What is the function of MUTYH?
What occurs due to loss of MUTYH function?
DNA glycosylase enzyme involved in the most frequent form of oxidative DNA damage repair, excising adenine bases from the DNA backbone where inappropriately paired with guanine or cytosine
Result in G:C to T:A transversions and these somatic mutations frequently occur in APC, KRAS and BRCA1/2
Which two kinase are important in controlling cell cycle in the presence of double strand breaks and stalled replication forks?
ATM - phosphorylates p53 to stop passage through G1 checkpoint and CHK2 to stop intra-S passage for DS breaks
ATR - Phosphorylates CHK2 to stop passage through G2 checkpoint after replication
What are the types of DNA repair mechanisms?
What type of damage do they fix?
Base excision repair - Single strand breaks and removing damaged bases
Nucleotide excision repair - DNA adducts, crosslinks and oxidised bases
Homologous recombination - DSB
Non-homologous end joining - DSB
Mismatch Match repair - base mismatches
What are the common causes of each type of DNA damage?
Base mismatch - replication stress
SSB - O2 radicals, ionizing radiation, chemotherapeutics
DSB - ionizing radiation, chemotherapeutics
DNA adducts, crosslinks and oxidised bases - UV light, hydrocarbons
Outline Base Excision Repair
1) DNA glycosylase (e.g. MUTYH) recognise and remove damaged or inappropriate base to from an abasic site
2) AP endonuclease cleave to create SSB
3) DNA polymerase and ligase then fill gap (either ligase out and then fill or displace old strand and then ligase that out)
PARP essential for protein recruitment in BER
Outline Nucleotide excision repair
NER enzymes recognise bulky distortions in the shape of the DNA double helix and undertake either
- Global excision repair (GER) which repairs all DNA, or
- Transcription-coupled repair (TCR) where DNA undergoing transcription is repaired (when RNA polymerase stalls)
Name a cancer syndrome associated with NER
Xeroderma pigmentosum
Outline Homologous recombination
DSB - resection around to create single strand overhangs. RAD51 binds to overhangs. One single stranded molecules invades between regions of homology. Formation of either single or Holliday junction.
Single Holliday resolves by invading strand reversing when has overlap with its partner which can then be used as template - resulting in no crossover
Double Holliday non-DSB allele used as template for both strands of broken allele. Forming a D loop. Which can resolved to produce a small area of crossover on each copy or a full recombination
Outline non-homologous end joining (NHEJ)
DSB - resection around to create single strand overhangs. NHEJ complex recognises these - they are removed and both ends ligated together resulting in loss of section of DNA
What is Ewing sarcoma?
primary bone cancer (and the soft tissue around the bones). Mostly in children and young adults. Often begins in the leg bones and in the pelvis
What is the underlying genetic abnormalities of Ewing sarcoma?
What are the two most common?
Balanced chromosomal translocations in which a member of the FET gene family (FUS, EWSR1 and TAF15) is fused with an ETS transcription factor (FLI1, ERG)
- EWSR1-FLI1 balanced t(11;22)(q24;q12). 85-90% of cases.
- EWSR1-ERG, t(21;22)(q22;q12). 10-15% of cases
How do the FET-ETS translocations cause malignancy?
FET promoter causes constitutive expression of ETS genes.
These aberrant transcription factors hundreds of genes involved in cell-cycle regulation, cell migration, signal transduction, chromatin architecture, telomerase activity.
Outline one MAPK pathway
ERK (extracellular signal-regulated kinase) MAPK pathway
TGFalpha binds EGFR and causes signalling through Ras, Raf, MEK and ERK to phosphorylate and activate transcription factors in the nucleus (including cyclin D and cdk2/4 which promote cell cycling).
Represents a autocrine feedback loop as ERK promotes more expression of EGFR ligands
How can the ERK pathway be dis-regulated in cancer?
EGFR overexpression, EGFR GoF variants, Ras GoF variants, RAF GoF variants
Outline the WNT signalling pathway
WNT signalling inhibits the complex from ubiquitinating b-catenin to mark it for destruction. b-catenin then accumulates and has transcriptional effects
Outline to the P13K/AKT pathway
Growth factor binding to tyrosine kinase receptor and dimerisation activates P13K through G-protein coupled receptor inside the cell. P13K in turn activates AKT. AKT activates mTOR for cell growth and proliferation (and inhibits TSC1/TSC2). And inhibits FOXO to stop apoptosis.
Which protein inhibits AKT?
PTEN
How can the P13K/AKT pathway be dis-regulated in cancer?
Somatic mutations in PIK3CA
Somatic mutations of PTEN
Loss of PTEN expression
Amplification of AKT
Somatic mutations in AKT1
Activating MTOR mutations
Outline the TGFβ pathway
TGF-β binds TGF-β receptor 1 or 2. Activated TGF-β R1 phosphorylates and activates SMAD2 and 3 to form the SMAD complex with SMAD4. This complex then moves to nucleus to activate gene expression.
What are the clinical features of ALL?
fever, fatigue, bone/joint pain, headache, weight loss, shortness of breath, swollen lymph nodes, particularly lymph nodes in the neck, armpit, or groin, swelling or discomfort in the abdomen, bruising, infections, lymphadenopathy, hepato/splenomegaly, anaemia, leucocytosis, neutropenia, thrombocytopenia.
What is ALL?
Acute lymphoblastic leukemia - Neoplastic disease characterized by clonal expansion of leukemic cells in the bone marrow (BM), lymph nodes, thymus, or spleen.
What is difference between leukaemia and lymphoma?
Disease presenting in BM or peripheral blood (PB) = leukaemia
Disease confirmed primarily nodal or extranodal sites with minimal BM/PB infiltration = lymphoma
What are the most significant genetic prognostic factors for adult B-cell ALL?
- t(9;22)(q34;q11) BCR-ABL1 Philadelphia chromosome
- t(4;11)(q21;q23) KMT2A (MLL)-AFF1
- Complex karyotype (5 or more abnormalities)
- Ploidy High hyperdiploidy 51-65 chromosomes
- Hypodiplody (<44 chromosomes) and near triploidy
What is the pathophysiology of of the t(9;22)(q34;q11)?
Why is it useful to know?
ABL1 encodes tyrosine kinase. The BRC-ABL1 fusion gene codes for a protein that replaces the myristoylated cap region, which would normally induce a conformational change to keep kinase domain inactive, with a truncated portion of the BCR protein. The produce constitutively activated kinase which effect cell divison.
TKI therapy available
What are the two forms of BRC-ABL1?
75% p190 (minor BCR breakpoint). p190 is only found in de novo ALL
25% p210 is seen in de novo ALL and CML in lymphoid blast crisis
What is the pathophysiology of of the t(4;11)(q21;q23) KMT2A (MLL)-AFF1
KMT2A encodes MLL - a histone methyltransferase deemed a positive global regulator of gene transcription
translocation leads to the loss of the methyltransferase domain of MLL but mechanism unknown
What is High hyperdiploid?
What is important to consider? Why?
51-65 chromosomes
4, 6, 10, 14, 17,18 , 21 (often 2 copies) and X.
True hyperdiploid - gained chromosome tend to be trisomic (other than 21 and X), OR
Doubled up near haploid/low hypodiploid: usually 4 copies of gained chromosomes
Important as hypodiploidy worse prognosis
What is Hypodiplody?
<44 chromosome
common losses of 3 and 7
Poor prognosis
What are most common genetic abnormalities in T-cell ALL?
Tetraploidy
Rearrangements of TCR loci at 7q34 (TCRB) or 14q11 (TCRA/D)
NOTCH1 receptor activating variants
NOTCH1;TCRB t(7;9) translocation
What is the master regulator of lymphocyte development?
How often are variants seen in B-ALL?
IKZF1
15% of B-ALL and are associated with a poor outcome. Deletions/mutations of IKZF1 are found in 80% of Ph+ve ALL
What differentiates Infant ALL from childhood ALL?
Infant ALL having an immature B phenotype lacking CD10 expression, with higher tumour load at presentation. Overall survival is considerably worse for infant ALL than for older children
What are the most prognostic re-arrangement in paediatric B-ALL ?
- t(9;22)(q34;q11) BCR-ABL1 rearrangement
- KMT2A (MLL) rearrangements
- t(12;21) ETV6-RUNX1 rearrangement
- iAMP21 (intrachromosomal amplification of chrm 21)
- High Hyperdiploidy (51-65 chromosomes).
- Near haploidy (23-29 chromosome) /low hypodiploidy (30-39 chromosomes)/ high hypodiploidy (40-44 chromosomes)
- TCF3 rearrangements
What is the most common cytogenic abnormalities in infant ALL?
KMT2A (MLL) rearrangements
What is the most common cytogenic abnormalities in childhoof B-ALL?
What is the pathophysiology?
t(12;21) ETV6-RUNX1 rearrangement
Promote RAG1 expression. RAG complex cleaves DNA at recombination signal sequence (RSS), and is responsible for the V(D)J rearrangement. Lead to excessive RAG recombinase activity in other regions of DNA
Why might near haploid/low hypodiploid B-ALL may be missed as normal by G-banding ?
clone may undergo doubling up (endoreduplication). BUT Chromosomes 1, 11 and 17 are usually disomic in haploid clone and tetrasomic in doubled up clone.
What characterises childhood T-ALL?
Recurring rearrangements that commonly juxtapose regulatory elements of TCR loci with transcription factors or homeobox genes.
What defines a diagnosis of AML?
Clonal expansion of myeloid progenitors (blasts). 20% blasts are present in PB or BM. Or <20% blasts but
myeloid sarcoma is present, AML-related chromosome abnormality detectedor, erythroid leukaemia
What are the recurrent AML cytogenetic abnormalities?
- t(8;21)(q22;q22); (RUNX1T1-RUNX1)
- inv(16)(p13.1q22) or t(16;16)(p13.1q22); CBFB (16q22)-MYH11 (16p13)
- t(15;17)(q24.1;q21.2); PML-RARA
- t(9;11)(p21.3;q23.3); MLLT3- KMT2A (KMT2A previously known as MLL)
- t(6;9)(p23;q34.1); DEK-NUP214
- inv(3)(q21,3qq26.2) or t(3;3)(q21.3;q26.2); GATA2, MECOM
- t(1;22)(p13.3;q13.3); RBM15-MKL1
What secondary abnormality is very specific to inv(16)? What is the implication?
+22
Better prognosis
How do the RUNX1T1-RUNX1 and CBFB-MYH11 fusion proteins interact?
RUNX1-CBFB proteins normally heterodimerise to create core binding factor (CBF)that binds target genes via the RUNX1 transcriptional activation domain, which regulates normal blood cell differentiation, and cell survival.
Fusions rearrangements allow the CBF to bind to the target genes, but the transcriptional activation is lost leading to arrest of differentiation and TP53 induction being inhibited resulting to increased cell survival.
What is the pathophysiology of the t(15;17) in AML?
Normally, PML codes for a tumour suppressor which blocks cell growth and proliferation and induces apoptosis. RARA protein represses transcription of retinoic acid target genes until needed to control white blood cell (WBC) maturation.
PML-RARA represses transcription of retinoic acid target genes always and does not block proliferation or induce apoptosis. This leads to accumulation of leukemic WBCs that do not mature or differentiate beyond the promyelocyte stage and do not apoptose.
What is the therapy for t(15;17) in AML?
ATRA (all-trans-retinoic acid) binds to the fusion protein and induced subsequent degradation to allow downstream signaling and maturation of WBCs
Remission in about 80-90%
Which AML translocations are associated with poor prognosis?
t(6;9)(p23;q34.1) DEK-NUP214
inv(3)(q21,3qq26.2) or t(3;3)(q21.3;q26.2) GATA2, MECOM
What is Myeloid Sarcoma?
A tumour mass consisting of myeloid blasts occurring at a site other than the bone marrow.
Outline the relationship between AML and T21
Children with DS have a 50-fold increased risk of developing AML in the first 5 years of life.
Approximately 1-2% of children with DS develop AML, usually M7. Usually de novo, but sometimes preceded by Transient abnormal myelopoiesis (TAM). Blast cells carry mutations of GATA1.
What percentage of AML harbour somatic variants?
95%
What are the five functional class of AML variants?
Give an example for each
Signalling and Kinase - FLT3
Epigenetic modifiers - KMT2A
Nucleophosmin - NPM1
Transcription factors - RUNX1
Tumour supressor - TP52
Spliceosome complex - SRSF2
Cohesin complex - STAG1
What is the function of FLT3 and what types of variants are seen in AML?
receptor tyrosine kinase important for cell differentiation, proliferation and survival. Expressed in normal myeloid and lymphoid hematopoietic progenitor cells but expression lost as cells differentiate.
Internal tandem duplications (ITDs) in exons 14 and 15 = loss of structure of autoinhibitory domain and ligand-independent activation of FLT3.
Tyrosine kinase domain mutations = folding out of activation loop enabling ATP to access catalytic site resulting in constitutive kinase activation.
What are the three phases of CML?
Chronic phase (CP) - 40% are asymptomatic, mean length is 3-4 years but can last for more than 10 years.
Accelerated phase (AP) - mutant stem cells persist within bone marrow, they eventually accumulate further mutations and disease enters the accelerated stage. Cell proliferation increases rapidly, symptoms quickly become more severe.
Blast crisis (BC) - >20% blasts in BM
What is the most common BCR-ABL fusion in CML?
p210Bcr-Abl
BCR exon 13/14 to exon 2 of ABL
What are two more rare BCR-ABL fusions in CML?
p190Bcr-Abl =BCR exon 1/2 and ABL exon 2
P230Bcr-Abl = BCR intron 19 and ABL exon 2
What is involved in MRD for CML?
minimal residual disease (MRD) monitoring
blood cell counts and differential cell counts every 2 weeks until a complete hematologic response is achieved.
qPCR on blood cells, expressed as BCR-ABL1 % according to the IS, must be performed at least every 3 months even after an MMR is achieved and confirmed
cytogenetics should be done in patients with atypical translocations, rare or atypical BCR-ABL1 transcripts that cannot be measured by qPCR
What level of MRD predicts 100% survival?
BCR-ABL1 ≤ 0.1% predicts a CML-specific survival close to 100% as disease progression is uncommon once this level of cytoreduction has been achieved.
What is imatinib?
1st line tyrosine-kinase inhibitors used for CML
What testing is recommended if milestones are not reached or secondary resistance arises?
ABL1 mutation detection
What are the three stages of CML reponse?
Haematological response (HR) - WBC and platelet counts normalise and splenomegaly is reversed. This has approximate sensitivity of 5%.
Cytogenetic response (CyR)
-Number of cells with Ph chromosome as a percentage. G-banding on metaphase chromosomes has a sensitivity of 1% -5%. FISH has a sensitivity of 0.1%-1%
Molecular response (MR) – Detect abnormal transcripts at much lower level. Major MR is said to be achieved if number of BCR-ABL1 copies is reduced to 3-log below level at initial diagnosis. Complete MR response is achieved if no cells are detected.
What are the second and third generation TKIs?
2nd - Dasatinib and nilotinib
3rd - Ponatinib
Which common ABL variant is resistant to first and second generation TKI?
T315I
What is difference between 1° and 2° resistance?
1° is initial failure to achieve HR or CyR
2° respond to treatment, but then have subsequent loss of CHR or CyR
What underlies 1° resistance?
Increased expression of PTGS1 which metabolises imatinib.
Increased ABCB1 expression, a drug efflux pump, increases imatinib resistance
Low levels of OCT1, a drug intake protein, are associated with resistance
What is the mechanism of action of Imatinib?
It out-competes ATP for binding to ABL1. Without being able to bind ATP ABL1 has no substrate and cannot phosphorylate downstream targets. This blocks the dysfunctional activity of the oncoprotein and once the oncogenic signal is disrupted the cells go into apoptosis.
What is Lymphoma?
Malignant lymphocytes (B and T cells) that accumulate in lymph nodes (lymphatic system) to form tumours
What cell type are characteristic of Hodgkin’s lymphoma?
RS cells (B-cell lineage)
In what cell type does Burkitt’s Lymphoma (BL) arise?
IgM+ memory B-cell
What is the underlying genetic cause of Burkitt’s Lymphoma (BL)?
Translocation which result in constitutional expression of MYC by bringing regulatory elements of the immunoglobulin loci to the MYC 5’ regulatory regions :
t(8;14)(q24;q32) is present in ~85% of cases
t(8;22)(q24;q11) is present in ~10% of cases
t(2;8)(p12;q24) is present in ~5% of cases
What treatment is used for Burkitt’s Lymphoma (BL)?
CODOX-M
What treatment is used for Follicular Lymphoma (FL)?
Rituximab - chimeric monoclonal antibody against CD20 cell surface antigen which is found on the surface of B cells (normal and malignant)
What is the most common underlying genetic cause of Follicular Lymphoma (BL)?
80% carry t(14;18)(q32;q21) as the primary chromosome abnormality
BCL2 with IGH, resulting in over-expression of BCL2 protein. BCL2 protein prevents cells from apoptosing
What is a highly specific biomarker for Mantle Cell Lymphoma (MCL)?
SOX11
What is the most common underlying genetic cause of Mantle Cell Lymphoma (MCL)?
t(11;14)(q13;q32) is seen in >95% of cases
IGH and CCND1 (aka BCL1). IGH enhancer stimulates expression of CCND1. Over expression of Cyclin D1 accelerates the passage through G1 phase of the cell cycle, causing cells to divide before they are mature.
Name a T cell lymphoma
Anaplastic large cell lymphoma (ALCL)
What gene is commonly involved in translocations in Anaplastic large cell lymphoma (ALCL)?
ALK - tyrosine kinase receptor normally silent in lymphoid cells.
t(2;5)(p23;q35) or t(1;2)(q25;p23) = Generation of the fusion protein results in a constitutively active tyrosine kinase
What is CHIP?
What can CHIP become?
Clonal hematopoiesis of indeterminate potential (CHIP) is the presence of a clonally expanded hematopoietic stem cell caused by a leukemogenic mutation without hematologic malignancy, dysplasia, or cytopenia. CHIP is associated with a 0.5-1.0% risk per year of leukemia.
What are myelodysplastic syndromes (MDS)?
group of hematologic malignancies characterised by:
- Clonal expansion of bone marrow myeloid cells with impaired differentiation
- development of peripheral cytopenias due to ineffective haemopoiesis and dysplasia in one or more myeloid lineages (hallmark of MDS)
- Increased risk of transformation to AML (5-65% depending on subtype).
Give an example cytogenetic abnormality for each MDS prognostic group
Very good = -Y
Good = del 5q
Intermediate = del 7q
Poor = inv3
Very poor = > 3 abnormalities
What is CLL?
Chronic Lymphocytic Leukaemia (CLL) - chronic mature B-cell neoplasm due to proliferation and accumulation of monomorphic small, round to slightly irregular B lymphocytes in the peripheral blood, bone marrow, spleen and lymph nodes
What are the four common cytogenetic abnormalities detected in CLL?
Isolated del(13q14.3)
del(11q23) (ATM)
Trisomy 12
del(17p13) (TP53)
What cytogenetic testing is used for CLL?
FISH for the common rearrangements. karyotyping in CLL is difficult due to the reluctance of these cells to divide in vitro
What drug is available to CLL patient with TP53 abnormalities?
Alemtuzumab
Which B call neoplasms is associated with plasma cells?
Multiple myeloma
What are the three stages of multiple myeloma?
Monoclonal gammopathy of undetermined significance (MGUS) - plasma cell content of <10%.
Smouldering myeloma - stable PC content 10-30%
Myeloma - accumulation of clonal plasma cells in the bone marrow. Secreted M-protein is detectable in the serum. CRAB- C- hypercalaemia, R- renal failure, A- Anaemia, B- Bone disease
What two genetic subgroups exist for multiple myeloma? Which has better prognosis?
Hyperdiploid - gains in the odd number chromosomes
Non-hyperdiploid - structural rearrangements of IGH@ (heavy chain at 14q32)
Hyperdiploid have better prognosis
What is the most common IGH rearrangement in multiple myeloma?
t(4;14)(p16.3;q32) FGFR3/MMSET
What other genetic changes are seen in both multiple myeloma subgroups?
Monosomy/del 13
Del 17p/TP53
Loss 1p/gain 1q
Translocations and/or amplifications of MYC
What is a myeloproliferative neoplasm?
Clonal haematological malignancies derived from myeloid lineage leading to increased number of mature cells
What is JAK2?
What is the most common JAK2 variant? What is its pathophysiology?
Non-receptor tyrosine kinase which is a signal transducer and activator in both the MAPK and PI3K pathways
V617F - Gain of function releasing auto inhibition
In which MPNs is the JAK2 V617F variant most common (%)?And what are their phenotypes?
Polycythemia Vera - 95% - increased red blood cell production
Primary myelofibrosis - 50% - Proliferation of megakaryocytes and granulocytes in BM that is associated with deposition of fibrous connective tissue and extramedullary haematopoiesis.
Essential Thrombocythaemia - 50% - Involves primarily the megakaryocytic lineage. Sustained thrombocytosis in PB, increase in mature megakaryocytes in BM.
What other two genes are commonly associated with PMF and ET?
MPL and CALR
How do MPL variants cause MPNs?
MPL encodes thrombopoietin which regulates the differentiation of megakaryocytes and platelets. Mutations constitutively activate signalling pathways including JAK/STAT, MAPK and PI3K
What clinical features are associated with Neurofibromatosis type 1?
Café-au-lait (CAL) spots/freckling
Neurofibromas
Benign tumours in brain and spinal cord (can become malignant)
Juvenile Myelomonocytic Leukaemia
What is the pathophysiology of Neurofibromatosis type 1 ?
Loss of function variants in NF1 gene on 17q
NF1 encodes neurofibromin which is negative regulator of RAS (activates RasGTPase which converts active RASGTP to inactive RASGDP) to control ERK and PI3K signalling pathways
What tumours are associated with Neurofibromatosis type 2?
Vestibular schwannomas
meningioma
glioma
neurofibroma
What are schwannomas? What are the symptoms?
Acoustic neuroma, is a benign intracranial tumour of the myelin-forming cells of the vestibulocochlear nerve
Gradual hearing loss, tinnitus and ● Balance problems
What is the pathophysiology of Neurofibromatosis type 2?
Loss of function NF2 variants on 22q
NF2 encodes neurofibromin 2 (aka merlin) which is produced in Schwann cells. Cyotskeletion protein which regulates the PI3 kinase/Akt, Raf/MEK/ERK and mTOR signalling pathways
What other gene can be associated with Schwannomatosis?
SMARCB1
What are the five broad classes of oncogene?
Secreted Growth Factors
Growth Factor Receptors
Signal Transducers
Inhibitors of apoptosis
Transcription Factors
Outline an example Secreted Growth Factor oncogene
Wnt signalling family in breast cancer/medulloblastoma. Wnt binding causing the APC complex to be inhibited. Subsequent accumulation of beta-catenin and associated gene transcription
Outline an example Growth Factor Receptor oncogene
EGFR in NSCLC
Activating variants in tyrosine kinase domain = increased signalling for proliferation and survival. Can be targeted by TKI (e.g. Gefitinib) which outcompete ATP
Outline an example Signal Transducer oncogene
PIK3CA (in ~15% of tumours) - enzyme which transmits signals from receptor tyrosine kinases for cell metabolism, growth, survival, cell cycle regulation and motility
Outline an example Inhibitors of apoptosis oncogene
BCL2 in follicular lymphoma (t(14;18))
BCL2 inhibits apoptosis through stress pathway - overexpression using Ig promoter leads to increased levels
Outline an example Transcription Factors oncogene
EWS/Fli1 - in Ewing sarcoma (t(11;22).
chimeric oncoprotein produced, EWS/Fli1, acts as an aberrant transcription factor
Give an example for each of the 5 mechanisms for cancer causing activation of Oncogenes
- Point mutations, deletions, or insertions that lead to a hyperactive gene product - BRAF V600E in CRC
- Point mutations, deletions, or insertions in the promoter region of a proto-oncogene that lead to increased transcription - TERT promoter variants
- Gene amplification events leading to extra chromosomal copies of a proto-oncogene - HER2 in breast cancer
- Chromosomal translocation events that relocate a proto-oncogene to a new chromosomal site that leads to higher expression - MYC translocations in Burkitt Lymphoma
- Chromosomal translocations that lead to a fusion between a proto-oncogene and a second gene, which produces a fusion protein with oncogenic activity - BCR-ABL in AML and ALL
Name a cancer syndrome which is associated with both activating and inactivating variants
Multiple Endocrine Neoplasia (MEN) - combined occurrence of tumours involving two or more endocrine glands within single patient
What are the four 4 major types of Multiple Endocrine Neoplasia (MEN)?
MEN1 (aka Wermer syndrome) associated with menin (MEN1) germline-inactivating mutations and copy number changes
MEN2 (previously MEN2A, aka Sipple syndrome) associated with germline-activating mutations of the tyrosine kinase receptor encoded by the (RET)
MEN3 (previously MEN2B, aka Gorlin Syndrome) associated with germline-activating RET mutations
MEN4 associated with Cyclin-Dependent KiNase Inhibitor (CDKN1B) germline-inactivating gene mutations.
What type of tumours are commonly observed in MEN1?
parathyroid and pancreatic islet neuroendocrine tumours
How is MEN1 screened for in families?
Biochemical tests for secretion of endocrine substances from different glands. Imaging less often
What is only type of malignant MEN1 tumour?
Gastrinoma - excessive gastric acid production, causing severe peptic ulcer disease and diarrhea
What is pathophysiology of MEN1?
Not fully known - but though to
Interacting with transcription factors that induce or suppress gene transcription.
Interacting with various histone-modifying enzymes (KMT2A (MLL) protein; HDACs and EZH2)
Directly interacting with gene promoters and acting as a transcription factor
What type of tumours are seen in MEN2 and MEN3?
What differentiates between the two?
Medullary Thyroid Carcinoma, Phaeochromocytoma and parathyroid tumours
MEN2 - all three tumour types and Hirschsprung’s disease
MEN3 - Very early-childhood onset. MTC + PCC + other features (e.g. marfanoid)
What is pathophysiology of RET variants?
RET usually binds its ligand and dimerises to have tyrosine kinase domain phosphorylated and downstream signalling occur
1st intracellular tyrosine kinase sub-domain = Familial Medullary Thyroid Carcinoma (least severe adult onset)
Transmembrane domain = MEN2 (constitutively dimer)
Second tyrosine kinase sub-domain (=constitutively active) = MEN3 (most common p.Met918Thr) (most severe)
What is pathophysiology in MEN4?
CDKN1B encodes cyclin-dependent kinase inhibitor p27 which inhibits cyclin E-CDK2 complexes to stop G1-S transition. phosphorylation of p27 causes export to the cytoplasmic ubiquitination and subsequent degradation can occur and degradation
CDKN1B variant in MEN4 reduces the cellular expression of p27, alter its intracellular location or disrupt its ability to interact with CDK2
What group of cancer syndromes are caused by PTEN variants?
PTEN Hamartoma Tumour Syndromes
What are the clinical features of Cowden syndrome?
macrocephaly, trichilemmomas. breast cancer is 85%, thyroid cancer (35%), and endometrial cancer (28%).
What are Wilms Tumours?
Malignant neoplasm of the kidney
What is nephrogenic rest?
Benign foci of embryonal kidney cells that persist abnormally into postnatal life. These rests are considered to be Wilms tumour precursors. Nephrogenic rests that sustain additional mutations transform into a Wilms tumour.
What three syndromes are associated with Wilms tumour?
What is the genetics of each?
WAGR syndrome (Wilms tumor, aniridia, genital anomalies, retardation) - 11p13 deletion including WT1
Denys-Drash syndrome (DDS) - early-onset renal failure, intersex disorders, and a high risk of Wilms tumor- heterozygous germline missense pathogenic variant in WT1 exon 8 or 9
Beckwith-Wiedemann syndrome - paternal UPD of 11p15.5
What is the difference between hereditary and non-hereditary Retinoblastoma?
Hereditary (60%) - germline RB1 variant and gain of second somatic variant = bi-lateral retinoblastoma and increased lifetime risk of other cancer
Non-hereditary (40%) - Somatic mutations present on both RB1 alleles = unilateral retinoblastoma
What theory is underpinned/proved by Retinoblastoma?
Knudson’s two hit hypothesis
Which two genes are associated with familial Neuroblastoma?
ALK and PHOX2B variants
KIF1B deletions
What are the two classes of ploidy in Neuroblastoma? What is the implication of each?
Near triploidy = good prognosis
Di-/Tetraploid = poor prognosis (also associated with MYCN amplification)
Outline one example drug where pharmacogenetics may be used to direct dosage/use
Warfarin - acts by reducing vitamin K availability (needed for clotting)
CYP2C9 - carriers of the CYP2C92 (rs1799853) and CYP2C93 (rs1057910) alleles have 70% and 20% activity, respectively, so give strong risk of over anticoagulation and require lower doses of Warfarin
VKORC1 SNPs (1173C>T and -1639G>A) are associated with increased warfarin sensitivity and require a reduced maintenance dose
Name 6 methods of MRD
FISH
RT-qPCR
qPCR
Tandem duplication PCR
Immunological (Flow)
QF-PCR (Chimerism)
What therapy is NICE approved for HER2 overexpression in Breast cancer?
trastuzumab (Herceptin; a monoclonal antibody with specificity for the extracellular domain of HER2)
What are the clinical features of TSC?
Abnormalities of the central nervous system
Abnormalities of skin
Abnormalities of the kidneys
Abnormalities of the heart
Abnormalities of the lungs (mainly women)
Abnormalities of the eyes
What genes are associated with TSC? Which is most common cause?
TSC1 (30%) and TSC2 (70%)
What contiguous gene syndrome is also associated with TSC2?
TSC2/PKD1 = involves deletion of both the TSC2 and PKD1 genes at 16p13.3. Typically associated with tuberous sclerosis with severe and early onset polycystic disease
What treatment is being trialed for TSC?
mTOR inhibitors (e.g. rapamycin)
TO ADD - THE MYC’s
