Genetics 10 - Cancer & Genomic Medicine (lessons) Flashcards
learning outcomes
neoplasm
an abnormal mass of tissue unresponsive to normal growth controls
neoplastic cells have clonally expanded as a result of somatic mutation
BENIGN - uncontrolled growth of tumour, but cannot metastasize
MALIGNANT - acquired ability to metastasize (seed other places)
cell growth/division
Cancer is closely linked to cell cycle
Most cancers have inactivating mutations in 1+ proteins that normally function to restrict progression through G1 phase of cell cycle
Virtually all human tumours have inactivating mutations in proteins - p53 - stopping cell if previous step has occurred incorrectly or DNA has been damaged
Growth factors
Growth factor receptors
Signal transduction proteins
Transcription factors
Pro and anti apoptotic proteins
Cell cycle control proteins
hallmarks of cancer
progressive
not overnight - changes accumulate
role of oncogene
developed from protooncogene
accelerator
genes involved in growth, proliferation, cell cycle
tyrosine kinases (Src, ABL)
growth factors (PDGF-B)
receptor tyrosine kinases (ERBB2, EGFR, HER2/neu)
IC signalling cascade components (Ras)
cell cycle regulators (Myc)
role of TSGs
brakes
gatekeeper genes
APC - familial colon cancer
RB1 - retinoblastoma
inhibits tumour growth, proliferation or cell cycle progression
caretaker genes
stability genes
MLH1
MSH2
stabilise the genome (provide mutational (DNA repair) or chr stability)
oncogene
a gene that when expressed confers resistance to programmed cell death
protooncogene
can become an oncogene following
point mutation
chromosomal translocation
increase in gene expression e.g. change in promoter
protooncogene to oncogene - type of mutation
change in just 1 of 2 alleles may result in malignant transformation e.g. epidermal growth factor (EGFR)
dominant activating/hypermorphic (GOF) mutation
tumour suppressor genes - what do they code for
products of this family of genes regulate cell cycle or direct cells towards apoptosis - code for:
- proteins that repress expression of genes essential for continuation of cell cycle
- proteins that prevent cell cycle progression in presence of damaged DNA
- proteins that promote apoptosis if DNA is damaged
- proteins that promote cell adhesion (prevent metastasis)
- proteins involved in DNA repair
2 hit hypothesis - type of mutation
typically need change in both alleles for malignant transformation
recessive amorph/hypomorphic (LOF) mutations
Probability of 1 cell being hit is high - especially if it’s a large cell
2nd hit is unlikely
big TS gene
size
activity depends on…
function
protein - p53
gene is TP53 on chr 17 (17p13.1)
393 AAs
activity depends on forming a tetramer
multiple TS functions - growth arrest, apoptosis, DNA repair
hereditary mutation associated with TP53
Li-Fraumeni Syndrome
rare but highly penetrant
can result in tumorigenesis in different places
mutation in core domain of TP53
mutation in C terminal of TP53
type of mutation
No tetramer formed
Interferes with normal protein folding - binds in an abhorrent fashion
Monoallelic change is enough
Dominant negative mutation - antimorph
Protein with a no of subunits and a mutation in 1 allele means the tetramer cannot form properly to carry out its function
Vogelstein’s tumour progression model
e.g. Colorectal cancer
10 years to get to carcinoma stage
More and more mutations over time
Initially in DNA repair genes, TSGs, built up to oncogenes which acecelerated tumorigenesis - loss of p53 can lead to chromosomal aneuploidy
CA = change no of chromosomes in the cell - increases dysplasia (presence of abnormal cells within a tissue)
life time risk of BC
molecular progression of BC is complex
different subtypes arising from different pathways
histology of BC
sporadic BC - risk factors
female gender
oestrogen exposure
age of menarche/menopause (<12/>55)
reproductive Hx
exposure to exogenous oestrogens
alcohol, obesity, radiation exposure
null parity
having 1st child > 35
sporadic vs familial BC
majority of BC is sporadic
family history of BC not synonymous with hereditary BC
13% of women have family history of BC but most do not get BC
what does oestrogen do
fuels growth and division of cancer cells, especially those with oestrogen receptors
triple -ve BC
negative for oestrogen receptors, progesterone receptors and excess HER2 protein
common mechanisms of genetic change in BC
- amplification of DNA sequences
- changes in chr number (aneuploidy)
- epigenetic modification
- point mutations
- changes in micro-RNA regulation
amplification
commonly of oncogenes
increase in gene copy number
results in over-expression of proteins
up to 24 ‘amplicons’ (tandemly repeated copies) in invasive BC
many genes amplified simultaneously
17q12-22 (“HER2 amplicon”) contains HER2, amplicon and Top2A, TSG (responsive to anticyclins)
changes in chr number
common
advanced tumours
significance uncertain
epigenetic modification
common mechanism of genetic change
reversible
methylation of DNA and histone acetylation
regulates expression of many genes e.g. ER, PR, p16, p21, BRCA1
point mutations
E-cadherin (CDH1) mutated in lobular carcinomas (putative TSG)
discrete point mutations are more common in hereditary BC
BRCA1 and BRCA2 - TSGs, transcriptional regulation, repair of double strand breaks
TP53 - TSG, guardian of genome, mutated in > 50% of BCs
Checkpoint Kinase 2 (CHEK2) - cell cycle TSG - DNA repair and cell cycle arrest
micro-RNAs
non-coding ss RNA
contribute to post-transcriptional gene silencing by binding to mRNA
altered in BC by e.g. amplification, deletion
affect expression of many gene products e.g. ER, p27, Bcl-2
Abhorrently expressed in cancer, they can function as TUMOUR SUPPRESSORS and/or ONCOGENES
Oncogenes - oncomeres/oncomicroRNAs
chr translocations in cancer - chimeric oncogenes
can create chimeric oncogenes (neomorphic) - Take a protoncogene and move it to another position in chromosome - usually a fusion protein with another gene
e. g. Philadelphia chr (Ph1: (t9;22)) - BCR-ABL in CML - constitutively active ABL tyrosine kinase - growth signal
e. g. PML-RARα fusion (t15;17) in APML - blocks PML TSG function and retinoic acid induced myeloid differentiation
chr translocations in cancer - transcriptionally upregulated oncogenes
e.g. MYC oncogene in Burkitt lymphoma (t8;14) or occasionally (t8;2, t8;22)
MYC oncogene moved to IGH (Ig heavy chain) region (chr 14)
MYC overexpression in lymphocytes (high expression from IGH promoter)
constitutive B lymphocyte activation - characteristic lymphoma tumour in jaw
things to remember
learning outcomes
hypermorphic - GOF - new or stronger expression
symptoms of RB
white reflection in eye - leukocoria
strabismus - cross-eyed
hereditary cancer syndromes ⇒
first hit in a TSG is inherited as a constitutional mutation
e.g. hereditary. RB - OMIM 180200
gene - hereditary RB
RB1 TS gene on 1 copy of chr 13q14 in all cells (including retina)
subsequent 2nd hit in RB1 in retinal cells lead to retinoblastoma tumour
sporadic form of RB where 2 hits occur de novo (somatic) - 2/3 of cases
sporadic RB difference
2/3 of cases
tumours are generally. UNILATERAL
in hereditary RB, tumours are BILATERAL or MULTIPLE PER EYE (multifocal)
tumour suppressor gene
typically need change in both alleles for malignant transformation
recessive amorph/hypomorphic (LOF) mutations
Knudson’s 2 hit hypothesis
loss of heterozygosity
a TSG locus that is heterozygous in a normal cell becomes homozygous or hemizygous (lose good allele and only left with bad one) in derived cancer cell
most important mechanism of 2nd hit in hereditary cancer syndromes
how does LOH occur
acquired UPD - copy neutral
monosomy (by nondisjunction) - hemizygous
gene conversion (copy neutral) - hybrid chr
mitotic recombination between parental homologs (copy neutral)
deletion
inactivating mechanisms in 2nd hit
proportion of children with RB with a +ve family history
10% - 95% risk for RB
de novo mutation for RB
in the parental (USUALLY PATERNAL) germ line accounts for the other (3/4) of hereditary retinoblastoma
what are hereditary cancer syndrome patients also prone to
other forms of cancer
for RB this includes pineoblastoma, osteosarcoma and melanoma
3 other hereditary cancer syndromes
familial adenomatous polyposis
Lynch syndrome - hereditary non polyposis colon cancer - HNPCC
Li-Fraumeni syndrome
FAP
gene
symptoms
OMIM 175100 - APC - chr5q21
colon polyps that become malignant at 40
extracolonic manifestations
Lynch syndrome
HNPCC
usually MLH1 (chr3p22) or MSH2 (chr2p21)
early age of onset (44) colon cancer, often multiple tumours and often multiple forms of cancer
Li-Fraumeni syndrome
OMIM 151623 - TP53 - chr17p13
multiple forms of cancer
50% have cancer by 30, 90% by 65
are hereditary syndromes inherited in a dominant or recessive pattern
DOMINANT, even though technically recessive
1 hit already there
Increased chance because mutations occur all the time
What would usually be recessive becomes dominant because if you already have 1 hit then you don’t have a good allele to balance it
hereditary BC - 5% of BC
suggested if multiple 1st degree relatives affected
germline mutations in cancer susceptible genes
cancer susceptibility genes
BRCA1 or 2 - mutations in 25% HBC
others: ATM, CHEK2, p53, PTEN, LKB1
many susceptibility genes unknown
BRCA1 - type of gene
TSG
germ line inherited non-functioning allele in 1 homolog of chr 17
subsequent somatic mutation in BRCA1 in the other homolog of chr 17 of 1 breast cell
potential for neoplastic transformation
summary of BC
multiple mutations must accrue for cancer to develop
cancer progression - the result of
importance of balance
cancer is the result of the accumulation of several genetic and chr changes
often accompanied by reversible epigenetic modifications which perturb the function of 100s-1000s of genes
impact cellular control pathways
BALANCE
uncontrolled growth (tumour) is common and not equal to cancer
if balance between cell division/growth and apoptosis is disrupted can get undifferentiated tumour - more likely to become malignant
match the cancer to the oncogene
should screening for BRCA1/BRCA2 be encouraged to prevent breast cancer
BreastCheck Screening in Ireland
US
Tumour found - staging - TNM, type of tumour, is it in any lymph nodes, biopsy (look under microscope - how poorly differentiated it is)
BC - molecular (gene expression) profiling
evaluation of multiple genes/proteins in parallel
ER, PR, HER2 etc
expressive microarray profiling, quantitative RT-PCR for multiple genes e.g. oncotype DX
genome sequencing
immunohistochemistry
basic science + high throughput clinical studies
helps to guide patient management - surgery? Radiation? Hormone therapy? Chemo?
how does NGS work
RNA sequencing (NGS)
whole exome sequencing
NGS allows for
personalised medicine
causation
progression
recurrence
treatment response
risk prediction
therapeutic development
challenges of NGS in clinical medicine and public health
things to remember
