7. Chromosomal Aberrations Flashcards
1
Q
describe a circus plot
A
outside ring shows all human chromosomes
- blue = deletions, red = gains
- intensity of red/blue = amount of tumours with that deletion or gain
- purple lines show chromosomal translocations
2
Q
describe the packing of chromatin
A
- 30nm fiber forms series of loops that fold to compact the chromatin
- loops wrap around histone proteins
- 300nm fiber has multiple loops
3
Q
what are the 2 major functions of packing chromatin
A
- packages linear info so it occupies as little space as possible
- make specific domains with specific functions
4
Q
why is it important that specific regions of chromatin contacts other regions of chromatin
A
for DNA organization and timing of metabolism
5
Q
what is the assay for determining the specific localization of diff chromosomes? (3 steps)
A
- make tiny damage in nuclei to damage the DNA in small spots
- fed cells with radiolabelled nucleotides
- when DNA was repaired, the areas where DNA was damaged could be detected
6
Q
what were the 2 hypotheses for localization of chromosomes?
A
- all chromosomes have distinct locations in nucleus
- all chromosomes are loose and mixed together
7
Q
what does the radiolabelling assay show if chromosomes have distinct locations?
A
will see damage on very few chromosomes bc the damage will only be in a certain spot
8
Q
what does the radiolabelling assay show if chromosomes are mixed together?
A
will see damage on all chromosomes
9
Q
which hypothesis is correct for the localization of chromosomes?
A
chromosomes are highly organized in specific locations
10
Q
what is the inter-chromatin space?
A
chromosome has loop protruding into inter-chromatin space where processes occur
11
Q
are all chromosomes and different parts of chromosomes in the same regions?
A
diff chromosomes occupy diff regions and diff parts of chromosomes occupy diff regions
12
Q
what is the consequence of diff parts of chromosomes occupying diff regions?
A
this affects gene function
13
Q
where are actively-transcribed genes located on the chromosomes?
A
located far from the centromere
14
Q
do chromosomal territories have uniform or varying levels of compactness?
A
chromosomal territories have varying levels of compactness
15
Q
describe the difference in location of early/late-replicating chromatin in chromosomal territories
A
Early –> center of chromosomal territory
Late –> periphery of chromosomal territory
16
Q
how do genes move around?
A
based on metabolism, active genes will move to the surface of convoluted chromatin fibers
17
Q
what does the inter-chromatin region contain?(5)
A
complexes and non-chromatin domains for:
1. transcription
2. splicing
3. DNA
4. replication
5. repair
18
Q
what happens to chromatin during mitosis?
A
loose chromatin must form compact, cylindrical, chromosomal bodies that can be sorted into daughter cells
19
Q
what is Wee1?
A
S phase checkpoint
20
Q
what does Wee1 control? (2)
A
- speed of replication fork
- replication Common Fragile Site
21
Q
what is the replication Common Fragile Site?
A
this region is replicated late and lags behind –> commonly has mutations
22
Q
why does Wee1 control the replication common fragile site?
A
the common replicating site may still be replicating when the cell wants to divide (bad) so Wee1 controls this
23
Q
what is the spindle assembly checkpoint (SAC)?
A
controls that chromosomes are attached to microtubules for division
24
Q
when is SAC activated?
A
if chromosomes are UNattached
25
what does SAC activation lead to?
MCC forms and blocks mitosis by inhibiting cell cycle proteins
26
when is SAC inactivated?
if chromosomes are attached
27
what does SAC inactivation lead to?
MCC is inactivated and mitosis can proceed so chromosomes can separate
28
why are all chromosomal aberrations NOT equal?
chromosomal aberrations are usually lethal but sometimes a specific combination of chromosomes can make a malignant cell with growth advantage
29
describe the first experiment for observing abnormal chromosomes in CML cells and the results
chromosomes stained with Giemsa at metaphase stage of mitosis --> detects A-T base pairs
found many patients have small chromosome 22, assumed to be a deletion
30
why did they assume the small chromosome 22 was a deletion? what actually occurs in CML?
the resolution of the experiment was low so they couldn't detect that the missing piece of chromosome 22 was actually on chromosome 9 (translocation)
31
describe the experiment to determine that the short chromosome 22 was due to translocation?
stain with QUINACRINE fluorescence and Giemsa staining to give higher resolution and detect translocations --> can detect BREAK POINT and which genes are affected that
32
what genes were found with the quinacrine+giemsa experiment?
BCR on chromosome 22
ABL on chromosome 9
33
describe the BCR and ABL translocations
conserved across patients but slightly diff ones with diff molecular weight
34
what gene forms with BCR/ABL fusion
gene with 5' of BCR and 3' of ABL
35
what happens when proteins fuse in frame?
domains are translated in the correct open reading frame to make chimeric protein with functional domains from both proteins
36
what type of protein is BCR?
serine threonine kinase
37
what type of protein is ABL?
tyrosine kinase
38
what do BCR and ABL do normally when not fused?
normally, each controls differentiation and proliferation from extracellular signals
39
what do BCR and ABL do when fused?
BCR portion activates MAPK
ABL portion activates other survival pathways
less regulation
40
3 phases of CML
1. chronic phase
2. accelerated phase
3. blast phase
41
what happens during chronic phase of CML?
5-6 years
ASYMPTOMATIC
mostly just presence of BCR-ABL
42
what happens during accelerated phase of CML?
6-9 months
symptoms appear
15-50% of myeloid cells gain new cytogenetic abnormalities
43
what happens during blast crisis of CML?
3-6 months
bad cells occupy whole bone marrow and blood and prevent the bone marrow from doing its function --> severe disease
increased genetic instability
44
why do cells with the BCR-ABL fusion protein outcompete the normal cells?
BCR-ABL fusion protein acts as a potent ONCOGENE
45
what is Gleevec?
kinase inhibitor to block BCR-ABL --> very successful
46
what causes resistance to Gleevec
mutation could alter structure of protein or use diff pathway
47
what happens if a patient responds to Gleevec and doesn't reach accelerated phase of CML after 5 years? why?
likely will not reach accelerated phase ever
48
why does the rate of CML relapse depends on the resistant variant at BEGINNING of treatment?
at beginning of treatment, there are cells that are already resistant to treatment --> these will outcompete other cells
So the drug can only work if there are cells WITHOUT resistance at the beginning
49
if you don't relapse, why will you never relapse?
if cells without resistance at beginning of treatment can be killed --> the drug is successful and will not relapse
50
where are most mutations in BCR-ABL found?
most mutations are found in the kinase domain
51
2 general types of chromosomal aberrations
1. balanced chromosomal rearrangements
2. chromosomal imbalances
52
2 types of BALANCED CHROMOSOMAL REARRANGEMENTS
1. Formation of chimeric fusion gene
2. Deregulated expression of structurally normal gene
53
describe deregulated expression of structurally normal gene
enhancer hijacking --> breakpoint puts gene under control of diff promoter, enhancer, etc.
54
2 types of chromosomal imbalances
1. gain
2. loss
55
4 types of genomic GAINS
1. complete trisomy
2. partial trisomy
3. intrachromosomal amplification
4. extrachromosomal amplification
56
what is intrachromosomal amplification?
specific region has been amplified, chromosomes look diff
57
what is extrachromosomal amplification?
sorted independently of chromosome as an episome
58
3 types of genomic LOSS
1. monosomy
2. large-scale deletion
3. submicroscopical deletion
59
what is submicroscopical deletion?
can only detect the change by sequencing
60
2 types of chimeric genes generated from chromosomal translocation
1. Involves tyrosine kinase
2. involves TFs
61
what do chromosomal rearrangements that involve TFs lead to?
fusion proteins that cause ENHANCED, ABERRANT, or REPRESSED transcriptional activity
62
describe the FLI1-EWRS1 fusion protein and its role
forms chimeric TF
maintains DNA binding domain of FLI1 so it recognizes the same target but has diff transactivation property, causing aberrant expression of genes normally activated by FLI1
63
describe the function of PML-RARA fusion protein
conserves DNA binding domain to induce transcription and cause aberrant expression of genes normally activated by RARA
64
what causes deregulated expression of structurally normal gene? and consequence?
loses REGULATION, doesn't lose pieces --> increases selective growth advantage
65
2 examples of deregulated expression of structural normal gene
1. MYC
2. ERG
66
describe normal MYC and dysregulated MYC
normally on chromosome 8 and induces cell survival and proliferation
can be translocated to be under control of heavy chain Ig promoter on chromosome14
67
consequence of dysregulated MYC
when B cells want to make heavy chain Ig, they will make MYC instead
68
describe normal ERG and dysregulated ERG
normally not expressed in prostate tissue
but translocated to other chromosomes and turned on
69
3 groups of chromosomal aberrations found in sarcomas
1. FUSION-DRIVEN
2. NON-TRANSLOCATION-ASSOCIATED
3. HIGHLY UNBALANCED KARYOTYPES
70
how do fusion-driven sarcomas arise?
de novo
71
describe the driver event in fusion-driven sarcomas
may only have 1 cytogenetic abnormality that is maintained --> the driver event is the fusion event
72
most gene fusions from translocations encode:
most gene fusions from translocations encode chimeric TFs that dysregulate genes
73
are gene fusions in sarcomas consistent btwn cases and cells?
gene fusions in sarcomas are HIGHLY RECURRENT and found in all cases and cells
74
4 common themes of fusion-driven sarcomas
1. DBD of TF fuses with transactivation domain of another TF to cause changes in gene expression
2. fusion gene makes constitutively active form of RTK that activates proliferation/survival pathways
3. fusion gene makes chimeric chromatin regulator
4. fusion gene enables autocrine mechanism that feeds tumour thru specific growth factors
75
why is a chimeric chromatin regulator different than TF?
binds DNA less specifically than TF
76
describe PAX3 and FOXO1 separately and the PAX3-FOXO1 fusion
PAX3: TF that directs developmental processes in muscle
FOXO1: TF that is normally regulated thru phosphorylation by AKT
PAX3-FOXO1: DNA binding domain of FOXO1 is lost so PAX3 directs DNA binding
77
is a function of a fusion protein the sum of the 2 proteins?
no, there are other factors involved
78
what disease is FLI1-EWSR1 involved in?
Ewing-Sarcoma
79
why does FLI1-EWSR1 have unexpected/neomorphic function?
fusion protein can bind genes normally targeted by FLI1 but also binds unexpected sites
80
consequence of FLI1-EWSR1
opens chromatin labelled by acetylation to turn genes on/off as a pioneer TF
81
what happens if you overexpress FLI1-EWSR1 fusion protein? (2)
variable results depending on cell type
on non-Ewing sarcoma cells --> may cause neuronal and endothelial features of gene expression
mesenchymal progenitor cells have most similar expression to Ewing sarcoma cells
82
what happens in non-translocation-associated sarcoma?
increased number of chromosomal abnormalities with intermediate genomic complexity
83
what type of sarcoma is commonly non-translocated associated sarcoma?
liposarcomas
84
why is genetic complexity "intermediate" in non-translocated-associated liposarcoma?
all the abnormalities are in chromosome 12
85
what type of abnormality is in liposarcoma? is it high or low prevalence?
gains in chromosome 12 --> high prevalence (90%)
86
what is the non-translocation change that occurs in liposarcoma?
consequence?
oncogenes CDK4 and MDM2 are co-amplified on chromosome 12 to inhibit p53
causes cancer with downregulation of p53 tumour suppressor WITHOUT production of a chimeric protein
87
what occurs in sarcoma with highly unbalanced karyotypes?
complex genomes with many areas of gains, losses, translocations
often aneuploidy with complex cytogenetic changes that lack specificity
88
what do highly unbalanced karyotype sarcomas often involve?
often involves mutated tumour suppressors (p53, Rb)
89
is it common for cancers to have complex karyotypes AND point mutatins?
rare
90
what is called when there is a mix of chromosomal abnormalities and point mutations?
kataegis
91
describe kataegis
hypermutations in regions of structural variants (gain/loss/translocations)
92
is location of structural variants recurrent?
no --> not found among all patients
93
do mutations or structural variants occur first in kataegis?
structural variants occur first, then mutations occur on top of that
94
besides mutations, what occurs in addition to chromosomal abnormalities? (4)
increase of pathways that promote growth:
1. IGF1-receptor pathway
2. PDGFR pathway
3. c-KIT receptor pathway
4. c-MET receptor pathway
95
is the increase of pathways that promote growth independent or related to chromosomal abnormality?
the increase of these pathways is independent of chromosomal abnormality
96
5 ways that genomic rearrangements happen in cancer
1. epigenetic modifications
2. structural configuration
3. dsDNA breaks
4. replication stress
5. ionizing radiation
97
how do structural configurations promote genomic rearrangements?
some parts of DNA can be configured to cause more breaks --> non-typical DNA structure
98
how does replications stress promote genomic rearrangements?
inefficient replication/replication forks can cause stress in DNA
99
is there one factor that must occur for genomic rearrangement to occur?
no, all the diff factors must be combined for rearrangement to occur
100
how does vicinity of genes allow rearrangement? (3 examples)
BCR and ABL in close proximity for CML --> fusion protein more likely in this case
In other leukemia, PML and RARA in close proximity --> fusion protein more likely in this case
MYC fuses more with IgH than IgK bc of proximity
101
why are some gene loci brought closer together under certain circumstances?
active genes are dynamically organized into shared nuclear SUBCOMPARTMENTS --> rather than recruiting and assembling transcriptional machinery at each site, the genes migrate to pre-assembled transcription and become close to other genes
102
how can cells attenuate effects of chromosomal instability?
cells adapt their physiology and homeostasis
103
3 ways cells can adapt their physiology and homeostasis
1. APC/C dysfunction
2. if aneuploidy, will be making more proteins so take over protein synthesis to trigger apoptosis
3. near-triploid karyotype
104
describe APC/C dysfunction to attenuate chromosomal instability
downstream of spindle assembly checkpoint
NORMAL APC/C
- no mitosis
- allows error correction to prevent excessive chromosomal instability
DYSFUNCTIONAL APC/C
- induces tolerance to chromosomal instability
105
describe how tumour cells induce apoptosis to counteract chromosomal aberrations
if aneuploidy and making lots of proteins, will take over ribosomes, protein synthesis, and golgi to trigger apoptosis
i.e. reduce protein load
106
in tumours with high level of chromosomal instability but also high level of tolerance, what type of tumour do we see?
faster growth rate and tumour can be maintained --> this is the tumour we see
107
how do tumours adapt to LOW levels of chromosomal instability?
low levels of instability are selected against and removed
108
how do tumours adapt to HIGH levels of chromosomal instability?
high levels of instability are balanced by tolerance mechanisms
109
what type of cancers are most helpful to diagnose with chromosomal abnormalities? why?
sarcoma --> bc high level of chromosomal abnormalities
110
how can we diagnose sarcomas with chromosomal translocations?
molecular profiling
use FISH probes to visualize fusion proteins to diagnose diff types
111
how are sarcomas defined? how is this different than carcinomas?
defined by their molecular alterations
carcinomas are defined by their organ of origin
112
why is molecular profiling helpful?
can see two sarcomas that seem unrelated but find that they both have same translocation leading to same fusion protein
this helps with treatment --> both will have same resistance and transformation mechanisms
113
how are chromosomal abnormalities related to prognosis?
chromosomal abnormalities are correlated with outcome
114
2 examples of chromosomal abnormalities correlated to outcome
1. copy number status of chromosome 14 and amplification of Gli2 predicts outcome
2. amplification of Gli1 family TFs will be resistant to target therapies
