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Molecular Genetics College Notes (5052MOGE6Y)
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Summary of the molecular genetics courses during the third year of the bachelor's degree in biomedical sciences at the UvA
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Lecture 1 NeuroblastomaNeuroblastoma is childhood tumor, can happen very early (peak incidence: 0-4
years). Sometimes even at birth. Is tumor of peripheral sympathetic nervous system.
is 10% of all tumors and about 30 cases per year. Very often leads to fatality.
Mostly located in abdomen and associate with adrenal gland
Primary tumor: adrenal gland, peripheral nerve.
Metastasis: bone, bone marrow, liver.
Low stage tumors: localized diseased
High stage: neuroblastoma are metastasized at diagnosis
Have stage 1-4 and then also 4S, where 1 is low stage and 4 is high stage. Stage 4S
has metastasis limited to skin and liver.
Neuroblastoma does not represent progressive stages, so stage 3 and 4 are
diagnosed as such.
Stage 4S
- S= special
- Has nothing to do with stage 4
- Metastasis to liver
- Spontaneous regression
- ‘wait-and-see’ in the clinic → not doing a lot of treatments
- Good prognosis
First diagnosis to see which stage it is. Then several rounds of chemotherapy, usually
combination of therapies (high dose). Usually then remission. Remaining tumor
material removed during surgery, as much as possible. Often then stem cell
transplantation for new bone marrow. And then often followed by consolidation
therapy → differentiational therapy or immune therapy → keep disease low.
In stage 4 only about 40% survival rate.
Major problem → firstly in regression where tumor falls under detection limit. But
eventually after few years often relapse of the tumor and then they are fully
resistance to therapy. So no response to earlier treatment nor to new treatment. So
die from the relapse mostly.
Nervous system cells originated from neural crest. Then migrate and then
differentiation (EMT) into lineage-committed precursors. Can then differentiate into
adrenal chromaffin cells and sympathetic ganglia.
Expression of PHOX2A and PHOX2B are specific for neuroblastomas, they regulate
DBH → also specific for neuroblastoma. DBH is essential for conversion dopamine to
noradrenalin. Neurobalsts are precursors of adrenalin-producing cells → neural crest
gives rise to neuroblasts.
Neuroblastoma diagnosis: MIBG scintigraphy
, - Tyrosine → dopa → dopamine → noradrenalin → adrenalin
- Differentiated neuroblasts produce adrenalin
- They express adrenalin re-uptake receptors
- Meta-iodobenzylguanidie (MIBG) → binds to re-uptake receptors
- So light up on a scan
Genes that drive neuroblastoma
- Amplification of MYC oncogene in neuroblastoma
o With this amplification the survival rate drops dramatically
o Use THpromotor-MYCN transgenic mouse → without MYCN they survive,
but with overexpression they all die due to tumors.
- Mutations in PHOX2B
o Mutations: expansion of alanine tract at C term of protein
o Mutations act as repressors
o Mutant represses DBH, while wild-type activates DBH
o PHOX2B: master gene sympathetic nervous system development
- ALK is recurrently mutated in neuroblastoma
o Is a kinase. Intracellular domain has different regions that can be
mutated
o When you overexpress mutated ALK this leads to activation of different
downstream signaling pathways, so the mutations are activating
mutations
o Mutant ALK is oncogenic in mice since activation of the gene led to
arise of neuroblastoma’s
o Can use crizotinib to inhibit the ALK and induce tumor regression. Works
a little bit so need other options. Other one really kills the tumors. Works
for different mutation sites
2
,Lecture 3 Genomic defects in cancer
Neuroblastoma
- Frequent loss of one copy of chromosome 1p36, 11q and 14q
- Probably reflecting tumor suppressor gene inactivations
- 1980-2012: difficult to identify → had to await full genome sequencing
But whole genome sequencing did not identify mutations in 1p36, 11q or 14q
There are very few mutations in childhood tumors
No tumor suppressor genes inactivated by chromosomal deletions.
Chromosomal deletions are frequent and recurrent
Color coding the genome for loss and gain gives overview of patterns in type of
cancer.
Low stage neuroblastoma → whole chromosome gains and losses
High stage neuroblastoma → partial chromosome gains and losses (deletions,
insertions)
- Pattern 1; +17q, -1p, MYCN amplification
- Pattern 2; +17q, -11q, +7, -3p
- Pattern 3; +17q, +7
So copy numbers matter. Many consistently deleted and gained regions in
neuroblastoma genomes. Deletions/gains are more consistent than mutations.
Deletions do not reflect homozygous inactivation of classic tumor suppressors. Low
stage neuroblastoma only have chromosomal imbalances, no recurrent mutations.
Can chromosomal copy number aberrations cause diseases? → YES
- Trisomy 21 → down syndrome
- Trisomy 13, 14 → very severe syndromes
- Any other trisomy → prenatal lethal
- 1 copy lost; 30-50% reduction in expression of hundreds of genes
Cancer pathways consist of hundreds of regulatory genes.
Copy number defects could have exponential regulatory effects →
way more signaling.
All assays were directed to the detection of mutated genes, no assay
exists to measure effect of chromosomal gains and losses.
Chromosomal imbalance may be major cause of cancer as well. Evident in
childhood tumors, as they have few gene mutations. Adult cancers have way more
mutations, masking role of chromosomes. Adult equally frequent chromosomal
defects as childhood tumors. Gains and losses form recurrent patterns. Mechanism
of action might be activation of pathways by gene dosage effects.
3
, Lecture 4 Epithelial-mesenchymal transition
Relevance of EMT in neuroblastoma
1. Sequencing hardly identified mutated genes in neuroblastoma
➔ Neuroblastoma remained poorly understood
2. Discovered two divergent neuroblastoma cell types
3. Adrenergic (ADRN) and mesenchymal (MES) neuroblastoma cell types
4. Analogy with epithelial-mesenchymal transition (EMT)
In EMT you have epithelial cells that
are connected to each other
through different connections such
as tight junctions. And attached via
integrins to basement membrane.
In transition the connections are resolved and start to loose contact with neighbors.
Then able to go through basal membrane and go into body, leaving epithelial.
EMT = loss of epithelial characters and acquire mesenchymal features.
Mesoderm EMT → epiblast gives rise to different cell types
Neural crest EMT → epithelial cells undergo transition and move
downstream where they differentiate into different cell types such as
neurons
EMT is necessary for development but can also cause disease in like
fibrosis. Also known to play role in tumor progression, where the cells can detach
and invade local tissues and bloodstream → metastasis.
EMT is reverse of MET (mesenchymal-
epithelial transition)
Core transcription factors orchestrating EMT
- Snail
- Slug
- Twist
- Goosecoid
- FOXC2
- ZEB1
- ZEB2
4
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