Lecture 5 Flashcards
What are the four most common features of the nuclear morphology of cancer cells?
- Nucelar shape and magrin irregularities
- Changes to chromatin compaction/texture
- Altered Nuclei
- Variations ins size within a population (polymorphism)
What are the two main types of chromatin?
Heterochromatin- Highly compacted and generally inactive, found around the egde of the nucleus. Replicated in late S phase
Euchromatin - Less compacted and conatins active genes. Replicated in early S phase
How are chromatin loops formed?
scaffolding/matrix attachment regions (S/MARS)
Create 100kb loops
What makes up the nuclear matrix?
Filamentous and granular network of proteins and RNA
What further level os the nuclear matrix has been hypothesised?
The tissue matrix
The matrix connects cells possibly allowing communication
Molecular machines for what processes assemble on the nuclear matrix?
Transcription, splicing and DNA replication at the bases on chromatin loops
What protein is important for ensuring the correct spatial arrangement of genes in the nuclear matrix during transcription?
SATB1
Where will DNA replication occur?
At one of the immobolised sites on the nuclear matrix, spooling DNA through the machinery
Where are chromosomes found in the interphase nucleus?
As chromatid - but each would be chromatid has its own segregated area. But some do mingle for functional reasons
Outline 3C chromatin conformation capture
- Cross link chromatin with associated proteins
- Digest away any chromatin not crosslinked
- Ligate together ends of chromatin
- Analyse the pieces
What is Hi-C?
Uses sequenced product of 3C and whole genome map to map location of associated protein and chromatin in normal nucleus
What is 4C?
Look at interactions from Hi-C over time
How can mingling between the chromatid cause translocation?
Double strand breaks that occur in areas of mingling may be repaired by fusing chromatid from two different chromosomes together
Outline an example translocation seen due to chromatid mingling
BRC-ABL fusion
BCR gene from chromosome 22 and ABL gene from chromosome 9
Creates a tyrosine kinase which is hyper activated - causing cell growth and proliferation. Seen in chronic myeloid leukemia
What are balanced translocation associted with?
Leukemias and lymphomas - which can be cured by chemotherapy
What are unbalanced rearrangements associated with?
Solid tumours - more disorganisation and more difficult to cure
Give some examples unbalanced rearrangements
- Ploidy
- Variation in copy number
- Inversion
- Duplications
- Deletions
- Nonreciprocal translocations
Which nuclear matrix protein has been implicated in unbalanced rearrangements?
High-mobility-group protein (HMGI) in prostate cancer
What two models exist to explain the order in the nucleus matrix?
Derministic model - Underlieing nuclear matrix gives rise to factories
Self-organisation models- Factories form and recruits nuclear matrix proteins
What controls whether cyclin E is soluble or associated with the nuclear matrix?
Differentiation state
Soluble in stem cell
Associated in differentiated cell
Where was cyclin E in cancer cell lines?
Soluble in nucleus - so no control
What does having factors, such as cyclin E, associated with the nuclear matrix give normal cells?
An immobolising platform - which can control and stop cell cycle
Outline the halo method
- Solubilise the nuclear membrane with detergent
- Extract histones
- Nick DNA us UV light and allow chromatid to spread out from attachment points on nuclear matrix to full length
How does the addition oncogenes affect the halo?
Giving H-Ras to immortalised cells causes halo to increase in size
Addition of oncogenes past immortalisation will decrease stability of the halo
What is nuclear morphology traditionally used for?
Staining and visualisation down the microscope used by pathologists for cancer diagnosis
What can nuclear morphology tell pathologists?
The grade of a tumour but not the stage
What could be used as a replacement to nuclear morphology?
Biomarkers
High content imaging
High throughput
What could be used as biomarkers for cancer cells?
Nuclear matrix protein
E.g. NMP22 - however, not tumour specific can only be used if know base level of NMP22 so can see if increases on cancer reoccurence
