12. Chromosomes and Cancer 1 Flashcards
1. Types of chromosome abnormalities in cancers 2. How these lead to activation of oncogenes and inactivation of tumour suppressor genes. 3. Common chromosomal defects in tumours
What is cytogenetics?
The study of the genetics of the cell and the number of chromosomes and how this leads to cancer
What is FISH?
Fluorescent in situ hybridisation
How is FISH done?
- Fluorescent probes that are specific to bits of the chromosome
- use the markers to decorate the chromosomes
- identify changes and abnormalitites
What is CGH?
comparative genomic hybridisation
How is CGH done?
- Take a sample of normal DNA to be control DNA and label with red
- Take a sample of cancer DNA and label it green
- see lots of red = loss of DNA in the tumour sample
- see lots of green = gain of DNA in the tumour sample
What is a human karyotype?
- Chromosomes are organised into a karyotype according to the size of the chromosomes, largest to smallest
- Chromosomes are recognised by size, position of the centromere and the banding
- most recognition is done by position of the centromere
What are banding patterns?
- Stained using Giemsa
- dividing and sub dividing the chromosome into regions
- easy identification and for communication with other labs
What are telomeres?
- sections of the DNA that protect the ends
- If the cell sees the linear DNA ends it sees them as breaks as tries to repair them
- telomeres signal the cell to not repair the ends
What stain is used for banding patterns?
Giemsa
What do banding patterns show?
- they divide the chromosome up into regions
- and further into subdivisions
- can use the specific banding patterns to identify abnormalities and locations
Why were banding patterns really useful?
It gave specific locations on the chromosome when you could just send a photo of where to look
What is the international system for chromosome nomenclature?
name in this order:
1. the total chromosome number
2. sex chromosomes
3. gains and losses of whole chromosomes
4. structural rearrangements
What does 47, XX, +8 mean?
1 gained chromosome.
the patient is female.
there are 8 gained regions.
What does t(9;22)(q34;q11) mean?
A translocation between chr9 and chr22 between the regions q34 on chr9 and q11 on chr22
Changes in banding patterns: deletions
Smaller bands
Changes in banding patterns: duplications
larger bands
Changes in banding patterns: pericentric inversion
Much larger band that crosses the centromere
Changes in banding patterns: paracentric inversion
larger band that doesn’t cross the centromere
Changes in banding patterns: insertions
Extra bands or different bands
What are the 2 types of karyotypic differences in cancer cells?
- changes in the structure of individual chromosomes like insertions, deletions and translocations
- changes in the chromosome number
What are chromosomal abnormalities that can contribute to carcinogenesis?
- chromosome abnormalities that are initiating events and increase the risk of developing cancer
- Chromosome instability that accelerates tumour progression
What chromosome abnormalities can be initiating events?
- mutations as a result of exposure to clastogens
- chromosome instability syndromes
What are clastogens?
a compound that causes DNA breaks
What chromosomal abnormalities accelerate tumour progression?
- defects in DNA repair
- defects in chromosomal segregation
What are primary abnormalities?
chromosomal abnormalities that are involved in establishing the tumour
What are secondary abnormalities?
chromosomal abnormalities that occur after the tumour has developed and may be important in tumour progression
What is cytogenetic noise?
chromosomal abnormalities that are causing disturbance in the genome but they don’t contribute to the cancer.
(A background level of non-consequential abnormalities)
Ways of gene amplification: Trisomy
- There are more copies of the gene so the copy number increases and proteins are over expressed.
- This gives a fitness or growth advantage to allow survival in harsh environments
Ways of gene amplification: duplication of part of the chromosome
- Isochromosomes where the p arm is lost and the sequences are replaced by duplicating the q arm sequences
- This increases the number of the copied gene and therefore the amount of expression
Ways of gene amplification: Tandem repeats
- many repeats of the same allele
- the more repeats correlates with a more aggressive tumour
- examples include MYCN
- Visualise using stains
What are homogeneously staining regions?
the regions of tandem repeats stained to visualise the scale of the amplification and is an important diagnostic tool
Ways of gene amplification: small repeat sequences
Microsatellites or short tandem repeats = <10 nucleotides
Minisatellites or variable number tandem repeats = 10-60 nucleotides
More repeats can cause gene amplification
Ways of gene amplification: Double minutes
- Very small pairs of extrachromosomal DNA that form a loop
- A sign of amplification and gives the cell an advantage
- double minutes frequently contain oncogenes
- replicated with the cells but segregation doesn’t occur and uneven numbers end up daughter cells
How can gene inactivation of TSGs occur?
- Deletions
- Whole chromosome loss (aneuploidy) usually due to a segregation error
- mutation in the second allele
What should the ratio of chromosome number to gene number be?
1:1
How can small deletions be detected?
Using FISH to label the genes and the chromosomes and count the numbers of colours
What are the common chromosomal defects in haematopoietic tumours?
- rearrangements involving only a few abnormal chromosomes in an otherwise diploid cell
- many cells dividing
What are the common chromosomal defects in solid tumours?
- numerous chromosome rearrangements with gross aneuploidy
- chromosome preparations are harder due to fewer dividing cells
- It is harder to obtain biopsies in solid tumours also making it harder to study
What is Burkitt’s lymphoma?
A highly aggressive B-cell lymphoma
What are the causes of Burkitt’s lymphoma?
- Translocation: t(8;14)(q24;q32) which causes 75-85% of cancers
- translocation: t(8;22)(q24;q11)
- translocation: t(2;8)(p12;q24)
The break point is always q24 on chr8
What is the main oncogene in Burkitt’s lymphoma?
- c-Myc
- protein is unchanged in its amino acid sequence but is constitutively produced at high levels
- This means the cells are prevented from exiting the cell cycle leading to uncontrolled proliferation
Details of the Burkitt’s lymphoma translocation
- Myc region on chr8 moves to the IgH region on chr14
- IgH is an immune loci so it has enhancers to keep expression high
- by putting myc into the Ig loci it also is constitutively expressed
How can we view burkitt’s lymphoma translocations?
using FISH
What is Follicular lymphoma?
The most common indolent (lazy) B-cell lymphoma
What causes follicular lymphoma?
translocation t(14;18)(q32;q21) which moves the bcl-2 gene with to IgH region
What is the t(14;18) translocation used for?
Diagnosis and monitoring of lymphomas with high prevalence for this aberration
What are the consequences of the translocation t(14;18)(q32;q21)?
- The entire coding sequence on bcl-2 is translocated
- same protein just produced in significantly higher levels
- bcl-2 prevents apoptosis so in follicular lymphoma the cells don’t die
- this mutation doesn’t increase cell proliferation
- bcl-2 often interacts with c-myc mutations
- This translation can also be a 1st hit in somatic cancers
What is chronic myeloid leukaemia?
- A clonal bone marrow disease
- abnormality happens in the pluripotent stem cell phase so all haematopoietic lineages
- accounts for 1/4 of all leukaemia cases in the western world
- CML was the 1st malignancy to be linked to a clear genetic abnormality called the Philadelphia chromosome
What is the Philadelphia chromosome?
- present in 90% of cases of CML
- A truncated chr22 generated by the reciprocal translation between chr9 and chr22
- t(9;22)(q34;q11)
- results in the fusion protein bcr-abl
bcr-abl fusion protein generation
- proto-oncogene c-abl moves from 9q34 to 22q
- the 1st exon of c-abl remains on chr9
- 1st and 2nd exons of bcr gene fuse to the rest of c-abl
- This fusion makes bcr-abl
What is the function of c-abl?
A tyrosine kinase which is involved in signalling pathways for growth and DNA repair
What is the difference between bcr-abl and c-abl?
- bcr-abl has enhanced tyrosine kinase activity driving cell proliferation.
- prevents DNA repair pathways and increases genome instability
- both promote tumorgenesis
How can we use bcr-abl origins to develop treatment?
- we can design an inhibitor to prevent the tyrosine kinase activity and signalling
- A drug called Gleevec
- Shows how understanding the origins of a disease is important for finding treatments
What was the development for Gleevec like?
- Thought it could be a wonder drug
- Couldn’t originally get the funding so had to use it as a proof concept to apply to loads of other cancers
- Was tested on 30 patients and all showed improvement and has been used clinically since
- transformed survival from <5 years to 10+ years
- Major benefit is significantly less side effects and toxicity
