Genetic Changes in Cancer Part One

Question 1

Outline cytogenetic preparation required for leukaemia bone marrow samples.

Answer 1

• Nearly always going to be a bone marrow sample when talking about leukaemia - occasionally will get a blood sample. Should not be receiving a blood sample unless sure that there are a significant proportion of the leukaemic cells within this. Blood is not an ideal sample.
• Fresh BM and blood is cultured for between 1 and 96 hours.
• Cells are generally spontaneously dividing so a mitogen is not usually required. The cells we are interested in should be the ones that are spontaneously dividing. Are some exceptions - may use mitogens when looking specifically at a T-cell or B-cell disease.
• Usually work with multiple cultures and base the leukaemia analysis on 2, 3 or more cultures.
• It is usual to establish the number of cells in your cultures at the start. Most cells will do some sort of lab count or dilution process to make sure that they don’t overseed their cultures.

Question 2

Outline the issues with cytogenetic nomenclature that are key to leukaemia analysis.

Answer 2

• In most other cases we are working with diploid preparations.
• There are certain important words in defining chromosome numbers within a cell - e.g. haploid (n), diploid (2n).
• Hypodiploid = 35-45 chromosomes.
• Hyperdiploid = 47-57 chromosomes.
• Pseudodiploid = 46 chromosomes (abnormal).
• Near triploid = number close to 69 (3n).
• May have to describe a chimera (such as post BMT) - separated by //
• [*] square brackets signify the numbers of cells within a cell line.
• Will have difference cell lines to present - related abnormal clones presented in order of evolution. Normal cells always presented last separated by /.
• Where cells vary but have a consistent clonal pattern a composite karyotype may be written - cp[*].

Question 3

How many chromosomes would are present if a cell is described as ‘hypodiploid’?

Answer 3

• Hypodiploid = 35-45 chromosomes.

Question 4

How many chromosomes would are present if a cell is described as ‘hyperdiploid’?

Answer 4

• Hyperdiploid = 47-57 chromosomes.

Question 5

How many chromosomes would are present if a cell is described as ‘pseudodiploid’?

Answer 5

• Pseudodiploid = 46 chromosomes (abnormal).

Question 6

How many chromosomes would are present if a cell is described as ‘near triploid’?

Answer 6

• Near triploid = number close to 69 (3n).

Question 7

In cytogenetic nomenclature what symbol is used to describe a chimera?

Answer 7

• // is used to separate the karyotype descriptions.

Question 8

What are square brackets used to signify in cytogenetic nomenclature?

Answer 8

• [*] used the signify the number of cells within a cell line.

Question 9

How do we present related abnormal clones using cytogenetic nomenclature?

Answer 9

Will have difference cell lines to present - related abnormal clones presented in order of evolution. Normal cells always presented last separated by /.

Question 10

When you have a complex marrow and almost every cell is slightly different but they have common themes what ‘cheat’ may we use to describe it using cytogenetic nomenclature?

Answer 10

• Where cells vary but have a consistent clonal pattern a composite karyotype may be written - cp[*]. Basically combine all the information into a single karyotype and use the letters ‘cp’ to signify a composite karyotype.
• Can also use inc[*} when it has been analysed as well as possible but is incomplete.

Question 11

What genetic information do clinicians tend to want to know about a leukaemia sample?

Answer 11

Clinicians will usually want to know:

• The cell number/ploidy.
• If abnormal diagnostic rearrangements are present.
• If there is a robust prognostic association.
• Interpretation in relation to stage of disease.

Question 12

What are the categories of acquired genetic change in cancer?

Answer 12

1) . Formation of a chimeric protein.
2a) . Gain
2b) . Amplification (of a gene or of a product).
3) . Deletion/loss of function of a gene.

Question 13

1). Discuss the formation of a chimeric protein as an acquired genetic change in cancer.

Answer 13

• Fusion of 2 genes to produce 2 new chimeric genes > chimeric proteins.
• Usually involves a transcription factor.
• Results in a change to the control mechanism of the transcription factor - often removes the transcription factor control element.
• Transcription factor continuously switched on.
• Cascade of other genes switched on as a result - uncontrolled transcription factor can go off and switch other genes on.
• Single genetic change that has enormous potential to produce changes down the line.
• Chimeric protein forming rearrangements are usually balanced chromosome rearrangements - translocations, inversions, insertions.
• Often diagnostically specific e.g:
• t(9;22)(q34;q11) in CML
• t(15;17)(q22;q11-21) in AML
• Inv(16)(p13q22) in AML
• t(11;22)(q24;q12) Ewings/PNET/Askins

Question 14

In what cancer would may the following inversion be found in? - t(9;22)(q34;q11)

Answer 14

• CML - forms the philadelphia chromosome
• Is also seen in other leukaemias but if a sample comes in specifically querying CML and it has this mutation then the answer is yes.

Question 15

In what cancer would may the following inversion be found in? - t(15;17)(q22;q11-21)

Answer 15

AML (formerly AML M3/APML).

Question 16

In what cancer would may the following inversion be found in? - Inv(16)(p13q22)

Answer 16

• AML (formerly M4Eo)

- AML subtype with eosinophilia - associated with good prognosis

Question 17

In what cancer would may the following inversion be found in? - t(11;22)(q24;q12)

Answer 17

Ewings/PNET/Askins.

Question 18

What is the translocation that results in the formation of the Philadelphia chromosome?

Answer 18

t(9;22)(q34;q11) - CML

Question 19

2). Discuss how cancers can arise as a result of the increase of a gene (copy number) or gene produce.

Answer 19

• Increase in copy number of an oncogene
  OR
• Increase in the rate that the oncogene is expressed.
• Increase in copy number of a gene occurs due to the gain of copies of a gene or genes by unbalanced cytogenetic abnormality.
• Can get duplication of part of a chromosome, gain a whole chromosome, or get the amplification of a smaller segment of DNA including an oncogene in the form of double minutes (dmin) or homogeneous staining regions (hsr).
• An example of an increase in gene copy number causing a cancer is the gain of chromosome 8 leading to MDS/AML. Very non-specific finding but is generally specific to myeloid disease. Often sole abnormality but may be seen as part of a more complex karyotype. No specific prognosis or disease subtype is indicated by trisomy 8.
• Gaining copies of a gene by amplification can be a bit more diagnostically specific. Amplification of a gene is a many-fold increase in copy but is defined differently for different diseases - e.g. in neuroblastoma an increase in copy number in excess of a fourfold increase relative to ploidy level. Usually many fold increase.

Question 20

What type of cancer is trisomy 8 usually a marker for?

Answer 20

Myeloid-derived cancers.

Question 21

Give an example of where a copy number increase may lead to cancer.

Answer 21

An example of an increase in gene copy number causing a cancer is the gain of chromosome 8 leading to MDS/AML. Very non-specific finding but is generally specific to myeloid disease. Often sole abnormality but may be seen as part of a more complex karyotype. No specific prognosis or disease subtype is indicated by trisomy 8.

Question 22

What might be seen on metaphase analysis that could reveal the amplification of an oncogene in a Neuroblastoma case?

Answer 22

• Double minutes containing many copies of MYCN can be seen on analysis of metaphase spread.
• Double minutes can be FISH probed for the MYCN gene.
• The difference between ‘gain of’ and amplification is huge - talking hundreds of extra copies of MYCN.

Question 23

2b). Discuss how cancers can arise as a result of the increase of the expression of a gene rather than copy number.

Answer 23

Up-regulation of an oncogene.
- A balanced rearrangement can place an unaltered oncogene next to the promoter of another highly transcribed gene region resulting in massive up-regulation of the oncogene - e.g. translocations between the control elements of immunoglobulin gene loci (which are expressed at a high level in B-lymphocytes) and oncogenes in lymphoid malignancies.

• e.g. t(8;14)(q24;q32) in ALL and Burkitt’s lymphomaa

variant forms t(2;8) (IGK/MYC) and t(8;22) (MYC/IGL).

Question 24

Give an example of a cancer that arises as a result of the increased expression of a gene.

Answer 24

• e.g. t(8;14)(q24;q32) in ALL and Burkitt’s lymphomaa

variant forms t(2;8) (IGK/MYC) and t(8;22) (MYC/IGL).