Pocket Oncology (Pocket Notebook Series), 1st Ed.

CYTOGENETICS

Chung-Han Lee

Cytogenetics

• Definition: The study of the structures of chromosomes as related to the structure & function of the cell

• Nl: 46 chromosomes, 22 pairs + XX vs. XY

Chromosomes numbered from largest to smallest chromosomes

Chromosome joined by central centromere

Short arm = p arm

Long arm = q arm

• Aneuploidy: Additions or deletions of entire chromosomes

Karyotyping

• The principle:

Cells are arrested in metaphase, while chromosomes are condensed

Cells/chromosomes are stained w/a dye

Images of the chromosomes are isolated & compared

• The observed info:

Differences in absolute size of chromosomes

Differences in position of the centromeres

Differences in relative size of the chromosomes

Differences in numbers of chromosomes

Differences in position & number of satellites

Differences in degree & distribution of heterochromatic regions

• Reciprocal translocations:

AKA balanced translocations

Rearrangement of part between nonhomologous chromosomes

No net loss of genetic data; however, genes may be disrupted at the translocation sites

At translocation sites, fusion genes created vs. genes prematurely terminated

• Unbalanced translocation:

AKA Robertsonian translocation

Fusion of two chromosomes near the centromere typically leading to loss of the p arms

Often occurring w/chromosomes 13, 14, 15, 21, 22

Fusions of 13 & 14 do not lead to loss of genetic material

• Nomenclature more commonly seen in oncology:

Selected Translocations in Oncology

Fluorescent in Situ Hybridizations (FISH)

• Goal: Detection of the presence or absence of a specific seq of DNA

• The Principle:

Probes are generated that are complementary to the gene/seq of DNA of interest

Fluorophores are attached to the probes to allow for detection

Tissues or cells are fixed & permeablized

Probes are allowed to hybridize to the permeablized samples

Fluorescence is detected as a marker for the gene of interest

• Applications:

Gene amp

Gene deletions

Gene translocations

• Benefits:

Specific probes can be designed to detect multiple targets simultaneously

Multiple cells can be assayed simultaneously

Spatial organization of the genes can be assayed

• Limitations:

Detection of targets depends on design & quality of the probes

Target identities must be known in advance to design probes

• Select Targets for FISH in oncology

Therapeutic Application of Cytogenetics

Risk Stratification in AML (JCO 2011; 29:487)

Del(3p) in multiple solid tumors

87% breast CA, 97% lung CA (Cancer Res 2000;60:1949)

87% kidney CA (Nature 2010;463:360)

Congenital 3p loss: Low birth weight, microcephaly, trigonocephaly, hypotonia, intellectual disability, growth delay, ptosis of eye, micrognathia, polydactyly, renal/heart/GI/ear abnormalities

Sx depend on size of 3p deletion

Critical deletion @ 3p25

Multiple TSGs likely on 3p

3p loss-dependent pathogenesis in solid tumors remains to be determined