Chromosome Abnormalities and Cancer Cytogenetics

In 1960, Peter Nowell and David Hungerford discovered the first chromosomal abnormality associated with cancer using cytogenetics (Nowell & Hungerford, 1960). Specifically, they identified an abnormal minute chromosome that was present in patients with chronic myeloid leukemia, a form of cancer that causes unrestricted growth of myeloid cells in the bone marrow. Nowell and Hungerford named the minute chromosome the Philadelphia chromosome, and the alteration associated with this chromosome was presumed to be a deletion. Later, in 1973, Janet Rowley used new cytogenetic techniques, namely quinacrine fluorescence and G-banding, to examine patients' karyotypes, and in doing so, she discovered that the Philadelphia chromosome actually formed from a specific translocation of DNA between chromosomes 9 and 22. This translocation shortened chromosome 22 to form the Philadelphia chromosome (Ph¹), while simultaneously lengthening chromosome 9 (9q⁺), as shown in Figure 1 (Rowley, 1973). But how does this DNA rearrangement trigger leukemia? It turns out that the translocation leads to the formation of an abnormal, fused gene called bcr-abl, which codes for an aberrant, new protein. This abnormal protein functions as a kinase molecule, which is constitutively, or always, active and can, in turn, activate cell cycle controlling proteins and enzymes (Trask, 2002). This interferes with normal cell cycle regulation and allows cells that express the aberrant protein to divide more rapidly. Such unrestricted cell growth can result in cancer.

Since the discovery of this particular chromosomal rearrangement, thousands of other chromosomal aberrations have been determined to be associated with cancer (Mitelman, 2005). These chromosomal changes are the signature of gene deregulation in cancer and lead to instability of the genome (Albertson et al., 2003). Chromosomal changes are highly variable in different cancers, and the resultant phenotypic effects are equally variable.

Although chromosomal changes are highly variable, they can be grouped into two general categories. In balanced structural changes, the genetic material is exchanged evenly. An example of a balanced structural change is the Philadelphia chromosome translocation previously described. In that case, although genetic information was rearranged into an abnormal gene, it resulted from an even exchange of DNA. Conversely, in nonreciprocal or unbalanced structural changes, the exchange is not equal, and genetic material is added or lost. This can range from the loss or gain of a single base pair to the loss or gain of entire chromosomes.

Scientists have hypothesized that the primary pathogenetic changes in cancer result from balanced rearrangements, while the secondary changes that occur during cancer progression are from unbalanced changes (Mitelman, 2005). Cancer is a multistep, progressive disease, and early chromosomal changes provide the cell with a proliferative advantage. Often, these changes hijack or interfere with the normal cellular control mechanisms by disrupting proto-oncogenes and tumor suppressor genes and allowing additional changes to occur in the genome. Different types of chromosomal changes and the cytogenetic methods commonly used to identify them are shown in Figure 2 (Albertson et al., 2003).

Cancer cells generally gain multiple types of chromosomal aberrations during tumor progression, including rearrangements, deletions, and duplications. As a result, the genome becomes progressively more unstable.

So far, technical methods for detecting cytogenetic changes have favored detection of hematological cancers, or cancers of the blood, such as leukemias; however, the majority of human cancers are solid tumors. Balanced chromosomal changes have been detected in 30% of acute leukemias but only in 5% of epithelial cancers (Mitelman, 2005). This is because hematological cancers can be detected earlier, when the cells have fewer cytogenetic changes. In contrast, solid tumors are often diagnosed later, after a multitude of unbalanced chromosomal mutations have taken place.

Mutations that provide growth or other advantages to cancer cells accumulate at different times during cancer progression, so cells in solid tumors are generally heterogeneous when the cancer is detected. A schematic illustration of epithelial tumor progression is shown in Figure 3 (Albertson et al., 2003). A single mutation in a single cell can allow the cell to escape from its normal tissue organization. An example is the loss of the adenomatous polyposis coli (APC) tumor suppressor gene, which occurs in many colorectal cancers (Fearon & Vogelstein, 1990). Additional mutations in genes such as RAS, CCND, CMYC, CDKN1A, or RB1 can allow a cell to deregulate its normal cell cycle controls, to live longer, and to increase its proliferation (Albertson et al., 2003). Cancer is clonal in origin and begins from mutations like these within a single cell that provide an environment for abnormal cell growth. As a tumor develops, the genome grows more unstable and complex. The telomeres can erode, centromeres might be duplicated, and double-stranded breaks might occur as cancer development progresses. Eventually, the instability of the genome results in more complicated karyotypes as a cancer becomes invasive and metastatic (Albertson et al., 2003).

This complexity can complicate the process of identifying the critical early mutations that promoted the development of the cancer and genomic instability. In fact, to identify common early changes, it is necessary to characterize many clonal lines and identify common mutations. These mutations and aberrations can be identified using modern cytogenetic approaches, including fluorescence in situ hybridization, PCR-based screening, copy number measurements, and comparative genomic hybridization. The common mutations are more likely to be relevant early in cancer development. Therefore, identification of these mutations is critical in order to consistently diagnose cancer at early stages and provide targeted therapies.