Cytogenetics and molecular genetics of soft tissue tumors and bone tumors

Abstract

This chapter presents the genetic changes (cytogenetic and molecular) in bone tumors and soft tissue tumors applicable to fuller understanding and evaluation of their in the clinical setting. Thus, in keeping with the aims and nature of this volume, the genetic changes are addressed primarily to radiologists,but also to orthopedists, oncologists, and surgeons. The genetic changes in tumors can be established by a number of methodologies: cytogenetics, fluorescence in situ hybridization (FISH), and molecular approaches [1, 2]. Chromosomal (karyotypic, cytogenetic) changes in human tumors are confined to the involved tissues and cells and are not reflected in other somatic cells, e.g., blood cells. The establishment of chromosomal changes in a tumor requires fresh (not fixed) tissue; following short-term culture, dividing cells can be examined in late prophase or metaphase, when the chromosomes are morphologically well defined and readily recognized. These chromosomal changes may be either numerical (gain or loss or chromosomes) or structural (morphological; Fig. 7.4). Since space limitations for this chapter preclude detailed presentations of cytogenetic terminology (Figs. 7.17.4) and of the genetics of soft tissue and bone tumors, proportionally more space has been given to pictorial presentations (Figs. 110). The salient cytogenetic changes in these tumors are listed in Tables 1 and 2, accompanied by short discussions of particular tumors. Human tumors are primarily caused by anomalies affecting two types of genes: (1) Dominantly acting oncogenes, whose protein products serve to accelerate cell growth and whose functions are altered by increased gene dosage (amplification) or by activating mutations or participation in fusion genes, resulting from chromosomal translocations, inversions, or insertions; and (2) tumor-suppressor genes (TSG), whose products normally serve as brakes on cell growth and runaway cell proliferation and whose inactivation leads to uncontrolled cell proliferation and downregulation of apoptosis (programmed cell death). Such inactivation is typically altered by physical elimination of TSG or by inactivating mutations (Fig. 7.7). The recurrent and specific translocations in many soft tissue and bone tumors are unique in that they are diagnostic of the tumor and usually affect the oncogenes that have been identified in almost all of these conditions (Table 7.1). The translocations lead to the genesis of abnormal fusion genes of varying parts of the oncogenes involved and result in the mutation and/or overexpression of components of the fused genes. The occurrence of specific chromosome changes in benign tumors (e.g., lipoma, leiomyoma; Table 7.2), i.e., translocations, as well as nonspecific changes in a number of others,bears witness to the role of genetic events in cellular proliferation but without malignant aspects. In parfact, the specific chromosome alterations in benign tumors not only serve diagnostic purposes, but also serve as a means of differentiating them from their malignant counterparts (e.g., liposarcomas, leiomyosarcoma). Some of the genes (particularly TSG) affected in malignant tumors may be involved in the genesis of benign tumors. In fact, the same genes can be altered in a number of different tumors, but apparently at varying chronologies in tumor development and associated with different genetic changes and milieus (Fig. 7.10). The preponderant number of human cancers, including tumors of the bones and soft tissues, are not characterized by specific translocations affecting oncogenes, but develop through a stepwise and orchestrated sequence of genetic events, primarily loss of heterozygosity (LOH) of TSG (Fig. 7.10). Some of these losses are evident as deletions of chromosomal material established microscopically, ranging from partial loss of a band to loss of the whole arm of a chromosome or a whole chromosome. Other LOH changes are submicroscopic. Advantage has been taken of the composition and structure of fusion genes by tailoring therapies affecting the function of these genes, e.g., blocking of expression of the mutated tyrosine kinase present in the fusion gene of chronic myelocytic leukemia and in the mutated KIT gene in gastrointestinal stromal tumors (GIST). The uniqueness of such therapy is reflected by the successful treatment of GIST with imatinib, which inhibits the tyrosine kinase of KIT, but only if the mutation occurs at exon 11 and not, for example, at exon 17. In many tumors specific translocations may be the only alterations; however, in a significant number of cases, additional karyotypic changes appear and are possibly responsible (or at least associated with) progression of the disease. This is also reflected by alterations in the expression of a number of genes (not evident microscopically and hence cytogenetically) aside from those involved in the translocation. The exact cause(s) for these alterations is not known, i.e.,whether the translocation per se is responsible or the process leading to the translocation or other factors. In some of these conditions, e.g., Ewing-type tumors (Table 7.1), variant translocations may occur, but they always involve the EWS gene located on chromosome 22. The genetic and molecular consequences of inversions and insertions, quite rare events in soft tissue tumors and bone tumors, are probably similar to those associated with translocations in that they lead to the genesis of fusion genes. The specific translocations shown in Table 7.1 are diagnostic of the tumors in which they are found; they have not been observed in other tumor types and can be of crucial value in establishing the correct diagnosis in confusing cases.As mentioned above, fresh tumor tissue is required for cytogenetic analysis and, hence, both the surgeon and pathologist must be alert to the possibility of a tumor requiring cytogenetic analysis and obtain appropriate tissue for such an analysis. Such an alert could originate with the radiologist (see Things to remember). Having failed to obtain fresh tissue for cytogenetic analysis, the presence of specific translocations can be established by several interphase FISH techniques, par ticularly with cosmid probes, which can be applied to frozen or archival tissues. In fact, results have been obtained in fixed specimens a number of years old. The presence of translocations may also be ascertained by molecular analysis (usually reverse transcriptase polymerase chain reaction, RT-PCR), based on messenger ribonucleic acid (mRNA) or deoxyribonucleic acid (DNA) extracted from fresh or archival tissues and in which the products of fusion genes can be identified. This approach may also detect varying transcripts of such fusion genes. Examples of genetic changes not reflected in recognizable cytogenetic anomalies but determinable with molecular techniques or FISH are the KIT mutation in GIST, amplification of HER2/neu in breast cancer, and NMYC in neuroblastoma. The genetic findings in Ewing tumors based on a number of techniques (Figs. 7.5 and 7.6) are examples of the approaches available in the diagnosis of the tumors associated with specific translocations shown in Table 7.1. The translocation t(11;12)(q24;q12) in Ewing sarcoma and related tumors leads to the genesis of an abnormal fusion gene containing elements of the EWS and FUL genes involved by the breaks in the t(11;12). However, the products of this translocation show variability in the breaks in these genes occurring at different exons (but still in the chromosomal bands indicated), leading to variable transcripts. The clinical consequences of such variability is the demonstration that patients with tumors with type 1 transcript do much better than those with type 2. Though as many as 18 different transcripts have been identified as a result of the EWS-FUL fusion gene, insufficient numbers of cases with the other fusion products have been examined and hence clinical significance of these varying transcripts is unknown. The appearance of chromosomal changes, numerical and/or structural, in addition to the translocations seen in bone tumors and soft tissue tumors is usually associated with biological progression, manifested by invasion and metastases. These additional changes are usually variable from tumor to tumor, even those with the same diagnosis. With or without additional chromosome changes, tumors with specific translocations may show a variety of anomalies at the molecular level which may involve a number of genes.