Deletions

20q deletion

The importance of del(20q) is exemplified in a study of 3996 consecutive abnormal bone marrow samples performed by Dewald et al. (1993). Almost 3000 of these samples possessed a sole chromosomal abnormality and, of these, del(20q) was the second most common structural abnormality after t(9;22). In addition to the MPDs, 20q deletions are also seen in approximately 4% of patients with myelodysplastic syndrome (MDS) and in 1-2% of patients with AML. However, 20q deletions are rarely seen in lymphoid malignancies. This pattern of disease association suggests that the deleted region of chromosome 20 marks the site of one or more genes, loss or inactivation of which perturbs the regulation of hemato-poietic progenitors. The finding of 20q deletions at diagnosis and as a sole abnormality suggests that, in at least some cases, it plays an early role in disease pathogenesis.

There have been a number of studies concerning the prognostic significance of the 20q deletion in both MPD and MDS. As far as MPD is concerned, there is no significant difference in the survival rate of patients with and without a 20q deletion, although only a small number of patients have been studied. For MDS, a 20q deletion is associated with a relatively good prognosis, if it is observed without any other karyotypic abnormalities. Deletions of chromosome 20q may be particularly associated with a subset of myeloid disorders characterized by megakaryocytic and erythroid dysplasia with only infrequent granulocytic dysplasia. However, it is not clear whether such a pattern is also seen in patients lacking a 20q deletion and so the significance of these findings is unclear.

Since both MPD and MDS are believed to result from transformation of a hematopoietic stem cell, it was of interest to determine whether 20q deletions arise in a pluripotent progenitor or a later, committed progenitor. White et al. (1994) described a patient with MDS whose granulocytes and monocytes were clonal (as assessed by X-inactivation patterns) and clearly contained the deletion, whereas B cells and T cells were polyclonal and did not contain the deletion. However, EBV-transformed B-cell lines carrying the 20q deletion were derived from this patient. Similarly, in another patient, a 20q deletion was reported in EBV-transformed B-cell lines as well as in CFU-GM, CFU-GEMM and BFU-E colonies. Clearly, the 20q deletion can arise in a very early progenitor with both lymphoid and myeloid potential.

In most patients with a 20q deletion, the deletion can readily be detected in peripheral blood neutrophils using microsatellite PCR to demonstrate loss of heterozygosity (LOH) (Figure 9.4). However, this is not always the case. Asimakopoulos et al. (1996) described an interesting subset of patients with a 20q deletion in the majority of bone marrow metaphases but with no deletion detectable in peripheral blood granulocytes by microsatellite PCR. This observation suggests that, in some patients, granulocytes carrying the deletion may be preferentially destroyed or retained within the bone marrow. Granu-locytes from the female patients displayed a clonal pattern of X inactivation, implying that either the 20q deletion was not the initiating event or the clonal X-inactivation pattern in granulocytes was age-related (see above) and not part of the pathogenesis of these disorders.

Molecular analysis of the 20q deletion has been undertaken to identify the gene or genes involved. Using fluorescence in situ hybridization (FISH), microsatellite PCR (Figure 9.4)

Deletion

Fig. 9.4 Use of microsatellite PCR to map deletions

Granulocytes (G) contain the deletion whereas T cells (T) do not. Using markers A and C, two alleles are present in granulocytes and therefore these markers lie outside the deletion. Using marker B, two alleles are present in T cells but only one in granulocytes. Hence, marker B lies within the deletion. Reproduced from Bench et al. (1998) with permission from Elsevier Science.

and quantitative Southern blotting, a common deleted region (CDR) spanning 20q11-20q13 has been defined and is likely to contain one or more tumor suppressor genes. Deletion of part of 20q has also been demonstrated by LOH and FISH in CML patients.

Given that MPD and MDS are overlapping but clinically different diseases, it remains possible that different or additional genes are involved in the two disorders. Therefore, two overlapping common deleted regions have been defined. The MPD CDR spans 3 Mb. Two different MDS/AML CDRs have been constructed (Figure 9.5). A 3-Mb CDR based entirely on patients with a simple interstitial deletion overlaps the MPD CDR by 2 Mb. A smaller 700-kb CDR has been constructed using patients with complex rearrangements of chromosome 20. Within the CDRs identified by Bench et al. (Figure 9.5), 40 genes lie within the MPD CDR and 18 within the MDS CDR. Of the 16 that lie within both CDRs, 6 are expressed within normal CD34+ progenitor cells, making them good positional and expression candidates (Figure 9.5). These include the SFRS6, L3MBTL and MYBL2 genes.

13q deletion

In contrast to 20q deletions, molecular analysis of chromosome 13q deletions in myeloid malignancies has only recently been initiated. CDRs of 4 centimorgans (cM) and of 14 cM have been constructed in MDS and MPD patients respectively. LOH at the RB1 locus has been observed in the bone marrow or peripheral blood from 13 of 30 MPD patients, suggesting that abnormalities of chromosome 13 may be relatively more common than conventional karyotyping suggests. No mutations of the RB1 gene have been found in MPD patients.

Deletion of chromosome 13q is the commonest structural chromosomal abnormality seen in chronic lymphocytic leukemia (CLL). Deletions and unbalanced translocations involving 13q14 are seen in approximately 18% of all CLL cases. Several small common deleted regions have been constructed and a number of candidate genes identified. These include RFP2, BCMSUN and BCMS, a large gene spanning all the CDRs and likely to represent non-coding RNA. Quantitative RT-PCR has demonstrated that many genes in this region are underexpressed compared with normal B cells. However, only RFP2 showed significant loss of expression in B-CLL patients without a 13q deletion. No mutations have been found in any of these genes, suggesting that downregulation of one or more of these genes by an unknown mechanism may contribute to the pathogenesis of CLL. Whether the same mechanism contributes to the pathogenesis of myeloid malignancies with 13q deletions is not known.

Models of deletion syndromes

Loss and/or inactivation of candidate genes on 20q may be responsible for the pathogenesis of MPD by a number of possible mechanisms (Figure 9.6). A simple 'two-hit' model with a single target gene, reminiscent of Knudson's two-hit

Fig. 9.5 Summary of common deleted regions on 20q for MPD and MDS

The MPD CDR is bordered by D20S108 and D20S481. Two distinct CDRs for MDS/ AML have been published. MDS CDR (1) is flanked by PACs 620E11 and 196H17. MDS CDR (2) is flanked by PACs 29M7 and 179M20. Data taken from Bench et al. (2000) and Wang etal. (2000). Reproduced from Bench et al. (2001) with permission from Elsevier Science.

11.2

Fig. 9.5 Summary of common deleted regions on 20q for MPD and MDS

The MPD CDR is bordered by D20S108 and D20S481. Two distinct CDRs for MDS/ AML have been published. MDS CDR (1) is flanked by PACs 620E11 and 196H17. MDS CDR (2) is flanked by PACs 29M7 and 179M20. Data taken from Bench et al. (2000) and Wang etal. (2000). Reproduced from Bench et al. (2001) with permission from Elsevier Science.

11.2

Chromosome 20

13.1

13.2

13.3

Chromosome 20

D20S106 D20S174

D20S107

D20S108

D20S110

D20S96

PLC1

D20S481

D20S17

D20S178

q hypothesis, might involve inactivation of one copy of the gene by a subtle genetic alteration, such as a point mutation followed by loss of the second copy by deletion. Alternatively, the intact copy may be transcriptionally silenced; for example, by methylation, as has been demonstrated for the VHL, p16 and p15 genes. In a 'one-hit' model, loss of only a single copy of the gene may result in haploinsufficiency and be sufficient to contribute to disease pathogenesis. A number of tumor suppressor genes, such as p27 and p53, show retention of one active allele in human tumors. Furthermore, heterozygous knockout mice develop tumors without any apparent inactivation of the wild-type allele. In addition, loss of two or more genes may be required (Figure 9.6). Again, inactivation of one or both copies of critical genes may be necessary to perturb progenitor cell behavior. Perhaps the inactivation of different combinations of genes is responsible for distinct myeloid disorders. The generation of mouse models of acquired deletions may offer ways of investigating such multigene hypotheses.

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