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Molecular Oncology, Markers, Clinical Correlates |
1 Leukemia Research Fund Centre for Cell and Molecular Biology, Institute of Cancer Research, London, United Kingdom; 2 Childhood Leukaemia Investigation Prague (CLIP), Department of Paediatric Haematology and Oncology, 2nd Medical School, Charles University, Prague, Czech Republic; 3 Childrens Cancer Research Institute and St Anna Kinderspital, Vienna, Austria; 4 Cancer Research UK Childrens Cancer Group, Royal London Hospital, London, United Kingdom; and 5 Charite, Department of Paediatric Oncology/Haematology, Humboldt-University, Campus Virchow-Klinikum, Berlin, Germany
ABSTRACT
Purpose: TEL (ETV6)-AML1 (RUNX1) chimeric gene fusions are frequent genetic abnormalities in childhood acute lymphoblastic leukemia (ALL). They often arise prenatally as early events or initiating events and are complemented by secondary postnatal genetic events of which deletion of the non-rearranged, second TEL allele is the most common. This consistent sequence of molecular pathogenesis facilitates an analysis of the clonal origins of relapse in this leukemia, which has some unusual clinical features.
Experimental Design: We compared the boundaries, by microsatellite mapping, of TEL deletions at relapse versus diagnosis in 15 informative patients. Moreover, we compared the relatedness of diagnostic and relapse clones using immunoglobulin and T-cell receptor genes rearrangements and clonotypic TEL-AML1 genomic fusion.
Results: Five patients retained the apparent same size TEL deletion, seven had larger deletions, and three had smaller deletions at relapse. In all of the cases evaluated, the clonal relatedness of diagnostic and relapse cells was confirmed by the retention of clonotypic TEL-AML1 genomic sequence and/or at least one identical immunoreceptor gene rearrangement.
Conclusions: These data provide further evidence that TEL deletions are secondary to TEL-AML1 fusions in ALL. They are compatible with the novel idea that in at least some cases of childhood ALL, remission occurs with persistence of a preleukemic "fetal" clone, and subsequent relapse reflects the emergence of a new subclone from this reservoir after an independent "second hit," i.e., independent TEL deletion. To our knowledge, the study is the most extensive and comprehensive analysis of the relationship between diagnostic and relapse clones in childhood ALL presented thus far.
INTRODUCTION
TEL-AML1 (ETV6-RUNX1) fusion, via the t(12;21)(p13;q22) chromosomal translocation is a common genetic abnormality in childhood B-cell precursor acute lymphoblastic leukemia (ALL) present in
20 to 25% of cases (1, 2, 3, 4, 5)
. Studies on identical twins with concordant ALL (6, 7, 8)
and retrospective scrutiny of neonatal blood spots (Guthrie cards; refs. 8, 9, 10, 11
) have provided evidence that TEL-AML1 often arises prenatally, possibly as a first or initiating event. A corollary of these data are that a "preleukemic" clone with TEL-AML1 can persist postnatally for extended periods, up to
14 years (7)
and that at least one other postnatal genetic event is required for overt leukemia. The majority of cases of TEL-AML1-positive ALL have deletion of the nontranslocated TEL allele at diagnosis (12, 13, 14)
. TEL deletions vary in size from 10 kb to >10 megabases as judged by microsatellite loss of heterozygosity (LOH) but the minimally deleted regions always affect at least some part of the TEL transcription framework (15
, 16)
. Studies on both singletons (12
, 14)
and twins (8)
with ALL indicate that such TEL deletions are subclonal or secondary to TEL-AML1 and almost certainly postnatal. Candidate preleukemic clones in normal cord blood with TEL-AML1 fusions retain the normal TEL allele (17)
. Whether other genetic changes in addition to TEL deletion, e.g., kinase mutations (18)
, are necessary for the clinical development of ALL remains to be established.
These data throw light on the natural history of childhood ALL (19) , but they also have clinical implications. One particular issue is whether the putative preleukemic clone with TEL-AML1 fusion but no TEL deletion responds to therapy as does the dominant clone of overt leukemic blasts at diagnosis. One possibility is that they might persist in some patients and, in so doing, provide a reservoir of "at risk" cells for later independent second hits, i.e., TEL deletion and/or other events that would precipitate a de novo ALL masquerading as relapse. The plausibility of this unconventional interpretation of "late" relapse in ALL is supported by the clinical responsiveness of many cases of late or off-treatment ALL relapses (20) . In a small pilot study of this issue, we reported that in two patients with off-treatment relapse of TEL-AML1-positive ALL, the TEL deletions that were present at relapse had different genomic boundaries and were smaller than the deletions observed at diagnosis (21) . This result was possible only if TEL deletions were secondary and further suggested that the dominant clone at diagnosis might not be that which appeared in relapse.
In view of the potential clinical importance of these preliminary data, we have carried out a systematic analysis of TEL deletion by microsatellite mapping in a series of patients with TEL-AML1-positive ALL in relapse. Importantly, in addition to the TEL deletion analysis, in this series we have sought confirmation of the clonal relatedness of diagnostic and relapse clones via sequence analysis of rearrangements of immunoglobulin and T-cell receptor (TCR) genes and, in some cases, genomic TEL-AML1 fusion.
PATIENTS, MATERIALS, AND METHODS
Patients.
Clinical features of the 19 analyzed patients with relapsed TEL-AML1-positive ALL are summarized in Table 1
. The patients were selected on the basis of DNA availability. Presentation and relapse samples were available from 17 patients, and samples from 2 children were analyzed at first and second relapse. A remission DNA sample was obtainable in 11 cases. In the remaining eight patients, only TEL deletion in samples from presentation and relapse (or first and second relapse) could be compared. Patients with Unique Patient Numbers (UPN) 1 to 16 were treated according to Berlin-Frankfurt-Munster (BFM)-based protocols, patients UPN 17 to 19 according to Medical Research Council (MRC), United Kingdom, ALL-based protocols. None of the patients underwent allogeneic hematopoietic stem cell transplantation before first relapse (or before second relapse for patients UPN 14 and 19). Informed consent was obtained from each subject or subjects guardian.
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-32P]dCTP at a final concentration of 37 kBq was added. After denaturation for 3 minutes at 94°C, amplification was performed for 28 cycles at 94°C for 30 seconds, at 55°C for 60 seconds, and at 72°C for 60 seconds. Before electrophoresis on 6% polyacrylamide gels containing 7 mol/L Urea, samples were denatured in 98% formamide, 0,02% bromphenol blue, and 10 mmol/L EDTA by heating to 90°C for 3 minutes; the samples were then chilled on ice. LOH was scored if the relative intensity of one allele was lost or diminished in the same patient either at presentation or at relapse when compared with remission DNA.
Immunoreceptor Gene Rearrangement Analysis.
In bone marrow samples, we examined the pattern of immunoglobulin/TCR gene rearrangements using 18 screening PCR reactions (23
, 24)
. The set of reactions covers the vast majority (>90%) of immunoglobulin heavy chain (IgH), Ig
, TCR-
and TCR-
gene rearrangements in B-cell precursor ALL. The primers and PCR conditions were published elsewhere (23
, 24)
. To reliably distinguish clonal PCR products from polyclonal, we performed heteroduplex analyses of fragments using polyacrylamide gels (25)
. Homoduplexes were cut from the gel, were reamplified, and were sequenced. Sequences of rearrangements at presentation and relapse were compared.
Characterization of TEL-AML1 Fusion at DNA Level.
Amplification of the genomic breakpoint fusion sequences for TEL-AML1 at relapse was performed by long-range PCR using conditions and primers previously described (8
, 26)
. Primers TEL6B and TEL8B were used in combination with each of 11 AML1 primers. The breakpoint sequence was obtained through restriction analysis by primer walking and sequencing. Patient-specific primers for amplification of fusion breakpoints were designed so that PCR yielded a product of 130 to 300 base-pairs. DNA from presentation material was then amplified using these primers, and resulting products were sequenced to confirm identity with TEL-AML1 intronic fusion in relapse samples.
RESULTS
Deletions of the Second TEL Allele.
We analyzed bone marrow samples of 19 patients with relapsed TEL-AML1-positive ALL. In 11 patients in which remission DNA was available, we were able to assess microsatellite markers within the 12p locus and screen the informative loci (heterozygous) for LOH at presentation and relapse (at first and second relapse in patient UPN 19). In the remaining eight patients, remission samples were not available. Thus, we were able to compare only the diagnostic and relapse samples in each patient (first and second relapse samples in patient UPN 14), and LOH was determined only at markers where the two samples differed.
The results of the presentation versus relapse analyses can be divided into four groups (Table 1)
. Group U (unchanged) consists of five patients with an apparent similar pattern of LOH analysis at both presentation and relapse (patients 3, 6, 12, 17, and 18). Patients from group L (larger at relapse; n = 7; patients 1, 2, 7, 8, 13, 15, and 16) had a larger deletion at relapse than in the presentation sample. LOH at relapse was longer by one to six markers in these patients, compared with diagnostic material. Group S (shorter at relapse) comprises three patients (patients 4, 14, and 19), in which the deletion at relapse was shorter than the deletion seen at presentation. We found at least one informative microsatellite marker at first relapse or second relapse that was deleted at either original presentation or first relapse, respectively. Group N (noninformative) includes four cases in which LOH data were not informative. Illustrative examples of patients from each group are shown in Fig. 1
.
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DISCUSSION
This molecular scrutiny of clonal relatedness in relapsed versus diagnostic TEL-AML1 ALL was designed to confirm that the same or related clones are involved and to assess the consistency with which TEL deletions alter in relapse compared with diagnosis (21) . We previously argued that the appearance of smaller TEL deletions in late relapses (i.e., off treatment) of TEL-AML1 might reflect a new ALL generated from a persistent preleukemic clone rather than a conventional relapse (21) . One attraction of this idea was that it might rationalize the otherwise surprising clinical observation that late relapses of B-cell precursor/common ALL are often as therapeutically sensitive as ALLs of first diagnosis, with sustained remissions and cures achievable in most cases (20) .
In all but one (15 of 16) cases of relapse in which we evaluated for immunoglobulin/TCR rearrangements, there was definitive molecular evidence that a related clone was involved, i.e., at least one clonotypic rearrangement was shared. In the remaining case (UPN 15) and also in another four cases, we were able to evaluate and confirm that the clonotypic genomic TEL-AML1 fusion sequence, believed to mark the initiated preleukemic clone (8 , 17 , 28) , was identical at relapse and diagnosis. A prediction of the hypothesis is that TEL deletions, as common but secondary events, should be different in their genomic boundaries at diagnosis and relapse. In practice, the only result that is unequivocal in this respect is relapse with a smaller TEL deletion (three cases described here). Relapse cases with a larger deletion would also be anticipated to occur, and the seven cases described here are, therefore, compatible with this view; however, we cannot exclude the possibility that larger deletions arise by attrition of boundaries of prior smaller deletions. Cases with identical TEL deletions at diagnosis and relapse may contradict the hypothesis and one third (5 of 15) of our informative patients had this feature. This could indicate that the dominant clone at diagnosis reappeared in relapse. A caveat here is, however, that the genomic boundaries are defined only with respect to the available microsatellite markers for which the patient is heterozygous. Boundary differences of a modest size (i.e., <0.5 cM) would be undetected. In a recent study, Takeuchi et al. (29) found that LOH at loci other than 12p/TEL were also divergent between diagnosis and relapse of childhood ALL, and, in some cases, a deletion present at diagnosis was not evident in relapse cells. The authors suggested that this might indicate the emergence of relapse from a small subpopulation of cells present at diagnosis.
The conclusion from these studies is therefore that late relapse in childhood ALL with TEL-AML1 does represent, as anticipated, emergence of a related subclone, but in some cases, it is a different dominant clone from that seen at initial diagnosis. Clearly, this result indicates persistence of a subclone in complete remission possibly at levels undetectable in PCR-based minimal residual disease screening. One possibility is that the "different" subclone in relapse is present as a very minor subclone at diagnosis, evades elimination by therapy, and re-emerges over time, particularly after cessation of therapy. Evidence for this is now available from immunoglobulin/TCR analysis, which indicates that dominant TEL-AML1-positive clones in relapse may be present at low levels (104 to 5 x 103 total) at diagnosis and are poorly or only slowly responsive to induction chemotherapy (27
, 28)
. This is compatible with the view that these cells represent the reservoir of relatively drug-resistant preleukemic cells (28)
. We assume that these cells may remain in a dormant state during hematologic remission, may be gradually lost, or, if suffering a second hit (i.e., TEL deletion or other), will amplify as an overt ALL cell population in later "relapse" (see Fig. 2
). This interpretation is difficult to prove unequivocally but accords best with the clinical observations and parallels similar views on the persistence of AML1-ETO-positive preleukemic clones in remission of acute myeloid leukemia (30, 31, 32)
. The results of the study are influential for the understanding of pathogenesis and natural history of childhood ALL (33)
. If correct, they change our understanding of the biology of remission and relapse and may have possible implications for the detection of minimal residual disease. Furthermore, the proposed interpretation might influence the treatment approach to the TEL-AML1-positive relapses.
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FOOTNOTES
Grant support: Supported by grant GACR 301/P041, projects of MSMT-CR 111300001 and 111300003, the Österreichische Kinder-krebshilfe, and a specialist program grant from the Leukaemia Research Fund, United Kingdom (M. Greaves).
The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
Requests for reprints: Jan Zuna, Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, 2nd Medical School, Charles University Prague, V Uvalu 84, 150 06, Prague 5, Czech Republic. Phone: 420-224432280; Fax: 420-224432268; E-mail: jan.zuna{at}lfmotol.cuni.cz
6 Internet address for the Genome database is http://gdbwww.gdb.org/. ![]()
Received 3/26/04; accepted 4/21/04.
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