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New frontiers in the stratification of acute lymphoblastic leukemia (ALL): integration between non-conventional cytogenetics, genomics and post-genomics.

Università degli Studi di Roma "La Sapienza"

Abstract

Acute lymphoblastic leukemia (ALL) is one the most frequent neoplasms in pediatric cohorts, while it is more rare in adult patients. Prognosis varies widely between the two cohorts: in children, the overall five-year event-free survival rate is nowadays greater than 75%, while in adults the results are much less favorable. The improved results in children have led researchers to try to identify who, among the small patients, may benefit from less intense chemotherapeutic regimes; in addition, the evaluation of Minimal Residual Disease (MRD) during the course of the disease has become a fundamental parameter. This "surrogate" marker, beyond measuring the response to treatment, offers unique opportunities to raise scientific questions with potential clinical implications. In particular, MRD allows to identify subgroups of patients displaying a poor early response to treatment in the absence of any other known prognostic factor, as well as subgroups with very rapid tumor clearance and good outcome, even in subgroups with poor prognostic genetic lesions.
In both groups of patients - children and adults -, there is still the need of understanding the mechanism/s that lead to malignant transformation. In fact, in both adults and children within B-lineage ALL (B-ALL) it has been possible to identify several recurrent molecular aberrations that are strictly associated to leukemia development. Nonetheless, with the exception of BCR/ABL, which is per se causal of the >>>

Principal Investigator

Roberto Foà Università degli Studi di ROMA "La Sapienza"

Research Objectives

The analysis of acute lymphoblastic leukemia (ALL) has provided in the last twenty years extremely useful results. In fact, studies performed in this disease have allowed to identify recurrent molecular lesions strictly associated to this neoplasm, such as BCR/ABL, ALL1 rearrangements, E2A/PBX and TEL/AML1. As a general premise, three main issues must be kept in mind: 1) the occurrence of the aforementioned lesions varies widely between children and adults; 2) the presence of these aberrations is more frequently detected in B-ALL, while in T-ALL up to recently the mechanisms of transformation were scarcely known; as a matter of fact, up to 2004, in about 80% of T-ALL patients it was not possible to recognize any genetic lesion; 3) the impact on the clinical behavior is well-established with some lesions, as for example BCR/ABL, being associated with a particularly poor outcome (lower percentage of responses to induction chemotherapy, as well as a higher incidence of relapse), and others, e.g. TEL/AML1, that is almost exclusively detected in children, which are associated to a favorable clinical outcome.
Overall, this body of information has represented an ideal background for the definition of stratification criteria and, ultimately, for the design of tailored chemotherapeutic regimens that in some cases include the use of transplant procedures, while in other circumstances allow to reduce treatment intensity. Moreover, in the last ten years the role of minimal >>>

First Results

This project is absolutely feasible because all the units are using, with high proficiency, powerful technologies, such as gene expression profiling arrays, array-CGH, SNP array and a handful set of non-conventional cytogenetic techniques.
In the pediatric setting, the expected results are:
1) Discovery, by applying high resolution SNP array-based and CGH array-based technologies, of secondary genomic imbalances of possible prognostic and pathogenic importance for ALL stratification that have so far gone undetected. Hopefully, these lesions will be detected not only in samples without known molecular aberrations, but also in those cases, as recently reported in the literature, that display some known recurrent lesion (for example TEL/AML1), and may therefore be useful in further stratification of patients also in these cases.
2) Re-analysis and revision, in light of the lesions identified by array-CGH and SNP array, the gene expression profiling results of pediatric ALL, and if possible, to explain the reason/s of the presence of subgroups that are identified by unsupervised and semi-supervised approaches that, presently, do not appear to correlate with any of current biological knowledge.
3) Correlation of the results of MRM with those obtained by gene profiling, array-CGH and SNP-array.
4) Investigation of the role of microRNA to: 1) directly infer the variation of transcript/microRNA levels in deleted or amplified regions, and 2 >>>

Timescale

24 months

National and international background

Acute lymphoblastic leukemia (ALL) is an heterogeneous disease with a highly heterogeneous clinical course; its incidence varies widely between children and adults. Clinical heterogeneity is known to be correlated with recurrent patterns of genetic changes in the leukemic cells and current acute leukemia subclassifications utilize genomic hallmarks for treatment stratification. The analyses used to recognize leukemia subclasses have evolved along several lines, including flow cytometry for lineage-specific marker proteins and DNA-indexing of blast cells, karyotyping to recognize gross chromosomal aberrations, FISH utilizing probes for recurrent aberrations and molecular biology, which uses RT-PCR and quantitative PCR (Q-PCR) for the screening and quantification of recurrent translocations.
Altogether, these approaches have so far allowed to distinguish among acute leukemias the following B-lineage (B-ALL) subclasses: mature B-ALL with t(8;14), pro-B-ALL with rearrangements involving the ALL1 (MLL) gene, c-ALL/pre-B-ALL with t(9;22), ALL with t(12;21), ALL with t(1;19), ALL with hyperdiploid karyotype, c-ALL/pre-B-ALL without any of the above aberrations. The incidence of these abnormalities is different in pediatric and adult cohorts: more specifically, the t(9;22) is much more frequent in adults (and more so in the elderly), as well as rearrangements involving the MLL, with the exception of infants; contrariwise, the t(12;21) is exclusively detected in children and >>>