Genomic and trascriptomic analyses of pediatric T-cell lynphoblastic leukemia/limphoma

ABSTRACT In the first part of our work we focused our attention on the biological question about the differences between two pathologies: T-cell lymphoblastic leukemia and T-cell lymphoblastic lymphoma. These two diseases share many features such as immunophenotypic features, lymphoblast morphology and clinical characteristics and are differentially diagnosed only on the base of bone marrow involvement. We tried to understand whether T-cell leukemia and lymphoma are a unique pathology with a different manifestation or whether they are two different diseases. The results obtained by gene expression profiling revealed an intrinsic difference in the expression of 78 genes between T-ALL and T-LBL. In particular since these genes belong to the angiogenesis and the chemotactic response we supposed that the two malignancies have different ability to respond to several cyto- and chemokines and that T-LBL need to modulate transcription to promote angiogenesis as well as to deal with hypoxic conditions. Also by analysis of copy number we were able to identify some abnormalities that seemed to be specific for each group regardless the limited data set of patients. Although this work provides additional elements in the characterization of these two pathologies, many studies have yet to be done, especially on the comprehension of the different capability of cells to migrate and invade the bone marrow compartment. The complete understanding of the molecular characteristics of T-LBL and T-ALL represents the driving element toward the design of fully successful therapeutic approaches. The second part of the study focused on the genetic characterization of two different groups of T-ALL patients on the basis of MRD response. With the aim to find biological correlates with the outcome for HR and nonHR patients, we performed many analyses, starting from copy number analysis to microRNAs expression profiling. Furthermore, we tried to integrate all the data in order to delineate common characteristics for each group of patients. First of all, the study of copy number revealed the presence of multiple abnormalities in all patients: we found known and unknown lesions, and in some cases we were able to associate them with HR or nonHR patients. The improvement of copy number results was obtained by the study of translocations. Also in this case we found one or more translocation in the majority of patients and we identified that the most recurrent were SIL-TAL1 and TLX3 translocations. Moreover, we tested the Notch1 mutations and, as expected, about 60% of patients were mutated for Notch1, with a tendency for Notch1 mutations to be more frequent in the nonHR group. The second step was the analysis of gene and microRNAs expression. The initial unsupervised analysis between HR and nonHR group failed to distinguish the two groups; but the successively supervised analysis revealed the distribution of MR patients in an equal manner between HR and SR patients. Thus an unsupervised analysis without MR patients showed a specific pattern of expression for each group (SR and HR). The GSEA analysis performed highlighted the enrichment of two specific pathways: the mir-215/192 pathway and the methylation pathway. The results obtained by the expression profile of about 700 microRNAs in the HR and nonHR group and those achieved by the combined analysis of GEP and microRNAs suggested miR-215 and miR-107 as the most differentially expressed and provided some possible target genes of these microRNAs. Moreover, to delineate specific pattern of expression not driven by MRD but by other alterations, we used the data derived from copy number, translocation and mutational analyses to supervise genetic subgroups. Significant results were obtained for Nocth1 mutated vs non-mutated, TLX3 translocated vs non-translocated, PTEN and LEF1 deleted vs non-deleted. We also tried to integrate all the data provided by both genomic and trasncriptomic analyses to understand whether the distribution of MR and the different signature of HR and SR were correlated with specific gene lesions. SIL-TAL1 fusion gene and the deletion of LEF1 and PTEN seemed to be specific for the HR group while the TLX3-translocation seemed to be peculiar for the nonHR group of patients. In conclusion HR and nonHR patients seemed to show some peculiar lesions and patterns of expression that could be justify the different response to therapy. In summary, several high throughput methodologies have been applied to the selected subgroup of patients to study the biological correlates of the different response to therapy. By this work we tried to provide a better characterization of T-ALL and to give a way of interpretation for the different outcome of T-ALL patients.