Analysis of Clonal T-Cell Receptor Gamma Gene Rearrangements, NOTCH1, FBW7 and PTEN Mutations in Paired Pediatric T-Cell Acute Lymphoblastic Leukemia Samples at Diagnosis and Relapse Reveals Evidence of Relapse in New Leukemic Clones.
Authors: Chen Qing , Gedman Amanda Larson , Matherly Larry H. , Taub Jeffrey W. 
Published: April 2020

Abstract
Relapse following remission induction chemotherapy remains the major challenge in the successful treatment of childhood T cell acute lymphoblastic leukemia (T-ALL). Relapse often results from the outgrowth of residual leukemia cells that are present below the limit of detection or involves a new therapy-related secondary leukemia. Individualization of treatment might improve the outcome and long-term quality of life for T-ALL patients. Molecular genetic markers represent clinically useful factors which predict responses to therapy. T-cell receptor gamma (TCRG) gene rearrangements occur in more than 90% of T-ALL and provide markers of lymphoblast clonality. Determining rearrangements in the TCRG could be critical to the diagnosis and treatment of T-ALL in children and adults. Mutations in the NOTCH1, FBW7, and PTEN genes have been identified at high frequencies in pediatric T-ALL cases. Activating NOTCH1 mutations have been found in more than 50% of ALL patients, resulting in constitutive NOTCH1 signalling, whereas PTEN mutations are inactivating, resulting in increased PI3K/AKT signalling. FBW7 has been identified as an important tumor suppressor. Several studies reported that frequent mutations in the substrate binding domain (e.g. Arg465, Arg479, Arg505) for FBW7 in T-ALL cell lines and primary T-ALL specimens result in sustained NOTCH1 levels and downstream signalling and gamma secretase inhibitor resistance, suggesting an alternate mechanism for NOTCH1 deregulation. To investigate the mechanism of T-ALL relapse, we analyzed the TCRG gene rearrangements and mutational status of the NOTCH1, FBW7, and PTEN genes by comparing sequences in paired diagnostic and relapsed T-ALL samples from 11 children to evaluate their stabilities throughout disease progression and association with treatment failure. The age distribution of 11 patients ranged from four years to fifteen years. Original TCRG sequence (a measure of leukemia clonality) was fully preserved at relapse in 3 (27.3%) patients. Clonal evolution was identified in 8 (72.7%) patients, reflected in changes in TCRG sequence. In 3 patients at diagnosis, NOTCH1 mutations were detected. At relapse, the major leukemia clones exhibited different NOTCH1 mutations. For another patient, a NOTCH1 mutation was detected at relapse but not at diagnosis. No FBW7 mutations were detected either at diagnosis or relapse. In 5 patients at diagnosis, PTEN mutations were detected and at relapse, 2 preserved the same mutation and 2 lost their mutations, while the additional sample harbored a different PTEN mutation. Our comparative sequence analysis of pediatric T-ALL samples provided detailed insight in the stabilities and changes of TCRG rearrangements and NOTCH1, FBW7 and PTEN mutation status during disease development. Re-emergence of the initial ALL clone or the occurrence of a secondary ALL clone may be clinically important to guide subsequent therapy. Collectively, our results suggest that for the majority of cases, relapse is associated with appearance of a new leukemic clone. For a subset of these cases, this is accompanied by a distinct subset of NOTCH1 mutations and, to a lesser extent, PTEN mutations. FBW7 mutations are rare. Better understanding of the changes in oncogenes and tumor suppressor genes with progression of T-ALL may identify new targets for therapy and facilitate the design of individualized therapy for this disease. Further study is needed to determine whether the newly identified relapse ALL clones were present at diagnosis as minor subclinical populations.