NOTCH1 pathway activating mutations and clonal evolution in pediatric T‐cell acute lymphoblastic leukemia

Abstract

Molecular mechanisms involved in the relapse of T‐cell acute lymphoblastic leukemia (T‐ALL) are not fully understood, although activating NOTCH1 signaling due to NOTCH1/FBXW7 alterations is a major oncogenic driver. To unravel the relevance of NOTCH1/FBXW7 mutations associated with relapse, we performed whole–exome sequencing in 30 pediatric T‐ALL cases, among which 11 diagnosis‐relapse paired cases were further investigated to track the clonal evolution of relapse using amplicon–based deep sequencing. NOTCH1/FBXW7 alterations were detected in 73.3% (diagnosis) and 72.7% (relapse) of cases. Single nucleotide variations in the heterodimerization domain were the most frequent (40.0%) at diagnosis, whereas proline, glutamic acid, serine, threonine–rich (PEST) domain alterations were the most frequent at relapse (54.5%). Comparison between non–relapsed and relapsed cases at diagnosis showed a predominance of PEST alterations in relapsed cases (P = .045), although we failed to validate this in the TARGET cohort. Based on the clonal analysis of diagnosis‐relapse samples, we identified NOTCH1 “switching” characterized by different NOTCH1 mutations in a major clone between diagnosis and relapse samples in 2 out of 11 diagnosis‐relapse paired cases analyzed. We found another NOTCH1 “switching” case in a previously reported Berlin‐Frankfurt‐Münster cohort (n = 13), indicating NOTCH1 importance in both the development and progression of T‐ALL. Despite the limitations of having a small sample size and a non–minimal residual disease–based protocol, our results suggest that the presence of NOTCH1 mutations might contribute to the disease relapse of T‐ALL.

Next-Generation Sequencing in Acute Lymphoblastic Leukemia

“…To explore the pathogenic mechanisms of relapse and to detect the occurrence of NOTCH1 / FBXW7 alterations in relapsed T-ALL, a WES study was conducted in 30 paediatric patients, among which 11 diagnosis-relapse paired cases [104] NOTCH1 / FBXW7 mutations were identified in 73.3% of cases at the onset and 72.7% of the relapses. At diagnosis, mutations in the heterodimerization domain predominated (40.0%), while at relapse PEST domain alterations were more frequent (54.5%).…”

“…In the diagnosis-relapse paired cases, there was a prevalence of PEST mutations in relapsed cases, although this observation was not confirmed in the target cohort. Indeed, in two of 11 diagnosis-relapse paired cases a mutation switch was observed from diagnosis to relapse [104] Despite the small sample size, these data suggested that the presence of NOTCH1 mutations might contribute to the T-ALL relapse.…”

Phase 1 study to evaluate Crenigacestat (LY3039478) in combination with dexamethasone in patients with T‐cell acute lymphoblastic leukemia and lymphoma

“…The limited efficacy of Crenigacestat in this study could be due to several reasons, including dosing interruptions due to gastrointestinal toxicities and less dependence of the disease on the Notch pathway after multiple relapses 22 . The low frequency of Notch‐1 mutations in our study population is in contrast to the high frequency of such mutations in newly diagnosed and early‐relapse T‐ALL 22,23 . The mutational composition among patients with multiple relapses has not been well studied.…”

Next‐generation sequencing of PTEN mutations for monitoring minimal residual disease in T‐cell acute lymphoblastic leukemia

“…On the other hand, the use of a single mutation to follow a leukemic clone could be limiting compared with the repertoire of antigen receptors. However, both methods may also suffer from the clonal evolution of leukemic cells during disease and treatment that can affect MRD monitoring . In addition, the sensitivity and the MRD quantification of the NGS‐PTEN method depend on several factors, such as coverage, type of mutation, and quantity of DNA used for the PCR.…”