Identification of a genetically defined ultra-high-risk group in relapsed pediatric T-lymphoblastic leukemia

Abstract

In the search for genes that define critical steps of relapse in pediatric T-cell acute lymphoblastic leukemia (T-ALL) and can serve as prognostic markers, we performed targeted sequencing of 313 leukemia-related genes in 214 patients: 67 samples collected at the time of relapse and 147 at initial diagnosis. As relapse-specific genetic events, we identified activating mutations in NT5C2 (P=0.0001, Fisher's exact test), inactivation of TP53 (P=0.0007, Fisher's exact test) and duplication of chr17:q11.2-24.3 (P=0.0068, Fisher's exact test) in 32/67 of T-ALL relapse samples. Alterations of TP53 were frequently homozygous events, which significantly correlated with higher rates of copy number alterations in other genes compared with wild-type TP53 (P=0.0004, Mann–Whitney's test). We subsequently focused on mutations with prognostic impact and identified genes governing DNA integrity (TP53, n=8; USP7, n=4; MSH6, n=4), having key roles in the RAS signaling pathway (KRAS, NRAS, n=8), as well as IL7R (n=4) and CNOT3 (n=4) to be exclusively mutated in fatal relapses. These markers recognize 24/49 patients with a second event. In 17 of these patients with mostly refractory relapse and dire need for efficient treatment, we identified candidate targets for personalized therapy with p53 reactivating compounds, MEK inhibitors or JAK/STAT-inhibitors that may be incorporated in future treatment strategies.

Cost‐effective screening of DNMT3A coding sequence identifies somatic mutation in pediatric T‐cell acute lymphoblastic leukemia

“…Our results indicate that DNMT3A is not recurrently altered by mutations in pediatric T‐ALL, although it frequently mutates in many types of hematological malignancies. This observation is in line with a previous study that utilized Sanger sequencing to screen the hotspot locus of DNMT3A in a group of 170 T‐ALL pediatric patients and with data resulting from more recent NGS‐based studies in cohorts of pediatric T‐ALL: 13 patients, 12 patients, 5 patients, 47 patients, 111 patients, 214 patients, and in 67 patients, both pediatric and adult cases . Our results add data from a relatively large independent cohort of 74 patients that support the low frequency of DNMT3A mutations in pediatric T‐ALL.…”

“…Some DNMT3A mutations in pediatric T‐ALL were discovered with NGS technology, but none of them has been confirmed to have somatic origin. These include two nonsense mutations: (p.R320X) and (p400E>X), two amino acid insertions: (p.531D>DN) and (p.562C>CR), frameshift mutation, and splice variant, all these detected in diagnostic samples, and one mutation (p.M250T) detected in a relapse sample . Thus, for the first time in pediatric T‐ALL, we describe DNMT3A mutation with confirmed somatic origin.…”

PDX models recapitulate the genetic and epigenetic landscape of pediatric T‐cell leukemia

“…The commercially available SALSA MLPA P383 T‐ALL probe mix (MRC‐Holland, Amsterdam, The Netherlands) and a custom‐made probe set based on the SALSA MLPA P200‐A1 probemix (MRC‐Holland) were used for the detection of specific copy number variations as described before (Richter‐Pechanska et al , ).…”

Deleterious and Oncogenic Mutations in the IL7RA

“…So far, all IL7RA mutations previously associated with oncogenic disease have been gain of function mutations. Oncogenic IL7RA mutations were described by our group and others [61][62][63][64][65][66] in approximately 9% of T-ALL cases [61], 7.8% of early T phenotype ALL (ETP-ALL) cases [67], 2%-3% of B-ALL cases [62,68] and 12% of Ph-like B-ALL subtype [68][69][70]. Oncogenic mutations are almost always in exon six and appear to be more common (two-fold) in children than in adults [67,68,71].…”