Relapsed precursor T-cell acute lymphoblastic leukemia is characterized by resistance against chemotherapy and is frequently fatal. We aimed at understanding the molecular mechanisms resulting in relapse of T-cell acute lymphoblastic leukemia and analyzed 13 patients at first diagnosis, remission and relapse by whole exome sequencing, targeted ultra-deep sequencing, multiplex ligation dependent probe amplification and DNA methylation array. Compared to primary T-cell acute lymphoblastic leukemia, in relapse the number of single nucleotide variants and small insertions and deletions approximately doubled from 11.5 to 26. Targeted ultra-deep sequencing sensitively detected subclones that were selected for in relapse. The mutational pattern defined two types of relapses. While both are characterized by selection of subclones and acquisition of novel mutations, 'type 1' relapse derives from the primary leukemia whereas 'type 2' relapse originates from a common pre-leukemic ancestor. Relapse-specific changes included activation of the nucleotidase NT5C2 resulting in resistance to chemotherapy and mutations of epigenetic modulators, exemplified by SUZ12, WHSC1 and SMARCA4. While mutations present in primary leukemia and in relapse were enriched for known drivers of leukemia, relapse-specific changes revealed an association with general cancer-promoting mechanisms. This study thus identifies mechanisms that drive progression of pediatric T-cell acute lymphoblastic leukemia to relapse and may explain the characteristic treatment resistance of this condition. ALL-BFM 86/90, 1989-1998 INS 98 protocol based on ALL-BFM 95 40 , 1998-2003 and ALL Intercontinental (IC) -BFM 200315, 2003-2005 analyzed at the time of primary diagnosis, during remission and at relapse. Pediatric T-cell lymphoblastic leukemia evolves into relapse by clonal selection, acquisition of mutations and promoter hypomethylation ABSTRACT © F e r r a t a S t o r t i F o u n d a t i o n Methods Patients' clinical characteristics Patients were treated according to ALL-BFM 2000 or related frontline protocols 14 IC 15 ). One patient was aged 18 at diagnosis, all others were children or adolescents. The 13 patients This study was approved by the institutional review boards of the Charité Universitätsmedizin Berlin and the Medical Faculty Heidelberg. Informed consent was obtained in accordance with the Declaration of Helsinki. Exome capture, target capture and Illumina sequencing The Agilent SureSelect Target Enrichment Kit (Agilent, Santa Clara, CA, USA; vendor's protocol version 2.0.1) was used to capture all human exons for sequencing. The HaloPlex Target Enrichment Kit (Agilent, Santa Clara, CA, USA; vendor's protocol version D.5, May 2013) was used according to the manufacturer's instructions. The starting material consisted of 225 ng of genomic DNA. The captured fragments were sequenced as 100 bp paired reads using an Illumina HiSeq instrument (Illumina, San Diego, CA, USA). Analysis of whole exome sequencing and targeted ultra-deep sequencing data The analysis of sequencing data is detailed in the Online Supplementary Methods. DNA methylation analysis using 450k BeadChip arrays Genomic DNA (200 ng) was bisulfite-converted using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA, USA). The Infinium methylation assay (Illumina) was carried out as previously described. 17 Data from the 450k Human Methylation Array were normalized by the Beta Mixture Quantile (BMIQ) method 18 using the RnBeads analysis software package. 19 Multiplex ligation dependent probe amplification Multiplex ligation dependent probe amplification (MLPA) was done using the MRC Holland (Amsterdam, The Netherlands) SALSA MLPA probe mix P383-A1 T-ALL according to the manufacturer's instructions. Polymerase chain reaction products were separated by capillary electrophoresis on an ABI-3130XL device; the size standard was GeneScan 500-250 (Applied Biosystems). Coffalyser software, available at http://www.mlpa.com, was used for the analyses. Integrated analysis In order to evaluate functions that were altered by mutation or DNA methylation at relapse, Ingenuity Results Relapsed T-cell acute lymphoblastic leukemia acquires single nucleotide variants and small insertions and deletions We performed whole exome sampling (WES) of DNA samples obtained from 13 patients (see Comparing all mutations in primary disease to those in relapse, no significant difference in the types of single nucleotide exchanges and in the ratio of transversions and transitions was identified (Online Supplementary 20 Somatic copy number alterations can represent subclonal, "late" events We used MLPA in order to identify CNA in genes commonly altered in T-ALL. On average, 3.5 CNA were detected in each primary leukemia sample and 3.2 in each relapse sample, whereas 2.7 CNA were detected in both samples from the same patient (Online Targeted ultra-deep sequencing detects rare subclones In order to track the clonal evolution of the relapses, we performed targeted ultra-deep sequencing of all mutations that had previously been identified by WES using the HaloPlex target capture (Agilent). Allele frequencies inferred by HaloPlex were highly reproducible (Online Supplementary . The rate of SNV that were detected as false positives in samples from patients who never carried the respective SNV was 1.8% (Online Supplementary In ten of 13 of the first disease/relapse pairs a DNA sample obtained at the time of remission (for 7 patients, MRD level from the same sample was available and ≤ 10 -2 , J.B. Kunz et al. 1444 haematologica | 2015; 100 Evolution of pediatric T-ALL into relapse haematologica | 2015; 100(11) 1445 r r a t a S t o r t i F o u n d a t i o n 0.0120). Twenty-six SNV that were detected in remission were not detected in the corresponding primary disease sample with a sensitivity of 0.01 or higher. We propose that these 26 SNV may have originated from a mutational event during treatment, although clonal selection starting from a very small subclone present at initial diagnosis cannot be ruled out. In all 13 patients a minimal set of common genetic changes (at least one concordant MRD marker, Online Supplementary Table S3, or at least six concordant SNV and InDels, The example of mutations in the nucleotidase NT5C2 illustrates the genetic plasticity of T-ALL. NT5C2 mutations were identified in five of 13 relapse samples (R367Q in patients A61, S00207, S00285, T92; D407Y in patient T92; P414S in S00456; Online Supplementary Tables S1 and S5). R367Q has been shown to activate the nucleotidase activity of NT5C2 and to confer resistance against nucleoside analogs. Patient E114 demonstrated that the evolution of the relapse-specific clone from a pre-leukemic ancestor may be facilitated by intensive induction treatment of the primary leukemia. In this patient, two preserved MRD markers confirmed the relationship between primary leukemia and relapse. In addition, targeted ultra-deep sequencing identified five mutations that had been present at a subclonal level in primary disease, persisted in remission and became predominant in relapse (Figure 1C, Online Supplementary Tables S6 and S7). Already in the remission sample, which was taken immediately after induction treatment had been completed, 16 newly acquired mutations were detected and later predominated at relapse (Online Relapse-specific alterations in T-acute lymphoblastic leukemia do not show association with leukemogenesis, but with cancerogenesis in general In nine of 13 patients we identified relapse-specific mutations that, based on current knowledge, are likely to contribute to the evolution of relapse In order to obtain an unsupervised view of the contribution of mutations to relapse we investigated whether the genetic alterations that are specific for relapse can be linked to certain biological functions. To this end, we grouped genetic alterations, which had been detected either by WES or by MLPA, according to the time points at which they were found. Using Ingenuity Pathway Analysis (IPA) software, genes that were mutated or deleted in the major clones at both times, primary leukemia J.B. Kunz et al. 1446 haematologica | 2015; 100(11) © F e r r a t a S t o r t i F o u n d a t i o n and relapse, were compared to those genes that were found to be mutated or deleted in the major clone at relapse but not in the corresponding primary leukemia (Online Using genes altered both in primary leukemia and in relapse, IPA constructed a dense network involving the nodes NOTCH, IL7R, MTOR, GATA3 and AKT, reflecting the frequent occurrence of somatic DNA alterations in established leukemia drivers in this gene set (Online Hypermutation caused by somatic DNA repair deficiency can contribute to genetic instability in relapsed T-cell acute lymphoblastic leukemia Patient S00285 carried a moderate number of eight mutations in primary disease, but an extraordinarily high number of 106 mutations in relapse, many of which were subclonal (Online Hypomethylated promoters in relapsed T-cell acute lymphoblastic leukemia do not show association with leukemogenesis, but with cancerogenesis in general We used Illumina 450k arrays to compare DNA methylation in relapse samples to that in the corresponding primary T-ALL samples. In contrast to the situation in relapsed BCP-ALL, In order to identify promoters that may undergo differential methylation in relapse, we filtered for promoters that: (i) were represented on the 450k array by at least three different probes; (ii) had a gene symbol assigned; and (iii) had a decrease or an increase of the β-value of at least 0.2 in absolute numbers in at least three different patients. According to these criteria, a total of 239 promoters were recurrently hypermethylated and 579 promoters recurrently hypomethylated in relapse. The lists of hyper-and hypomethylated promoters (Online Discussion By applying a deep coverage target enrichment technique to sensitively and quantitatively detect rare mutations in primary disease, remission and relapse of pediatric T-ALL, we distinguish between relapses arising from the major clone of the primary leukemia (type 1) and relapses arising from a pre-leukemic ancestral clone (type 2). In both types, selection of subclones and acquisition of novel mutations contributed to clonal evolution. Similar observations have been made before for BCP-leukemia 6,7,9 and for acute myeloid leukemia. 2,14 More than three-quarters (187 of 241) of relapse-specific mutations could not be detected in primary disease samples despite a sensitivity of detection that exceeded 1:100 for most mutations. The mutational load during relapse is more than doubled compared to that during primary leukemia, suggesting that mutations are truly acquired de novo during treatment and/or during remission. Relapsespecific patterns of mutations attributed to chemotherapy have been described by others. The leukemia that acquired a BLM mutation during treatment was of particular interest. This mutation first appeared at the time of remission and was clonal at the time of relapse. The presence of this mutation was associated with an unusually high number of mostly subclonal relapse-specific mutations, indicating that acquired mutations of DNA repair genes may result in somatic hypermutation during the clonal evolution of T-ALL. While haploinsufficiency is not evident in heterozygous carriers of germline BLM mutations, 32,33 the effect of somatic BLM mutations in the context of leukemia may be amplified by mutagenic stress induced by chemotherapy. While the genetic alterations shared by primary leukemia and relapse are, as expected, enriched in genes that are known to be implicated in leukemogenesis, An analysis of the 450k methylome data revealed that, in contrast to BCP-ALL, 1448 haematologica | 2015; 100(11) © F e r r a t a S t o r t i F o u n d a t i o n relapse. However, a set of promoters was found to be recurrently hypomethylated in relapse compared to primary disease. This set contains many genes related to cancer, albeit not specifically involved in leukemogenesis. The correlation between DNA methylation and RNA abundance could not be analyzed due to lack of RNA samples. However, a strong inverse correlation between promoter methylation and RNA expression has been described before in ALL. 6,10 Hence, both relapse-specific mutations and changes of the DNA methylome are consistent with the activation of additional oncogenic mechanisms in relapsed T-ALL. The importance of epigenetic changes is specifically highlighted by the findings in patient S00169 ( The only gene that was recurrently mutated in a relapsespecific manner was NT5C2, 38 In our small series of patients, no other mutation was recurrent and many mutations present in the primary leukemia were lost in relapse. The application of novel, targeted therapies to patients with relapsed T-ALL will, therefore, likely require a thorough genetic characterization of relapse-specific targets. In conclusion, the data presented here identify two molecularly defined types of relapse in pediatric T-ALL and implicate the selection of subclones, the acquisition of novel somatic mutations and the hypomethylation of promoters as mechanisms driving the progression of T-ALL from primary disease to relapse. It is noteworthy that the relapsespecific alterations tend to activate general mechanisms of carcinogenesis rather than known leukemia-specific drivers. (BMBF, NGFN Plus), "Tour der Hoffnung", Manfred Lautenschläger Stiftung, European Commission (FP7, ERA-NET on Translational Cancer Research, TRANSCALL to MUM; Health-F2-2010-260791 The β value for each promoter in relapse was compared to that in primary leukemia. Promoters with a β value in relapse that was at least 0.2 higher than in primary leukemia were considered to be hypermethylated. Promoters with a β value in relapse that was at least 0.2 lower than in primary leukemia were considered to be hypomethylated. Only promoters of those genes for which at least one gene symbol is assigned and which are represented by at least three probes on the 450k array are represented here. © F e r r a t a S t o r t i F o u n d a t i o n Acknowledgments The authors would like to thank the following institutions for grants: German Consortium for Translational Cancer Research (DKTK), German Ministry of Education and Research A B © F e r r a t a S t o r t i F o u n d a t i o n