TY - JOUR
T1 - Pediatric T-cell lymphoblastic leukemia evolves into relapse by clonal selection, acquisition of mutations and promoter hypomethylation
AU - Kunz, Joachim B.
AU - Rausch, Tobias
AU - Bandapalli, Obul R.
AU - Eilers, Juliane
AU - Pechanska, Paulina
AU - Schuessele, Stephanie
AU - Assenov, Yassen
AU - Stütz, Adrian M.
AU - Kirschner-Schwabe, Renate
AU - Hof, Jana
AU - Eckert, Cornelia
AU - von Stackelberg, Arend
AU - Schrappe, Martin
AU - Stanulla, Martin
AU - Koehler, Rolf
AU - Avigad, Smadar
AU - Elitzur, Sarah
AU - Handgretinger, Rupert
AU - Benes, Vladimir
AU - Weischenfeldt, Joachim
AU - Korbel, Jan O.
AU - Muckenthaler, Martina U.
AU - Kulozik, Andreas E.
PY - 2015/10/31
Y1 - 2015/10/31
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84946239254&partnerID=8YFLogxK
U2 - 10.3324/haematol.2015.129692
DO - 10.3324/haematol.2015.129692
M3 - Journal article
C2 - 26294725
AN - SCOPUS:84946239254
SN - 0390-6078
VL - 100
SP - 1442
EP - 1450
JO - Haematologica
JF - Haematologica
IS - 11
ER -