Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia.

Xiaotu Ma,Mary V Relling,Richard C Harvey,Michael Rusch,Donald Yergeau,Daniela S Gerhard,Gang Wu,Harshavardhan Doddapaneni,William L Carroll,David A Wheeler,Malcolm A Smith,Charles G Mullighan,Stephen P Hunger,Guangchun Song,Cheryl L Willman,Meenakshi Devidas,Jinghui Zhang,John Easton,Jaime M Guidry Auvil,Panduka Nagahawatte,Donna M Muzny,Mignon L Loh,Bhavin Vadodaria,Jing Ma,James R Downing,Oliver Hampton ,Julie M Gastier‐Foster ,Michael N Edmonson ,I‐Ming Chen

doi:10.1038/ncomms7604

Abstract

There is incomplete understanding of genetic heterogeneity and clonal evolution during cancer progression. Here we use deep whole-exome sequencing to describe the clonal architecture and evolution of 20 pediatric B-acute lymphoblastic leukaemias from diagnosis to relapse. We show that clonal diversity is comparable at diagnosis and relapse and clonal survival from diagnosis to relapse is not associated with mutation burden. Six pathways were frequently mutated, with NT5C2, CREBBP, WHSC1, TP53, USH2A, NRAS and IKZF1 mutations enriched at relapse. Half of the leukaemias had multiple subclonal mutations in a pathway or gene at diagnosis, but mostly with only one, usually minor clone, surviving therapy to acquire additional mutations and become the relapse founder clone. Relapse-specific mutations in NT5C2 were found in nine cases, with mutations in four cases being in descendants of the relapse founder clone. These results provide important insights into the genetic basis of treatment failure in ALL and have implications for the early detection of mutations driving relapse.

Highlights

ResultsSomatic mutation profile at diagnosis and relapse. We performed WXS at high coverage (B200-fold) of samples obtained at diagnosis, remission and relapse from 20 patients treated on recent COG B-ALL trials (Methods, Supplementary Data 1 and Supplementary Fig. 1)
S) and a subset of SVs selected from WXS and CGI WGS analysis were subjected to experimental verification
We evaluated the clonal original of mutation clusters present in the dominant clone in the relapsed tumour of case PASLZM

Summary

Results

Somatic mutation profile at diagnosis and relapse. We performed WXS at high coverage (B200-fold) of samples obtained at diagnosis, remission and relapse from 20 patients treated on recent COG B-ALL trials (Methods, Supplementary Data 1 and Supplementary Fig. 1). The WHSC1 p.Glu1099Lys mutation in case PARFTR exhibited an increase in MAF from 0.01 at diagnosis to 0.49 at relapse, while an intragenic deletion of CREBBP in PARBRK, detectable at diagnosis only by high-coverage capture sequencing, was found to be clonal at relapse by analysis of WGS and SNP array data In addition to these six pathways, frequent non-silent sequence mutations were found in FCGBP (immunoglobulin Fc gammabinding protein; n 1⁄4 4) and USH2A (mutated in Usher syndrome and retinitis pigmentosa; n 1⁄4 4; Supplementary Fig. 5c). Case PAPSPN illustrates how clonal evolution resulted in the turnover of the predominant mutations in genes involved in multiple cellular pathways, including JAK-STAT signalling (JAK2), Ras signalling (KRAS) and lymphoid development (PAX5) as well as acquisition of relapse-associated mutations in epigenetic regulators (MLL2) and drug-metabolizing genes (NT5C2). The loss of clone 1 coupled with the expansion of clone 3 resulted in switching of the predominant JAK2 mutation from p.Arg683Ser in diagnosis to p.Arg683Gly in relapse

D CNV loss: CDKN2A CNV loss

Discussion

Methods