Eye on the B-ALL: B-cell receptor repertoires reveal persistence of numerous B-lymphoblastic leukemia subclones from diagnosis to relapse.

R J M Bashford-Rogers,P Kellam,J Chi,K A Nicolaou,G S Vassiliou,N J Goulden,L Loizou,M Hubank,J Bartram,L Koumas,P A Costeas

doi:10.1038/leu.2016.142

Abstract

The strongest predictor of relapse in B-cell acute lymphoblastic leukemia (B-ALL) is the level of persistence of tumor cells after initial therapy. The high mutation rate of the B-cell receptor (BCR) locus allows high-resolution tracking of the architecture, evolution and clonal dynamics of B-ALL. Using longitudinal BCR repertoire sequencing, we find that the BCR undergoes an unexpectedly high level of clonal diversification in B-ALL cells through both somatic hypermutation and secondary rearrangements, which can be used for tracking the subclonal composition of the disease and detect minimal residual disease with unprecedented sensitivity. We go on to investigate clonal dynamics of B-ALL using BCR phylogenetic analyses of paired diagnosis-relapse samples and find that large numbers of small leukemic subclones present at diagnosis re-emerge at relapse alongside a dominant clone. Our findings suggest that in all informative relapsed patients, the survival of large numbers of clonogenic cells beyond initial chemotherapy is a surrogate for inherent partial chemoresistance or inadequate therapy, providing an increased opportunity for subsequent emergence of fully resistant clones. These results frame early cytoreduction as an important determinant of long-term outcome.

Highlights

Advances in the treatment of B-cell acute lymphoblastic leukemia (B-ALL) have increased long-term survival of pediatric patients to above 80%, the equivalent rate for adults remains poor at 30–40%,1,2 with relapse representing the leading cause of mortality at all ages
The samples were studied by analysis of B-cell receptor (BCR) sequencing repertoires and mining of leukemiaspecific BCR sequences derived from RNA (UKALL2003 samples) or DNA (UKALL XI samples) (Table 1)
Using the BCR stem regions (IgHD-J) as molecular barcodes, we reveal the disparate dynamics of cellular clones suggesting differential responses to therapy, different growth rates within different anatomical sites and emergence of novel clones at relapse corresponding with the cytogenetic

Summary

Introduction

Advances in the treatment of B-cell acute lymphoblastic leukemia (B-ALL) have increased long-term survival of pediatric patients to above 80%, the equivalent rate for adults remains poor at 30–40%,1,2 with relapse representing the leading cause of mortality at all ages. B-cells express distinct cell-surface B-cell receptors (BCRs), generated during B-cell differentiation through the rearrangement and assembly of heavy- and light-chain gene variable (V), diverse (D) and joining (J) elements into V(D)J segments through V (D)J recombination.[3] BCRs represent unique markers for each B-cell clone, where the accumulation of BCR mutational variants have been reported to occur at significantly greater rates than that of the rest of the genome,[4,5,6] making this genomic region ideal for characterization of B-cell population dynamics by high-throughput sequencing.[7,8] The BCR sequence repertoire of an individual represents a snapshot of their B-cell population structure and can identify the presence of clonal proliferations, making it useful in the diagnosis and monitoring of B-cell malignancies.[9] Next-generation sequencing of BCR repertoires[10] can facilitate the longitudinal study of the clonal dynamics of malignant B-cell populations from diagnosis to relapse

Methods

Results

Conclusion