Abstract
Acute lymphoblastic leukemia (ALL) is often composed of numerous subclones. Here we test whether the clonal composition of the blood is representative of the bone marrow at leukemia onset. Using ultra-deep IGH sequencing, we detected 28 clones across 16 patients; 5/28 were only in the marrow. In 4 patients, the most abundant clones differed between sites, including 3 in which the dominant medullary clones were minimally detectable in the blood. These findings demonstrate that the peripheral blood often underrepresents the genetic heterogeneity in a B-ALL and highlight the potential impact of tissue site selection on the detection of minor subclones.
Introduction
Acute lymphoblastic leukemia (ALL) remains a leading cause of cancer mortality in children and adolescents [1]. The inherent genetic diversity within each ALL illustrates its complexity. Next generation sequencing (NGS) approaches have expanded our awareness of numerous clinically-relevant genetic alternations in ALL [2-4], some of which are often present at the subclone level [5]. Still, the presence of minimal residual disease (MRD) remains the primary predictor of ALL relapse [6, 7], which is often characterized by the expansion of minor subclones present at the time of diagnosis [8]. NGS methods for detection of subclonal antigen receptor gene rearrangements thus hold promise for refining patient risk stratification [9-13].
As the field begins to study NGS-based MRD in clinical trials, enhanced detection sensitivity will have numerous potential applications. For instance, the Children’s Oncology Group (COG) has previously studied Induction day 8 peripheral blood (PB) MRD as a means of sub-stratifying particularly treatment-responsive patients [6]. Recently published day 15 flow cytometry (FC) MRD data from patients treated on AIEOP-BFM ALL 2000 demonstrate relatively higher MRD levels in BM than PB but also support the hypothesis that PB MRD findings may independently correlate with outcome [14]. Thus, in the context of new and evolving detection methods and their potential applications for enhancing patient prognostication perhaps even by PB surveillance, it will be critical to ascertain the impact of the tissue sampling site on molecular marker detection and to define whether the clonal composition of each site – namely the BM and PB – adequately represents the malignancy as a whole.
Materials and Methods
Using NGS of the immunoglobulin heavy chain (IGH) variable, diversity, and joining segment junctional region (Vh-D-Jh) from 16 patients with B-ALL, we aimed to discern the relative dissemination patterns of B-ALL clones between BM and PB.
Samples
Matched BM and PB specimens were collected from residual clinically obtained pre-treatment tissue from 16 pediatric and adult patients with newly diagnosed B-ALL in accordance with a University of Rochester Institutional Review Board-approved protocol (within 24h for 15 patients, within 48h for 1 patient, P4). Associated data included age, white blood cell (WBC) count, blast percentage (by morphology), immunophenotype, and cytogenetic data as reported in associated, de-identified pathology reports.
IGH amplification and NGS
Isolated DNA from each sample underwent PCR amplification of the rearranged IGH junctional region (Supplemental Methods). NGS was performed by the University of Rochester Genomics Research Center on a MiSeqDx using Illumina® protocol.
Defining “early clones”
Reads above a conservative sequencing noise threshold were clustered according to shared clonal lineage as represented by a common Jh identity and 6 identical upstream D-Jh junctional nucleotides (termed “6NJx”) according to defined methods [15]; 6NJx clusters comprising ≥5% read frequency defined each “early clone” (Supplemental Methods).
Results
Matched pre-treatment BM and PB B-ALL specimens were analyzed from 16 patients aged 3-63 years (median: 17.5) (Table 1). Deep IGH sequencing yielded a median of 331,974 ~300 base pair paired-end IGH Vh-D-Jh rearranged sequences per specimen.
TABLE 1.
Patient characteristics and B-ALL clonal composition
| Age | WBC | Blast % | No. clones | ||||
|---|---|---|---|---|---|---|---|
| Patient | (y) | (x103/μL) | BM | PB | Cytogenetics | BM | PB |
| P1 | 4 | 20.9 | 97 | 60 | other/complex | 1 | 1 |
| P2 | 3 | 8.1 | 90 | 16 | ETV6/RUNX1 | 2 | 2 |
| P3 | 11 | 4.9 | 90 | 78 | ETV6/RUNX1 | 2 | 2 |
| P4 | 63 | 3.4 | 74 | 44 | hypodiploid | 1 | 1 |
| P5 | 3 | 13.4 | 98 | 68 | normal | 1 | 1 |
| P6 | 61 | 3.1 | 86 | 21 | other/complex | *2 | *1 |
| P7 | 40 | 100.0 | >90 | >90 | KMT2Ar | 4 | 3 |
| P8 | 49 | 106.7 | 97 | 74 | other/complex | 1 | 2 |
| P9 | 26 | 2.7 | 88 | 18 | other/complex | 1 | 1 |
| P10 | 17 | 129.1 | n/a | 92 | other/complex | 1 | 1 |
| P11 | 58 | 2.2 | n/a | 27 | other/complex | 2 | 2 |
| P12 | 5 | 17.2 | 97 | 40 | ETV6/RUNX1 | 2 | 2 |
| P13 | 13 | 2.4 | 96 | 6 | Trisomy 4&10 | 2 | 0 |
| P14 | 6 | 15.5 | 93 | 13 | ETV6/RUNX1 & Trisomy 4&10 | 2 | 2 |
| P15 | 18 | 101 | 92 | 90 | normal | 2 | 2 |
| P16 | 40 | 127.4 | 38 | 30 | BCR/ABL1 | 0 | 0 |
n/a=not available
In P6, a total of 3 distinct clones were detected across tissue sites; 2 were in the BM and 1 was in the PB.
Early clone detection
Fifteen of 16 patients had at least 1 early clone at ≥5% read frequency; 10/15 demonstrated multiple early clones in one or both tissue sites (median: 2, range: 1-4) (Table 1).
Distinct clone abundance between BM & PB
Fourteen patients (8 pediatric, 6 adult) had at least 1 early clone in both BM and PB, while 1 pediatric patient (P13) demonstrated clonal involvement of the BM alone. A total of 28 early clones were detected across all patients. Five of these 28 were above clone threshold only in the BM.
Eleven patients showed comparable predominant clones between BM and PB (Figure 1A). In the other 4 patients, the most abundant clone differed between sites. In P6, the 2 most prevalent clones in the BM were minimally detectable in the PB, while the most prevalent clone in the PB (5.6%) was below but approaching the 5% threshold in the BM (4.8%). In P7, the most prevalent clone in the BM was below 5% in the PB, while the top 3 in the PB were far less abundant in the BM than the predominant BM clone. P8 showed a prevalent clone in the BM which was also represented in the PB, but the most frequent clone in the PB (8.3%) was not detected at all in the BM. P13 had 2 abundant clones in the BM which were minimally detectable with inverted prevalence in the PB. (Figure 1B)
FIGURE 1. Distribution of early clones between matched, pre-treatment BM and PB B-ALL specimens.
All early clones detected above the 5% read threshold (dotted lines) in at least 1 site are shown according to their total read frequencies in the BM vs. PB. A) In 11/15 patients, the most abundant early clones were proportionately shared (*or closely comparable, as in P12) between the BM and PB. B) In 4/15 patients, the most abundant early clones differed between the BM and PB. In 3 (P6, P7, P8), the relative blast percentage (gray lines) of the PB vs. that of the BM did not correspond to the differences observed. P13 highlights the potential impact of a disproportionate blast percentage on reliable clone detection across sites. C) The read frequency (% of total) of the most prevalent clones are shown from the 4 patients with discrepant clonal predominance between BM and PB. Read frequencies above the 5% clone threshold are shown in bold.
Discussion
Numerous techniques have demonstrated abundant clonal heterogeneity detectable by antigen receptor rearrangements in ALL [15-18]. Historically, IGH PCR showed that differences in gene rearrangement patterns between BM and PB may represent preferential subclone generation in the tissue compartment in which the leukemia precursor cell originated [19]. Analysis of numerous bony and extramedullary tissue sites in murine xenografts further suggested that clonal composition can be variable between sites, with some clones continuing to evolve upon tissue site dissemination [20].
More recently, NGS of antigen receptor rearrangements has further enhanced the detectability of minor subclones in B-ALL [15]. In order to optimize the potential of NGS assays for refining MRD risk stratification in clinical trials [9, 21], it will be critical to recognize all diagnostic subclones to reliably search for them at the MRD level. By these methods, Theunissen et al.’s 2017 analysis of 12 children with B-ALL showed comparable clonal distribution between 7 patients’ paired left and right-sided diagnostic BM samples and 5 patients’ BM and PB, suggesting the notion of homogenous medullary clonal involvement potentially via PB migration [22]. While 11/15 cases reported here show similar findings, our data expand upon Theunissen’s by demonstrating that the PB does not consistently portray a sufficient representation of medullary clonal composition in B-ALL, often providing an underestimate of the extent of clonal heterogeneity.
Our data demonstrate differential distribution of leukemic clones between BM and PB in 4/15 cases. In 1 case (P13), this discrepancy may have been related to a disproportionate blast percentage in the BM vs. the PB, suggesting that PB blast count may be an important feature to consider in determining the reliability of PB clonality assessment. Nevertheless, of the 11 total clones in these 4 patients, 5 (45%) were observed at ≥5% frequency in the BM alone. One case (P16) did not reveal evidence of a clonal IGH rearrangement, suggesting that future analyses may be enhanced by the addition of D region primers to amplify those subclones which have not yet fully recombined the Vh region.
Conclusions
Genetic heterogeneity is a prevalent and increasingly clinically relevant feature of B-ALL. The presented data show differences in the most abundant clone between BM and PB in a substantial subset of patients, most often with the PB providing an underrepresentation of BM clonal heterogeneity and in some cases presenting an entirely distinct pattern of clonal dominance. These findings highlight the potential impact of the tissue sampling site on the detection of minor subclones, a notion to be considered in the context of optimizing NGS-based MRD analysis, interpreting mid-Induction PB MRD sub-stratification, and as potentially subclonal molecular markers are used to refine patient risk stratification and inform targeted therapy decisions. The data underscore the relevance of a standardized approach to specimen collection in optimizing the detection of all minor subclones in a patient’s disease.
Supplementary Material
SUPPLEMENTAL FIGURE 1. Detection of a 6NJx read cluster above the 5% clonal threshold is exclusively a feature of active B-ALL disease specimens. The 2 most prevalent 6NJx clusters detected from each patient’s B-ALL are depicted by total read frequency (%). Five patients (P1, P4, P5, P9, P10) demonstrated only 1 ≥5% early clone. End of induction (EOI) minimal residual disease (MRD) control data are depicted for 2 specimens not included in the primary analysis as well as for Patient P5. Control 1: Refractory disease (EOI PB), Control 2: MRD negative (EOI BM and PB). Control 3 (P5): MRD negative (EOI BM).
Acknowledgements
This work was supported by a University of Rochester Clinical and Translational Science Institute Trainee Pilot Award and a University of Rochester Department of Pediatrics Dean’s Fellowship Award.
NGS was performed in the University of Rochester Genomics Research Center.
Footnotes
Conflict of Interest
The authors have no relevant conflicts of interest to disclose.
Data Sharing
The data that support the findings of this study are available from the corresponding author upon reasonable request.
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Associated Data
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Supplementary Materials
SUPPLEMENTAL FIGURE 1. Detection of a 6NJx read cluster above the 5% clonal threshold is exclusively a feature of active B-ALL disease specimens. The 2 most prevalent 6NJx clusters detected from each patient’s B-ALL are depicted by total read frequency (%). Five patients (P1, P4, P5, P9, P10) demonstrated only 1 ≥5% early clone. End of induction (EOI) minimal residual disease (MRD) control data are depicted for 2 specimens not included in the primary analysis as well as for Patient P5. Control 1: Refractory disease (EOI PB), Control 2: MRD negative (EOI BM and PB). Control 3 (P5): MRD negative (EOI BM).