Tamara Law

Integration of genetic and clinical risk factors improves prognostication in relapsed childhood B-cell precursor acute lymphoblastic leukemia.

Somatic genetic abnormalities are initiators and drivers of disease and have proven clinical utility at initial diagnosis. However, the genetic landscape and its clinical utility at relapse are less well understood and have not been studied comprehensively. We analyzed cytogenetic data from 427 children with relapsed B-cell precursor ALL treated on the international trial, ALLR3. Also we screened 238 patients with a marrow relapse for selected copy number alterations (CNAs) and mutations. Cytogenetic risk groups were predictive of outcome postrelapse and survival rates at 5 years for patients with good, intermediate-, and high-risk cytogenetics were 68%, 47%, and 26%, respectively (P < .001). TP53 alterations and NR3C1/BTG1 deletions were associated with a higher risk of progression: hazard ratio 2.36 (95% confidence interval, 1.51-3.70, P < .001) and 2.15 (1.32-3.48, P = .002). NRAS mutations were associated with an increased risk of progression among standard-risk patients with high hyperdiploidy: 3.17 (1.15-8.71, P = .026). Patients classified clinically as standard and high risk had distinct genetic profiles. The outcome of clinical standard-risk patients with high-risk cytogenetics was equivalent to clinical high-risk patients. Screening patients at relapse for key genetic abnormalities will enable the integration of genetic and clinical risk factors to improve patient stratification and outcome. This study is registered at www.clinicaltrials.org as #ISCRTN45724312.

Highly sensitive MRD tests for ALL based on the IKZF1 Δ3–6 microdeletion

Current clinical trials for patients with acute lymphoblastic leukemia (ALL) depend upon the measurement of minimal residual disease (MRD) at early stages of therapy to determine the risk of relapse for each patient who is being used for treatment stratification.1 PCR-based MRD tests are usually designed to detect the specific rearrangements of immunoglobulin and T-cell receptor (Ig/TCR) genes found in the leukemic clone. We now present evidence supporting the hypothesis that the most common deletion in the IKZF1 gene in ALL also provides the basis for highly sensitive MRD tests that give MRD results in close agreement with Ig/TCR MRD markers.

Persistent MRD before and after allogeneic BMT predicts relapse in children with acute lymphoblastic leukaemia

Minimal residual disease (MRD) during early chemotherapy is a powerful predictor of relapse in acute lymphoblastic leukaemia (ALL) and is used in children to determine eligibility for allogeneic haematopoietic stem cell transplantation (HSCT) in first (CR1) or later complete remission (CR2/CR3). Variables affecting HSCT outcome were analysed in 81 children from the ANZCHOG ALL8 trial. The major cause of treatment failure was relapse, with a cumulative incidence of relapse at 5 years (CIR) of 32% and treatment‐related mortality of 8%. Leukaemia‐free survival (LFS) and overall survival (OS) were similar for HSCT in CR1 (LFS 62%, OS 83%, n = 41) or CR2/CR3 (LFS 60%, OS 72%, n = 40). Patients achieving bone marrow MRD negativity pre‐HSCT had better outcomes (LFS 83%, OS 92%) than those with persistent MRD pre‐HSCT (LFS 41%, OS 64%, P < 0·0001) or post‐HSCT (LFS 35%, OS 55%, P < 0·0001). Patients with B‐other ALL had more relapses (CIR 50%, LFS 41%) than T‐ALL and the main precursor‐B subtypes including BCR‐ABL1, KMT2A (MLL), ETV6‐RUNX1 (TEL‐AML1) and hyperdiploidy >50. A Cox multivariate regression model for LFS retained both B‐other ALL subtype (hazard ratio 4·1, P = 0·0062) and MRD persistence post‐HSCT (hazard ratio 3·9, P = 0·0070) as independent adverse prognostic variables. Persistent MRD could be used to direct post‐HSCT therapy.

Improving the Identification of High Risk Precursor B Acute Lymphoblastic Leukemia Patients with Earlier Quantification of Minimal Residual Disease

The stratification of patients with acute lymphoblastic leukemia (ALL) into treatment risk groups based on quantification of minimal residual disease (MRD) after induction therapy is now well accepted but the relapse rate of about 20% in intermediate risk patients remains a challenge. The purpose of this study was to further improve stratification by MRD measurement at an earlier stage. MRD was measured in stored day 15 bone marrow samples for pediatric patients enrolled on ANZCHOG ALL8 using Real-time Quantitative PCR to detect immunoglobulin and T-cell receptor gene rearrangements with the same assays used at day 33 and day 79 in the original MRD stratification. MRD levels in bone marrow at day 15 and 33 were highly predictive of outcome in 223 precursor B-ALL patients (log rank Mantel-Cox tests both P<0.001) and identified patients with poor, intermediate and very good outcomes. The combined use of MRD at day 15 (≥1×10−2) and day 33 (≥5×1−5) identified a subgroup of medium risk precursor B-ALL patients as poor MRD responders with 5 year relapse-free survival of 55% compared to 84% for other medium risk patients (log rank Mantel-Cox test, Pu200a=u200a0.0005). Risk stratification of precursor B-ALL but not T-ALL could be improved by using MRD measurement at day 15 and day 33 instead of day 33 and day 79 in similar BFM-based protocols for children with this disease.

High prevalence of relapse in children with Philadelphia-like acute lymphoblastic leukemia despite risk-adapted treatment

Acute lymphoblastic leukemia (ALL) remains a leading cause of cancer-related death in children and young adults. Since the 1960s, improvements in the treatment of children with ALL have led to 10-year survival rates now exceeding 85%.[1][1] Philadelphia-like (Ph-like) ALL is characterized by a gene

Xenograft-directed personalized therapy for a patient with post-transplant relapse of ALL

The outcome for ALL relapsing after BM transplantation (BMT) remains poor. International Bone Marrow Transplant Register data suggest that about 30% of patients can be cured with a second BMT and that younger age (o20 years), longer interval between transplants (46 months) and deeper molecular remission contribute to greater likelihood of success. The selection of chemotherapy to achieve deep remission before second BMT is often complicated by the patient’s previous exposures to agents with cumulative toxicities such as anthracyclines and/or slow minimal residual disease (MRD) responses to previous induction therapy. The use of novel therapies targeted to specific ALL biology is attractive and has been pioneered for tyrosine kinase inhibitors in Ph-like ALL. Although integrated genomic analysis may identify novel treatment options for relapsed ALL, it is important to establish if targeted therapy will be more effective than conventional remission induction which works in 60–70% of cases. Xenograft models accurately reproduce ALL in preclinical studies and patient-derived xenografts (PDX) could be used to assess this and to prioritize therapy for individual ALL relapse cases. We demonstrate that biologic, genetic and expression analyses combined with the treatment of a patient’s ALL in PDX mice were able to provide relevant information in time to guide therapy selection for a patient with a post-transplant relapse resulting in a complete molecular remission and enabling a second BMT. A 3-year-old girl diagnosed with pre-B-ALL was treated as a high standard-risk patient following the Children’s Oncology Group protocol (ALL0331) due to a slow early marrow response with high minimal residual disease (MRD410 ; Supplementary Table S1). She completed therapy but had an isolated BM relapse 35 months after diagnosis. The patient was enrolled in the UKALL-R3 trial in the intermediate risk group and had high MRD (1 × 10 ) at end of induction. As per trial recommendation, she received a matched-sibling-donor BMT. She had low level MRD (positive o5 × 10 ) pre-BMT and a second isolated BM relapse occurred 15 months after the first transplant. The family wished to pursue curative therapy, with the plan to induce a third remission followed by a second BMT. Treatment with fludarabine, cytarabine and mitoxantrone (FLAG-M) was commenced 5 days after the second relapse (Figure 1, Table 1). A multi-disciplinary panel was convened to determine whether alternate treatment(s) could be identified and validated in real-time in the event of failure of FLAG-M to achieve a third remission. The panel reviewed diagnostic information, results from the literature and the Pediatric Preclinical Testing Program (PPTP) and chose targeted genetic analyses to be performed to facilitate rapid analysis and enable PDX validation. In particular we tested for a BCR-ABL1-like expression signature including specific targetable fusions, performed phospho-flow cytometry for targetable kinase activity; low-density genomic analysis by multiplex ligation-dependent PCR (MLPA); and screened for activating RAS or JAK mutations. Twenty non-irradiated, immune-deficient, NOD/SCID/IL-2 receptor gamma /− (NOD.Cg-Prkdc Il2rg/SzJ, NSG) mice were inoculated by tail vein injection 8 days after the 2nd relapse with 2 × 10 BM cells (from the 2nd relapse) to establish the PDX.

A risk score including microdeletions improves relapse prediction for standard and medium risk precursor B-cell acute lymphoblastic leukaemia in children

To prevent relapse, high risk paediatric acute lymphoblastic leukaemia (ALL) is treated very intensively. However, most patients who eventually relapse have standard or medium risk ALL with low minimal residual disease (MRD) levels. We analysed recurrent microdeletions and other clinical prognostic factors in a cohort of 475 uniformly treated non‐high risk precursor B‐cell ALL patients with the aim of better predicting relapse and refining risk stratification. Lower relapse‐free survival at 7 years (RFS) was associated with IKZF1 intragenic deletions (P < 0·0001); P2RY8‐CRLF2 gene fusion (P < 0·0004); Day 33 MRD>5 × 10−5 (P < 0·0001) and High National Cancer Institute (NCI) risk (P < 0·0001). We created a predictive model based on a risk score (RS) for deletions, MRD and NCI risk, extending from an RS of 0 (RS0) for patients with no unfavourable factors to RS2 + for patients with 2 or 3 high risk factors. RS0, RS1, and RS2 + groups had RFS of 93%, 78% and 49%, respectively, and overall survival (OS) of 99%, 91% and 71%. The RS provided greater discrimination than MRD‐based risk stratification into standard (89% RFS, 96% OS) and medium risk groups (79% RFS, 91% OS). We conclude that this RS may enable better early therapeutic stratification and thus improve cure rates for childhood ALL.