Faculty Bibliography

PURPOSE: Five-year overall survival (OS) for children with B-cell precursor acute lymphoblastic leukemia (B-ALL) exceeds 90% with risk-adapted therapy. Age, initial WBC count, genetic aberrations, and minimal residual disease (MRD) are used for risk stratification. Intrachromosomal amplification of a region of chromosome 21 (iAMP21; three or more extra copies of RUNX1 on an abnormal chromosome 21) is a recently identified recurrent genomic lesion associated with inferior outcome in some studies. We investigated the impact of iAMP21 in a large cohort treated in contemporary Children's Oncology Group (COG) ALL trials. PATIENTS AND METHODS: Fluorescent in situ hybridization for specific genetic aberrations was required at diagnosis. MRD was measured by flow cytometry at end induction. Outcome was measured as event-free survival (EFS) and OS. RESULTS: iAMP21 was found in 158 (2%) of 7,793 patients with B-ALL age >/= 1 year; 74 (1.5%) of 5,057 standard-risk (SR) patients, and 84 (3.1%) of 2,736 high-risk (HR) patients. iAMP21 was associated with age >/= 10 years, WBC less than 50,000/muL, female sex, and detectable MRD at day 29. Four-year EFS and OS were significantly worse for patients with iAMP21 and SR B-ALL, but iAMP21 was not a statistically significant prognostic factor in HR patients. There was no interaction between MRD and iAMP21. Among SR patients, day 29 MRD >/= 0.01% and iAMP21 were associated with the poorest EFS and OS; absence of both was associated with the best outcome. CONCLUSION: iAMP21 is associated with inferior outcome in pediatric B-ALL, particularly SR patients who require more intensive therapy and are now treated on HR COG ALL protocols.

The Sox4 transcription factor mediates early B-cell differentiation. Compared with normal pre-B cells, SOX4 promoter regions in Ph(+) ALL cells are significantly hypomethylated. Loss and gain-of-function experiments identified Sox4 as a critical activator of PI3K/AKT and MAPK signaling in ALL cells. ChIP experiments confirmed that SOX4 binds to and transcriptionally activates promoters of multiple components within the PI3K/AKT and MAPK signaling pathways. Cre-mediated deletion of Sox4 had little effect on normal pre-B cells but compromised proliferation and viability of leukemia cells, which was rescued by BCL2L1 and constitutively active AKT and p110 PI3K. Consistent with these findings, high levels of SOX4 expression in ALL cells at the time of diagnosis predicted poor outcome in a pediatric clinical trial (COG P9906). Collectively, these studies identify SOX4 as a central mediator of oncogenic PI3K/AKT and MAPK signaling in ALL.

BACKGROUND: Acute lymphoblastic leukemia (ALL) is the most common cancer in children and the incidence of ALL varies by ethnicity. Although accumulating evidence indicates inherited predisposition to ALL, the genetic basis of ALL susceptibility in diverse ancestry has not been comprehensively examined. METHODS: We performed a multiethnic genome-wide association study in 1605 children with ALL and 6661 control subjects after adjusting for population structure, with validation in three replication series of 845 case subjects and 4316 control subjects. Association was tested by two-sided logistic regression. RESULTS: A novel ALL susceptibility locus at 10p12.31-12.2 (BMI1-PIP4K2A, rs7088318, P = 1.1 x 10(-11)) was identified in the genome-wide association study, with independent replication in European Americans, African Americans, and Hispanic Americans (P = .001, .009, and .04, respectively). Association was also validated at four known ALL susceptibility loci: ARID5B, IKZF1, CEBPE, and CDKN2A/2B. Associations at ARID5B, IKZF1, and BMI1-PIP4K2A variants were consistent across ethnicity, with multiple independent signals at IKZF1 and BMI1-PIP4K2A loci. The frequency of ARID5B and BMI1-PIP4K2A variants differed by ethnicity, in parallel with ethnic differences in ALL incidence. Suggestive evidence for modifying effects of age on genetic predisposition to ALL was also observed. ARID5B, IKZF1, CEBPE, and BMI1-PIP4K2A variants cumulatively conferred strong predisposition to ALL, with children carrying six to eight copies of risk alleles at a ninefold (95% confidence interval = 6.9 to 11.8) higher ALL risk relative to those carrying zero to one risk allele at these four single nucleotide polymorphisms. CONCLUSIONS: These findings indicate strong associations between inherited genetic variation and ALL susceptibility in children and shed new light on ALL molecular etiology in diverse ancestry.

Children's Oncology Group AALL07P2 tested whether substitution of Erwinia asparaginase 25,000-IU/m2 for 6 doses intramuscularly (IM) given Monday/Wednesday/Friday to children and young adults with acute lymphoblastic leukemia (ALL) and clinical allergy to pegaspargase would provide a 48-hour nadir serum asparaginase activity (NSAA) >/=0.10-IU/mL in at least 70% of patients. AALL07P2 enrolled 55 eligible/evaluable patients. NSAA >/=0.1-IU/mL was achieved in 38/41 patients (92.7%) with samples meeting acceptability criteria 48-hours after dosing and in 38/43 patients (88.4%) 72-hours after dosing during course 1. Among acceptable samples obtained during all therapy courses, 95.8% (252/263) of 48-hour samples and 84.5% (125/148) of 72-hour samples had NSAA >/=0.10-IU/mL. Pharmacokinetic parameters were estimated by fitting the serum asparaginase activity-time course for all 6 doses given during course 1 to a one compartment open model with first order absorption. Erwinia asparaginase administered with this schedule achieved therapeutic NSAA at both 48- and 72-hours and was well tolerated with no reports of hemorrhage, thrombosis, or death, and few cases of grade 2-3 allergic reaction (n=6), grade 1-3 hyperglycemia (n=6), and grade 1 pancreatitis (n=1). Following allergy to pegaspargase, Erwinia asparaginase 25,000-IU/m2 x 6 doses IM Monday/Wednesday/Friday for 2 weeks can be substituted for a single dose of pegaspargase.

The B cell-specific transcription factor BACH2 is required for affinity maturation of B cells. Here we show that Bach2-mediated activation of p53 is required for stringent elimination of pre-B cells that failed to productively rearrange immunoglobulin VH-DJH gene segments. After productive VH-DJH gene rearrangement, pre-B cell receptor signaling ends BACH2-mediated negative selection through B cell lymphoma 6 (BCL6)-mediated repression of p53. In patients with pre-B acute lymphoblastic leukemia, the BACH2-mediated checkpoint control is compromised by deletions, rare somatic mutations and loss of its upstream activator, PAX5. Low levels of BACH2 expression in these patients represent a strong independent predictor of poor clinical outcome. In this study, we demonstrate that Bach2+/+ pre-B cells resist leukemic transformation by Myc through Bach2-dependent upregulation of p53 and do not initiate fatal leukemia in transplant-recipient mice. Chromatin immunoprecipitation sequencing and gene expression analyses carried out by us revealed that BACH2 competes with BCL6 for promoter binding and reverses BCL6-mediated repression of p53 and other cell cycle checkpoint-control genes. These findings identify BACH2 as a crucial mediator of negative selection at the pre-B cell receptor checkpoint and a safeguard against leukemogenesis.

Background: The poor prognosis of relapsed ALL warrants the need for new insights into drug resistance mechanisms. We have previously shown that relapsed blasts can be re-sensitized to chemotherapy by the reversal of their gene expression signature using epigenetic agents.[1] Objectives: We hypothesize that aberrant epigenetic mechanisms may play a role in chemoresistance. To assess the degree to which the histone code evolves from diagnosis to relapse, we have used an unbiased, whole genome approach to examine changes in the epigenomic landscape by mapping the genome-wide location of key histone marks in diagnosis/relapse patient pairs with ALL enrolled on Children's Oncology Group protocols. Design/Method: We have performed Chromatin-immunoprecipitation sequencing (ChIP-seq) on two cryopreserved matched diagnosis/relapse pairs using active (H3K4me3, H3K9ac) and repressive (H3K9me3, H3K27me3) histone "mark" antibodies, with non-immunoprecipitated DNA (input) as control. Libraries for each patient pair were multiplexed in a single lane and sequenced in duplicate. 51-cycle single-end sequencing was performed using the Illumina HiSeq2000 Analyzer. Reads were aligned to reference genome using BWA and filtered using Samtools to remove multiple mapping reads. Peaks were called using MACS (v2.0.9) with default settings for histone marks. Results: 94.2% of the sequence reads passed filter (PF) and 96.4% of PF reads had quality score of more than 30. Using a p-value<0.00001, we identified 83,380 and 74,453 peaks (enriched regions) for activating and, 37,483 and 46,143 peaks for repressive histone marks at diagnosis and relapse respectively; suggesting that relapsed blasts are enriched with repressive marks and depleted of activating marks compared to those at diagnosis. Sixty-six genes had shared peaks for various histone marks between the two patients. Upon analyzing the top most differentially expressed transcripts at relapse from our previous cohort[2],64% genes showed concordant histone modificatio!

The bone marrow environment (BME) has been shown to promote resistance of leukemia cells towards chemotherapy, which has been attributed to several proteins, including integrins. Our analysis of 207 children with high-risk (BCR/ABL1-) pre-B ALL revealed that high expression of the integrin alpha6 (alpha6beta1) portends poor clinical outcomes in patients with minimal residual disease (MRD+) on day 29 of induction. Therefore, we hypothesized that alpha6-mediated adhesion of ALL cells to the bone marrow stromal niche contributes to drug resistance. We evaluated the role of alpha6 in BCR-ABL1+ leukemia using two of our established models of leukemia, a conditional knockout model of alpha6 in murine BCR-ABL1+ leukemia and a xenograft model of human BCR-ABL1+ leukemia. alpha6fl/fl cells were oncogenically transformed using BCR-ABL1 (p210). Subsequent transduction with CreERT2 or EmptyERT2 generated leukemia cells in which alpha6 ablation could be induced (CreERT2) or not (EmptyERT2) by addition of Tamoxifen. Conditional ablation of alpha6 in vitro decreased adhesion significantly compared to undeleted controls. Moreover, alpha6 deletion sensitized murine ALL to a tyrosine kinase inhibitor (TKI), Nilotinib. To test the effect of alpha6 deletion on leukemic progression in vivo, alpha6 BCR/ABL1+ pre-B CreERT2+ or control ALL cells were transferred into NOD/SCIDmice. 3 days thereafter, in vivo deletion of alpha6 alone delayed leukemia progression compared to controls (Median survival time, MST, 43 days versus 30 days post-leukemia injection; p=0.008). Nilotinib-treated recipients of to alpha6-competent cells have uniformly died with aMSTof 39.5 days, however the Nilotinib treated alpha6-deleted recipients stayed completely alive. Moreover, we show that alpha6 blockade de-adheres primary ALL cells from their cognate counter receptor laminin in vitro, and sensitizes them to TKI. Taken together, inhibition of alpha6 offers a new approach to overcome drug resistance in pre-B ALL