Faculty Bibliography

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!

BUBR1 is a mitotic phosphoprotein essential for the maintenance of chromosome stability by promoting chromosome congression and proper kinetochore-microtubule (K-fiber) attachment, but the underlying mechanism(s) has remained elusive. Here we identify BUBR1 as a binding partner of the B56 family of Protein Phosphatase 2A regulatory subunits. The interaction between BUBR1 and the B56 family is required for chromosome congression, since point mutations in BUBR1 that block B56 binding abolish chromosome congression. The BUBR1:B56-PP2A complex opposes Aurora B kinase activity, since loss of the complex can be reverted by inhibiting Aurora B. Importantly, we show that the failure of BUBR1 to recruit B56-PP2A also contributes to the chromosome congression defects found in cells derived from patients with the Mosaic Variegated Aneuploidy (MVA) syndrome. Together, we propose that B56-PP2A is a key mediator of BUBR1's role in chromosome congression and functions by antagonizing Aurora B activity at the kinetochore for establishing stable kinetochore-microtubule attachment at the metaphase plate.

Relapsed childhood acute lymphoblastic leukemia (ALL) carries a poor prognosis, despite intensive retreatment, owing to intrinsic drug resistance. The biological pathways that mediate resistance are unknown. Here, we report the transcriptome profiles of matched diagnosis and relapse bone marrow specimens from ten individuals with pediatric B-lymphoblastic leukemia using RNA sequencing. Transcriptome sequencing identified 20 newly acquired, novel nonsynonymous mutations not present at initial diagnosis, with 2 individuals harboring relapse-specific mutations in the same gene, NT5C2, encoding a 5'-nucleotidase. Full-exon sequencing of NT5C2 was completed in 61 further relapse specimens, identifying additional mutations in 5 cases. Enzymatic analysis of mutant proteins showed that base substitutions conferred increased enzymatic activity and resistance to treatment with nucleoside analog therapies. Clinically, all individuals who harbored NT5C2 mutations relapsed early, within 36 months of initial diagnosis (P = 0.03). These results suggest that mutations in NT5C2 are associated with the outgrowth of drug-resistant clones in ALL.

One recently identified subtype of pediatric B-precursor acute lymphoblastic leukemia (ALL) has been termed BCR-ABL1-like or Ph-like because of similarity of the gene expression profile to BCR-ABL1 positive ALL suggesting the presence of lesions activating tyrosine kinases, frequent alteration of IKZF1, and poor outcome. Prior studies demonstrated that approximately half of these patients had genomic lesions leading to CRLF2 overexpression, with half of such cases harboring somatic mutations in the Janus kinases JAK1 and JAK2. To determine whether mutations in other tyrosine kinases might also occur in ALL, we sequenced the tyrosine kinome and downstream signaling genes in 45 high-risk pediatric ALL cases with either a Ph-like gene expression profile or other alterations suggestive of activated kinase signaling. Aside from JAK mutations and 1 FLT3 mutation, no somatic mutations were found in any other tyrosine kinases, suggesting that alternative mechanisms are responsible for activated kinase signaling in high-risk ALL.

Leukaemia is the single most common childhood malignancy. With modern treatment regimens, survival in acute lymphoblastic leukaemia (ALL) approaches 90%. Only about 70% of children with acute myeloid leukaemia (AML) achieve long term survival. Patients who relapse have a dismal prognosis. Novel therapeutic approaches are needed to improve treatment outcomes in newly-diagnosed patients with a poor prognosis and for patients with relapsed/refractory disease that have limited treatment options. One promising approach in treating haematological malignancies has been the use of monoclonal antibodies to target cell surface antigens expressed on malignant cells. Most success with monoclonal antibody therapy in the treatment of haematological malignancies has come in the setting of adult B-cell non-Hodgkin lymphoma with the addition of the anti-CD20 monoclonal antibody rituximab to standard treatment regimens. In order to further advance treatment of haematological malignancies, novel monoclonal antibodies continue to be developed that target a variety of cell surface antigens. Several antibodies continue to be investigated in childhood leukaemias. This review will discuss the development of monoclonal antibodies that target a variety of cell surface antigens for the treatment of childhood ALL and the use of the anti-CD33 antibody gemtuzumab ozogamicin in the treatment of childhood AML.

PURPOSE OF REVIEW: Acute lymphoblastic leukemia (ALL) is the most common and one of the most curable malignancies in children; however, it presents unique challenges in adolescents and young adults (AYAs). The purpose of this review is to discuss factors that contribute to the outcome disparities in AYAs with ALL as well as approaches that can be taken to optimize the care of this patient population. RECENT FINDINGS: AYAs with ALL are unique and have outcomes that have lagged behind those observed in children with ALL. Contributing factors to the challenges faced by this group include distinctive disease biology, different drug pharmacology and toxicity profiles, and complex psychosocial and socioeconomic factors. Several clinical trials conducted worldwide have demonstrated that treatment with pediatric protocols significantly improves outcomes in the AYA population. SUMMARY: Initiatives to improve outcomes for AYAs with ALL include treatment with pediatric regimens tailored to be delivered without excessive toxicity and in centers with the necessary supportive care and medical services to address the specific needs of this population. As more is understood about the unique disease biology of AYA ALL, targeted therapeutic approaches may offer promise for the future.