33 research outputs found
Genomic characterization of pediatric Bâlymphoblastic lymphoma and Bâlymphoblastic leukemia using formalinâfixed tissues
BackgroundRecurrent genomic changes in Bâlymphoblastic leukemia (BâALL) identified by genomeâwide singleânucleotide polymorphism (SNP) microarray analysis provide important prognostic information, but gene copy number analysis of its rare lymphoma counterpart, Bâlymphoblastic lymphoma (BâLBL), is limited by the low incidence and lack of fresh tissue for genomic testing.ProcedureWe used molecular inversion probe (MIP) technology to analyze and compare copy number alterations (CNAs) in archival formalinâfixed paraffinâembedded pediatric BâLBL (n = 23) and BâALL (n = 55).ResultsSimilar to BâALL, CDKN2A/B deletions were the most common alteration identified in 6/23 (26%) BâLBL cases. Eleven of 23 (48%) BâLBL patients were hyperdiploid, but none showed triple trisomies (chromosomes 4, 10, and 17) characteristic of BâALL. IKZF1 and PAX5 deletions were observed in 13 and 17% of BâLBL, respectively, which was similar to the reported frequency in BâALL. Immunoglobulin light chain lambda (IGL) locus deletions consistent with normal light chain rearrangement were observed in 5/23 (22%) BâLBL cases, compared with only 1% in BâALL samples. None of the BâLBL cases showed abnormal, isolated VPREB1 deletion adjacent to IGL locus, which we identified in 25% of BâALL.ConclusionsOur study demonstrates that the copy number profile of BâLBL is distinct from BâALL, suggesting possible differences in pathogenesis between these closely related diseases.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137353/1/pbc26363.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/137353/2/pbc26363_am.pd
Genomic analyses identify recurrent MEF2D fusions in acute lymphoblastic leukemia
Chromosomal rearrangements are initiating events in acute lymphoblastic leukaemia (ALL). Here using RNA sequencing of 560 ALL cases, we identify rearrangements between MEF2D (myocyte enhancer factor 2D) and five genes (BCL9, CSF1R, DAZAP1, HNRNPUL1 and SS18) in 22 B progenitor ALL (B-ALL) cases with a distinct gene expression profile, the most common of which is MEF2DBCL9. Examination of an extended cohort of 1,164 B-ALL cases identified 30 cases with MEF2D rearrangements, which include an additional fusion partner, FOXJ2; thus, MEF2D-rearranged cases comprise 5.3% of cases lacking recurring alterations. MEF2D-rearranged ALL is characterized by a distinct immunophenotype, DNA copy number alterations at the rearrangement sites, older diagnosis age and poor outcome. The rearrangements result in enhanced MEF2D transcriptional activity, lymphoid transformation, activation of HDAC9 expression and sensitive to histone deacetylase inhibitor treatment. Thus, MEF2D-rearranged ALL represents a distinct form of high-risk leukaemia, for which new therapeutic approaches should be considered.This work was supported in part by
the American Lebanese Syrian Associated Charities of St. Jude Childrenâs Research
Hospital; by a Stand Up to Cancer Innovative Research Grant and St. Baldrickâs
Foundation Scholar Award (to C.G.M.); by a St. Baldrickâs Consortium Award (S.P.H.),
by a Leukemia and Lymphoma Society Specialized Center of Research grant (S.P.H. and
C.G.M.), by a Lady Tata Memorial Trust Award (I.I.), by a Leukemia and Lymphoma
Society Special Fellow Award and Alexâs Lemonade Stand Foundation Young Investigator
Awards (K.R.), by an Alexâs Lemonade Stand Foundation Award (M.L.) and by
National Cancer Institute Grants CA21765 (St Jude Cancer Center Support Grant), U01
CA157937 (C.L.W. and S.P.H.), U24 CA114737 (to Dr Gastier-Foster), NCI Contract
HHSN261200800001E (to Dr Gastier-Foster), U10 CA180820 (ECOG-ACRIN
Operations) and CA180827 (E.P.); U10 CA180861 (C.D.B. and G.M.); U24 CA196171
(The Alliance NCTN Biorepository and Biospecimen Resource); CA145707 (C.L.W. and
C.G.M.); and grants to the COG: U10 CA98543 (Chairâs grant and supplement to
support the COG ALL TARGET project), U10 CA98413 (Statistical Center) and U24
CA114766 (Specimen Banking). This project has been funded in whole or in part with
Federal funds from the National Cancer Institute, National Institutes of Health, under
Contract Number HHSN261200800001E
Molecular characterization of genetic diversity, structure, and differentiation in the olive (Olea europaea L.) germplasm collection of the United States Department of Agriculture
Prolonged Complete Response in a Pediatric Patient With Primary Peripheral T-Cell Lymphoma of the Central Nervous System.
We describe a child with a 2-week history of progressive headaches, blurry vision, and intermittent vomiting. Magnetic resonance imaging (MRI) of the brain showed a deep left hemispheric lesion with extension into the corpus callosum. Histology and immunophenotyping of the lesion was consistent with peripheral T-cell lymphoma, not otherwise specified. Chemotherapy was initiated and a complete remission was achieved. This case illustrates that a chemotherapeutic regimen used in adults with central nervous system (CNS) lymphoma can achieve durable remissions in pediatric patients with peripheral T-cell lymphoma, not otherwise specified of the CNS
Prolonged Complete Response in a Pediatric Patient With Primary Peripheral T-Cell Lymphoma of the Central Nervous System
Targetable kinase gene fusions in high-risk B-ALL: a study from the Children\u27s Oncology Group.
Plasma Asparaginase Activity and Asparagine Depletion in Acute Lymphoblastic Leukemia Patients Treated with Pegaspargase on Children\u27s Oncology Group AALL07P4
Plasma asparaginase activity and asparagine depletion in patients with acute lymphoblastic leukemia (ALL) treated with pegaspargase (SS-PEG E. coli
Detection of minimal residual disease in B lymphoblastic leukemia by high-throughput sequencing of IGH.
PURPOSE: High-throughput sequencing (HTS) of immunoglobulin heavy chain genes (IGH) in unselected clinical samples for minimal residual disease (MRD) in B lymphoblastic leukemia (B-ALL) has not been tested. As current methods for MRD detection, such as flow cytometry or patient-specific qPCR are complex or difficult to standardize in the clinical laboratory, sequencing may enhance clinical prognostication. EXPERIMENTAL DESIGN: We sequenced IGH in paired pre- and day 29 post-treatment samples using residual material from consecutive, unselected samples from Children's Oncology Group AALL0932 trial to measure MRD as compared to flow cytometry. We assessed the impact of on-going recombination at IGH on MRD detection in post-treatment samples. Lastly, we evaluated a subset of cases with discordant MRD results between flow cytometry and sequencing. RESULTS: We find clonal IGH rearrangements in 92 of 98 pre-treatment patient samples. Further, while on-going recombination of IGH was evident, index clones typically prevailed in MRD-positive post-treatment samples, suggesting that clonal evolution at IGH does not contribute substantively to tumor fitness. MRD was detected by sequencing in all flow cytometry positive cases with no false negative results. Additionally, in a subset of patients, MRD was detected by sequencing, but not by flow cytometry, including a fraction with MRD levels within the sensitivity of flow cytometry. We provide data that suggest that this discordance in some patients may be due to the phenotypic maturation of the transformed cell. CONCLUSION: Our results provide strong support for high-throughput sequencing of IGH to enhance clinical prognostication in B-ALL