title: Differential gene expression patterns and interaction networks in BCR-ABL-positive and -negative adult acute lymphoblastic leukemias.
abstract: OBJECTIVE
  To identify gene expression patterns and interaction networks related to BCR-ABL status and clinical outcome in adults with acute lymphoblastic leukemia (ALL).
  
  
  METHODS
  DNA microarrays were used to profile a set of 54 adult ALL specimens from the Medical Research Council UKALL XII/Eastern Cooperative Oncology Group E2993 trial (21 p185BCR-ABL-positive, 16 p210BCR-ABL-positive and 17 BCR-ABL-negative specimens).
  
  
  RESULTS
  Using supervised and unsupervised analysis tools, we detected significant transcriptomic changes in BCR-ABL-positive versus -negative specimens, and assessed their validity in an independent cohort of 128 adult ALL specimens. This set of 271 differentially expressed genes (including GAB1, CIITA, XBP1, CD83, SERPINB9, PTP4A3, NOV, LOX, CTNND1, BAALC, and RAB21) is enriched for genes involved in cell death, cellular growth and proliferation, and hematologic system development and function. Network analysis demonstrated complex interaction patterns of these genes, and identified FYN and IL15 as the hubs of the top-scoring network. Within the BCR-ABL-positive subgroups, we identified genes overexpressed (PILRB, STS-1, SPRY1) or underexpressed (TSPAN16, ADAMTSL4) in p185BCR-ABL-positive ALL relative to p210BCR-ABL-positive ALL. Finally, we constructed a gene expression- and interaction-based outcome predictor consisting of 27 genes (including GRB2, GAB1, GLI1, IRS1, RUNX2, and SPP1), which correlated with overall survival in BCR-ABL-positive adult ALL (P = .0001), independent of age (P = .25) and WBC count at presentation (P = .003).
  
  
  CONCLUSIONS
  We identified prominent molecular features of BCR-ABL-positive adult ALL, which may be useful for developing novel therapeutic targets and prognostic markers in this disease.
authors.affiliation: Division of Medical Oncology, Stanford University School of Medicine, Stanford, CA 94305-5151, USA.
authors.forename: Dejan
authors.initials: D
authors.lastname: Juric
authors.forename: Norman J
authors.initials: NJ
authors.lastname: Lacayo
authors.forename: Meghan C
authors.initials: MC
authors.lastname: Ramsey
authors.forename: Janis
authors.initials: J
authors.lastname: Racevskis
authors.forename: Peter H
authors.initials: PH
authors.lastname: Wiernik
authors.forename: Jacob M
authors.initials: JM
authors.lastname: Rowe
authors.forename: Anthony H
authors.initials: AH
authors.lastname: Goldstone
authors.forename: Peter J
authors.initials: PJ
authors.lastname: O'Dwyer
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Paietta
authors.forename: Branimir I
authors.initials: BI
authors.lastname: Sikic
mesh_terms: D000328:Adult; D016044:Fusion Proteins, bcr-abl / Q000235:genetics*; D020869:Gene Expression Profiling; D015973:Gene Expression Regulation, Leukemic; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics* / Q000473:pathology; D016016:Proportional Hazards Models; D020133:Reverse Transcriptase Polymerase Chain Reaction; D018709:Statistics, Nonparametric; D016019:Survival Analysis
chemical_list: D016044:Fusion Proteins, bcr-abl