Differential gene expression patterns and interaction networks in BCR-ABL-positive and -negative adult acute lymphoblastic leukemias

Dejan Juric, Norman J. Lacayo, Meghan C. Ramsey, Janis Racevskis, Peter H. Wiernik, Jacob M. Rowe, Anthony H. Goldstone, Peter J. O'Dwyer, Elisabeth M. Paietta, Branimir I. Sikic

Research output: Contribution to journalArticle

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Abstract

Purpose: To identify gene expression patterns and interaction networks related to BCR-ABL status and clinical outcome in adults with acute lymphoblastic leukemia (ALL). Patients and 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 p210 BCR-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). Conclusion: 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.

Original languageEnglish (US)
Pages (from-to)1341-1349
Number of pages9
JournalJournal of Clinical Oncology
Volume25
Issue number11
DOIs
StatePublished - Apr 10 2007
Externally publishedYes

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Precursor Cell Lymphoblastic Leukemia-Lymphoma
Gene Expression
Genes
Interleukin-15
Oligonucleotide Array Sequence Analysis
Biomedical Research
Cell Death
Cell Proliferation
Survival
Growth

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

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Differential gene expression patterns and interaction networks in BCR-ABL-positive and -negative adult acute lymphoblastic leukemias. / Juric, Dejan; Lacayo, Norman J.; Ramsey, Meghan C.; Racevskis, Janis; Wiernik, Peter H.; Rowe, Jacob M.; Goldstone, Anthony H.; O'Dwyer, Peter J.; Paietta, Elisabeth M.; Sikic, Branimir I.

In: Journal of Clinical Oncology, Vol. 25, No. 11, 10.04.2007, p. 1341-1349.

Research output: Contribution to journalArticle

Juric, Dejan ; Lacayo, Norman J. ; Ramsey, Meghan C. ; Racevskis, Janis ; Wiernik, Peter H. ; Rowe, Jacob M. ; Goldstone, Anthony H. ; O'Dwyer, Peter J. ; Paietta, Elisabeth M. ; Sikic, Branimir I. / Differential gene expression patterns and interaction networks in BCR-ABL-positive and -negative adult acute lymphoblastic leukemias. In: Journal of Clinical Oncology. 2007 ; Vol. 25, No. 11. pp. 1341-1349.
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abstract = "Purpose: To identify gene expression patterns and interaction networks related to BCR-ABL status and clinical outcome in adults with acute lymphoblastic leukemia (ALL). Patients and 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 p210 BCR-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). Conclusion: 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.",
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T1 - Differential gene expression patterns and interaction networks in BCR-ABL-positive and -negative adult acute lymphoblastic leukemias

AU - Juric, Dejan

AU - Lacayo, Norman J.

AU - Ramsey, Meghan C.

AU - Racevskis, Janis

AU - Wiernik, Peter H.

AU - Rowe, Jacob M.

AU - Goldstone, Anthony H.

AU - O'Dwyer, Peter J.

AU - Paietta, Elisabeth M.

AU - Sikic, Branimir I.

PY - 2007/4/10

Y1 - 2007/4/10

N2 - Purpose: To identify gene expression patterns and interaction networks related to BCR-ABL status and clinical outcome in adults with acute lymphoblastic leukemia (ALL). Patients and 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 p210 BCR-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). Conclusion: 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.

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