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A p53-regulated apoptotic gene signature predicts treatment response and outcome in pediatric acute lymphoblastic leukemia

Authors Bainer RO, Trendowski MR, Cheng C, Pei D, Yang W, Paugh SW, Goss KH, Skol AD, Pavlidis P, Pui CH, Gilliam TC, Evans WE, Onel K

Received 18 April 2017

Accepted for publication 14 July 2017

Published 13 September 2017 Volume 2017:9 Pages 397—410

DOI https://doi.org/10.2147/CMAR.S139864

Checked for plagiarism Yes

Review by Single-blind

Peer reviewers approved by Dr Akshita Wason

Peer reviewer comments 4

Editor who approved publication: Dr Alexandra R. Fernandes


Russell O Bainer,1 Matthew R Trendowski,2 Cheng Cheng,3 Deqing Pei,3 Wenjian Yang,3 Steven W Paugh,4 Kathleen H Goss,5 Andrew D Skol,6 Paul Pavlidis,7 Ching-Hon Pui,4,8 T Conrad Gilliam,1 William E Evans,4,9,* Kenan Onel10–13,*

1Department of Human Genetics, 2Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, IL, 3Department of Biostatistics, 4Hematological Malignancy Program, St Jude Children’s Research Hospital, Memphis, TN, 5University of Chicago Medicine Comprehensive Cancer Center, 6Department of Pediatrics, The University of Chicago, Chicago, IL, USA; 7Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada; 8Department of Oncology, 9Department of Pharmaceutical Sciences, St Jude Children’s Research Hospital, Memphis, TN, 10Division of Human Genetics and Genomics, 11Division of Hematology/Oncology and Stem Cell Transplantation, Cohen Children’s Medical Center, New Hyde Park, 12The Feinstein Institute for Medical Research, Manhasset, NY, 13Hofstra Northwell School of Medicine, Hofstra University, Hempstead, NY, USA

*These authors contributed equally to this work

Abstract: Gene signatures have been associated with outcome in pediatric acute lymphoblastic leukemia (ALL) and other malignancies. However, determining the molecular drivers of these expression changes remains challenging. In ALL blasts, the p53 tumor suppressor is the primary regulator of the apoptotic response to genotoxic chemotherapy, which is predictive of outcome. Consequently, we hypothesized that the normal p53-regulated apoptotic response to DNA damage would be altered in ALL and that this alteration would influence drug response and treatment outcome. To test this, we first used global expression profiling in related human B-lineage lymphoblastoid cell lines with either wild type or mutant TP53 to characterize the normal p53-mediated transcriptional response to ionizing radiation (IR) and identified 747 p53-regulated apoptotic target genes. We then sorted these genes into six temporal expression clusters (TECs) based upon differences over time in their IR-induced p53-regulated gene expression patterns, and found that one cluster (TEC1) was associated with multidrug resistance in leukemic blasts in one cohort of children with ALL and was an independent predictor of survival in two others. Therefore, by investigating p53-mediated apoptosis in vitro, we identified a gene signature significantly associated with drug resistance and treatment outcome in ALL. These results suggest that intersecting pathway-derived and clinically derived expression data may be a powerful method to discover driver gene signatures with functional and clinical implications in pediatric ALL and perhaps other cancers as well.

Keywords: pediatric acute lymphoblastic leukemia, p53, gene expression signature, outcomes analysis

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