title: High throughput digital quantification of mRNA abundance in primary human acute myeloid leukemia samples.
abstract: Acute promyelocytic leukemia (APL) is characterized by the t(15;17) chromosomal translocation, which results in fusion of the retinoic acid receptor alpha (RARA) gene to another gene, most commonly promyelocytic leukemia (PML). The resulting fusion protein, PML-RARA, initiates APL, which is a subtype (M3) of acute myeloid leukemia (AML). In this report, we identify a gene expression signature that is specific to M3 samples; it was not found in other AML subtypes and did not simply represent the normal gene expression pattern of primary promyelocytes. To validate this signature for a large number of genes, we tested a recently developed high throughput digital technology (NanoString nCounter). Nearly all of the genes tested demonstrated highly significant concordance with our microarray data (P < 0.05). The validated gene signature reliably identified M3 samples in 2 other AML datasets, and the validated genes were substantially enriched in our mouse model of APL, but not in a cell line that inducibly expressed PML-RARA. These results demonstrate that nCounter is a highly reproducible, customizable system for mRNA quantification using limited amounts of clinical material, which provides a valuable tool for biomarker measurement in low-abundance patient samples.
authors.affiliation: Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University Medical School, St. Louis, Missouri 63110, USA.
authors.forename: Jacqueline E
authors.initials: JE
authors.lastname: Payton
authors.forename: Nicole R
authors.initials: NR
authors.lastname: Grieselhuber
authors.forename: Li-Wei
authors.initials: LW
authors.lastname: Chang
authors.forename: Mark
authors.initials: M
authors.lastname: Murakami
authors.forename: Gary K
authors.initials: GK
authors.lastname: Geiss
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Link
authors.forename: Rakesh
authors.initials: R
authors.lastname: Nagarajan
authors.forename: Mark A
authors.initials: MA
authors.lastname: Watson
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Ley
mesh_terms: D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics; D012815:Signal Processing, Computer-Assisted
chemical_list: D012333:RNA, Messenger