title: Genetic variants in cytosolic 5'-nucleotidase II are associated with its expression and cytarabine sensitivity in HapMap cell lines and in patients with acute myeloid leukemia.
abstract: Cytosolic 5'-nucleotidase II (NT5C2) is involved in the development of 1-β-d-arabinofuranosylcytosine (ara-C) resistance and has been associated with clinical outcome in patients receiving ara-C-based chemotherapy. NT5C2 inactivates ara-C by dephosphorylating ara-C monophosphate to ara-C. In this study, we sequenced NT5C2 in genomic DNA samples from International HapMap project panels with European [Centre d'Etude du Polymorphisme Humain (CEU); n = 90] or African [Yoruba people in Ibadan, Nigeria (YRI); n = 90] ancestry. We identified 41 genetic variants [one insertion-deletion and 40 single nucleotide polymorphisms (SNPs)], including three nonsynonymous SNPs (Y3A, K47R, and Q136R). Twenty-five SNPs were novel and 16 overlapped with the HapMap data. Subjects with African ancestry had NT5C2 mRNA expression levels that was significantly higher than those with European ancestry (p = 0.005). Furthermore, there was a correlation between NT5C2 mRNA expression and ara-C sensitivity in CEU but not in YRI cell lines. None of the nonsynonymous SNPs demonstrated any effect on NT5C2 activity. The genotypes of several SNPs were significantly associated with NT5C2 mRNA expression and/or ara-C sensitivity in CEU cell lines, but very few were significant in YRI cell lines. Of most interest, SNPs (linkage disequilibrium group CEU.12) in the 5'-untranslated region were associated with NT5C2 expression and ara-C sensitivity in HapMap cell lines and with NT5C2 mRNA expression and ara-C sensitivity in diagnostic leukemic blasts from pediatric patients with acute myeloid leukemia. Functional genomics analysis demonstrated that the promoter SNP rs11191612 was associated with altered luciferase activation in reporter assays and altered DNA-protein binding in gel shift assays. These results suggest that genetic variations in NT5C2 influence its expression and, potentially, cellular responses to nucleoside analogs.
authors.affiliation: Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, USA.
authors.forename: Amit K
authors.initials: AK
authors.lastname: Mitra
authors.forename: Kristine R
authors.initials: KR
authors.lastname: Crews
authors.forename: Stanley
authors.initials: S
authors.lastname: Pounds
authors.forename: Xueyuan
authors.initials: X
authors.lastname: Cao
authors.forename: Tanya
authors.initials: T
authors.lastname: Feldberg
authors.forename: Yogita
authors.initials: Y
authors.lastname: Ghodke
authors.forename: Varsha
authors.initials: V
authors.lastname: Gandhi
authors.forename: William
authors.initials: W
authors.lastname: Plunkett
authors.forename: M Eileen
authors.initials: ME
authors.lastname: Dolan
authors.forename: Christine
authors.initials: C
authors.lastname: Hartford
authors.forename: Susana
authors.initials: S
authors.lastname: Raimondi
authors.forename: Dario
authors.initials: D
authors.lastname: Campana
authors.forename: James
authors.initials: J
authors.lastname: Downing
authors.forename: Jeffrey E
authors.initials: JE
authors.lastname: Rubnitz
authors.forename: Raul C
authors.initials: RC
authors.lastname: Ribeiro
authors.forename: Jatinder K
authors.initials: JK
authors.lastname: Lamba
mesh_terms: D015720:5'-Nucleotidase / Q000037:antagonists & inhibitors / Q000096:biosynthesis / Q000235:genetics*; D000964:Antimetabolites, Antineoplastic / Q000494:pharmacology / Q000627:therapeutic use; D001483:Base Sequence; D015153:Blotting, Western; D002460:Cell Line; D045744:Cell Line, Tumor; D002648:Child; D003561:Cytarabine / Q000494:pharmacology / Q000627:therapeutic use; D003600:Cytosol / Q000201:enzymology*; D004247:DNA / Q000235:genetics; D024202:Electrophoretic Mobility Shift Assay; D005091:Exons / Q000235:genetics; D014644:Genetic Variation; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000188:drug therapy / Q000201:enzymology* / Q000235:genetics*; D008156:Luciferases / Q000378:metabolism; D008745:Methylation; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D000964:Antimetabolites, Antineoplastic; D012333:RNA, Messenger; D014157:Transcription Factors; D003561:Cytarabine; D004247:DNA; D008156:Luciferases; D015720:5'-Nucleotidase; C508048:NT5C2 protein, human