Journal Article

Array-based genomic resequencing of human leukemia

Naoe, T, Ueno, T, Haruta, H, Yamashita, Y, Iwama, A, Takada, S, Ito, E, Tajima, S, Ishikawa, Y, Choi, Y L, Kiyoi, H, Suetake, I, Suzuki, H, Yuan, J, Mano, H, Toyota, M, Hamada, T, Miyazaki, Y, Tomonaga, M, Soda, M

2010

Overview

To identify oncogenes in leukemias, we performed large-scale resequencing of the leukemia genome using DNA sequence arrays that determine ∼9 Mbp of sequence corresponding to the exons or exon–intron boundaries of 5648 protein-coding genes. Hybridization of genomic DNA from CD34-positive blasts of acute myeloid leukemia ( n =19) or myeloproliferative disorder ( n =1) with the arrays identified 9148 nonsynonymous nucleotide changes. Subsequent analysis showed that most of these changes were also present in the genomic DNA of the paired controls, with 11 somatic changes identified only in the leukemic blasts. One of these latter changes results in a Met-to-Ile substitution at amino-acid position 511 of Janus kinase 3 (JAK3), and the JAK3(M511I) protein exhibited transforming potential both in vitro and in vivo . Further screening for JAK3 mutations showed novel and known transforming changes in a total of 9 out of 286 cases of leukemia. Our experiments also showed a somatic change responsible for an Arg-to-His substitution at amino-acid position 882 of DNA methyltransferase 3A, which resulted in a loss of DNA methylation activity of >50%. Our data have thus shown a unique profile of gene mutations in human leukemia.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/1647/514/1948 / 692/420/2489/68 / 692/699/67/1990/283 / Acute myeloid leukemia / Amino Acid Sequence / Amino acid substitution / Animals / Apoptosis / Arrays / Base Sequence / Biological and medical sciences / c-Met protein / CD34 antigen / Cell Biology / Cell physiology / Cell transformation and carcinogenesis. Action of oncogenes and antioncogenes / Cell Transformation, Neoplastic / Diverse techniques / DNA (Cytosine-5-)-Methyltransferases - chemistry / DNA (Cytosine-5-)-Methyltransferases - genetics / DNA methylation / DNA methyltransferase / DNA microarrays / DNA sequencing / Exons / Fundamental and applied biological sciences. Psychology / Gene mutations / Genetic aspects / Genome, Human - genetics / Genomics / Genomics - methods / Health aspects / Hematologic and hematopoietic diseases / Human Genetics / Humans / Hybridization / Internal Medicine / Janus kinase / Janus kinase 3 / Janus Kinase 3 - genetics / Leukemia / Leukemia - genetics / Leukemia - pathology / Leukemias. Malignant lymphomas. Malignant reticulosis. Myelofibrosis / Medical sciences / Medicine / Medicine & Public Health / Mice / Molecular and cellular biology / Molecular Sequence Data / Mutation / Myeloproliferative diseases / Nucleotide sequence / Nucleotide sequencing / Oligonucleotide Array Sequence Analysis - methods / oncogenomics / Oncology / Risk factors / Sequence Analysis, DNA - methods