Hiroko Tanaka, Jacqueline Boultwood, Yuichi Shiraishi, Satoru Miyano, Reda Z. Mahfouz, Jaroslaw P. Maciejewski, Edward D. Cui, Bartlomiej P Przychodzen, Andres Jerez, Seishi Ogawa, Amit Verma, Alan F. List, Masashi Sanada, Yogen Saunthararajah, Michael J. Clemente, Kenichi Chiba, Michael A. McDevitt, Kenichi Yoshida, Naoko Hosono, Mikkael A. Sekeres, Chantana Polprasert, Hideki Makishima, and Thomas LaFramboise
// Naoko Hosono 1, 2 , Hideki Makishima 1, * , Reda Mahfouz 1 , Bartlomiej Przychodzen 1 , Kenichi Yoshida 3, 4 , Andres Jerez 1 , Thomas LaFramboise 5 , Chantana Polprasert 1 , Michael J. Clemente 1 , Yuichi Shiraishi 6 , Kenichi Chiba 6 , Hiroko Tanaka 7 , Satoru Miyano 6, 7 , Masashi Sanada 3, 4 , Edward Cui 5 , Amit K. Verma 8 , Michael A. McDevitt 9 , Alan F. List 10 , Yogen Saunthararajah 1 , Mikkael A. Sekeres 1, 12, 13 , Jacqueline Boultwood 13 , Seishi Ogawa 3, 4 , Jaroslaw P. Maciejewski 1, 11, * 1 Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA 2 First Department of Internal Medicine, Faculty of Medical Sciences, University of Fukui, Fukui, Japan 3 Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan 4 Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan 5 Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA 6 Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan 7 Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan 8 Department of Oncology, Albert Einstein College of Medicine, Bronx, NY, USA 9 Division of Hematology and Hematological Malignancy, Department of Internal Medicine and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA 10 H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA 11 Leukemia Program, Cleveland Clinic, Taussig Cancer Institute, Cleveland, OH, USA 12 Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA 13 LLR Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom * These authors contributed equally to this work Correspondence to: Jaroslaw P. Maciejewski, email: maciejj@ccf.org Keywords: MDS, del(5q), TP53, G3BP1 Received: June 20, 2016 Accepted: December 16, 2016 Published: December 23, 2016 ABSTRACT Background: Deletion of chromosome 5q (del(5q)) is the most common karyotypic abnormality in myeloid neoplasms. Materials and Methods: To define the pathogenic molecular features associated with del(5q), next–generation sequencing was applied to 133 patients with myeloid neoplasms (MDS; N = 69, MDS/MPN; N = 5, sAML; N = 29, pAML; N = 30) with del(5q) as a sole abnormally or a part of complex karyotype and results were compared to molecular features of patients diploid for chr5. Findings: A number of 5q genes with haploinsufficient expression and/or recurrent somatic mutations were identified; for these genes, CSNK1A1 and G3BP1 within the commonly deleted 5q region and DDX41 within a commonly retained region were most commonly affected by somatic mutations. These genes showed consistent haploinsufficiency in deleted cases; low expression/mutations of G3BP1 or DDX41 were associated with poor survival, likely due to decreased cellular function. The most common mutations on other chromosomes in patients with del(5q) included TP53 , and mutations of FLT3 (ITD or TKD), NPM1 or TET2 and were mutually exclusive. Serial sequencing allowed for definition of clonal architecture and dynamics, in patients with exome sequencing allelic imbalance for informative SNPs facilitated simultaneous approximation of clonal size of del(5q) and clonal burden for somatic mutations. Interpretation: Our results illuminate the spectrum of molecular defects characteristic of del(5q), their clinical impact and succession of stepwise evolution.