title: Whole-exome sequencing in relapsing chronic lymphocytic leukemia: clinical impact of recurrent RPS15 mutations.
abstract: Fludarabine, cyclophosphamide, and rituximab (FCR) is first-line treatment of medically fit chronic lymphocytic leukemia (CLL) patients; however, despite good response rates, many patients eventually relapse. Although recent high-throughput studies have identified novel recurrent genetic lesions in adverse prognostic CLL, the mechanisms leading to relapse after FCR therapy are not completely understood. To gain insight into this issue, we performed whole-exome sequencing of sequential samples from 41 CLL patients who were uniformly treated with FCR but relapsed after a median of 2 years. In addition to mutations with known adverse-prognostic impact (TP53, NOTCH1, ATM, SF3B1, NFKBIE, and BIRC3), a large proportion of cases (19.5%) harbored mutations in RPS15, a gene encoding a component of the 40S ribosomal subunit. Extended screening, totaling 1119 patients, supported a role for RPS15 mutations in aggressive CLL, with one-third of RPS15-mutant cases also carrying TP53 aberrations. In most cases, selection of dominant, relapse-specific subclones was observed over time. However, RPS15 mutations were clonal before treatment and remained stable at relapse. Notably, all RPS15 mutations represented somatic missense variants and resided within a 7 amino-acid, evolutionarily conserved region. We confirmed the recently postulated direct interaction between RPS15 and MDM2/MDMX and transient expression of mutant RPS15 revealed defective regulation of endogenous p53 compared with wild-type RPS15. In summary, we provide novel insights into the heterogeneous genetic landscape of CLL relapsing after FCR treatment and highlight a novel mechanism underlying clinical aggressiveness involving a mutated ribosomal protein, potentially representing an early genetic lesion in CLL pathobiology.
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden;
authors.forename: Viktor
authors.initials: V
authors.lastname: Ljungström
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden;
authors.forename: Diego
authors.initials: D
authors.lastname: Cortese
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden;
authors.forename: Emma
authors.initials: E
authors.lastname: Young
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden;
authors.forename: Tatjana
authors.initials: T
authors.lastname: Pandzic
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden;
authors.forename: Larry
authors.initials: L
authors.lastname: Mansouri
authors.affiliation: Central European Institute of Technology, Masaryk University and University Hospital Brno, Brno, Czech Republic;
authors.forename: Karla
authors.initials: K
authors.lastname: Plevova
authors.affiliation: Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece;
authors.forename: Stavroula
authors.initials: S
authors.lastname: Ntoufa
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden;
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Baliakas
authors.affiliation: Oxford National Institutes of Health Research Biomedical Research Centre, University of Oxford, Oxford, United Kingdom;
authors.forename: Ruth
authors.initials: R
authors.lastname: Clifford
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden;
authors.forename: Lesley-Ann
authors.initials: LA
authors.lastname: Sutton
authors.affiliation: Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom;
authors.forename: Stuart J
authors.initials: SJ
authors.lastname: Blakemore
authors.affiliation: Hematology Department and Hematopoietic Cell Transplantation Unit, G. Papanicolaou Hospital, Thessaloniki, Greece;
authors.forename: Niki
authors.initials: N
authors.lastname: Stavroyianni
authors.affiliation: Università Vita-Salute San Raffaele and Division of Experimental Oncology and Department of Onco-Hematology, Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele Scientific Institute, Milan, Italy;
authors.forename: Andreas
authors.initials: A
authors.lastname: Agathangelidis
authors.affiliation: Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy;
authors.forename: Davide
authors.initials: D
authors.lastname: Rossi
authors.affiliation: Department of Medical Sciences, Section of Hematology, Uppsala University, Uppsala, Sweden;
authors.forename: Martin
authors.initials: M
authors.lastname: Höglund
authors.affiliation: Central European Institute of Technology, Masaryk University and University Hospital Brno, Brno, Czech Republic;
authors.forename: Jana
authors.initials: J
authors.lastname: Kotaskova
authors.affiliation: Department of Laboratory Medicine, Stem Cell Center, Lund University, Lund, Sweden;
authors.forename: Gunnar
authors.initials: G
authors.lastname: Juliusson
authors.affiliation: Hematology Department, General Hospital of Nikea, Piraeus, Greece;
authors.forename: Chrysoula
authors.initials: C
authors.lastname: Belessi
authors.affiliation: Karches Center for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Manhasset, New York;
authors.forename: Nicholas
authors.initials: N
authors.lastname: Chiorazzi
authors.affiliation: First Department of Propaedeutic Medicine, School of Medicine, University of Athens, Athens, Greece;
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Panagiotidis
authors.affiliation: Department of Immunology, Laboratory for Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands;
authors.forename: Anton W
authors.initials: AW
authors.lastname: Langerak
authors.affiliation: Department of Medicine Solna, Clinical Epidemiology Unit, Karolinska Institutet, Stockholm, Sweden;
authors.forename: Karin E
authors.initials: KE
authors.lastname: Smedby
authors.affiliation: Department of Haematology, Royal Bournemouth Hospital, Bournemouth, United Kingdom;
authors.forename: David
authors.initials: D
authors.lastname: Oscier
authors.affiliation: Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy;
authors.forename: Gianluca
authors.initials: G
authors.lastname: Gaidano
authors.affiliation: Oxford National Institutes of Health Research Biomedical Research Centre, University of Oxford, Oxford, United Kingdom;
authors.forename: Anna
authors.initials: A
authors.lastname: Schuh
authors.affiliation: Laboratory of Hematology and Universite Pierre et Marie Curie, Hopital Pitie-Salpetriere, Paris, France;
authors.forename: Frederic
authors.initials: F
authors.lastname: Davi
authors.affiliation: Second Medical Department, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; and.
authors.forename: Christiane
authors.initials: C
authors.lastname: Pott
authors.affiliation: Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom;
authors.forename: Jonathan C
authors.initials: JC
authors.lastname: Strefford
authors.affiliation: Department of Medicine, Hematology and Clinical Immunology Branch, Padua University School of Medicine, Padua, Italy.
authors.forename: Livio
authors.initials: L
authors.lastname: Trentin
authors.affiliation: Central European Institute of Technology, Masaryk University and University Hospital Brno, Brno, Czech Republic;
authors.forename: Sarka
authors.initials: S
authors.lastname: Pospisilova
authors.affiliation: Università Vita-Salute San Raffaele and Division of Experimental Oncology and Department of Onco-Hematology, Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele Scientific Institute, Milan, Italy;
authors.forename: Paolo
authors.initials: P
authors.lastname: Ghia
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece; Hematology Department and Hematopoietic Cell Transplantation Unit, G. Papanicolaou Hospital, Thessaloniki, Greece;
authors.forename: Kostas
authors.initials: K
authors.lastname: Stamatopoulos
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden;
authors.forename: Tobias
authors.initials: T
authors.lastname: Sjöblom
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden;
authors.forename: Richard
authors.initials: R
authors.lastname: Rosenquist
mesh_terms: D000971:Antineoplastic Combined Chemotherapy Protocols / Q000627:therapeutic use; D015153:Blotting, Western; D002469:Cell Separation; D003520:Cyclophosphamide / Q000008:administration & dosage; D004252:DNA Mutational Analysis; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D059472:Exome; D006801:Humans; D047468:Immunoprecipitation; D053208:Kaplan-Meier Estimate; D015451:Leukemia, Lymphocytic, Chronic, B-Cell / Q000188:drug therapy / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D020125:Mutation, Missense; D009364:Neoplasm Recurrence, Local / Q000235:genetics* / Q000473:pathology; D012269:Ribosomal Proteins / Q000235:genetics*; D000069283:Rituximab / Q000008:administration & dosage; D014162:Transfection; D016159:Tumor Suppressor Protein p53 / Q000235:genetics; D014740:Vidarabine / Q000008:administration & dosage / Q000031:analogs & derivatives
chemical_list: D012269:Ribosomal Proteins; D016159:Tumor Suppressor Protein p53; C036004:ribosomal protein S15; D000069283:Rituximab; D003520:Cyclophosphamide; D014740:Vidarabine; C024352:fludarabine