title: PTEN microdeletions in T-cell acute lymphoblastic leukemia are caused by illegitimate RAG-mediated recombination events.
abstract: Phosphatase and tensin homolog (PTEN)-inactivating mutations and/or deletions are an independent risk factor for relapse of T-cell acute lymphoblastic leukemia (T-ALL) patients treated on Dutch Childhood Oncology Group or German Cooperative Study Group for Childhood Acute Lymphoblastic Leukemia protocols. Some monoallelic mutated or PTEN wild-type patients lack PTEN protein, implying that additional PTEN inactivation mechanisms exist. We show that PTEN is inactivated by small deletions affecting a few exons in 8% of pediatric T-ALL patients. These microdeletions were clonal in 3% and subclonal in 5% of patients. Conserved deletion breakpoints are flanked by cryptic recombination signal sequences (cRSSs) and frequently have non-template-derived nucleotides inserted in between breakpoints, pointing to an illegitimate RAG recombination-driven activity. Identified cRSSs drive RAG-dependent recombination in a reporter system as efficiently as bona fide RSSs that flank gene segments of the T-cell receptor locus. Remarkably, equivalent microdeletions were detected in thymocytes of healthy individuals. Microdeletions strongly associate with the TALLMO subtype characterized by TAL1 or LMO2 rearrangements. Primary and secondary xenotransplantation of TAL1-rearranged leukemia allowed development of leukemic subclones with newly acquired PTEN microdeletions. Ongoing RAG activity may therefore actively contribute to the acquisition of preleukemic hits, clonal diversification, and disease progression.
authors.affiliation: Department of Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands;
authors.forename: Rui D
authors.initials: RD
authors.lastname: Mendes
authors.affiliation: Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal;
authors.forename: Leonor M
authors.initials: LM
authors.lastname: Sarmento
authors.affiliation: Department of Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands;
authors.forename: Kirsten
authors.initials: K
authors.lastname: Canté-Barrett
authors.affiliation: Department of Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands;
authors.forename: Linda
authors.initials: L
authors.lastname: Zuurbier
authors.affiliation: Department of Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands;
authors.forename: Jessica G C A M
authors.initials: JG
authors.lastname: Buijs-Gladdines
authors.affiliation: Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal;
authors.forename: Vanda
authors.initials: V
authors.lastname: Póvoa
authors.affiliation: Department of Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands;
authors.forename: Willem K
authors.initials: WK
authors.lastname: Smits
authors.affiliation: Cardiologia Pediatrica Medico Cirúrgica, Hospital Sta. Cruz, Lisboa, Portugal;
authors.forename: Miguel
authors.initials: M
authors.lastname: Abecasis
authors.affiliation: Centro Infantil Boldrini, Campinas, São Paulo, Brazil;
authors.forename: J Andres
authors.initials: JA
authors.lastname: Yunes
authors.affiliation: Dutch Childhood Oncology Group, The Hague, The Netherlands;
authors.forename: Edwin
authors.initials: E
authors.lastname: Sonneveld
authors.affiliation: German Cooperative Study Group for Childhood Acute Lymphoblastic Leukemia, Hamburg, Germany; Research Institute Children's Cancer Center Hamburg, Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; and.
authors.forename: Martin A
authors.initials: MA
authors.lastname: Horstmann
authors.affiliation: Department of Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands; Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
authors.forename: Rob
authors.initials: R
authors.lastname: Pieters
authors.affiliation: Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal;
authors.forename: João T
authors.initials: JT
authors.lastname: Barata
authors.affiliation: Department of Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands;
authors.forename: Jules P P
authors.initials: JP
authors.lastname: Meijerink
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics*; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics*; D017353:Gene Deletion; D015321:Gene Rearrangement; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D060588:LIM Domain Proteins / Q000235:genetics*; D051379:Mice; D008969:Molecular Sequence Data; D051059:PTEN Phosphohydrolase / Q000235:genetics*; D016133:Polymerase Chain Reaction; D054218:Precursor T-Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics*; D011518:Proto-Oncogene Proteins / Q000235:genetics*; D011995:Recombination, Genetic / Q000235:genetics*; D000073942:T-Cell Acute Lymphocytic Leukemia Protein 1; D014183:Transplantation, Heterologous
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D051792:Basic Helix-Loop-Helix Proteins; D018398:Homeodomain Proteins; D060588:LIM Domain Proteins; D051059:PTEN Phosphohydrolase; D011518:Proto-Oncogene Proteins; D000073942:T-Cell Acute Lymphocytic Leukemia Protein 1; C085117:LMO2 protein, human; C064658:RAG-1 protein; C067143:TAL1 protein, human; C494929:PTEN protein, human