1
|
Abla O, Ries RE, Triche T, Gerbing RB, Hirsch B, Raimondi S, Cooper T, Farrar JE, Buteyn N, Harmon LM, Wen H, Deshpande AJ, Kolb EA, Gamis AS, Aplenc R, Alonzo T, Meshinchi S. Structural variants involving MLLT10 fusion are associated with adverse outcomes in pediatric acute myeloid leukemia. Blood Adv 2024; 8:2005-2017. [PMID: 38306602 PMCID: PMC11024924 DOI: 10.1182/bloodadvances.2023010805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 02/04/2024] Open
Abstract
ABSTRACT MLLT10 gene rearrangements with KMT2A occur in pediatric acute myeloid leukemia (AML) and confer poor prognosis, but the prognostic impact of MLLT10 in partnership with other genes is unknown. We conducted a retrospective study with 2080 children and young adults with AML registered on the Children's Oncology Group AAML0531 (NCT00372593) and AAML1031 trials (NCT01371981). Transcriptome profiling and/or karyotyping were performed to identify leukemia-associated fusions associated with prognosis. Collectively, 127 patients (6.1%) were identified with MLLT10 fusions: 104 (81.9%) with KMT2A::MLLT10, 13 (10.2%) with PICALM::MLLT10, and 10 (7.9%) X::MLLT10: (2 each of DDX3X and TEC), with 6 partners (DDX3Y, CEP164, SCN2B, TREH, NAP1L1, and XPO1) observed in single patients. Patients with MLLT10 (n = 127) demonstrated adverse outcomes, with 5-year event-free survival (EFS) of 18.6% vs 49% in patients without MLLT10 (n = 1953, P < .001), inferior 5-year overall survival (OS) of 38.2% vs 65.7% (P ≤ .001), and a higher relapse risk of 76% vs 38.6% (P < .001). Patients with KMT2A::MLLT10 had an EFS from study entry of 19.5% vs 12.7% (P = .628), and an OS from study entry of 40.4% vs 27.6% (P = .361) in those with other MLLT10 fusion partners. Patients with PICALM::MLLT10 had an EFS of 9.2% vs 20% in other MLLT10- without PICALM (X::MLLT10; P = .788). Patients with PICALM::MLLT10 and X::MLLT10 fusions exhibit a DNA hypermethylation signature resembling NUP98::NSD1 fusions, whereas patients with KMT2A::MLLT10 bear aberrations primarily affecting distal regulatory elements. Regardless of the fusion partner, patients with AML harboring MLLT10 fusions exhibit very high-risk features and should be prioritized for alternative therapeutic interventions.
Collapse
Affiliation(s)
- Oussama Abla
- Division of Hematology/Oncology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Rhonda E. Ries
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Tim Triche
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI
| | | | - Betsy Hirsch
- Division of Laboratory Medicine, University of Minnesota Medical Center, Minneapolis, MN
| | - Susana Raimondi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Todd Cooper
- Division of Hematology-Oncology, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Jason E. Farrar
- Department of Pediatrics, Hematology-Oncology Section, Arkansas Children's Research Institute, Little Rock, AR
| | | | | | - Hong Wen
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI
| | | | - E. Anders Kolb
- Nemours Center for Cancer and Blood Disorders and Alfred I. DuPont Hospital for Children, Wilmington, DE
| | - Alan S. Gamis
- Division of Hematology, Oncology and Bone Marrow Transplantation, Children's Mercy Hospitals and Clinics, Kansas City, MO
| | | | - Todd Alonzo
- Department of Translational Genomics, University of Southern California, Los Angeles, CA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Hematology-Oncology, Seattle Children's Hospital, University of Washington, Seattle, WA
| |
Collapse
|
2
|
Hare L, Trotman J, Tarpey P, Hook E, Burke GAA. Challenging our understanding of B-cell lymphomagenesis and risk: Paediatric high-grade B-cell lymphoma, not otherwise specified with a DDX3X::MLLT10 fusion and an IGH deletion. Pediatr Blood Cancer 2024; 71:e30810. [PMID: 38102963 DOI: 10.1002/pbc.30810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023]
Abstract
We report a unique case of high-grade B-cell lymphoma, not otherwise specified in a 5-year-old child. Whole-genome sequencing revealed a DDX3X::MLLT10 fusion, usually seen in T-cell acute lymphoblastic leukaemia (ALL). This suggests the novel idea that MLLT10 fusions are capable of driving B-cell malignancies. An IGH deletion usually only seen in adults was also found. These unique genetic findings provide novel insights into B-cell lymphomagenesis. The child remains in remission 7 year post chemotherapy, which demonstrates that novel complex molecular findings do not always denote high-risk disease.
Collapse
Affiliation(s)
- Lucy Hare
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Paediatric Haematology, Oncology and Palliative Care, Addenbrooke's Hospital, Cambridge, UK
| | - Jamie Trotman
- East-Genomics Laboratory Hub (GLH) Genetics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Patrick Tarpey
- East-Genomics Laboratory Hub (GLH) Genetics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Elizabeth Hook
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Pathology, Addenbrooke's Hospital, Cambridge, UK
| | - G A Amos Burke
- Department of Paediatric Haematology, Oncology and Palliative Care, Addenbrooke's Hospital, Cambridge, UK
| |
Collapse
|
3
|
Buckley J, Schmidt RJ, Ostrow D, Maglinte D, Bootwalla M, Ruble D, Govindarajan A, Ji J, Kovach AE, Orgel E, Raca G, Navid F, Mascarenhas L, Pawel B, Robison N, Gai X, Biegel JA. An Exome Capture-Based RNA-Sequencing Assay for Genome-Wide Identification and Prioritization of Clinically Important Fusions in Pediatric Tumors. J Mol Diagn 2024; 26:127-139. [PMID: 38008288 DOI: 10.1016/j.jmoldx.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 08/14/2023] [Accepted: 11/07/2023] [Indexed: 11/28/2023] Open
Abstract
This study reports the development of an exome capture-based RNA-sequencing assay to detect recurring and novel fusions in hematologic, solid, and central nervous system tumors. The assay used Twist Comprehensive Exome capture with either fresh or formalin-fixed samples and a bioinformatic platform that provides fusion detection, prioritization, and downstream curation. A minimum of 50 million uniquely mapped reads, a consensus read alignment/fusion calling approach using four callers (Arriba, FusionCatcher, STAR-Fusion, and Dragen), and custom software were used to integrate, annotate, and rank the candidate fusion calls. In an evaluation of 50 samples, the number of calls varied substantially by caller, from a mean of 24.8 with STAR-Fusion to 259.6 with FusionCatcher; only 1.1% of calls were made by all four callers. Therefore a filtering and ranking algorithm was developed based on multiple criteria, including number of supporting reads, calling consensus, genes involved, and cross-reference against databases of known cancer-associated or likely false-positive fusions. This approach was highly effective in pinpointing known clinically relevant fusions, ranking them first in 47 of 50 samples (94%). Detection of pathogenic gene fusions in three diagnostically challenging cases highlights the importance of a genome-wide and nontargeted method for fusion detection in pediatric cancer.
Collapse
Affiliation(s)
- Jonathan Buckley
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Ryan J Schmidt
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Dejerianne Ostrow
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Dennis Maglinte
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Moiz Bootwalla
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - David Ruble
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Ananthanarayanan Govindarajan
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Jianling Ji
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Alexandra E Kovach
- Keck School of Medicine of University of Southern California, Los Angeles, California; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Etan Orgel
- Keck School of Medicine of University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Gordana Raca
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Fariba Navid
- Keck School of Medicine of University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Leo Mascarenhas
- Keck School of Medicine of University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Bruce Pawel
- Keck School of Medicine of University of Southern California, Los Angeles, California; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Nathan Robison
- Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Jaclyn A Biegel
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Keck School of Medicine of University of Southern California, Los Angeles, California.
| |
Collapse
|
4
|
Su D, Ding C, Qiu J, Yang G, Wang R, Liu Y, Tao J, Luo W, Weng G, Zhang T. Ribosome profiling: a powerful tool in oncological research. Biomark Res 2024; 12:11. [PMID: 38273337 PMCID: PMC10809610 DOI: 10.1186/s40364-024-00562-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
Neoplastic cells need to adapt their gene expression pattern to survive in an ever-changing or unfavorable tumor microenvironment. Protein synthesis (or mRNA translation), an essential part of gene expression, is dysregulated in cancer. The emergence of distinct translatomic technologies has revolutionized oncological studies to elucidate translational regulatory mechanisms. Ribosome profiling can provide adequate information on diverse aspects of translation by aiding in quantitatively analyzing the intensity of translating ribosome-protected fragments. Here, we review the primary currently used translatomics techniques and highlight their advantages and disadvantages as tools for translatomics studies. Subsequently, we clarified the areas in which ribosome profiling could be applied to better understand translational control. Finally, we summarized the latest advances in cancer studies using ribosome profiling to highlight the extensive application of this powerful and promising translatomic tool.
Collapse
Affiliation(s)
- Dan Su
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Chen Ding
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Jiangdong Qiu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Gang Yang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Ruobing Wang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Yueze Liu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Jinxin Tao
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Wenhao Luo
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Guihu Weng
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
| | - Taiping Zhang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China.
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China.
| |
Collapse
|
5
|
Komata Y, Kanai A, Maeda T, Inaba T, Yokoyama A. MOZ/ENL complex is a recruiting factor of leukemic AF10 fusion proteins. Nat Commun 2023; 14:1979. [PMID: 37031220 PMCID: PMC10082848 DOI: 10.1038/s41467-023-37712-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 03/22/2023] [Indexed: 04/10/2023] Open
Abstract
Changes in the transcriptional machinery cause aberrant self-renewal of non-stem hematopoietic progenitors. AF10 fusions, such as CALM-AF10, are generated via chromosomal translocations, causing malignant leukemia. In this study, we demonstrate that AF10 fusion proteins cause aberrant self-renewal via ENL, which binds to MOZ/MORF lysine acetyltransferases (KATs). The interaction of ENL with MOZ, via its YEATS domain, is critical for CALM-AF10-mediated leukemic transformation. The MOZ/ENL complex recruits DOT1L/AF10 fusion complexes and maintains their chromatin retention via KAT activity. Therefore, inhibitors of MOZ/MORF KATs directly suppress the functions of AF10 fusion proteins, thereby exhibiting strong antitumor effects on AF10 translocation-induced leukemia. Combinatorial inhibition of MOZ/MORF and DOT1L cooperatively induces differentiation of CALM-AF10-leukemia cells. These results reveal roles for the MOZ/ENL complex as an essential recruiting factor of the AF10 fusion/DOT1L complex, providing a rationale for using MOZ/MORF KAT inhibitors in AF10 translocation-induced leukemia.
Collapse
Affiliation(s)
- Yosuke Komata
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata, 997-0052, Japan
| | - Akinori Kanai
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Hiroshima, 734-8553, Japan
| | - Takahiro Maeda
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, 812-8582, Japan
| | - Toshiya Inaba
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Hiroshima, 734-8553, Japan
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata, 997-0052, Japan.
| |
Collapse
|
6
|
Popov A, Tsaur G, Permikin Z, Henze G, Verzhbitskaya T, Plekhanova O, Nokhrina E, Valochnik A, Sibiryakov P, Zerkalenkova E, Olshanskaya Y, Gindina T, Movchan L, Shorikov E, Streneva O, Khlebnikova O, Makarova O, Arakaev O, Boichenko E, Kondratchik K, Ponomareva N, Lapotentova E, Aleinikova O, Miakova N, Novichkova G, Karachunskiy A, Fechina L. Genetic characteristics and treatment outcome in infants with KMT2A germline B-cell precursor acute lymphoblastic leukemia: Results of MLL-Baby protocol. Pediatr Blood Cancer 2023; 70:e30204. [PMID: 36715125 DOI: 10.1002/pbc.30204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 01/31/2023]
Abstract
The aim of this study was to present the diagnostic and outcome characteristics of infants with germline status of KMT2A gene (KMT2A-g) B-cell precursor acute lymphoblastic leukemia (BCP-ALL) treated consistently according to the MLL-Baby protocol, a moderate-intensity protocol. Of the 139 patients enrolled in the MLL-Baby study, 100 (71.9%) carried different types of rearranged KMT2A (KMT2A-r), while the remaining 39 infants (28.1%) had KMT2A-g. KMT2A-g patients were generally older (77% older than 6 months), less likely to have a very high white blood cell count (greater than 100 × 109 /L), less likely to be central nervous system (CNS)-positive, and more likely to be CD10-positive. The 6-year event-free survival and overall survival rates for all 39 patients were 0.74 (standard error [SE] 0.07) and 0.80 (SE 0.07), respectively. Relapse was the most common adverse event (n = 5), with a cumulative incidence of relapse (CIR) of 0.13 (SE 0.06), while the incidence of a second malignancy (n = 1) and death in remission (n = 3) was 0.03 (SE 0.04) and 0.08 (SE 0.04), respectively. None of the initial parameters, including genetics and the presence of recently described fusions of NUTM1 and PAX5 genes, was able to distinguish patients with different outcomes. Only rapidity of response, measured as minimal residual disease (MRD) by flow cytometry, showed a statistically significant impact. Moderate-intensity therapy, as used in the MLL-Baby protocol in infants with KMT2A-g BCP-ALL, yields results comparable to other infant studies. Patients with a slow multicolor flow cytometry (MFC)-MRD response should be subjected to advanced therapies, such as targeted or immunotherapies.
Collapse
Affiliation(s)
- Alexander Popov
- National Research and Clinical Centre for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Grigory Tsaur
- Regional Children's Hospital, Ekaterinburg, Russian Federation.,Ural State Medical University, Ekaterinburg, Russian Federation.,Research Institute of Medical Cell Technologies, Ekaterinburg, Russian Federation
| | - Zhan Permikin
- Regional Children's Hospital, Ekaterinburg, Russian Federation.,Ural State Medical University, Ekaterinburg, Russian Federation.,Research Institute of Medical Cell Technologies, Ekaterinburg, Russian Federation
| | - Guenter Henze
- Department of Pediatric Oncology Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Tatiana Verzhbitskaya
- Regional Children's Hospital, Ekaterinburg, Russian Federation.,Research Institute of Medical Cell Technologies, Ekaterinburg, Russian Federation
| | - Olga Plekhanova
- Regional Children's Hospital, Ekaterinburg, Russian Federation
| | | | - Alena Valochnik
- Belarussian Research Centre for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Petr Sibiryakov
- Regional Children's Hospital, Ekaterinburg, Russian Federation.,Research Institute of Medical Cell Technologies, Ekaterinburg, Russian Federation
| | - Elena Zerkalenkova
- National Research and Clinical Centre for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Yulia Olshanskaya
- National Research and Clinical Centre for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Tatiana Gindina
- R.M. Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University of Saint Petersburg, Saint Petersburg, Russian Federation
| | - Liudmila Movchan
- Belarussian Research Centre for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Egor Shorikov
- PET-Technology Centre of Nuclear Medicine, Ekaterinburg, Russian Federation
| | - Olga Streneva
- Regional Children's Hospital, Ekaterinburg, Russian Federation.,Research Institute of Medical Cell Technologies, Ekaterinburg, Russian Federation
| | | | - Olga Makarova
- Regional Children's Hospital, Ekaterinburg, Russian Federation
| | - Oleg Arakaev
- Regional Children's Hospital, Ekaterinburg, Russian Federation.,Research Institute of Medical Cell Technologies, Ekaterinburg, Russian Federation
| | - Elmira Boichenko
- City Children's Hospital No. 1, Saint Petersburg, Russian Federation
| | | | | | - Elena Lapotentova
- Belarussian Research Centre for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Olga Aleinikova
- National Research and Clinical Centre for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation.,Belarussian Research Centre for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Natalia Miakova
- National Research and Clinical Centre for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Galina Novichkova
- National Research and Clinical Centre for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Alexander Karachunskiy
- National Research and Clinical Centre for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Larisa Fechina
- Regional Children's Hospital, Ekaterinburg, Russian Federation.,Research Institute of Medical Cell Technologies, Ekaterinburg, Russian Federation
| |
Collapse
|
7
|
Salmerón-Villalobos J, Ramis-Zaldivar JE, Balagué O, Verdú-Amorós J, Celis V, Sábado C, Garrido M, Mato S, Uriz J, Ortega MJ, Gutierrez-Camino A, Sinnett D, Illarregi U, Carron M, Regueiro A, Galera A, Gonzalez-Farré B, Campo E, Garcia N, Colomer D, Astigarraga I, Andrés M, Llavador M, Martin-Guerrero I, Salaverria I. Diverse mutations and structural variations contribute to Notch signaling deregulation in paediatric T-cell lymphoblastic lymphoma. Pediatr Blood Cancer 2022; 69:e29926. [PMID: 36000950 DOI: 10.1002/pbc.29926] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/24/2022] [Accepted: 07/25/2022] [Indexed: 11/12/2022]
Abstract
BACKGROUND T-cell lymphoblastic lymphoma (T-LBL) is an aggressive neoplasm closely related to T-cell acute lymphoblastic leukaemia (T-ALL). Despite their similarities, and contrary to T-ALL, studies on paediatric T-LBL are scarce and, therefore, its molecular landscape has not yet been fully elucidated. Thus, the aims of this study were to characterize the genetic and molecular heterogeneity of paediatric T-LBL and to evaluate novel molecular markers differentiating this entity from T-ALL. PROCEDURE Thirty-three paediatric T-LBL patients were analyzed using an integrated approach, including targeted next-generation sequencing, RNA-sequencing transcriptome analysis and copy-number arrays. RESULTS Copy number and mutational analyses allowed the detection of recurrent homozygous deletions of 9p/CDKN2A (78%), trisomy 20 (19%) and gains of 17q24-q25 (16%), as well as frequent mutations of NOTCH1 (62%), followed by the BCL11B (23%), WT1 (19%) and FBXW7, PHF6 and RPL10 genes (15%, respectively). This genetic profile did not differ from that described in T-ALL in terms of mutation incidence and global genomic complexity level, but unveiled virtually exclusive 17q25 gains and trisomy 20 in T-LBL. Additionally, we identified novel gene fusions in paediatric T-LBL, including NOTCH1-IKZF2, RNGTT-SNAP91 and DDX3X-MLLT10, the last being the only one previously described in T-ALL. Moreover, clinical correlations highlighted the presence of Notch pathway alterations as a factor related to favourable outcome. CONCLUSIONS In summary, the genomic landscape of paediatric T-LBL is similar to that observed in T-ALL, and Notch signaling pathway deregulation remains the cornerstone in its pathogenesis, including not only mutations but fusion genes targeting NOTCH1.
Collapse
Affiliation(s)
- Julia Salmerón-Villalobos
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red-Oncología (CIBERONC), Madrid, Spain
| | - Joan Enric Ramis-Zaldivar
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red-Oncología (CIBERONC), Madrid, Spain
| | - Olga Balagué
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red-Oncología (CIBERONC), Madrid, Spain.,Haematopathology Unit, Hospital Clínic, Barcelona, Spain
| | | | - Verónica Celis
- Paediatric Oncology Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - Constantino Sábado
- Paediatric Oncology Department, Hospital Vall d'Hebron, Barcelona, Spain
| | - Marta Garrido
- Anatomic Pathology Department, Hospital Vall d'Hebron, Barcelona, Spain
| | - Sara Mato
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red-Oncología (CIBERONC), Madrid, Spain
| | - Javier Uriz
- Paediatric Oncohaematology Department, Donostia University Hospital, Biodonostia Health Research Institute, San Sebastian, Spain
| | - M José Ortega
- Paediatric Oncology Department, Hospital Universitario Virgen de la Nieves, Granada, Spain
| | | | - Daniel Sinnett
- Division of Haematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Canada.,Department of Paediatrics, Faculty of Medicine, University of Montreal, Montreal, Canada
| | - Unai Illarregi
- Genetics, Physics Anthropology and Animal Physiology, Faculty of Science and Technology, UPV/EHU, Leioa, Spain
| | - Máxime Carron
- Division of Haematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Canada
| | - Alexandra Regueiro
- Paediatric Haematology and Oncology Department, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana Galera
- Paediatric Oncohaematology Department, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Blanca Gonzalez-Farré
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red-Oncología (CIBERONC), Madrid, Spain.,Haematopathology Unit, Hospital Clínic, Barcelona, Spain
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red-Oncología (CIBERONC), Madrid, Spain.,Haematopathology Unit, Hospital Clínic, Barcelona, Spain
| | - Noelia Garcia
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red-Oncología (CIBERONC), Madrid, Spain.,Haematopathology Unit, Hospital Clínic, Barcelona, Spain
| | - Itziar Astigarraga
- Paediatric Department, Osakidetza, Biocruces Bizkaia Health Research Institute, Hospital Universitario Cruces, Barakaldo, Spain.,Paediatric Department, Universidad del Pais Vasco UPV/EHU, Leioa, Spain
| | - Mara Andrés
- Paediatric Oncology Department, Hospital La Fe, Valencia, Spain
| | | | - Idoia Martin-Guerrero
- Biocruces Bizkaia Health Research Institute, Department of Genetics, Physical Anthropology & Animal Physiology, Science and Technology Faculty, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Itziar Salaverria
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red-Oncología (CIBERONC), Madrid, Spain
| |
Collapse
|
8
|
Nilius-Eliliwi V, Tembrink M, Gerding WM, Lubieniecki KP, Lubieniecka JM, Kankel S, Liehr T, Mika T, Dimopoulos F, Döhner K, Schroers R, Nguyen HHP, Vangala DB. Broad genomic workup including optical genome mapping uncovers a DDX3X: MLLT10 gene fusion in acute myeloid leukemia. Front Oncol 2022; 12:959243. [PMID: 36158701 PMCID: PMC9501710 DOI: 10.3389/fonc.2022.959243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/12/2022] [Indexed: 11/24/2022] Open
Abstract
In acute myeloid leukemia (AML), treatment decisions are currently made according to the risk classification of the European LeukemiaNet (ELN), which is based on genetic alterations. Recently, optical genome mapping (OGM) as a novel method proved to yield a genome-wide and detailed cytogenetic characterization at the time of diagnosis. A young female patient suffered from a rather unexpected aggressive disease course under FLT3 targeted therapy in combination with induction chemotherapy. By applying a “next-generation diagnostic workup“ strategy with OGM and whole-exome sequencing (WES), a DDX3X: MLLT10 gene fusion could be detected, otherwise missed by routine diagnostics. Furthermore, several aspects of lineage ambiguity not shown by standard diagnostics were unraveled such as deletions of SUZ12 and ARPP21, as well as T-cell receptor recombination. In summary, the detection of this particular gene fusion DDX3X: MLLT10 in a female AML patient and the findings of lineage ambiguity are potential explanations for the aggressive course of disease. Our study demonstrates that OGM can yield novel clinically significant results, including additional information helpful in disease monitoring and disease biology.
Collapse
Affiliation(s)
- Verena Nilius-Eliliwi
- Department of Medicine, Hematology and Oncology, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | | | | | | | | | - Stefanie Kankel
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Thomas Mika
- Department of Medicine, Hematology and Oncology, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Fotios Dimopoulos
- Department of Medicine, Hematology and Oncology, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Roland Schroers
- Department of Medicine, Hematology and Oncology, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | | | - Deepak Ben Vangala
- Department of Medicine, Hematology and Oncology, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
- *Correspondence: Deepak Ben Vangala,
| |
Collapse
|
9
|
Lacroix M, Beauchemin H, Fraszczak J, Ross J, Shooshtarizadeh P, Chen R, Moroy T. The X-linked helicase DDX3X is required for lymphoid differentiation and MYC-driven lymphomagenesis. Cancer Res 2022; 82:3172-3186. [PMID: 35815807 DOI: 10.1158/0008-5472.can-21-2454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 03/29/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022]
Abstract
The X-linked gene DDX3X encodes an RNA helicase that is mutated at high frequencies in several types of human B-cell lymphoma. Females have two active DDX3X alleles and males carry a DDX3Y homolog on the Y chromosome. We show here that pan-hematopoietic, homozygous deletion of Ddx3x in female mice perturbs erythropoiesis, causing early developmental arrest. However, both hemizygous male and heterozygous female embryos develop normally, suggesting that one Ddx3x allele is sufficient for fetal hematopoietic development in females and that the Ddx3y allele can compensate for the loss of Ddx3x in males. In adult mice, DDX3X deficiency altered hematopoietic progenitors, early lymphoid development, marginal zone and germinal center B-cells, and lymphomagenesis in a sex-dependent manner. Loss of both Ddx3x alleles abrogated MYC-driven lymphomagenesis in females, while Ddx3x-deletion in males did not affect the formation of B-cell lymphoma in both mouse models. Moreover, tumors that appeared in male mice lacking DDX3X showed upregulated expression of DDX3Y, indicating a critical requirement for DDX3 activity for lymphomagenesis. These data reveal sex-specific roles of DDX3X in erythro- and lymphopoiesis as well as in MYC-driven lymphomagenesis.
Collapse
Affiliation(s)
- Marion Lacroix
- IRCM (Institut de Recherches Cliniques de Montr�al), Montreal, Quebec, Canada
| | | | | | - Julie Ross
- Montreal Clinical Research Institute, Montreal, Quebec, Canada
| | | | | | - Tarik Moroy
- Institut de recherches cliniques de Montr�al, Montreal, Canada
| |
Collapse
|
10
|
Abstract
Continuously renewing the proteome, translation is exquisitely controlled by a number of dedicated factors that interact with the ribosome. The RNA helicase DDX3 belonging to the DEAD box family has emerged as one of the critical regulators of translation, the failure of which is frequently observed in a wide range of proliferative, degenerative, and infectious diseases in humans. DDX3 unwinds double-stranded RNA molecules with coupled ATP hydrolysis and thereby remodels complex RNA structures present in various protein-coding and noncoding RNAs. By interacting with specific features on messenger RNAs (mRNAs) and 18S ribosomal RNA (rRNA), DDX3 facilitates translation, while repressing it under certain conditions. We review recent findings underlying these properties of DDX3 in diverse modes of translation, such as cap-dependent and cap-independent translation initiation, usage of upstream open reading frames, and stress-induced ribonucleoprotein granule formation. We further discuss how disease-associated DDX3 variants alter the translation landscape in the cell.
Collapse
Affiliation(s)
- Joon Tae Park
- Division of Life Sciences, Incheon National University, Incheon 22012, Korea
| | - Sekyung Oh
- Department of Medical Science, Catholic Kwandong University College of Medicine, Incheon 22711, Korea
| |
Collapse
|
11
|
T-Cell Acute Lymphoblastic Leukemia: Biomarkers and Their Clinical Usefulness. Genes (Basel) 2021; 12:genes12081118. [PMID: 34440292 PMCID: PMC8394887 DOI: 10.3390/genes12081118] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/17/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
T-cell acute lymphoblastic leukemias (T-ALL) are immature lymphoid tumors localizing in the bone marrow, mediastinum, central nervous system, and lymphoid organs. They account for 10-15% of pediatric and about 25% of adult acute lymphoblastic leukemia (ALL) cases. It is a widely heterogeneous disease that is caused by the co-occurrence of multiple genetic abnormalities, which are acquired over time, and once accumulated, lead to full-blown leukemia. Recurrently affected genes deregulate pivotal cell processes, such as cycling (CDKN1B, RB1, TP53), signaling transduction (RAS pathway, IL7R/JAK/STAT, PI3K/AKT), epigenetics (PRC2 members, PHF6), and protein translation (RPL10, CNOT3). A remarkable role is played by NOTCH1 and CDKN2A, as they are altered in more than half of the cases. The activation of the NOTCH1 signaling affects thymocyte specification and development, while CDKN2A haploinsufficiency/inactivation, promotes cell cycle progression. Among recurrently involved oncogenes, a major role is exerted by T-cell-specific transcription factors, whose deregulated expression interferes with normal thymocyte development and causes a stage-specific differentiation arrest. Hence, TAL and/or LMO deregulation is typical of T-ALL with a mature phenotype (sCD3 positive) that of TLX1, NKX2-1, or TLX3, of cortical T-ALL (CD1a positive); HOXA and MEF2C are instead over-expressed in subsets of Early T-cell Precursor (ETP; immature phenotype) and early T-ALL. Among immature T-ALL, genomic alterations, that cause BCL11B transcriptional deregulation, identify a specific genetic subgroup. Although comprehensive cytogenetic and molecular studies have shed light on the genetic background of T-ALL, biomarkers are not currently adopted in the diagnostic workup of T-ALL, and only a limited number of studies have assessed their clinical implications. In this review, we will focus on recurrent T-ALL abnormalities that define specific leukemogenic pathways and on oncogenes/oncosuppressors that can serve as diagnostic biomarkers. Moreover, we will discuss how the complex genomic profile of T-ALL can be used to address and test innovative/targeted therapeutic options.
Collapse
|
12
|
Klein BJ, Deshpande A, Cox KL, Xuan F, Zandian M, Barbosa K, Khanal S, Tong Q, Zhang Y, Zhang P, Sinha A, Bohlander SK, Shi X, Wen H, Poirier MG, Deshpande AJ, Kutateladze TG. The role of the PZP domain of AF10 in acute leukemia driven by AF10 translocations. Nat Commun 2021; 12:4130. [PMID: 34226546 PMCID: PMC8257627 DOI: 10.1038/s41467-021-24418-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 06/16/2021] [Indexed: 11/09/2022] Open
Abstract
Chromosomal translocations of the AF10 (or MLLT10) gene are frequently found in acute leukemias. Here, we show that the PZP domain of AF10 (AF10PZP), which is consistently impaired or deleted in leukemogenic AF10 translocations, plays a critical role in blocking malignant transformation. Incorporation of functional AF10PZP into the leukemogenic CALM-AF10 fusion prevents the transforming activity of the fusion in bone marrow-derived hematopoietic stem and progenitor cells in vitro and in vivo and abrogates CALM-AF10-mediated leukemogenesis in vivo. Crystallographic, biochemical and mutagenesis studies reveal that AF10PZP binds to the nucleosome core particle through multivalent contacts with the histone H3 tail and DNA and associates with chromatin in cells, colocalizing with active methylation marks and discriminating against the repressive H3K27me3 mark. AF10PZP promotes nuclear localization of CALM-AF10 and is required for association with chromatin. Our data indicate that the disruption of AF10PZP function in the CALM-AF10 fusion directly leads to transformation, whereas the inclusion of AF10PZP downregulates Hoxa genes and reverses cellular transformation. Our findings highlight the molecular mechanism by which AF10 targets chromatin and suggest a model for the AF10PZP-dependent CALM-AF10-mediated leukemogenesis.
Collapse
Affiliation(s)
- Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Anagha Deshpande
- Tumor Initiation and Maintenance Program, National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Khan L Cox
- Department of Physics, Ohio State University, Columbus, OH, USA
| | - Fan Xuan
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Mohamad Zandian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Karina Barbosa
- Tumor Initiation and Maintenance Program, National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Sujita Khanal
- Tumor Initiation and Maintenance Program, National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Qiong Tong
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Pan Zhang
- Tumor Initiation and Maintenance Program, National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Stefan K Bohlander
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Xiaobing Shi
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Hong Wen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | | | - Aniruddha J Deshpande
- Tumor Initiation and Maintenance Program, National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.
| |
Collapse
|
13
|
A JAK/STAT-mediated inflammatory signaling cascade drives oncogenesis in AF10-rearranged AML. Blood 2021; 137:3403-3415. [PMID: 33690798 DOI: 10.1182/blood.2020009023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/11/2021] [Indexed: 12/18/2022] Open
Abstract
Leukemias bearing fusions of the AF10/MLLT10 gene are associated with poor prognosis, and therapies targeting these fusion proteins (FPs) are lacking. To understand mechanisms underlying AF10 fusion-mediated leukemogenesis, we generated inducible mouse models of acute myeloid leukemia (AML) driven by the most common AF10 FPs, PICALM/CALM-AF10 and KMT2A/MLL-AF10, and performed comprehensive characterization of the disease using transcriptomic, epigenomic, proteomic, and functional genomic approaches. Our studies provide a detailed map of gene networks and protein interactors associated with key AF10 fusions involved in leukemia. Specifically, we report that AF10 fusions activate a cascade of JAK/STAT-mediated inflammatory signaling through direct recruitment of JAK1 kinase. Inhibition of the JAK/STAT signaling by genetic Jak1 deletion or through pharmacological JAK/STAT inhibition elicited potent antioncogenic effects in mouse and human models of AF10 fusion AML. Collectively, our study identifies JAK1 as a tractable therapeutic target in AF10-rearranged leukemias.
Collapse
|
14
|
Challenging conventional karyotyping by next-generation karyotyping in 281 intensively treated patients with AML. Blood Adv 2021; 5:1003-1016. [PMID: 33591326 DOI: 10.1182/bloodadvances.2020002517] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 12/10/2020] [Indexed: 12/19/2022] Open
Abstract
Although copy number alterations (CNAs) and translocations constitute the backbone of the diagnosis and prognostication of acute myeloid leukemia (AML), techniques used for their assessment in routine diagnostics have not been reconsidered for decades. We used a combination of 2 next-generation sequencing-based techniques to challenge the currently recommended conventional cytogenetic analysis (CCA), comparing the approaches in a series of 281 intensively treated patients with AML. Shallow whole-genome sequencing (sWGS) outperformed CCA in detecting European Leukemia Net (ELN)-defining CNAs and showed that CCA overestimated monosomies and suboptimally reported karyotype complexity. Still, the concordance between CCA and sWGS for all ELN CNA-related criteria was 94%. Moreover, using in silico dilution, we showed that 1 million reads per patient would be enough to accurately assess ELN-defining CNAs. Total genomic loss, defined as a total loss ≥200 Mb by sWGS, was found to be a better marker for genetic complexity and poor prognosis compared with the CCA-based definition of complex karyotype. For fusion detection, the concordance between CCA and whole-transcriptome sequencing (WTS) was 99%. WTS had better sensitivity in identifying inv(16) and KMT2A rearrangements while showing limitations in detecting lowly expressed PML-RARA fusions. Ligation-dependent reverse transcription polymerase chain reaction was used for validation and was shown to be a fast and reliable method for fusion detection. We conclude that a next-generation sequencing-based approach can replace conventional CCA for karyotyping, provided that efforts are made to cover lowly expressed fusion transcripts.
Collapse
|
15
|
Abstract
The DEAD-box helicase family member DDX3X (DBX, DDX3) functions in nearly all stages of RNA metabolism and participates in the progression of many diseases, including virus infection, inflammation, intellectual disabilities and cancer. Over two decades, many studies have gradually unveiled the role of DDX3X in tumorigenesis and tumour progression. In fact, DDX3X possesses numerous functions in cancer biology and is closely related to many well-known molecules. In this review, we describe the function of DDX3X in RNA metabolism, cellular stress response, innate immune response, metabolic stress response in pancreatic β cells and embryo development. Then, we focused on the role of DDX3X in cancer biology and systematically demonstrated its functions in various aspects of tumorigenesis and development. To provide a more intuitive understanding of the role of DDX3X in cancer, we summarized its functions and specific mechanisms in various types of cancer and presented its involvement in cancer-related signalling pathways.
Collapse
|
16
|
Triphenotypic acute leukaemia: the contribution of multimodality laboratory diagnostic techniques. Pathology 2021; 53:678-680. [PMID: 33461800 DOI: 10.1016/j.pathol.2020.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/03/2020] [Accepted: 09/10/2020] [Indexed: 11/21/2022]
|
17
|
Wong J, Wall M, Corboy GP, Taubenheim N, Gregory GP, Opat S, Shortt J. Failure of tofacitinib to achieve an objective response in a DDX3X-MLLT10 T-lymphoblastic leukemia with activating JAK3 mutations. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a004994. [PMID: 32843425 PMCID: PMC7476415 DOI: 10.1101/mcs.a004994] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 06/05/2020] [Indexed: 02/01/2023] Open
Abstract
T-cell lymphoblastic lymphoma/T-cell acute lymphoblastic leukemia (T-LBL/T ALL) is an aggressive hematological malignancy arising from malignant transformation of T-cell progenitors with poor prognosis in adult patients. Outcomes are particularly dismal in the relapsed/refractory setting, and therapeutic options are limited in this context. Genomic profiling has shown frequent aberrations in the JAK-STAT pathway, including recurrent mutations in JAK3 (15%–20% of T-ALL cases), suggesting that JAK kinase inhibition may be a promising therapeutic approach. Activating JAK3 mutations are capable of transforming cytokine-dependent progenitor cells in vitro and causing T-ALL-like disease when expressed in hematopoietic progenitors in vivo. We describe a case of relapsed T-ALL in an adult patient, with two JAK3 activating mutations identified by whole-exome sequencing (WES), leading to hypothesis-based treatment with the JAK1 and JAK3 inhibitor, tofacitinib, following failure of salvage chemotherapy reinduction. Despite the molecularly targeted rationale, tofacitinib did not induce an objective clinical response. Our report suggests that the presence of activating JAK3 mutations does not necessarily confer sensitivity to pharmacological JAK3 inhibition.
Collapse
Affiliation(s)
- Jonathan Wong
- Department of Hematology, Monash Health, Clayton, 3168, Victoria, Australia.,School of Clinical Sciences, Monash University, Clayton, 3168, Victoria, Australia
| | - Meaghan Wall
- School of Clinical Sciences, Monash University, Clayton, 3168, Victoria, Australia.,Victorian Cancer Cytogenetics Service, St Vincent's Hospital, Fitzroy, 3065, Victoria, Australia.,St Vincent's Institute, Fitzroy, 3065, Victoria, Australia.,Monash Pathology, Monash Health, Clayton, 3168, Victoria, Australia
| | - Gregory Philip Corboy
- Department of Hematology, Monash Health, Clayton, 3168, Victoria, Australia.,School of Clinical Sciences, Monash University, Clayton, 3168, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Nadine Taubenheim
- Monash Pathology, Monash Health, Clayton, 3168, Victoria, Australia.,Center for Cancer Research, Hudson Institute of Medical Research, Clayton, 3168, Victoria, Australia
| | - Gareth Peter Gregory
- Department of Hematology, Monash Health, Clayton, 3168, Victoria, Australia.,School of Clinical Sciences, Monash University, Clayton, 3168, Victoria, Australia
| | - Stephen Opat
- Department of Hematology, Monash Health, Clayton, 3168, Victoria, Australia.,School of Clinical Sciences, Monash University, Clayton, 3168, Victoria, Australia
| | - Jake Shortt
- Department of Hematology, Monash Health, Clayton, 3168, Victoria, Australia.,School of Clinical Sciences, Monash University, Clayton, 3168, Victoria, Australia
| |
Collapse
|
18
|
Forgione MO, McClure BJ, Yeung DT, Eadie LN, White DL. MLLT10 rearranged acute leukemia: Incidence, prognosis, and possible therapeutic strategies. Genes Chromosomes Cancer 2020; 59:709-721. [PMID: 32720323 DOI: 10.1002/gcc.22887] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/07/2020] [Accepted: 07/13/2020] [Indexed: 12/22/2022] Open
Abstract
Rearrangements of the MLLT10 gene occur in acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL), most commonly T-lineage ALL (T-ALL), in patients of all ages. MLLT10 rearranged (MLLT10r) acute leukemia presents a complex diagnostic and therapeutic challenge due to frequent presentation of immature or mixed phenotype, and a lack of consensus regarding optimal therapy. Cases of MLLT10r AML or T-ALL bearing immature phenotype are at high risk of poor outcome, but the underlying molecular mechanisms and sensitivity to targeted therapies remain poorly characterized. This review addresses the incidence and prognostic significance of MLLT10r in acute leukemia, and how the aberrant gene expression profile of this disease can inform potential targeted therapeutic strategies. Understanding the underlying genomics of MLLT10r acute leukemia, both clinically and molecularly, will improve prognostic stratification and accelerate the development of targeted therapeutic strategies, to improve patient outcomes.
Collapse
Affiliation(s)
- Michelle O Forgione
- Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Science, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Barbara J McClure
- Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - David T Yeung
- Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Department of Haematology, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Laura N Eadie
- Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Deborah L White
- Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Science, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Australian Genomics Health Alliance (AGHA), The Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Australian and New Zealand Children's Oncology Group (ANZCHOG), Hudson Institute, Clayton, Victoria, Australia
| |
Collapse
|
19
|
Kim B, Lee H, Shin S, Lee ST, Choi JR. Clinical Evaluation of Massively Parallel RNA Sequencing for Detecting Recurrent Gene Fusions in Hematologic Malignancies. J Mol Diagn 2019; 21:163-170. [DOI: 10.1016/j.jmoldx.2018.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 09/19/2018] [Accepted: 09/26/2018] [Indexed: 12/16/2022] Open
|
20
|
Targeting DDX3 in Medulloblastoma Using the Small Molecule Inhibitor RK-33. Transl Oncol 2018; 12:96-105. [PMID: 30292066 PMCID: PMC6171097 DOI: 10.1016/j.tranon.2018.09.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/31/2018] [Accepted: 09/07/2018] [Indexed: 02/08/2023] Open
Abstract
Medulloblastoma is the most common malignant tumor that arises from the cerebellum of the central nervous system. Clinically, medulloblastomas are treated by surgery, radiation, and chemotherapy, all of which result in toxicity and morbidity. Recent reports have identified that DDX3, a member of the RNA helicase family, is mutated in medulloblastoma. In this study, we demonstrate the role of DDX3 in driving medulloblastoma. With the use of a small molecule inhibitor of DDX3, RK-33, we could inhibit growth and promote cell death in two medulloblastoma cell lines, DAOY and UW228, with IC50 values of 2.5 μM and 3.5 μM, respectively. Treatment of DAOY and UW228 cells with RK-33 caused a G1 arrest, resulted in reduced TCF reporter activity, and reduced mRNA expression levels of downstream target genes of the WNT pathway, such as Axin2, CCND1, MYC, and Survivin. In addition, treatment of DAOY and UW228 cells with a combination of RK-33 and radiation exhibited a synergistic effect. Importantly, the combination of RK-33 and 5 Gy radiation caused tumor regression in a mouse xenograft model of medulloblastoma. Using immunohistochemistry, we observed DDX3 expression in both pediatric (55%) and adult (66%) medulloblastoma patients. Based on these results, we conclude that RK-33 is a promising radiosensitizing agent that inhibits DDX3 activity and down-regulates WNT/β-catenin signaling and could be used as a frontline therapeutic strategy for DDX3-expressing medulloblastomas in combination with radiation.
Collapse
|
21
|
Johnson SH, Smadbeck JB, Smoley SA, Gaitatzes A, Murphy SJ, Harris FR, Drucker TM, Zenka RM, Pitel BA, Rowsey RA, Hoppman NL, Aypar U, Sukov WR, Jenkins RB, Feldman AL, Kearney HM, Vasmatzis G. SVAtools for junction detection of genome-wide chromosomal rearrangements by mate-pair sequencing (MPseq). Cancer Genet 2017; 221:1-18. [PMID: 29405991 DOI: 10.1016/j.cancergen.2017.11.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/12/2017] [Accepted: 11/27/2017] [Indexed: 01/04/2023]
Abstract
Mate-pair sequencing (MPseq), using long-insert, paired-end genomic libraries, is a powerful next-generation sequencing-based approach for the detection of genomic structural variants. SVAtools is a set of algorithms to detect both chromosomal rearrangements and large (>10 kb) copy number variants (CNVs) in genome-wide MPseq data. SVAtools can also predict gene disruptions and gene fusions, and characterize the genomic structure of complex rearrangements. To illustrate the power of SVAtools' junction detection methods to provide comprehensive molecular karyotypes, MPseq data were compared against a set of samples previously characterized by traditional cytogenetic methods. Karyotype, FISH and chromosomal microarray (CMA), performed for 29 patients in a clinical laboratory setting, collectively revealed 285 breakpoints in 87 rearrangements. The junction detection methods of SVAtools detected 87% of these breakpoints compared to 48%, 42% and 57% for karyotype, FISH and CMA respectively. Breakpoint resolution was also reported to 1 kb or less and additional genomic rearrangement complexities not appreciable by standard cytogenetic techniques were revealed. For example, 63% of CNVs detected by CMA were shown by SVAtools' junction detection to occur secondary to a rearrangement other than a simple deletion or tandem duplication. SVAtools with MPseq provides comprehensive and accurate whole-genome junction detection with improved breakpoint resolution, compared to karyotype, FISH, and CMA combined. This approach to molecular karyotyping offers considerable diagnostic potential for the simultaneous detection of both novel and recurrent genomic rearrangements in hereditary and neoplastic disorders.
Collapse
Affiliation(s)
- Sarah H Johnson
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester MN, USA
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester MN, USA
| | - Stephanie A Smoley
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Stephen J Murphy
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester MN, USA
| | - Faye R Harris
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester MN, USA
| | | | - Roman M Zenka
- Bioinformatics Systems, Mayo Clinic Rochester, MN, USA
| | - Beth A Pitel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ross A Rowsey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Umut Aypar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hutton M Kearney
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester MN, USA; Department of Molecular Medicine, Mayo Clinic, Rochester MN, USA.
| |
Collapse
|
22
|
Russell LJ, Jones L, Enshaei A, Tonin S, Ryan SL, Eswaran J, Nakjang S, Papaemmanuil E, Tubio JMC, Fielding AK, Vora A, Campbell PJ, Moorman AV, Harrison CJ. Characterisation of the genomic landscape of CRLF2-rearranged acute lymphoblastic leukemia. Genes Chromosomes Cancer 2017; 56:363-372. [PMID: 28033648 PMCID: PMC5396319 DOI: 10.1002/gcc.22439] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/24/2016] [Accepted: 12/25/2016] [Indexed: 12/31/2022] Open
Abstract
Deregulated expression of the type I cytokine receptor, CRLF2, is observed in 5-15% of precursor B-cell acute lymphoblastic leukaemia (B-ALL). We aimed to determine the clinical and genetic landscape of those with IGH-CRLF2 or P2RY8-CRLF2 (CRLF2-r) using multiple genomic approaches. Clinical and demographic features of CRLF2-r patients were characteristic of B-ALL. Patients with IGH-CRLF2 were older (14 y vs. 4 y, P < .001), while the incidence of CRLF2-r among Down syndrome patients was high (50/161, 31%). CRLF2-r co-occurred with primary chromosomal rearrangements but the majority (111/161, 69%) had B-other ALL. Copy number alteration (CNA) profiles were similar to B-other ALL, although CRLF2-r patients harbored higher frequencies of IKZF1 (60/138, 43% vs. 77/1351, 24%) and BTG1 deletions (20/138, 15% vs. 3/1351, 1%). There were significant differences in CNA profiles between IGH-CRLF2 and P2RY8-CRLF2 patients: IKZF1 (25/35, 71% vs. 36/108, 33%, P < .001), BTG1 (11/35, 31% vs. 10/108, 9%, P =.004), and ADD3 deletions (9/19, 47% vs. 5/38, 13%, P =.008). A novel gene fusion, USP9X-DDX3X, was discovered in 10/54 (19%) of patients. Pathway analysis of the mutational profile revealed novel involvement for focal adhesion. Although the functional relevance of many of these abnormalities are unknown, they likely activate additional pathways, which may represent novel therapeutic targets.
Collapse
Affiliation(s)
- Lisa J. Russell
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Lisa Jones
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Amir Enshaei
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Stefano Tonin
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Sarra L. Ryan
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Jeyanthy Eswaran
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Sirintra Nakjang
- Bioinformatics Support Unit, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Elli Papaemmanuil
- Department of Epidemiology‐BiostatisticsMemorial Sloan Kettering Cancer CenterUSA
- Cancer Genome ProjectWellcome Trust Sanger InstituteHinxtonUK
| | | | | | - Ajay Vora
- Department of HaematologySheffield Children's HospitalSheffieldUK
| | | | - Anthony V. Moorman
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Christine J. Harrison
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle UniversityNewcastle‐upon‐TyneUK
| |
Collapse
|
23
|
Valentin-Vega YA, Wang YD, Parker M, Patmore DM, Kanagaraj A, Moore J, Rusch M, Finkelstein D, Ellison DW, Gilbertson RJ, Zhang J, Kim HJ, Taylor JP. Cancer-associated DDX3X mutations drive stress granule assembly and impair global translation. Sci Rep 2016; 6:25996. [PMID: 27180681 PMCID: PMC4867597 DOI: 10.1038/srep25996] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/21/2016] [Indexed: 12/26/2022] Open
Abstract
DDX3X is a DEAD-box RNA helicase that has been implicated in multiple aspects of RNA metabolism including translation initiation and the assembly of stress granules (SGs). Recent genomic studies have reported recurrent DDX3X mutations in numerous tumors including medulloblastoma (MB), but the physiological impact of these mutations is poorly understood. Here we show that a consistent feature of MB-associated mutations is SG hyper-assembly and concomitant translation impairment. We used CLIP-seq to obtain a comprehensive assessment of DDX3X binding targets and ribosome profiling for high-resolution assessment of global translation. Surprisingly, mutant DDX3X expression caused broad inhibition of translation that impacted DDX3X targeted and non-targeted mRNAs alike. Assessment of translation efficiency with single-cell resolution revealed that SG hyper-assembly correlated precisely with impaired global translation. SG hyper-assembly and translation impairment driven by mutant DDX3X were rescued by a genetic approach that limited SG assembly and by deletion of the N-terminal low complexity domain within DDX3X. Thus, in addition to a primary defect at the level of translation initiation caused by DDX3X mutation, SG assembly itself contributes to global translation inhibition. This work provides mechanistic insights into the consequences of cancer-related DDX3X mutations, suggesting that globally reduced translation may provide a context-dependent survival advantage that must be considered as a possible contributor to tumorigenesis.
Collapse
Affiliation(s)
- Yasmine A. Valentin-Vega
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yong-Dong Wang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Matthew Parker
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Deanna M. Patmore
- Department of Oncology, Cambridge Cancer Centre, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Anderson Kanagaraj
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jennifer Moore
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David W. Ellison
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Richard J. Gilbertson
- Department of Oncology, Cambridge Cancer Centre, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - J. Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| |
Collapse
|
24
|
Gianfelici V, Chiaretti S, Demeyer S, Di Giacomo F, Messina M, La Starza R, Peragine N, Paoloni F, Geerdens E, Pierini V, Elia L, Mancini M, De Propris MS, Apicella V, Gaidano G, Testi AM, Vitale A, Vignetti M, Mecucci C, Guarini A, Cools J, Foà R. RNA sequencing unravels the genetics of refractory/relapsed T-cell acute lymphoblastic leukemia. Prognostic and therapeutic implications. Haematologica 2016; 101:941-50. [PMID: 27151993 DOI: 10.3324/haematol.2015.139410] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/29/2016] [Indexed: 01/12/2023] Open
Abstract
Despite therapeutic improvements, a sizable number of patients with T-cell acute lymphoblastic leukemia still have a poor outcome. To unravel the genomic background associated with refractoriness, we evaluated the transcriptome of 19 cases of refractory/early relapsed T-cell acute lymphoblastic leukemia (discovery cohort) by performing RNA-sequencing on diagnostic material. The incidence and prognostic impact of the most frequently mutated pathways were validated by Sanger sequencing on genomic DNA from diagnostic samples of an independent cohort of 49 cases (validation cohort), including refractory, relapsed and responsive cases. Combined gene expression and fusion transcript analyses in the discovery cohort revealed the presence of known oncogenes and identified novel rearrangements inducing overexpression, as well as inactivation of tumor suppressor genes. Mutation analysis identified JAK/STAT and RAS/PTEN as the most commonly disrupted pathways in patients with chemorefractory disease or early relapse, frequently in association with NOTCH1/FBXW7 mutations. The analysis on the validation cohort documented a significantly higher risk of relapse, inferior overall survival, disease-free survival and event-free survival in patients with JAK/STAT or RAS/PTEN alterations. Conversely, a significantly better survival was observed in patients harboring only NOTCH1/FBXW7 mutations: this favorable prognostic effect was abrogated by the presence of concomitant mutations. Preliminary in vitro assays on primary cells demonstrated sensitivity to specific inhibitors. These data document the negative prognostic impact of JAK/STAT and RAS/PTEN mutations in T-cell acute lymphoblastic leukemia and suggest the potential clinical application of JAK and PI3K/mTOR inhibitors in patients harboring mutations in these pathways.
Collapse
Affiliation(s)
- Valentina Gianfelici
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Sabina Chiaretti
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Sofie Demeyer
- Center for Human Genetics, KU Leuven, Belgium Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Filomena Di Giacomo
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies (CeRMS), University of Turin, Italy
| | - Monica Messina
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Roberta La Starza
- Hematology and Bone Marrow Transplantation Unit, Department of Medicine, University of Perugia, Italy
| | - Nadia Peragine
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | | | - Ellen Geerdens
- Center for Human Genetics, KU Leuven, Belgium Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Valentina Pierini
- Hematology and Bone Marrow Transplantation Unit, Department of Medicine, University of Perugia, Italy
| | - Loredana Elia
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Marco Mancini
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | | | - Valerio Apicella
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Anna Maria Testi
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Antonella Vitale
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Marco Vignetti
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy GIMEMA Data Center, Rome, Italy
| | - Cristina Mecucci
- Hematology and Bone Marrow Transplantation Unit, Department of Medicine, University of Perugia, Italy
| | - Anna Guarini
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Belgium Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Robin Foà
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| |
Collapse
|
25
|
Bond J, Touzart A, Cieslak A, Trinquand A, Marchand T, Escoffre M, Contet A, Muller M, Schmitt C, Fest T, Asnafi V, Macintyre E. NAP1L1-MLLT10 is a rare recurrent translocation that is associated with HOXA activation and poor treatment response in T-cell acute lymphoblastic leukaemia. Br J Haematol 2015; 174:470-3. [PMID: 26455581 DOI: 10.1111/bjh.13772] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jonathan Bond
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, Paris, France.,Laboratory of Onco-Haematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - Aurore Touzart
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, Paris, France.,Laboratory of Onco-Haematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - Agata Cieslak
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, Paris, France.,Laboratory of Onco-Haematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - Amélie Trinquand
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, Paris, France.,Laboratory of Onco-Haematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - Tony Marchand
- Department of Haematology, University Hospital and INSERM UMR 917, Rennes 1 University, Rennes, France
| | - Martine Escoffre
- Department of Haematology, University Hospital and INSERM UMR 917, Rennes 1 University, Rennes, France
| | - Audrey Contet
- Department of Paediatric Haematology, University Hospital, Nancy, France
| | - Marc Muller
- Genetics Laboratory, University Hospital, Nancy, France
| | - Claudine Schmitt
- Department of Paediatric Haematology, University Hospital, Nancy, France
| | - Thierry Fest
- Department of Haematology, University Hospital and INSERM UMR 917, Rennes 1 University, Rennes, France
| | - Vahid Asnafi
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, Paris, France.,Laboratory of Onco-Haematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - Elizabeth Macintyre
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, Paris, France. .,Laboratory of Onco-Haematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France.
| |
Collapse
|