1
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Walia Y, de Bock CE, Huang Y. The landscape of alterations affecting epigenetic regulators in T-cell acute lymphoblastic leukemia: Roles in leukemogenesis and therapeutic opportunities. Int J Cancer 2024; 154:1522-1536. [PMID: 38155420 DOI: 10.1002/ijc.34819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/25/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy accounting for 10%-15% of pediatric and 20%-25% of adult ALL cases. Epigenetic irregularities in T-ALL include alterations in both DNA methylation and the post-translational modifications on histones which together play a critical role in the initiation and development of T-ALL. Characterizing the oncogenic mutations that result in these epigenetic changes combined with the reversibility of epigenetic modifications represents an opportunity for the development of epigenetic therapies. Oncogenic mutations and deregulated expression of DNA methyltransferases (DNMTs), Ten-Eleven Translocation dioxygenases (TETs), Histone acetyltransferases (HATs) and members of Polycomb Repressor Complex 2 (PRC2) have all been identified in T-ALL. This review focuses on the current understanding of how these mutations lead to epigenetic changes in T-ALL, their association with disease pathogenesis and the current efforts to exploit these clinically through the development of epigenetic therapies in T-ALL treatment.
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Affiliation(s)
- Yashna Walia
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, New South Wales, Australia
| | - Charles E de Bock
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, New South Wales, Australia
| | - Yizhou Huang
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, New South Wales, Australia
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2
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O'Connor D, Valle-Inclán JE, Conde L, Bloye G, Rahman S, Costa JR, Bartram J, Adams S, Wright G, Elrick H, Wall K, Dyer S, Howell C, Jigoulina G, Herrero J, Cortes-Ciriano I, Moorman AV, Mansour MR. Noncoding mutations drive persistence of a founder preleukemic clone which initiates late relapse in T-ALL. Blood 2024; 143:933-937. [PMID: 38194681 DOI: 10.1182/blood.2023021906] [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: 07/18/2023] [Revised: 11/14/2023] [Accepted: 12/01/2023] [Indexed: 01/11/2024] Open
Abstract
ABSTRACT T-ALL relapse usually occurs early but can occur much later, which has been suggested to represent a de novo leukemia. However, we conclusively demonstrate late relapse can evolve from a pre-leukemic subclone harbouring a non-coding mutation that evades initial chemotherapy.
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Affiliation(s)
- David O'Connor
- UCL Cancer Institute, University College London, London, United Kingdom
- Department of Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Jose Espejo Valle-Inclán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Lucia Conde
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Gianna Bloye
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Sunniyat Rahman
- UCL Cancer Institute, University College London, London, United Kingdom
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Joana R Costa
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Jack Bartram
- Department of Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Stuart Adams
- Specialist Integrated Haematology and Malignancy Diagnostic Service-Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Gary Wright
- Specialist Integrated Haematology and Malignancy Diagnostic Service-Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Hillary Elrick
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Kerry Wall
- West Midlands Regional Genetics Laboratory, Birmingham, United Kingdom
| | - Sara Dyer
- West Midlands Regional Genetics Laboratory, Birmingham, United Kingdom
| | | | | | - Javier Herrero
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Anthony V Moorman
- Leukaemia Research Cytogenetics Group, Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marc R Mansour
- UCL Cancer Institute, University College London, London, United Kingdom
- Department of Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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3
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Ding Y, Chen Q, Shan H, Liu J, Lv C, Wang Y, Yuan L, Chen Y, Wang Z, Yin Y, Xiao K, Li J, Liu W. SASH1: A Novel Eph Receptor Partner and Insights into SAM-SAM Interactions. J Mol Biol 2023; 435:168243. [PMID: 37619706 DOI: 10.1016/j.jmb.2023.168243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/16/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
The Eph (erythropoietin-producing human hepatocellular) receptor family, the largest subclass of receptor tyrosine kinases (RTKs), plays essential roles in embryonic development and neurogenesis. The intracellular Sterile Alpha Motif (SAM) domain presents a critical structural feature that distinguishes Eph receptors from other RTKs and participates in recruiting and binding downstream molecules. This study identified SASH1 (SAM and SH3 domain containing 1) as a novel Eph receptor-binding partner through SAM-SAM domain interactions. Our comprehensive biochemical analyses revealed that SASH1 selectively interacts with Eph receptors via its SAM1 domain, displaying the highest affinity for EphA8. The high-resolution crystal structure of the EphA8-SASH1 complex provided insights into the specific intermolecular interactions between these proteins. Cellular assays confirmed that EphA8 and SASH1 co-localize and co-precipitate in mammalian cells, with cancer mutations (EphA8 R942H or G978D) impairing this interaction. We demonstrated that SAM-SAM interaction is critical for SASH1-mediated regulation of EphA8 kinase activity, shedding new light on the Eph signaling pathway and expanding our understanding of the molecular basis of the tumor suppressor gene SASH1.
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Affiliation(s)
- Yuzhen Ding
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China. https://twitter.com/dingyuzhen8
| | - Qiangou Chen
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Hui Shan
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Jia Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Chunyu Lv
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Yanhui Wang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Lin Yuan
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen, Guangdong 518057, China
| | - Yu Chen
- Chinese Academy of Sciences Key Laboratory of Brain Connectome and Manipulation, Shenzhen Key Laboratory of Translational Research for Brain Diseases, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong 518055, China
| | - Ziyi Wang
- Innovative Institute of Basic Medical Sciences of Zhejiang University, Hangzhou 310058, China
| | - Yuxin Yin
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Kang Xiao
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China; HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, China.
| | - Jianchao Li
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China.
| | - Wei Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China; Institute of Geriatric Medicine, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China.
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4
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Bhasin SS, Thomas BE, Summers RJ, Sarkar D, Mumme H, Pilcher W, Emam M, Raikar SS, Park SI, Castellino SM, Graham DK, Bhasin MK, DeRyckere D. Pediatric T-cell acute lymphoblastic leukemia blast signature and MRD associated immune environment changes defined by single cell transcriptomics analysis. Sci Rep 2023; 13:12556. [PMID: 37532715 PMCID: PMC10397284 DOI: 10.1038/s41598-023-39152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/20/2023] [Indexed: 08/04/2023] Open
Abstract
Different driver mutations and/or chromosomal aberrations and dysregulated signaling interactions between leukemia cells and the immune microenvironment have been implicated in the development of T-cell acute lymphoblastic leukemia (T-ALL). To better understand changes in the bone marrow microenvironment and signaling pathways in pediatric T-ALL, bone marrows collected at diagnosis (Dx) and end of induction therapy (EOI) from 11 patients at a single center were profiled by single cell transcriptomics (10 Dx, 5 paired EOI, 1 relapse). T-ALL blasts were identified by comparison with healthy bone marrow cells. T-ALL blast-associated gene signature included SOX4, STMN1, JUN, HES4, CDK6, ARMH1 among the most significantly overexpressed genes, some of which are associated with poor prognosis in children with T-ALL. Transcriptome profiles of the blast cells exhibited significant inter-patient heterogeneity. Post induction therapy expression profiles of the immune cells revealed significant changes. Residual blast cells in MRD+ EOI samples exhibited significant upregulation (P < 0.01) of PD-1 and RhoGDI signaling pathways. Differences in cellular communication were noted in the presence of residual disease in T cell and hematopoietic stem cell compartments in the bone marrow. Together, these studies generate new insights and expand our understanding of the bone marrow landscape in pediatric T-ALL.
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Affiliation(s)
- Swati S Bhasin
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA.
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
| | - Beena E Thomas
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ryan J Summers
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Debasree Sarkar
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
| | - Hope Mumme
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
| | - William Pilcher
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mohamed Emam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sunil S Raikar
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sunita I Park
- Department of Pathology, Children's Healthcare of Atlanta, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Sharon M Castellino
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Douglas K Graham
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Manoj K Bhasin
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Deborah DeRyckere
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
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5
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Yu X, Sun R, Yang X, He X, Guo H, Ou C. The NT5DC family: expression profile and prognostic value in pancreatic adenocarcinoma. J Cancer 2023; 14:2274-2288. [PMID: 37576396 PMCID: PMC10414034 DOI: 10.7150/jca.85811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
Pancreatic adenocarcinoma (PAAD) is a malignant tumor with high morbidity and mortality rates. The NT5DC family is an evolutionarily-conserved family of 5'-nucleosidases that catalyze the intracellular hydrolysis of nucleotides. Although the NT5DC family has been linked to the initiation and growth of several cancers, its function in PAAD remains unclear. A series of bioinformatic analyses was used to ascertain the expression, prognosis, gene changes, functional enrichment, and immune regulatory functions of the NT5DC family in PAAD. NT5C2 and NT5DC1/2 mRNA and protein levels are increased in PAAD. Furthermore, the high mRNA expressions of NT5C2, NT5DC2, and NT5DC4 indicate a poor prognosis in patients with PAAD. The enrichment of biological processes and gene expression in the NT5DC family in PAAD were investigated using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses. Further investigations into immune infiltration revealed a close relationship between NT5DC gene expression and immune cell infiltration. These findings provide new insights into the biological function and prognostic value of the NT5DC gene family in PAAD.
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Affiliation(s)
- Xiaoqian Yu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Ru Sun
- Department of blood transfusion, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan, China
| | - Xuejie Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Hongbin Guo
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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6
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Zhou K, Gong D, He C, Xiao M, Zhang M, Huang W. Targeted therapy using larotrectinib and venetoclax for the relapsed/refractory T-cell acute lymphoblastic leukemia harboring a cryptic ETV6-NTRK3 fusion. Mol Carcinog 2023. [PMID: 37036164 DOI: 10.1002/mc.23534] [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: 12/22/2022] [Accepted: 03/17/2023] [Indexed: 04/11/2023]
Abstract
Outcomes for patients with relapsed and refractory (R/R) T-cell acute lymphoblastic leukemia (T-ALL) after allogeneic hematopoietic stem cell transplantation (allo-HSCT) are dismal, with few available treatments. Recently, identification of cancer patients harboring neurotrophic tropomyosin receptor kinase (NTRK) gene fusions is constantly increasing, especially with the advent of NTRK inhibitors. However, the role of ETV6-NTRK3 in T-ALL has not been investigated. This case represented the first detailed report of T-ALL patient harboring a cryptic ETV6-NTRK3 fusion with an unfavorable prognosis, not only because of leukemia resistant to the standard multiagent chemotherapy but also early relapse after allo-HSCT. Acquired EP300 mutation was found at relapse, which could explain the cause of recurrence and affect the follow-up treatment. Combined targeted therapy like larotrectinib allied with pan-targeted BCL-2 inhibitor venetoclax, may be a potential maintenance treatment in R/R ETV6-NTRK3 positive leukemia after allo-HSCT. The leukemic clonal evolution might be revealed through transcriptome sequencing and overcome by drugs with universal targets. Our case demonstrated that both comprehensive profiling techniques (such as transcriptome sequencing, multiparameter flow cytometry, and digital droplet polymerase chain reaction) and a multimodality treatment strategy were critical for anticipating an early relapse and personalized therapy of R/R T-cell leukemia.
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Affiliation(s)
- Kuangguo Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Duanhao Gong
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cheng He
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meilan Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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7
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Thatikonda V, Islam SMA, Autry RJ, Jones BC, Gröbner SN, Warsow G, Hutter B, Huebschmann D, Fröhling S, Kool M, Blattner-Johnson M, Jones DTW, Alexandrov LB, Pfister SM, Jäger N. Comprehensive analysis of mutational signatures reveals distinct patterns and molecular processes across 27 pediatric cancers. NATURE CANCER 2023; 4:276-289. [PMID: 36702933 PMCID: PMC9970869 DOI: 10.1038/s43018-022-00509-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 12/21/2022] [Indexed: 01/27/2023]
Abstract
Analysis of mutational signatures can reveal underlying molecular mechanisms of the processes that have imprinted the somatic mutations found in cancer genomes. Here, we analyze single base substitutions and small insertions and deletions in pediatric cancers encompassing 785 whole-genome sequenced tumors from 27 molecularly defined cancer subtypes. We identified only a small number of mutational signatures active in pediatric cancers, compared with previously analyzed adult cancers. Further, we report a significant difference in the proportion of pediatric tumors showing homologous recombination repair defect signatures compared with previous analyses. In pediatric leukemias, we identified an indel signature, not previously reported, characterized by long insertions in nonrepeat regions, affecting mainly intronic and intergenic regions, but also exons of known cancer genes. We provide a systematic overview of COSMIC v.3 mutational signatures active across pediatric cancers, which is highly relevant for understanding tumor biology and enabling future research in defining biomarkers of treatment response.
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Affiliation(s)
- Venu Thatikonda
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim RCV GmbH, Vienna, Austria
| | - S M Ashiqul Islam
- Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Robert J Autry
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Barbara C Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Pediatric Glioma Research Group, DKFZ, Heidelberg, Germany
| | - Susanne N Gröbner
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Gregor Warsow
- Omics IT and Data Management Core Facility (W610), DKFZ, Heidelberg, Germany
| | - Barbara Hutter
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg, DKFZ, Heidelberg, Germany
- Division of Applied Bioinformatics, DKFZ, Heidelberg, Germany
| | - Daniel Huebschmann
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg, DKFZ, Heidelberg, Germany
- Pattern Recognition and Digital Medicine, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, DKFZ, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Pediatric Glioma Research Group, DKFZ, Heidelberg, Germany
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany.
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
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8
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Pediatric T-ALL type-1 and type-2 relapses develop along distinct pathways of clonal evolution. Leukemia 2022; 36:1759-1768. [PMID: 35585141 PMCID: PMC9252914 DOI: 10.1038/s41375-022-01587-0] [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: 01/31/2022] [Revised: 04/18/2022] [Accepted: 04/27/2022] [Indexed: 11/08/2022]
Abstract
The mechanisms underlying T-ALL relapse remain essentially unknown. Multilevel-omics in 38 matched pairs of initial and relapsed T-ALL revealed 18 (47%) type-1 (defined by being derived from the major ancestral clone) and 20 (53%) type-2 relapses (derived from a minor ancestral clone). In both types of relapse, we observed known and novel drivers of multidrug resistance including MDR1 and MVP, NT5C2 and JAK-STAT activators. Patients with type-1 relapses were specifically characterized by IL7R upregulation. In remarkable contrast, type-2 relapses demonstrated (1) enrichment of constitutional cancer predisposition gene mutations, (2) divergent genetic and epigenetic remodeling, and (3) enrichment of somatic hypermutator phenotypes, related to BLM, BUB1B/PMS2 and TP53 mutations. T-ALLs that later progressed to type-2 relapses exhibited a complex subclonal architecture, unexpectedly, already at the time of initial diagnosis. Deconvolution analysis of ATAC-Seq profiles showed that T-ALLs later developing into type-1 relapses resembled a predominant immature thymic T-cell population, whereas T-ALLs developing into type-2 relapses resembled a mixture of normal T-cell precursors. In sum, our analyses revealed fundamentally different mechanisms driving either type-1 or type-2 T-ALL relapse and indicate that differential capacities of disease evolution are already inherent to the molecular setup of the initial leukemia. ![]()
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9
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Popa DC, Şerbănică A, Obrisca R, Şerbănică I, Radu L, Jercan C, Marcu A, Bica A, Asan M, Petran M, Dragomir M, Jardan C, Ţică V, Gheorghe A, Stoian I, Coriu D, Coliţă A, Coliţă A. Controversial Flow Cytometry Monitoring of a Relapse Case of Pediatric T Cell Acute Lymphoblastic Leukemia: A Case Report. Front Med (Lausanne) 2022; 9:858809. [PMID: 35391882 PMCID: PMC8982560 DOI: 10.3389/fmed.2022.858809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most frequent childhood cancer, with 80-85% represented by B cell ALL and only 15% by T cell ALL. T Cell ALL (T-ALL) carries a more reserved prognosis compared to B Cell ALL (B-ALL) with regard to response to treatment, risk of relapse, and overall survival. Progress made in current monitoring protocols such as via flow cytometry immunophenotyping (FCM) and by PCR-based amplification of antigen-receptor genes led to improved management of patients with ALL and superior rates of survival. Nevertheless, challenges remain in some clinical cases. This manuscript describes a unique case of T-ALL and raises awareness of such clinical challenges. The article presents an overview of the flow cytometry immunophenotyping at diagnosis and during treatment of a pediatric patient with T-ALL from Fundeni Clinical Institute. In this case, in spite of various therapeutic measures such as first-line chemotherapy for high risk group, salvage chemotherapy (FLAG), conditioning regimen (FLU-BU-TT-ATG), and stem cell transplant, a chemoresistance clone continued to be present.
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Affiliation(s)
- Delia Codruţa Popa
- Department of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Andreea Şerbănică
- Department of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Radu Obrisca
- Department of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Ionut Şerbănică
- Department of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Letiţia Radu
- Department of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Cristina Jercan
- Department of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Andra Marcu
- Department of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Ana Bica
- Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Minodora Asan
- Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Mădălina Petran
- Department of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Department of Toxicology, Grigore Alexandrescu Emergency Clinical Hospital for Children, Bucharest, Romania
| | - Mihaela Dragomir
- Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Cerasela Jardan
- Department of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Valeria Ţică
- Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Anca Gheorghe
- Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Irina Stoian
- Department of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Daniel Coriu
- Department of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Anca Coliţă
- Department of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Andrei Coliţă
- Department of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Department of Hematology, Coltea Hospital, Bucharest, Romania
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10
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Ruether C, Wuensch C, Randau G, Michgehl U, Trautmann M, Hartmann W, Sandmann S, Dugas M, Khanam T, Burkhardt B. Design of a targeted next-generation DNA sequencing panel for pediatric T-cell lymphoblastic lymphoma to unravel biology and optimize treatment. Genes Chromosomes Cancer 2022; 61:459-470. [PMID: 35278000 DOI: 10.1002/gcc.23037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/26/2022] [Accepted: 03/06/2022] [Indexed: 11/09/2022] Open
Abstract
Low incidence and molecular heterogeneity of pediatric T-cell lymphoblastic lymphoma (T-LBL) require an international, large-scale effort to identify novel clinical biomarkers. The ongoing international clinical trial LBL2018 (NCT04043494) represents an ideal opportunity to implement a common analytic approach. Targeted next-generation sequencing is well-suited for this purpose; however, selection of relevant target genes for T-LBL remains subject of ongoing debates. Our group has recently designed and evaluated a first target panel of 80 candidate genes for T-LBL. The present study aimed at developing a novel optimized gene panel for large-scale application and to promote an international agreement on a common core panel. Small sequence variants obtained from our former study were systematically analyzed and classified with regards to pathogenic relevance, to prioritize candidate genes. Additional genes were curated from literature and online databases for a more comprehensive analysis of relevant functions and signaling pathways. The new target panel TGP-T-LBL entails 84 candidate genes which are key actors in NOTCH, PI3K-AKT, JAK-STAT, RAS signaling, epigenetic regulation, transcription, DNA repair, cell cycle regulation and ribosomal function. From our former gene panel, 35 out of 80 candidate genes were selected for the novel panel. Forty-six out of 84 genes are currently being analyzed in the ongoing international trial LBL2018. Exploratory analysis of prognostic relevance on mutation-level suggested a potential association of PIK3CA variants c.1624G > A(p.Glu542Lys) and c.1633G > A(p.Glu545Lys) to occurrence of relapse, emphasizing particular relevance of mutation analysis in PI3K-AKT signaling. Our approach promotes comprehensive and clinically relevant mutational profiling of pediatric T-LBL. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Charlotte Ruether
- Paediatric Hematology and Oncology, University Hospital Muenster, Germany
| | | | - Gerrit Randau
- Paediatric Hematology and Oncology, University Hospital Muenster, Germany
| | - Ulf Michgehl
- Paediatric Hematology and Oncology, University Hospital Muenster, Germany
| | - Marcel Trautmann
- Division of Translational Pathology, Gerhard-Domagk-Institute of Pathology, University Hospital Muenster, Germany
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk-Institute of Pathology, University Hospital Muenster, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, Muenster University, Germany
| | - Martin Dugas
- Institute of Medical Informatics, Muenster University, Germany
| | - Tasneem Khanam
- Paediatric Hematology and Oncology, University Hospital Muenster, Germany
| | - Birgit Burkhardt
- Paediatric Hematology and Oncology, University Hospital Muenster, Germany
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11
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Grant AH, Ayala-Marin YM, Mohl JE, Robles-Escajeda E, Rodriguez G, Dutil J, Kirken RA. The Genomic Landscape of a Restricted ALL Cohort from Patients Residing on the U.S./Mexico Border. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18147345. [PMID: 34299796 PMCID: PMC8307122 DOI: 10.3390/ijerph18147345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/12/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS) has identified unique biomarkers yielding new strategies in precision medicine for the treatment of Acute lymphoblastic leukemia (ALL). Hispanics show marked health disparities in ALL, often absent in clinical trials or cancer research. Thus, it is unknown whether Hispanics would benefit equally from curated data currently guiding precision oncology. Using whole-exome sequencing, nine ALL patients were screened for mutations within genes known to possess diagnostic, prognostic and therapeutic value. Genes mutated in Hispanic ALL patients from the borderland were mined for potentially pathogenic variants within clinically relevant genes. KRAS G12A was detected in this unique cohort and its frequency in Hispanics from the TARGET-ALL Phase II database was three-fold greater than that of non-Hispanics. STAT5B N642H was also detected with low frequency in Hispanic and non-Hispanic individuals within TARGET. Its detection within this small cohort may reflect a common event in this demographic. Such variants occurring in the MAPK and JAK/STAT pathways may be contributing to Hispanic health disparities in ALL. Notable variants in ROS1, WT1, and NOTCH2 were observed in the ALL borderland cohort, with NOTCH2 C19W occurring most frequently. Further investigations on the pathogenicity of these variants are needed to assess their relevance in ALL.
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Affiliation(s)
- Alice Hernandez Grant
- Department of Biological Sciences, College of Science, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.H.G.); (Y.M.A.-M.); (E.R.-E.); (G.R.)
| | - Yoshira Marie Ayala-Marin
- Department of Biological Sciences, College of Science, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.H.G.); (Y.M.A.-M.); (E.R.-E.); (G.R.)
| | - Jonathon Edward Mohl
- Department of Mathematical Sciences, College of Science, The University of Texas at El Paso, El Paso, TX 79968, USA;
| | - Elisa Robles-Escajeda
- Department of Biological Sciences, College of Science, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.H.G.); (Y.M.A.-M.); (E.R.-E.); (G.R.)
| | - Georgialina Rodriguez
- Department of Biological Sciences, College of Science, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.H.G.); (Y.M.A.-M.); (E.R.-E.); (G.R.)
| | - Julie Dutil
- Department of Biochemistry, Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, PR 00716, USA;
| | - Robert Arthur Kirken
- Department of Biological Sciences, College of Science, The University of Texas at El Paso, El Paso, TX 79968, USA; (A.H.G.); (Y.M.A.-M.); (E.R.-E.); (G.R.)
- Correspondence: ; Tel.: +1-(915)-747-5536
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12
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Mansur MB, Furness CL, Nakjang S, Enshaei A, Alpar D, Colman SM, Minto L, Irving J, Poole BV, Noronha EP, Savola S, Iqbal S, Gribben J, Pombo-de-Oliveira MS, Ford TM, Greaves MF, van Delft FW. The genomic landscape of teenage and young adult T-cell acute lymphoblastic leukemia. Cancer Med 2021; 10:4864-4873. [PMID: 34080325 PMCID: PMC8290240 DOI: 10.1002/cam4.4024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/09/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Treatment on risk adapted intensive pediatric protocols has improved outcome for teenagers and young adults (TYA) with T-cell acute lymphoblastic leukemia (T-ALL). Understanding the biology of disease in this age group and the genetic basis of relapse is a key goal as patients with relapsed/refractory disease have poor outcomes with conventional chemotherapy and novel molecular targets are required. This study examines the question of whether TYA T-ALL has a specific biological-molecular profile distinct from pediatric or adult T-ALL. METHODS Genomic characterization was undertaken of a retrospective discovery cohort of 80 patients aged 15-26 years with primary or relapsed T-ALL, using a combination of Genome-Wide Human SNP Array 6.0, targeted gene mutation and promoter methylation analyses. Findings were confirmed by MLPA, real-time quantitative PCR, and FISH. Whole Exome Sequencing was performed in 4 patients with matched presentation and relapse to model clonal evolution. A prevalence analysis was performed on a final data set of 1,792 individual cases to identify genetic lesions with age specific frequency patterns, including 972 pediatric (1-14 years), 439 TYA (15-24 years) and 381 adult (≥25 years) cases. These cases were extracted from 19 publications with comparable genomic data identified through a PubMed search. RESULTS Genomic characterization of this large cohort of TYA T-ALL patients identified recurrent isochromosome 7q i(7q) in our discovery cohort (n = 3). Prevalence analysis did not identify any age specific genetic abnormalities. Genomic analysis of 6 pairs of matched presentation - relapsed T-ALL established that all relapses were clonally related to the initial leukemia. Whole exome sequencing analysis revealed recurrent, targetable, mutations disrupting NOTCH, PI3K/AKT/mTOR, FLT3, NRAS as well as drug metabolism pathways. CONCLUSIONS All genetic aberrations in TYA T-ALL occurred with an incidence similar or intermediate to that reported in the pediatric and adult literature, demonstrating that overall TYA T-ALL exhibits a transitional genomic profile. Analysis of matched presentation - relapse supported the hypothesis that relapse is driven by the Darwinian evolution of sub-clones associated with drug resistance (NT5C2 and TP53 mutations) and re-iterative mutation of known key T-ALL drivers, including NOTCH1.
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Affiliation(s)
- Marcela B Mansur
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.,Paediatric Haematology-Oncology Program, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.,Division of Clinical Research, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Caroline L Furness
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Sirintra Nakjang
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK.,Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Amir Enshaei
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Donat Alpar
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.,HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Sue M Colman
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Lynne Minto
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Julie Irving
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Beth V Poole
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Elda P Noronha
- Paediatric Haematology-Oncology Program, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Suvi Savola
- Oncogenetics, MRC-Holland, Amsterdam, The Netherlands
| | - Sameena Iqbal
- Centre for Haemato-Oncology, Barts Cancer Institute, London, UK
| | - John Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, London, UK
| | - Maria S Pombo-de-Oliveira
- Paediatric Haematology-Oncology Program, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Tony M Ford
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Mel F Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Frederik W van Delft
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.,Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
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13
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Lato MW, Przysucha A, Grosman S, Zawitkowska J, Lejman M. The New Therapeutic Strategies in Pediatric T-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2021; 22:ijms22094502. [PMID: 33925883 PMCID: PMC8123476 DOI: 10.3390/ijms22094502] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/23/2022] Open
Abstract
Childhood acute lymphoblastic leukemia is a genetically heterogeneous cancer that accounts for 10–15% of T-cell acute lymphoblastic leukemia (T-ALL) cases. The T-ALL event-free survival rate (EFS) is 85%. The evaluation of structural and numerical chromosomal changes is important for a comprehensive biological characterization of T-ALL, but there are currently no genetic prognostic markers. Despite chemotherapy regimens, steroids, and allogeneic transplantation, relapse is the main problem in children with T-ALL. Due to the development of high-throughput molecular methods, the ability to define subgroups of T-ALL has significantly improved in the last few years. The profiling of the gene expression of T-ALL has led to the identification of T-ALL subgroups, and it is important in determining prognostic factors and choosing an appropriate treatment. Novel therapies targeting molecular aberrations offer promise in achieving better first remission with the hope of preventing relapse. The employment of precisely targeted therapeutic approaches is expected to improve the cure of the disease and quality of life of patients. These include therapies that inhibit Notch1 activation (bortezomib), JAK inhibitors in ETP-ALL (ruxolitinib), BCL inhibitors (venetoclax), and anti-CD38 therapy (daratumumab). Chimeric antigen receptor T-cell therapy (CAR-T) is under investigation, but it requires further development and trials. Nelarabine-based regimens remain the standard for treating the relapse of T-ALL.
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Affiliation(s)
- Marta Weronika Lato
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland; (M.W.L.); (A.P.); (S.G.)
| | - Anna Przysucha
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland; (M.W.L.); (A.P.); (S.G.)
| | - Sylwia Grosman
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland; (M.W.L.); (A.P.); (S.G.)
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Monika Lejman
- Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
- Correspondence:
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14
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Mroczek A, Zawitkowska J, Kowalczyk J, Lejman M. Comprehensive Overview of Gene Rearrangements in Childhood T-Cell Acute Lymphoblastic Leukaemia. Int J Mol Sci 2021; 22:E808. [PMID: 33467425 PMCID: PMC7829804 DOI: 10.3390/ijms22020808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/11/2022] Open
Abstract
Acute lymphoblastic leukaemia (ALL) is a relevant form of childhood neoplasm, as it accounts for over 80% of all leukaemia cases. T-cell ALL constitutes a genetically heterogeneous cancer derived from T-lymphoid progenitors. The diagnosis of T-ALL is based on morphologic, immunophenotypic, cytogenetic, and molecular features, thus the results are used for patient stratification. Due to the expression of surface and intracellular antigens, several subtypes of T-ALL can be distinguished. Although the aetiology of T-ALL remains unclear, a wide spectrum of rearrangements and mutations affecting crucial signalling pathways has been described so far. Due to intensive chemotherapy regimens and supportive care, overall cure rates of more than 80% in paediatric T-ALL patients have been accomplished. However, improved knowledge of the mechanisms of relapse, drug resistance, and determination of risk factors are crucial for patients in the high-risk group. Even though some residual disease studies have allowed the optimization of therapy, the identification of novel diagnostic and prognostic markers is required to individualize therapy. The following review summarizes our current knowledge about genetic abnormalities in paediatric patients with T-ALL. As molecular biology techniques provide insights into the biology of cancer, our study focuses on new potential therapeutic targets and predictive factors which may improve the outcome of young patients with T-ALL.
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Affiliation(s)
- Anna Mroczek
- Department of Paediatric Haematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland; (A.M.); (J.Z.); (J.K.)
| | - Joanna Zawitkowska
- Department of Paediatric Haematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland; (A.M.); (J.Z.); (J.K.)
| | - Jerzy Kowalczyk
- Department of Paediatric Haematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland; (A.M.); (J.Z.); (J.K.)
| | - Monika Lejman
- Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
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15
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Sentís I, Gonzalez S, Genescà E, García-Hernández V, Muiños F, Gonzalez C, López-Arribillaga E, Gonzalez J, Fernandez-Ibarrondo L, Mularoni L, Espinosa L, Bellosillo B, Ribera JM, Bigas A, Gonzalez-Perez A, Lopez-Bigas N. The evolution of relapse of adult T cell acute lymphoblastic leukemia. Genome Biol 2020; 21:284. [PMID: 33225950 PMCID: PMC7682094 DOI: 10.1186/s13059-020-02192-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent. A higher percentage of the adult patients relapse, compared to children. It is thus essential to study the mechanisms of relapse of adult T-ALL cases. RESULTS We profile whole-genome somatic mutations of 19 primary T-ALLs from adult patients and the corresponding relapse malignancies and analyze their evolution upon treatment in comparison with 238 pediatric and young adult ALL cases. We compare the mutational processes and driver mutations active in primary and relapse adult T-ALLs with those of pediatric patients. A precise estimation of clock-like mutations in leukemic cells shows that the emergence of the relapse clone occurs several months before the diagnosis of the primary T-ALL. Specifically, through the doubling time of the leukemic population, we find that in at least 14 out of the 19 patients, the population of relapse leukemia present at the moment of diagnosis comprises more than one but fewer than 108 blasts. Using simulations, we show that in all patients the relapse appears to be driven by genetic mutations. CONCLUSIONS The early appearance of a population of leukemic cells with genetic mechanisms of resistance across adult T-ALL cases constitutes a challenge for treatment. Improving early detection of the malignancy is thus key to prevent its relapse.
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Affiliation(s)
- Inés Sentís
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Santiago Gonzalez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Eulalia Genescà
- Hematology Departments, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Violeta García-Hernández
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques, CIBERONC, Barcelona, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Celia Gonzalez
- Hematology Departments, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Erika López-Arribillaga
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jessica Gonzalez
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques, CIBERONC, Barcelona, Spain
| | | | - Loris Mularoni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- CMR[B] Center of Regenerative Medicine, Barcelona, Spain
| | - Lluís Espinosa
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques, CIBERONC, Barcelona, Spain
| | - Beatriz Bellosillo
- Pathology Department, CIBERONC, Hospital del Mar, IMIM, Barcelona, Spain
| | - Josep-Maria Ribera
- Hematology Departments, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Anna Bigas
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques, CIBERONC, Barcelona, Spain
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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16
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Vincristine and prednisone regulates cellular and exosomal miR-181a expression differently within the first time diagnosed and the relapsed leukemia B cells. Leuk Res Rep 2020; 14:100221. [PMID: 33094092 PMCID: PMC7568182 DOI: 10.1016/j.lrr.2020.100221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022] Open
Abstract
We explored the effect of vincristine and prednisone on cellular and exosomal miR-181a expression in first time diagnosed leukemia and relapsed leukemia. Vincristine and prednisone induced apoptosis/pro-apoptotic genes in first time diagnosed leukemia, and suppressed the cellular and exosomal miR-181a expression. In contrast, vincristine and prednisone could not induce apoptosis/pro-apoptotic genes in relapsed leukemia, and could not change the expression of cellular or exosomal miR-181a. In conclusion, the non-suppressive nature of miR-181a in relapsed leukemia might contribute to the chemo-resistance and this suggests a potential role of miR-181a-inhibitor along with the chemotherapy in the treatment of relapsed leukemia.
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17
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Oshima K, Zhao J, Pérez-Durán P, Brown JA, Patiño-Galindo JA, Chu T, Quinn A, Gunning T, Belver L, Ambesi-Impiombato A, Tosello V, Wang Z, Sulis ML, Kato M, Koh K, Paganin M, Basso G, Balbin M, Nicolas C, Gastier-Foster JM, Devidas M, Loh ML, Paietta E, Tallman MS, Rowe JM, Litzow M, Minden MD, Meijerink J, Rabadan R, Ferrando A. Mutational and functional genetics mapping of chemotherapy resistance mechanisms in relapsed acute lymphoblastic leukemia. ACTA ACUST UNITED AC 2020; 1:1113-1127. [PMID: 33796864 DOI: 10.1038/s43018-020-00124-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multi-agent combination chemotherapy can be curative in acute lymphoblastic leukemia (ALL). Still, patients with primary refractory disease or with relapsed leukemia have a very poor prognosis. Here we integrate an in-depth dissection of the mutational landscape across diagnostic and relapsed pediatric and adult ALL samples with genome-wide CRISPR screen analysis of gene-drug interactions across seven ALL chemotherapy drugs. By combining these analyses, we uncover diagnostic and relapse-specific mutational mechanisms as well as genetic drivers of chemoresistance. Functionally, our data identifies common and drug-specific pathways modulating chemotherapy response and underscores the effect of drug combinations in restricting the selection of resistance-driving genetic lesions. In addition, by identifying actionable targets for the reversal of chemotherapy resistance, these analyses open novel therapeutic opportunities for the treatment of relapse and refractory disease.
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Affiliation(s)
- Koichi Oshima
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,These authors contributed equally: Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown
| | - Junfei Zhao
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA.,These authors contributed equally: Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown
| | - Pablo Pérez-Durán
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,These authors contributed equally: Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown
| | - Jessie A Brown
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,These authors contributed equally: Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown
| | - Juan Angel Patiño-Galindo
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Timothy Chu
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Aidan Quinn
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Thomas Gunning
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Laura Belver
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Alberto Ambesi-Impiombato
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,Present address: PsychoGenics, Paramus, NJ, USA
| | | | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - Maria Luisa Sulis
- Department of Pediatric Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Motohiro Kato
- Department of Hematology-Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Katsuyoshi Koh
- Department of Hematology-Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Maddalena Paganin
- Fondazione Città della Speranza, Istituto di Ricerca Pediatrica, Padova, Italy.,Haematology-Oncology Division, Department of Woman's and Child's Health, University Hospital of Padua, Padua, Italy
| | - Giuseppe Basso
- Haematology-Oncology Division, Department of Woman's and Child's Health, University Hospital of Padua, Padua, Italy.,Present address: IIGM Italian Institute of Genomic Medicine, Turin, Italy
| | - Milagros Balbin
- Molecular Oncology Laboratory, Instituto Universitario de Oncologia del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Concepcion Nicolas
- Hematology Service, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Julie M Gastier-Foster
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Departments of Pathology and Pediatrics, Ohio State University School of Medicine, Columbus, OH, USA.,Children's Oncology Group, Arcadia, CA, USA
| | - Meenakshi Devidas
- Department of Biostatistics, University of Florida, Gainesville, FL, USA.,Present address: Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | | | - Martin S Tallman
- Department of Hematologic Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Mark D Minden
- Department of Oncology/Hematology, Princess Margaret Cancer Center, Toronto, ON, Canada
| | - Jules Meijerink
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Raul Rabadan
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.,Department of Pediatrics, Columbia University, New York, NY, USA
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18
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Determination of NUDT15 variants by targeted sequencing can identify compound heterozygosity in pediatric acute lymphoblastic leukemia patients. Sci Rep 2020; 10:14400. [PMID: 32873882 PMCID: PMC7463237 DOI: 10.1038/s41598-020-71468-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
Mercaptopurine intolerance is an adverse effect of mercaptopurine administration in pediatric acute lymphoblastic leukemia. Recently, NUDT15 variants were identified as a major determinant of mercaptopurine intolerance. Two NUDT15 variants, c.36_37insGGAGTC and c.415C > T, are located on exons 1 and 3, respectively. Patients with heterozygous c.36_37insGGAGTC and c.415C > T can be either compound heterozygous with two variants on different alleles or heterozygous with both variants on the same allele. Because patients with biallelic NUDT15 variants are extremely sensitive to mercaptopurine, clinical identification of NUDT15 diplotype would be advantageous. A cohort of 37 patients with c.36_37insGGAGTC and c.415C > T NUDT15 variants were selected for haplotyping by targeted sequencing. NUDT15 complementary DNA was amplified and sequenced by 300-bp paired-end sequencing on Illumina MiSeq. Of the 37 patients carrying NUDT15 variants, 35 had heterozygous NUDT15*1/*2 variants and two had compound heterozygous NUDT15*3/*6 and NUDT15*2/*7 variants. These two patients with compound heterozygous variants could only tolerate low doses of mercaptopurine, similar to patients with homozygous NUDT15 variants. Targeted sequencing of NUDT15 cDNA can be used to determine NUDT15 diplotype and identify patients with compound heterozygous NUDT15 variants.
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19
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Wandler AM, Huang BJ, Craig JW, Hayes K, Yan H, Meyer LK, Scacchetti A, Monsalve G, Dail M, Li Q, Wong JC, Weinberg O, Hasserjian RP, Kogan SC, Jonsson P, Yamamoto K, Sampath D, Nakitandwe J, Downing JR, Zhang J, Aster JC, Taylor BS, Shannon K. Loss of glucocorticoid receptor expression mediates in vivo dexamethasone resistance in T-cell acute lymphoblastic leukemia. Leukemia 2020; 34:2025-2037. [PMID: 32066867 PMCID: PMC7440098 DOI: 10.1038/s41375-020-0748-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/31/2020] [Accepted: 02/06/2020] [Indexed: 02/08/2023]
Abstract
Despite decades of clinical use, mechanisms of glucocorticoid resistance are poorly understood. We treated primary murine T lineage acute lymphoblastic leukemias (T-ALLs) with the glucocorticoid dexamethasone (DEX) alone and in combination with the pan-PI3 kinase inhibitor GDC-0941 and observed a robust response to DEX that was modestly enhanced by GDC-0941. Continuous in vivo treatment invariably resulted in outgrowth of drug-resistant clones, ~30% of which showed markedly reduced glucocorticoid receptor (GR) protein expression. A similar proportion of relapsed human T-ALLs also exhibited low GR protein levels. De novo or preexisting mutations in the gene encoding GR (Nr3c1) occurred in relapsed clones derived from multiple independent parental leukemias. CRISPR/Cas9 gene editing confirmed that loss of GR expression confers DEX resistance. Exposing drug-sensitive T-ALLs to DEX in vivo altered transcript levels of multiple genes, and this response was attenuated in relapsed T-ALLs. These data implicate reduced GR protein expression as a frequent cause of glucocorticoid resistance in T-ALL.
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Affiliation(s)
- Anica M Wandler
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Benjamin J Huang
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Jeffrey W Craig
- Department of Pathology, Brigham & Women's Hospital, Boston, MA, USA
| | - Kathryn Hayes
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Hannah Yan
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Lauren K Meyer
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Alessandro Scacchetti
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Gabriela Monsalve
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Monique Dail
- Department of Translational Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Qing Li
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jasmine C Wong
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Olga Weinberg
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | | | - Scott C Kogan
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Philip Jonsson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Keith Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Deepak Sampath
- Department of Translational Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Joy Nakitandwe
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jon C Aster
- Department of Pathology, Brigham & Women's Hospital, Boston, MA, USA
| | - Barry S Taylor
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevin Shannon
- Department of Pediatrics, University of California, San Francisco, CA, USA.
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20
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Barz MJ, Hof J, Groeneveld-Krentz S, Loh JW, Szymansky A, Astrahantseff K, von Stackelberg A, Khiabanian H, Ferrando AA, Eckert C, Kirschner-Schwabe R. Subclonal NT5C2 mutations are associated with poor outcomes after relapse of pediatric acute lymphoblastic leukemia. Blood 2020; 135:921-933. [PMID: 31971569 PMCID: PMC7218751 DOI: 10.1182/blood.2019002499] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/28/2019] [Indexed: 12/27/2022] Open
Abstract
Activating mutations in cytosolic 5'-nucleotidase II (NT5C2) are considered to drive relapse formation in acute lymphoblastic leukemia (ALL) by conferring purine analog resistance. To examine the clinical effects of NT5C2 mutations in relapsed ALL, we analyzed NT5C2 in 455 relapsed B-cell precursor ALL patients treated within the ALL-REZ BFM 2002 relapse trial using sequencing and sensitive allele-specific real-time polymerase chain reaction. We detected 110 NT5C2 mutations in 75 (16.5%) of 455 B-cell precursor ALL relapses. Two-thirds of relapses harbored subclonal mutations and only one-third harbored clonal mutations. Event-free survival after relapse was inferior in patients with relapses with clonal and subclonal NT5C2 mutations compared with those without (19% and 25% vs 53%, P < .001). However, subclonal, but not clonal, NT5C2 mutations were associated with reduced event-free survival in multivariable analysis (hazard ratio, 1.89; 95% confidence interval, 1.28-2.69; P = .001) and with an increased rate of nonresponse to relapse treatment (subclonal 32%, clonal 12%, wild type 9%, P < .001). Nevertheless, 27 (82%) of 33 subclonal NT5C2 mutations became undetectable at the time of nonresponse or second relapse, and in 10 (71%) of 14 patients subclonal NT5C2 mutations were undetectable already after relapse induction treatment. These results show that subclonal NT5C2 mutations define relapses associated with high risk of treatment failure in patients and at the same time emphasize that their role in outcome is complex and goes beyond mutant NT5C2 acting as a targetable driver during relapse progression. Sensitive, prospective identification of NT5C2 mutations is warranted to improve the understanding and treatment of this aggressive ALL relapse subtype.
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Affiliation(s)
- Malwine J Barz
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
| | - Jana Hof
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
| | - Stefanie Groeneveld-Krentz
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
| | - Jui Wan Loh
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ
- Graduate Program in Microbiology and Molecular Genetics, Rutgers University, Piscataway, NJ
| | - Annabell Szymansky
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Kathy Astrahantseff
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
| | - Arend von Stackelberg
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
| | - Hossein Khiabanian
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ
- Graduate Program in Microbiology and Molecular Genetics, Rutgers University, Piscataway, NJ
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ
| | - Adolfo A Ferrando
- Institute of Cancer Genetics, Columbia University, New York, NY; and
| | - Cornelia Eckert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Renate Kirschner-Schwabe
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
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21
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Sanders AD, Meiers S, Ghareghani M, Porubsky D, Jeong H, van Vliet MACC, Rausch T, Richter-Pechańska P, Kunz JB, Jenni S, Bolognini D, Longo GMC, Raeder B, Kinanen V, Zimmermann J, Benes V, Schrappe M, Mardin BR, Kulozik AE, Bornhauser B, Bourquin JP, Marschall T, Korbel JO. Single-cell analysis of structural variations and complex rearrangements with tri-channel processing. Nat Biotechnol 2020; 38:343-354. [PMID: 31873213 PMCID: PMC7612647 DOI: 10.1038/s41587-019-0366-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023]
Abstract
Structural variation (SV), involving deletions, duplications, inversions and translocations of DNA segments, is a major source of genetic variability in somatic cells and can dysregulate cancer-related pathways. However, discovering somatic SVs in single cells has been challenging, with copy-number-neutral and complex variants typically escaping detection. Here we describe single-cell tri-channel processing (scTRIP), a computational framework that integrates read depth, template strand and haplotype phase to comprehensively discover SVs in individual cells. We surveyed SV landscapes of 565 single cells, including transformed epithelial cells and patient-derived leukemic samples, to discover abundant SV classes, including inversions, translocations and complex DNA rearrangements. Analysis of the leukemic samples revealed four times more somatic SVs than cytogenetic karyotyping, submicroscopic copy-number alterations, oncogenic copy-neutral rearrangements and a subclonal chromothripsis event. Advancing current methods, single-cell tri-channel processing can directly measure SV mutational processes in individual cells, such as breakage-fusion-bridge cycles, facilitating studies of clonal evolution, genetic mosaicism and SV formation mechanisms, which could improve disease classification for precision medicine.
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Affiliation(s)
- Ashley D Sanders
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Sascha Meiers
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maryam Ghareghani
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarbrücken, Germany
- Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | - David Porubsky
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Hyobin Jeong
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | | | - Tobias Rausch
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - Paulina Richter-Pechańska
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Joachim B Kunz
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Silvia Jenni
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Davide Bolognini
- European Molecular Biology Laboratory, Genomics Core Facility, Heidelberg, Germany
| | - Gabriel M C Longo
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Benjamin Raeder
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Venla Kinanen
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jürgen Zimmermann
- European Molecular Biology Laboratory, Genomics Core Facility, Heidelberg, Germany
| | - Vladimir Benes
- European Molecular Biology Laboratory, Genomics Core Facility, Heidelberg, Germany
| | - Martin Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Balca R Mardin
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- BioMed X Innovation Center, Heidelberg, Germany
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Beat Bornhauser
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Jean-Pierre Bourquin
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Tobias Marschall
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.
- Max Planck Institute for Informatics, Saarbrücken, Germany.
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.
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22
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Aberuyi N, Rahgozar S, Ghodousi ES, Ghaedi K. Drug Resistance Biomarkers and Their Clinical Applications in Childhood Acute Lymphoblastic Leukemia. Front Oncol 2020; 9:1496. [PMID: 32010613 PMCID: PMC6978753 DOI: 10.3389/fonc.2019.01496] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022] Open
Abstract
Biomarkers are biological molecules found in body fluids or tissues, which can be considered as indications of a normal or abnormal process, or of a condition or disease. There are various types of biomarkers based on their application and molecular alterations. Treatment-sensitivity or drug resistance biomarkers include prognostic and predictive molecules with utmost importance in selecting appropriate treatment protocols and improving survival rates. Acute lymphoblastic leukemia (ALL) is the most prevalent hematological malignancy diagnosed in children with nearly 80% cure rate. Despite the favorable survival rates of childhood ALL (chALL), resistance to chemotherapeutic agents and, as a consequence, a dismal prognosis develops in a significant number of patients. Therefore, there are urgent needs to have robust, sensitive, and disease-specific molecular prognostic and predictive biomarkers, which could allow better risk classification and then better clinical results. In this article, we review the currently known drug resistance biomarkers, including somatic or germ line nucleic acids, epigenetic alterations, protein expressions and metabolic variations. Moreover, biomarkers with potential clinical applications are discussed.
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Affiliation(s)
- Narges Aberuyi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Soheila Rahgozar
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Elaheh Sadat Ghodousi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Kamran Ghaedi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
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23
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Roh V, Abramowski P, Hiou-Feige A, Cornils K, Rivals JP, Zougman A, Aranyossy T, Thielecke L, Truan Z, Mermod M, Monnier Y, Prassolov V, Glauche I, Nowrouzi A, Abdollahi A, Fehse B, Simon C, Tolstonog GV. Cellular Barcoding Identifies Clonal Substitution as a Hallmark of Local Recurrence in a Surgical Model of Head and Neck Squamous Cell Carcinoma. Cell Rep 2019; 25:2208-2222.e7. [PMID: 30463016 DOI: 10.1016/j.celrep.2018.10.090] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/04/2018] [Accepted: 10/24/2018] [Indexed: 01/04/2023] Open
Abstract
Local recurrence after surgery for head and neck squamous cell carcinoma (HNSCC) remains a common event associated with a dismal prognosis. Improving this outcome requires a better understanding of cancer cell populations that expand from postsurgical minimal residual disease (MRD). Therefore, we assessed clonal dynamics in a surgical model of barcoded HNSCC growing in the submental region of immunodeficient mice. Clonal substitution and massive reduction of clonal heterogeneity emerged as hallmarks of local recurrence, as the clones dominating in less heterogeneous recurrences were scarce in their matched primary tumors. These lineages were selected by their ability to persist after surgery and competitively expand from MRD. Clones enriched in recurrences exhibited both private and shared genetic features and likely originated from ancestors shared with clones dominating in primary tumors. They demonstrated high invasiveness and epithelial-to-mesenchymal transition, eventually providing an attractive target for obtaining better local control for these tumors.
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Affiliation(s)
- Vincent Roh
- Department of Otolaryngology - Head and Neck Surgery, University Hospital of Lausanne, Lausanne, Switzerland
| | - Pierre Abramowski
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Agnès Hiou-Feige
- Department of Otolaryngology - Head and Neck Surgery, University Hospital of Lausanne, Lausanne, Switzerland
| | - Kerstin Cornils
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Jean-Paul Rivals
- Department of Otolaryngology - Head and Neck Surgery, University Hospital of Lausanne, Lausanne, Switzerland
| | - Alexandre Zougman
- Clinical and Biomedical Proteomics Group, Cancer Research UK Centre, Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, UK
| | - Tim Aranyossy
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Lars Thielecke
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustave Carus, Technische Universität Dresden, Dresden, Germany
| | - Zinnia Truan
- Department of Otolaryngology - Head and Neck Surgery, University Hospital of Lausanne, Lausanne, Switzerland
| | - Maxime Mermod
- Department of Otolaryngology - Head and Neck Surgery, University Hospital of Lausanne, Lausanne, Switzerland
| | - Yan Monnier
- Department of Otolaryngology - Head and Neck Surgery, University Hospital of Lausanne, Lausanne, Switzerland
| | - Vladimir Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustave Carus, Technische Universität Dresden, Dresden, Germany
| | - Ali Nowrouzi
- German Cancer Consortium (DKTK), Translational Radiation Oncology, German Cancer Research Center (DKFZ), Core Center Heidelberg, Heidelberg, Germany; Division of Molecular and Translational Radiation Oncology, Heidelberg University Hospital (UKHD) and DKFZ, Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Amir Abdollahi
- German Cancer Consortium (DKTK), Translational Radiation Oncology, German Cancer Research Center (DKFZ), Core Center Heidelberg, Heidelberg, Germany; Division of Molecular and Translational Radiation Oncology, Heidelberg University Hospital (UKHD) and DKFZ, Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Boris Fehse
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.
| | - Christian Simon
- Department of Otolaryngology - Head and Neck Surgery, University Hospital of Lausanne, Lausanne, Switzerland.
| | - Genrich V Tolstonog
- Department of Otolaryngology - Head and Neck Surgery, University Hospital of Lausanne, Lausanne, Switzerland.
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24
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The effect of co-occurring lesions on leukaemogenesis and drug response in T-ALL and ETP-ALL. Br J Cancer 2019; 122:455-464. [PMID: 31792348 PMCID: PMC7028932 DOI: 10.1038/s41416-019-0647-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/14/2019] [Accepted: 10/30/2019] [Indexed: 01/27/2023] Open
Abstract
Despite advances in the management of acute lymphoblastic leukaemia (ALL), current regimens fail to significantly transform outcomes for patients with high-risk subtypes. Advances in genomic analyses have identified novel lesions including mutations in genes that encode chromatin modifiers and those that influence cytokine and kinase signalling, rendering many of these alterations potentially targetable by tyrosine kinase and epigenetic inhibitors currently in clinical use. Although specific genomic lesions, gene expression patterns, and immunophenotypic profiles have been associated with specific clinical outcomes in some cancers, the application of precision medicine approaches based on these data has been slow. This approach is complicated by the reality that patients often harbour multiple mutations, and in many cases, the precise functional significance and interaction of these mutations in driving leukaemia and drug responsiveness/resistance remains unknown. Given that signalling pathways driving leukaemic pathogenesis could plausibly result from the co-existence of specific lesions and the resultant perturbation of protein interactions, the use of combined therapeutics that target multiple aberrant pathways, according to an individual’s mutational profile, might improve outcomes and lower a patient’s risk of relapse. Here we outline the genomic alterations that occur in T cell ALL (T-ALL) and early T cell precursor (ETP)-ALL and review studies highlighting the possible effects of co-occurring lesions on leukaemogenesis and drug response.
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25
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van der Zwet JCG, Cordo' V, Canté-Barrett K, Meijerink JPP. Multi-omic approaches to improve outcome for T-cell acute lymphoblastic leukemia patients. Adv Biol Regul 2019; 74:100647. [PMID: 31523030 DOI: 10.1016/j.jbior.2019.100647] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/20/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
In the last decade, tremendous progress in curative treatment has been made for T-ALL patients using high-intensive, risk-adapted multi-agent chemotherapy. Further treatment intensification to improve the cure rate is not feasible as it will increase the number of toxic deaths. Hence, about 20% of pediatric patients relapse and often die due to acquired therapy resistance. Personalized medicine is of utmost importance to further increase cure rates and is achieved by targeting specific initiation, maintenance or resistance mechanisms of the disease. Genomic sequencing has revealed mutations that characterize genetic subtypes of many cancers including T-ALL. However, leukemia may have various activated pathways that are not accompanied by the presence of mutations. Therefore, screening for mutations alone is not sufficient to identify all molecular targets and leukemic dependencies for therapeutic inhibition. We review the extent of the driving type A and the secondary type B genomic mutations in pediatric T-ALL that may be targeted by specific inhibitors. Additionally, we review the need for additional screening methods on the transcriptional and protein levels. An integrated 'multi-omic' screening will identify potential targets and biomarkers to establish significant progress in future individualized treatment of T-ALL patients.
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Affiliation(s)
| | - Valentina Cordo'
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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26
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Structural insights into mutagenicity of anticancer nucleoside analog cytarabine during replication by DNA polymerase η. Sci Rep 2019; 9:16400. [PMID: 31704958 PMCID: PMC6841716 DOI: 10.1038/s41598-019-52703-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/22/2019] [Indexed: 01/08/2023] Open
Abstract
Cytarabine (AraC) is the mainstay chemotherapy for acute myeloid leukemia (AML). Whereas initial treatment with AraC is usually successful, most AML patients tend to relapse, and AraC treatment-induced mutagenesis may contribute to the development of chemo-resistant leukemic clones. We show here that whereas the high-fidelity replicative polymerase Polδ is blocked in the replication of AraC, the lower-fidelity translesion DNA synthesis (TLS) polymerase Polη is proficient, inserting both correct and incorrect nucleotides opposite a template AraC base. Furthermore, we present high-resolution crystal structures of human Polη with a template AraC residue positioned opposite correct (G) and incorrect (A) incoming deoxynucleotides. We show that Polη can accommodate local perturbation caused by the AraC via specific hydrogen bonding and maintain a reaction-ready active site alignment for insertion of both correct and incorrect incoming nucleotides. Taken together, the structures provide a novel basis for the ability of Polη to promote AraC induced mutagenesis in relapsed AML patients.
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27
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Yoon JH, Roy Choudhury J, Prakash L, Prakash S. Translesion synthesis DNA polymerases η, ι, and ν promote mutagenic replication through the anticancer nucleoside cytarabine. J Biol Chem 2019; 294:19048-19054. [PMID: 31685662 DOI: 10.1074/jbc.ra119.011381] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/30/2019] [Indexed: 11/06/2022] Open
Abstract
Cytarabine (AraC) is the mainstay for the treatment of acute myeloid leukemia. Although complete remission is observed in a large proportion of patients, relapse occurs in almost all the cases. The chemotherapeutic action of AraC derives from its ability to inhibit DNA synthesis by the replicative polymerases (Pols); the replicative Pols can insert AraCTP at the 3' terminus of the nascent DNA strand, but they are blocked at extending synthesis from AraC. By extending synthesis from the 3'-terminal AraC and by replicating through AraC that becomes incorporated into DNA, translesion synthesis (TLS) DNA Pols could reduce the effectiveness of AraC in chemotherapy. Here we identify the TLS Pols required for replicating through the AraC templating residue and determine their error-proneness. We provide evidence that TLS makes a consequential contribution to the replication of AraC-damaged DNA; that TLS through AraC is conducted by three different pathways dependent upon Polη, Polι, and Polν, respectively; and that TLS by all these Pols incurs considerable mutagenesis. The prominent role of TLS in promoting proficient and mutagenic replication through AraC suggests that TLS inhibition in acute myeloid leukemia patients would increase the effectiveness of AraC chemotherapy; and by reducing mutation formation, TLS inhibition may dampen the emergence of drug-resistant tumors and thereby the high incidence of relapse in AraC-treated patients.
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Affiliation(s)
- Jung-Hoon Yoon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555
| | - Jayati Roy Choudhury
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555
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28
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Pediatric ALL relapses after allo-SCT show high individuality, clonal dynamics, selective pressure, and druggable targets. Blood Adv 2019; 3:3143-3156. [PMID: 31648313 DOI: 10.1182/bloodadvances.2019000051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/08/2019] [Indexed: 12/11/2022] Open
Abstract
Survival of patients with pediatric acute lymphoblastic leukemia (ALL) after allogeneic hematopoietic stem cell transplantation (allo-SCT) is mainly compromised by leukemia relapse, carrying dismal prognosis. As novel individualized therapeutic approaches are urgently needed, we performed whole-exome sequencing of leukemic blasts of 10 children with post-allo-SCT relapses with the aim of thoroughly characterizing the mutational landscape and identifying druggable mutations. We found that post-allo-SCT ALL relapses display highly diverse and mostly patient-individual genetic lesions. Moreover, mutational cluster analysis showed substantial clonal dynamics during leukemia progression from initial diagnosis to relapse after allo-SCT. Only very few alterations stayed constant over time. This dynamic clonality was exemplified by the detection of thiopurine resistance-mediating mutations in the nucleotidase NT5C2 in 3 patients' first relapses, which disappeared in the post-allo-SCT relapses on relief of selective pressure of maintenance chemotherapy. Moreover, we identified TP53 mutations in 4 of 10 patients after allo-SCT, reflecting acquired chemoresistance associated with selective pressure of prior antineoplastic treatment. Finally, in 9 of 10 children's post-allo-SCT relapse, we found alterations in genes for which targeted therapies with novel agents are readily available. We could show efficient targeting of leukemic blasts by APR-246 in 2 patients carrying TP53 mutations. Our findings shed light on the genetic basis of post-allo-SCT relapse and may pave the way for unraveling novel therapeutic strategies in this challenging situation.
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29
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Richter-Pechańska P, Kunz JB, Bornhauser B, von Knebel Doeberitz C, Rausch T, Erarslan-Uysal B, Assenov Y, Frismantas V, Marovca B, Waszak SM, Zimmermann M, Seemann J, Happich M, Stanulla M, Schrappe M, Cario G, Escherich G, Bakharevich K, Kirschner-Schwabe R, Eckert C, Muckenthaler MU, Korbel JO, Bourquin JP, Kulozik AE. PDX models recapitulate the genetic and epigenetic landscape of pediatric T-cell leukemia. EMBO Mol Med 2019; 10:emmm.201809443. [PMID: 30389682 PMCID: PMC6284381 DOI: 10.15252/emmm.201809443] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We compared 24 primary pediatric T‐cell acute lymphoblastic leukemias (T‐ALL) collected at the time of initial diagnosis and relapse from 12 patients and 24 matched patient‐derived xenografts (PDXs). DNA methylation profile was preserved in PDX mice in 97.5% of the promoters (ρ = 0.99). Similarly, the genome‐wide chromatin accessibility (ATAC‐Seq) was preserved remarkably well (ρ = 0.96). Interestingly, both the ATAC regions, which showed a significant decrease in accessibility in PDXs and the regions hypermethylated in PDXs, were associated with immune response, which might reflect the immune deficiency of the mice and potentially the incomplete interaction between murine cytokines and human receptors. The longitudinal approach of this study allowed an observation that samples collected from patients who developed a type 1 relapse (clonal mutations maintained at relapse) preserved their genomic composition; whereas in patients who developed a type 2 relapse (subset of clonal mutations lost at relapse), the preservation of the leukemia's composition was more variable. In sum, this study underlines the remarkable genomic stability, and for the first time documents the preservation of the epigenomic landscape in T‐ALL‐derived PDX models.
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Affiliation(s)
- Paulina Richter-Pechańska
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Joachim B Kunz
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Beat Bornhauser
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Caroline von Knebel Doeberitz
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Tobias Rausch
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Büşra Erarslan-Uysal
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Yassen Assenov
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Viktoras Frismantas
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Blerim Marovca
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | | | - Martin Zimmermann
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Julia Seemann
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Margit Happich
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Martin Stanulla
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Martin Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gunnar Cario
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gabriele Escherich
- Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kseniya Bakharevich
- Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Renate Kirschner-Schwabe
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Cornelia Eckert
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Martina U Muckenthaler
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Jan O Korbel
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jean-Pierre Bourquin
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany .,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
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30
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Strategies to Overcome Resistance Mechanisms in T-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2019; 20:ijms20123021. [PMID: 31226848 PMCID: PMC6627878 DOI: 10.3390/ijms20123021] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/20/2022] Open
Abstract
Chemoresistance is a major cause of recurrence and death from T-cell acute lymphoblastic leukemia (T-ALL), both in adult and pediatric patients. In the majority of cases, drug-resistant disease is treated by selecting a combination of other drugs, without understanding the molecular mechanisms by which malignant cells escape chemotherapeutic treatments, even though a more detailed genomic characterization and the identification of actionable disease targets may enable informed decision of new agents to improve patient outcomes. In this work, we describe pathways of resistance to common chemotherapeutic agents including glucocorticoids and review the resistance mechanisms to targeted therapy such as IL7R, PI3K-AKT-mTOR, NOTCH1, BRD4/MYC, Cyclin D3: CDK4/CDK6, BCL2 inhibitors, and selective inhibitors of nuclear export (SINE). Finally, to overcome the limitations of the current trial-and-error method, we summarize the experiences of anti-cancer drug sensitivity resistance profiling (DSRP) approaches as a rapid and relevant strategy to infer drug activity and provide functional information to assist clinical decision one patient at a time.
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31
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Genetics and mechanisms of NT5C2-driven chemotherapy resistance in relapsed ALL. Blood 2019; 133:2263-2268. [PMID: 30910786 DOI: 10.1182/blood-2019-01-852392] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/18/2019] [Indexed: 01/01/2023] Open
Abstract
Mutations in the cytosolic 5' nucleotidase II (NT5C2) gene drive resistance to thiopurine chemotherapy in relapsed acute lymphoblastic leukemia (ALL). Mechanistically, NT5C2 mutant proteins have increased nucleotidase activity as a result of altered activating and autoregulatory switch-off mechanisms. Leukemias with NT5C2 mutations are chemoresistant to 6-mercaptopurine yet show impaired proliferation and self-renewal. Direct targeting of NT5C2 or inhibition of compensatory pathways active in NT5C2 mutant cells may antagonize the emergence of NT5C2 mutant clones driving resistance and relapse in ALL.
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32
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Jang W, Park J, Kwon A, Choi H, Kim J, Lee GD, Han E, Jekarl DW, Chae H, Han K, Yoon JH, Lee S, Chung NG, Cho B, Kim M, Kim Y. CDKN2B downregulation and other genetic characteristics in T-acute lymphoblastic leukemia. Exp Mol Med 2019; 51:1-15. [PMID: 30635552 PMCID: PMC6329696 DOI: 10.1038/s12276-018-0195-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 01/14/2023] Open
Abstract
We identified principal genetic alterations in 97.1% (99/102) of patients with T-acute lymphoblastic leukemia (T-ALL) using integrative genetic analyses, including massive parallel sequencing and multiplex ligation-dependent probe amplification (MLPA). A total of 133 mutations were identified in the following genes in descending order: NOTCH1 (66.7%), FBXW7 (19.6%), PHF6 (15.7%), RUNX1 (12.7%), NRAS (10.8%), and DNMT3A (9.8%). Copy number alterations were most frequently detected in CDKN2B, CDKN2A, and genes on 9p21.3 in T-ALL (45.1%). Gene expression data demonstrated the downregulation of CDKN2B in most cases of T-ALL, whereas CDKN2A downregulation was mainly restricted to deletions. Additional quantitative methylation analysis demonstrated that CDKN2B downregulation stemmed from deletion and hypermethylation. Analysis of 64 patients with CDKN2B hypermethylation indicated an association with an older age of onset and early T cell precursor ALL, which involved very early arrest of T cell differentiation. Genes associated with methylation and myeloid neoplasms, including DNMT3A and NRAS, were more commonly mutated in T-ALL with CDKN2B hypermethylation. In particular, a CDKN2B biallelic deletion or high methylation level (≥45%), the age of onset, and the GATA3 and SH2B3 mutations were factors associated with a poor prognosis. This study clarifies that one of the most important genetic events in T-ALL, namely, CDKN2B downregulation, occurs mechanistically via deletion and hypermethylation. Different susceptible genetic backgrounds exist based on the CDKN2B downregulation mechanism.
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Affiliation(s)
- Woori Jang
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahlm Kwon
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jiyeon Kim
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Gun Dong Lee
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eunhee Han
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Dong Wook Jekarl
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyojin Chae
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyungja Han
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jae-Ho Yoon
- Department of Hematology, Leukemia Research Institute, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seok Lee
- Department of Hematology, Leukemia Research Institute, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Nack-Gyun Chung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Bin Cho
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea. .,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea. .,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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33
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Kimura S, Seki M, Yoshida K, Shiraishi Y, Akiyama M, Koh K, Imamura T, Manabe A, Hayashi Y, Kobayashi M, Oka A, Miyano S, Ogawa S, Takita J. NOTCH1 pathway activating mutations and clonal evolution in pediatric T-cell acute lymphoblastic leukemia. Cancer Sci 2019; 110:784-794. [PMID: 30387229 PMCID: PMC6361559 DOI: 10.1111/cas.13859] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/31/2022] Open
Abstract
Molecular mechanisms involved in the relapse of T‐cell acute lymphoblastic leukemia (T‐ALL) are not fully understood, although activating NOTCH1 signaling due to NOTCH1/FBXW7 alterations is a major oncogenic driver. To unravel the relevance of NOTCH1/FBXW7 mutations associated with relapse, we performed whole–exome sequencing in 30 pediatric T‐ALL cases, among which 11 diagnosis‐relapse paired cases were further investigated to track the clonal evolution of relapse using amplicon–based deep sequencing. NOTCH1/FBXW7 alterations were detected in 73.3% (diagnosis) and 72.7% (relapse) of cases. Single nucleotide variations in the heterodimerization domain were the most frequent (40.0%) at diagnosis, whereas proline, glutamic acid, serine, threonine–rich (PEST) domain alterations were the most frequent at relapse (54.5%). Comparison between non–relapsed and relapsed cases at diagnosis showed a predominance of PEST alterations in relapsed cases (P = .045), although we failed to validate this in the TARGET cohort. Based on the clonal analysis of diagnosis‐relapse samples, we identified NOTCH1 “switching” characterized by different NOTCH1 mutations in a major clone between diagnosis and relapse samples in 2 out of 11 diagnosis‐relapse paired cases analyzed. We found another NOTCH1 “switching” case in a previously reported Berlin‐Frankfurt‐Münster cohort (n = 13), indicating NOTCH1 importance in both the development and progression of T‐ALL. Despite the limitations of having a small sample size and a non–minimal residual disease–based protocol, our results suggest that the presence of NOTCH1 mutations might contribute to the disease relapse of T‐ALL.
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Affiliation(s)
- Shunsuke Kimura
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Hiroshima University, Hiroshima, Japan
| | - Masafumi Seki
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masaharu Akiyama
- Department of Pediatrics, The Jikei University School of Medicine, Tokyo, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Toshihiko Imamura
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
| | - Atsushi Manabe
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan
| | | | - Masao Kobayashi
- Department of Pediatrics, Hiroshima University, Hiroshima, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Kyoto University, Kyoto, Japan
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34
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Expanding the clinical relevance of the 5'-nucleotidase cN-II/NT5C2. Purinergic Signal 2018; 14:321-329. [PMID: 30362044 DOI: 10.1007/s11302-018-9627-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/20/2018] [Indexed: 12/14/2022] Open
Abstract
Purine metabolism is depending on a large amount of enzymes to ensure cellular homeostasis. Among these enzymes, we have been interested in the 5'-nucleotidase cN-II and its role in cancer biology and in response of cancer cells to treatments. This protein has been cited and studied in a large number of papers published during the last decade for its involvement in non-cancerous pathologies such as hereditary spastic paraplegia, schizophrenia, and blood pressure regulation. Here, we review these articles in order to give an overview of the recently discovered clinical relevance of cN-II.
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35
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Biray Avci C, Goker Bagca B, Tetik Vardarli A, Saydam G, Gunduz C. Epigenetic modifications in chronic myeloid leukemia cells through ruxolitinib treatment. J Cell Biochem 2018; 120:4555-4563. [PMID: 30260022 DOI: 10.1002/jcb.27744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 08/31/2018] [Indexed: 12/28/2022]
Abstract
Chronic myeloid leukemia is a clonal malignancy of hematopoietic stem cell that is characterized by the occurrence of t(9;22)(q34;q11.2) translocation, named Philadelphia chromosome. Ruxolitinib is a powerful Janus tyrosine kinase 1 and 2 inhibitor that is used for myelofibrosis treatment. DNA-histone connection mediates a wide range of genes that code methylation, demethylation, acetylation, deacetylation, ubiquitination, and phosphorylation enzymes. Epigenetic modifications regulate chromatin compactness, which plays pivotal roles in critical biological processes including the transcriptional activity and cell proliferation as well as various pathological mechanisms, including CML. This study is aimed to determine the alterations of the expression levels of epigenetic modification-related genes after ruxolitinib treatment. Total RNA was isolated from K-562 cells treated with the IC50 value of ruxolitinib and untreated K-562 control cells. A reverse transcription procedure was performed for complementary DNA synthesis, and gene expressions were detected by real-time polymerase chain reaction compared with the untreated cells. Ruxolitinib treatment caused a significant alteration in the expression levels of epigenetic regulation-related genes in K-562 cells. Our novel results suggested that ruxolitinib has inhibitor effects on epigenetic modification-regulator genes.
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Affiliation(s)
- Cigir Biray Avci
- Department of Medical Biology, Medical Faculty, Ege University, Izmir, Turkey
| | - Bakiye Goker Bagca
- Department of Medical Biology, Medical Faculty, Ege University, Izmir, Turkey
| | - Asli Tetik Vardarli
- Department of Medical Biology, Medical Faculty, Ege University, Izmir, Turkey
| | - Guray Saydam
- Department of Internal Medicine, Division of Haematology, Medical Faculty, Ege University, Izmir, Turkey
| | - Cumhur Gunduz
- Department of Medical Biology, Medical Faculty, Ege University, Izmir, Turkey
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36
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Senft D, Jeremias I. A rare subgroup of leukemia stem cells harbors relapse-inducing potential in acute lymphoblastic leukemia. Exp Hematol 2018; 69:1-10. [PMID: 30261200 DOI: 10.1016/j.exphem.2018.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/10/2018] [Accepted: 09/18/2018] [Indexed: 01/08/2023]
Abstract
After initially successful chemotherapy, relapse frequently jeopardizes the outcome of patients with acute leukemia. Because of their adverse characteristics of self-renewal and dormancy, leukemia stem cells have been hypothesized to play a critical role in resistance to antiproliferative chemotherapy and the development of relapse. The high abundance of stem-like cells in acute lymphoblastic leukemia (ALL), however, suggests that not all leukemia-initiating cells carry these adverse characteristics, complicating the biological characterization of relapse-inducing cells in this malignancy. Here, we review sources of therapy resistance and relapse in acute leukemias, which include tumor cell plasticity and reversible characteristics. We discuss the development of patient-derived mouse models that are genetically engineered to mimic long-term dormancy and minimal residual disease in patients. These models allow the tracking and functional characterization of patient-derived ALL blasts that combine the properties of long-term dormancy, treatment resistance, and stemness. Finally, we discuss possible therapeutic avenues to target the functional plasticity of leukemia-initiating cells in ALL.
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Affiliation(s)
- Daniela Senft
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, German Center for Environmental Health (HMGU), Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, German Center for Environmental Health (HMGU), Munich, Germany; Department of Pediatrics, Dr. von Hauner Childrens Hospital, Ludwig Maximilians University, Munich, Germany; German Consortium for Translational Cancer Research (DKTK), Partnering Site Munich, Munich, Germany.
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37
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Nair RR, Piktel D, Geldenhuys WJ, Gibson LF. Combination of cabazitaxel and plicamycin induces cell death in drug resistant B-cell acute lymphoblastic leukemia. Leuk Res 2018; 72:59-66. [PMID: 30103201 DOI: 10.1016/j.leukres.2018.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/31/2018] [Accepted: 08/05/2018] [Indexed: 01/17/2023]
Abstract
Bone marrow microenvironment mediated downregulation of BCL6 is critical for maintaining cell quiescence and modulating therapeutic response in B-cell acute lymphoblastic leukemia (ALL). In the present study, we have performed a high throughput cell death assay using BCL6 knockdown REH ALL cell line to screen a library of FDA-approved oncology drugs. In the process, we have identified a microtubule inhibitor, cabazitaxel (CAB), and a RNA synthesis inhibitor, plicamycin (PLI) as potential anti-leukemic agents. CAB and PLI inhibited cell proliferation in not only the BCL6 knockdown REH cell line, but also six other ALL cell lines. Furthermore, combination of CAB and PLI had a synergistic effect in inhibiting proliferation in a cytarabine-resistant (REH/Ara-C) ALL cell line. Use of nanoparticles for delivery of CAB and PLI demonstrated that the combination was very effective when tested in a co-culture model that mimics the in vivo bone marrow microenvironment that typically supports ALL cell survival and migration into protective niches. Furthermore, exposure to PLI inhibited SOX2 transcription and exposure to CAB inhibited not only Mcl-1 expression but also chemotaxis in ALL cells. Taken together, our study demonstrates the utility of concomitantly targeting different critical regulatory pathways to induce cell death in drug resistant ALL cells.
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Affiliation(s)
- Rajesh R Nair
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, United States
| | - Debbie Piktel
- Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, United States
| | - Werner J Geldenhuys
- Department of Pharmaceutical Sciences, School of Pharmacy, and WVU Cancer Institute, West Virginia University, Morgantown, WV, United States
| | - Laura F Gibson
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, United States; Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, United States; WVU Cancer Institute, West Virginia University, Morgantown, WV, United States.
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38
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Ramos KN, Ramos IN, Zeng Y, Ramos KS. Genetics and epigenetics of pediatric leukemia in the era of precision medicine. F1000Res 2018; 7. [PMID: 30079227 PMCID: PMC6053694 DOI: 10.12688/f1000research.14634.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/11/2018] [Indexed: 01/06/2023] Open
Abstract
Pediatric leukemia represents a heterogeneous group of diseases characterized by germline and somatic mutations that manifest within the context of disturbances in the epigenetic machinery and genetic regulation. Advances in genomic medicine have allowed finer resolution of genetic and epigenetic strategies that can be effectively used to risk-stratify patients and identify novel targets for therapy. This review discusses the genetic and epigenetic mechanisms of leukemogenesis, particularly as it relates to acute lymphocytic leukemias, the mechanisms of epigenetic control of leukemogenesis, namely DNA methylation, histone modifications, microRNAs, and LINE-1 retroelements, and highlights opportunities for precision medicine therapeutics in further guiding disease management. Future efforts to broaden the integration of advances in genomic and epigenomic science into the practice of pediatric oncology will not only identify novel therapeutic strategies to improve clinical outcomes but also improve the quality of life for this unique patient population. Recent findings in precision therapeutics of acute lymphocytic leukemias over the past three years, along with some provocative areas of epigenetics research, are reviewed here.
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Affiliation(s)
- Kristie N Ramos
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Arizona College of Medicine-Tucson, Tucson, USA
| | - Irma N Ramos
- Department of Promotion Health Sciences, University of Arizona Mel and Enid Zucherman College of Public Health, Tucson, USA
| | - Yi Zeng
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Arizona College of Medicine-Tucson, Tucson, USA.,University of Arizona Cancer Center, Tucson, USA
| | - Kenneth S Ramos
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Arizona College of Medicine-Tucson, Tucson, USA.,University of Arizona Cancer Center, Tucson, USA.,Department of Medicine, Division of Clinical Support and Data Analytics, University of Arizona College of Medicine-Phoenix, Phoenix, USA
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39
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Dieck CL, Tzoneva G, Forouhar F, Carpenter Z, Ambesi-Impiombato A, Sánchez-Martín M, Kirschner-Schwabe R, Lew S, Seetharaman J, Tong L, Ferrando AA. Structure and Mechanisms of NT5C2 Mutations Driving Thiopurine Resistance in Relapsed Lymphoblastic Leukemia. Cancer Cell 2018; 34:136-147.e6. [PMID: 29990496 PMCID: PMC6049837 DOI: 10.1016/j.ccell.2018.06.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/06/2018] [Accepted: 06/06/2018] [Indexed: 11/25/2022]
Abstract
Activating mutations in the cytosolic 5'-nucleotidase II gene NT5C2 drive resistance to 6-mercaptopurine in acute lymphoblastic leukemia. Here we demonstrate that constitutively active NT5C2 mutations K359Q and L375F reconfigure the catalytic center for substrate access and catalysis in the absence of allosteric activator. In contrast, most relapse-associated mutations, which involve the arm segment and residues along the surface of the inter-monomeric cavity, disrupt a built-in switch-off mechanism responsible for turning off NT5C2. In addition, we show that the C-terminal acidic tail lost in the Q523X mutation functions to restrain NT5C2 activation. These results uncover dynamic mechanisms of enzyme regulation targeted by chemotherapy resistance-driving NT5C2 mutations, with important implications for the development of NT5C2 inhibitor therapies.
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Affiliation(s)
- Chelsea L Dieck
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Gannie Tzoneva
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Farhad Forouhar
- Hervert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA; Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, 1212 Amsterdam Avenue, 701 Fairchild Center, New York, NY 10027, USA
| | - Zachary Carpenter
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | | | | | - Renate Kirschner-Schwabe
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Scott Lew
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, 1212 Amsterdam Avenue, 701 Fairchild Center, New York, NY 10027, USA
| | | | - Liang Tong
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, 1212 Amsterdam Avenue, 701 Fairchild Center, New York, NY 10027, USA.
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Pediatrics, Columbia University Medical Center, 1130 St. Nicholas Avenue, ICRC 402, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA.
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40
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Cordas Dos Santos DM, Eilers J, Sosa Vizcaino A, Orlova E, Zimmermann M, Stanulla M, Schrappe M, Börner K, Grimm D, Muckenthaler MU, Kulozik AE, Kunz JB. MAP3K7 is recurrently deleted in pediatric T-lymphoblastic leukemia and affects cell proliferation independently of NF-κB. BMC Cancer 2018; 18:663. [PMID: 29914415 PMCID: PMC6006985 DOI: 10.1186/s12885-018-4525-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 05/18/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Deletions of 6q15-16.1 are recurrently found in pediatric T-cell acute lymphoblastic leukemia (T-ALL). This chromosomal region includes the mitogen-activated protein kinase kinase kinase 7 (MAP3K7) gene which has a crucial role in innate immune signaling and was observed to be functionally and prognostically relevant in different cancer entities. Therefore, we correlated the presence of MAP3K7 deletions with clinical parameters in a cohort of 327 pediatric T-ALL patients and investigated the function of MAP3K7 in the T-ALL cell lines CCRF-CEM, Jurkat and MOLT-4. METHODS MAP3K7 deletions were detected by multiplex ligation-dependent probe amplification (MLPA). T-ALL cell lines were transduced with adeno-associated virus (AAV) vectors expressing anti-MAP3K7 shRNA or a non-silencing shRNA together with a GFP reporter. Transduction efficiency was measured by flow cytometry and depletion efficiency by RT-PCR and Western blots. Induction of apoptosis was measured by flow cytometry after staining with PE-conjugated Annexin V. In order to assess the contribution of NF-κB signaling to the effects of MAP3K7 depletion, cells were treated with TNF-α and cell lysates analyzed for components of the NF-κB pathway by Western blotting and for expression of the NF-κB target genes BCL2, CMYC, FAS, PTEN and TNF-α by RT-PCR. RESULTS MAP3K7 is deleted in approximately 10% and point-mutated in approximately 1% of children with T-ALL. In 32 of 33 leukemias the deletion of MAP3K7 also included the adjacent CASP8AP2 gene. MAP3K7 deletions were associated with the occurrence of SIL-TAL1 fusions and a mature immunophenotype, but not with response to treatment and outcome. Depletion of MAP3K7 expression in T-ALL cell lines by shRNAs slowed down proliferation and induced apoptosis, but neither changed protein levels of components of NF-κB signaling nor NF-κB target gene expression after stimulation with TNF-α. CONCLUSIONS This study revealed that the recurrent deletion of MAP3K7/CASP8AP2 is associated with SIL-TAL1 fusions and a mature immunophenotype, but not with response to treatment and risk of relapse. Homozygous deletions of MAP3K7 were not observed, and efficient depletion of MAP3K7 interfered with viability of T-ALL cells, indicating that a residual expression of MAP3K7 is indispensable for T-lymphoblasts.
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Affiliation(s)
- David M Cordas Dos Santos
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Juliane Eilers
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Alfonso Sosa Vizcaino
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany
| | - Elena Orlova
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany
| | - Martin Zimmermann
- Department of Pediatric Hematology and Oncology, MH Hannover, Hannover, Germany
| | - Martin Stanulla
- Department of Pediatric Hematology and Oncology, MH Hannover, Hannover, Germany
| | - Martin Schrappe
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Kathleen Börner
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.,German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.,BioQuant Center, Heidelberg University, Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.,German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.,BioQuant Center, Heidelberg University, Heidelberg, Germany.,Cluster of Excellence CellNetworks, Heidelberg University, Heidelberg, Germany
| | - Martina U Muckenthaler
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Joachim B Kunz
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany. .,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.
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41
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Lindqvist CM, Lundmark A, Nordlund J, Freyhult E, Ekman D, Carlsson Almlöf J, Raine A, Övernäs E, Abrahamsson J, Frost BM, Grandér D, Heyman M, Palle J, Forestier E, Lönnerholm G, Berglund EC, Syvänen AC. Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes. Oncotarget 2018; 7:64071-64088. [PMID: 27590521 PMCID: PMC5325426 DOI: 10.18632/oncotarget.11773] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/25/2016] [Indexed: 12/29/2022] Open
Abstract
To characterize the mutational patterns of acute lymphoblastic leukemia (ALL) we performed deep next generation sequencing of 872 cancer genes in 172 diagnostic and 24 relapse samples from 172 pediatric ALL patients. We found an overall greater mutational burden and more driver mutations in T-cell ALL (T-ALL) patients compared to B-cell precursor ALL (BCP-ALL) patients. In addition, the majority of the mutations in T-ALL had occurred in the original leukemic clone, while most of the mutations in BCP-ALL were subclonal. BCP-ALL patients carrying any of the recurrent translocations ETV6-RUNX1, BCR-ABL or TCF3-PBX1 harbored few mutations in driver genes compared to other BCP-ALL patients. Specifically in BCP-ALL, we identified ATRX as a novel putative driver gene and uncovered an association between somatic mutations in the Notch signaling pathway at ALL diagnosis and increased risk of relapse. Furthermore, we identified EP300, ARID1A and SH2B3 as relapse-associated genes. The genes highlighted in our study were frequently involved in epigenetic regulation, associated with germline susceptibility to ALL, and present in minor subclones at diagnosis that became dominant at relapse. We observed a high degree of clonal heterogeneity and evolution between diagnosis and relapse in both BCP-ALL and T-ALL, which could have implications for the treatment efficiency.
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Affiliation(s)
- C Mårten Lindqvist
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anders Lundmark
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Eva Freyhult
- Cancer Pharmacology and Computational Medicine, Department of Medical Sciences, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Diana Ekman
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jonas Carlsson Almlöf
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Elin Övernäs
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonas Abrahamsson
- Department of Pediatrics, Queen Silvia Children's Hospital, Gothenburg, Sweden.,Nordic Society of Pediatric Hematology and Oncology
| | - Britt-Marie Frost
- Department of Women's and Children's Health, University Children's Hospital, Uppsala, Sweden.,Nordic Society of Pediatric Hematology and Oncology
| | - Dan Grandér
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Mats Heyman
- Childhood Cancer Research Unit, Department of Women and Child Health, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Nordic Society of Pediatric Hematology and Oncology
| | - Josefine Palle
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Women's and Children's Health, University Children's Hospital, Uppsala, Sweden.,Nordic Society of Pediatric Hematology and Oncology
| | - Erik Forestier
- Department of Medical Biosciences, University of Umeå, Umeå, Sweden.,Nordic Society of Pediatric Hematology and Oncology
| | - Gudmar Lönnerholm
- Department of Women's and Children's Health, University Children's Hospital, Uppsala, Sweden.,Nordic Society of Pediatric Hematology and Oncology
| | - Eva C Berglund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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42
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Drobna M, Szarzyńska-Zawadzka B, Dawidowska M. T-cell acute lymphoblastic leukemia from miRNA perspective: Basic concepts, experimental approaches, and potential biomarkers. Blood Rev 2018; 32:457-472. [PMID: 29703513 DOI: 10.1016/j.blre.2018.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/12/2018] [Accepted: 04/12/2018] [Indexed: 12/19/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a rare, aggressive and heterogeneous malignancy originating from T-cell precursors. The mechanisms of T-ALL pathogenesis related to non-protein coding part of the genome are currently intensively studied. miRNAs are short, non-coding molecules acting as negative regulators of gene expression which shape phenotype of cells in a complex and context-specific manner. miRNAs may act as oncogenes or tumor suppressors; several miRNAs have been related to drug resistance and treatment response in various malignancies. Here we present the review of the state-of-the-art knowledge on the role of miRNAs in T-ALL pathogenesis, with detailed overview of the studies reporting on miRNAs with oncogenic and tumor suppressor potential. We discuss whether miRNAs might be considered candidate biomarkers of prognosis in T-ALL and leukemia subtype-specific markers. We also describe experimental approaches and a typical workflow applied in research on the involvement of miRNAs in oncogenesis.
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Affiliation(s)
- Monika Drobna
- Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland.
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43
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Successful Treatment of a Very Late Isolated Relapse in an Adolescent With a PICALM-MLLT10 Positive T-lineage Acute Lymphoblastic Leukemia. J Pediatr Hematol Oncol 2018; 40:e191-e194. [PMID: 29189509 DOI: 10.1097/mph.0000000000000996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
T-lineage ALL is an aggressive disease that needs to be treated with intensive treatment schedules. A late relapse rarely occurs and a clear choice for second-line treatment is on debate. We report on a young adult with a very late isolated extramedullary relapse of PICALM-MLLT10 positive T-ALL, successfully treated with a chemotherapy-based and radiotherapy-based pediatric protocol. We demonstrate that relapse can occur in T-ALL although a SR-MRD behavior treated with a high-risk protocol; specific molecular diagnostic aberrations, as PICALM-MLLT10, are still conserved at very late relapse; a second-line treatment based on pediatric protocol can be effective.
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44
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The landscape of genomic alterations across childhood cancers. Nature 2018; 555:321-327. [PMID: 29489754 DOI: 10.1038/nature25480] [Citation(s) in RCA: 884] [Impact Index Per Article: 147.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 12/24/2017] [Indexed: 02/07/2023]
Abstract
Pan-cancer analyses that examine commonalities and differences among various cancer types have emerged as a powerful way to obtain novel insights into cancer biology. Here we present a comprehensive analysis of genetic alterations in a pan-cancer cohort including 961 tumours from children, adolescents, and young adults, comprising 24 distinct molecular types of cancer. Using a standardized workflow, we identified marked differences in terms of mutation frequency and significantly mutated genes in comparison to previously analysed adult cancers. Genetic alterations in 149 putative cancer driver genes separate the tumours into two classes: small mutation and structural/copy-number variant (correlating with germline variants). Structural variants, hyperdiploidy, and chromothripsis are linked to TP53 mutation status and mutational signatures. Our data suggest that 7-8% of the children in this cohort carry an unambiguous predisposing germline variant and that nearly 50% of paediatric neoplasms harbour a potentially druggable event, which is highly relevant for the design of future clinical trials.
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45
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Hnízda A, Fábry M, Moriyama T, Pachl P, Kugler M, Brinsa V, Ascher DB, Carroll WL, Novák P, Žaliová M, Trka J, Řezáčová P, Yang JJ, Veverka V. Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation. Leukemia 2018. [PMID: 29535428 DOI: 10.1038/s41375-018-0073-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Activating mutations in NT5C2, a gene encoding cytosolic purine 5'-nucleotidase (cN-II), confer chemoresistance in relapsed acute lymphoblastic leukemia. Here we show that all mutants became independent of allosteric effects of ATP and thus constitutively active. Structural mapping of mutations described in patients demonstrates that 90% of leukemia-specific allelles directly affect two regulatory hotspots within the cN-II molecule-the helix A region: residues 355-365, and the intersubunit interface: helix B (232-242) and flexible interhelical loop L (400-418). Furthermore, analysis of hetero-oligomeric complexes combining wild-type (WT) and mutant subunits showed that the activation is transmitted from the mutated to the WT subunit. This intersubunit interaction forms structural basis of hyperactive NT5C2 in drug-resistant leukemia in which heterozygous NT5C2 mutation gave rise to hetero-tetramer mutant and WT proteins. This enabled us to define criteria to aid the prediction of NT5C2 drug resistance mutations in leukemia.
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Affiliation(s)
- Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic. .,Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, UK.
| | - Milan Fábry
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Takaya Moriyama
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic
| | - Michael Kugler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic.,Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Vítězslav Brinsa
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic
| | - David B Ascher
- Department of Biochemistry, Sanger Building, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
| | | | - Petr Novák
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague, 4 142 20, Czech Republic
| | - Markéta Žaliová
- Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Trka
- Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic.,Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic
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Masetti R, Castelli I, Astolfi A, Bertuccio SN, Indio V, Togni M, Belotti T, Serravalle S, Tarantino G, Zecca M, Pigazzi M, Basso G, Pession A, Locatelli F. Genomic complexity and dynamics of clonal evolution in childhood acute myeloid leukemia studied with whole-exome sequencing. Oncotarget 2018; 7:56746-56757. [PMID: 27462774 PMCID: PMC5302950 DOI: 10.18632/oncotarget.10778] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/10/2016] [Indexed: 11/25/2022] Open
Abstract
Despite significant improvement in treatment of childhood acute myeloid leukemia (AML), 30% of patients experience disease recurrence, which is still the major cause of treatment failure and death in these patients. To investigate molecular mechanisms underlying relapse, we performed whole-exome sequencing of diagnosis-relapse pairs and matched remission samples from 4 pediatric AML patients without recurrent cytogenetic alterations. Candidate driver mutations were selected for targeted deep sequencing at high coverage, suitable to detect small subclones (0.12%). BiCEBPα mutation was found to be stable and highly penetrant, representing a separate biological and clinical entity, unlike WT1 mutations, which were extremely unstable. Among the mutational patterns underlying relapse, we detected the acquisition of proliferative advantage by signaling activation (PTPN11 and FLT3-TKD mutations) and the increased resistance to apoptosis (hyperactivation of TYK2). We also found a previously undescribed feature of AML, consisting of a hypermutator phenotype caused by SETD2 inactivation. The consequent accumulation of new mutations promotes the adaptability of the leukemia, contributing to clonal selection. We report a novel ASXL3 mutation characterizing a very small subclone (<1%) present at diagnosis and undergoing expansion (60%) at relapse. Taken together, these findings provide molecular clues for designing optimal therapeutic strategies, in terms of target selection, adequate schedule design and reliable response-monitoring techniques.
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Affiliation(s)
- Riccardo Masetti
- Department of Pediatrics "Lalla Seràgnoli", Hematology-Oncology Unit, University of Bologna, Bologna, Italy
| | - Ilaria Castelli
- Department of Pediatrics "Lalla Seràgnoli", Hematology-Oncology Unit, University of Bologna, Bologna, Italy
| | - Annalisa Astolfi
- Interdepartmental Centre of Cancer Research "G. Prodi", University of Bologna, Bologna, Italy
| | - Salvatore Nicola Bertuccio
- Department of Pediatrics "Lalla Seràgnoli", Hematology-Oncology Unit, University of Bologna, Bologna, Italy
| | - Valentina Indio
- Interdepartmental Centre of Cancer Research "G. Prodi", University of Bologna, Bologna, Italy
| | - Marco Togni
- Department of Pediatrics "Lalla Seràgnoli", Hematology-Oncology Unit, University of Bologna, Bologna, Italy.,Current address: Stem Cell Group, University College London Cancer Institute, University College London, London, United Kingdom
| | - Tamara Belotti
- Department of Pediatrics "Lalla Seràgnoli", Hematology-Oncology Unit, University of Bologna, Bologna, Italy
| | - Salvatore Serravalle
- Department of Pediatrics "Lalla Seràgnoli", Hematology-Oncology Unit, University of Bologna, Bologna, Italy
| | - Giuseppe Tarantino
- Interdepartmental Centre of Cancer Research "G. Prodi", University of Bologna, Bologna, Italy
| | - Marco Zecca
- Department of Pediatric Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Martina Pigazzi
- Department of Woman and Child Health, Laboratory of Hematology-Oncology, University of Padova, Padova, Italy
| | - Giuseppe Basso
- Department of Woman and Child Health, Laboratory of Hematology-Oncology, University of Padova, Padova, Italy
| | - Andrea Pession
- Department of Pediatrics "Lalla Seràgnoli", Hematology-Oncology Unit, University of Bologna, Bologna, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology-Oncology, IRCCS Ospedale Bambino Gesù, Rome, Italy.,University of Pavia, Pavia, Italy
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47
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Arumuggam N, Melong N, Too CKL, Berman JN, Rupasinghe HPV. Phloridzin docosahexaenoate, a novel flavonoid derivative, suppresses growth and induces apoptosis in T-cell acute lymphoblastic leukemia cells. Am J Cancer Res 2017; 7:2452-2464. [PMID: 29312799 PMCID: PMC5752686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/02/2017] [Indexed: 06/07/2023] Open
Abstract
The overall clinical outcome in T-cell acute lymphoblastic leukemia (T-ALL) can be improved by minimizing risk for treatment failure using effective pharmacological adjuvants. Phloridzin (PZ), a flavonoid precursor found in apple peels, was acylated with docosahexaenoic acid (DHA) yielding a novel ester known as phloridzin docosahexaenoate (PZ-DHA). Here, we have studied the cytotoxic effects of PZ-DHA on human leukemia cells using in vitro and in vivo models. The inhibitory effects of PZ-DHA were tested on human Jurkat T-ALL cells in comparison to K562 chronic myeloid leukemia (CML) cells and non-malignant murine T-cells. PZ-DHA, not PZ or DHA alone, reduced cell viability and ATP levels, increased intracellular LDH release, and caused extensive morphological alterations in both Jurkat and K562 cells. PZ-DHA also inhibited cell proliferation, and selectively induced apoptosis in Jurkat and K562 cells while sparing normal murine T-cells. The cytotoxic effects of PZ-DHA on Jurkat cells were associated with caspase activation, DNA fragmentation, and selective down-regulation of STAT3 phosphorylation. PZ-DHA significantly inhibited Jurkat cell proliferation in zebrafish larvae; however, the proliferation of K562 cells was not affected in vivo. We propose that PZ-DHA-induced cytotoxic response is selective towards T-ALL in the presence of a tumor-stromal microenvironment. Prospective studies evaluating the combinatorial effects of PZ-DHA with conventional chemotherapy for T-ALL are underway.
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Affiliation(s)
- Niroshaathevi Arumuggam
- Department of Plant, Food, & Environmental Sciences, Faculty of Agriculture, Dalhousie UniversityTruro, NS B2N 5E3, Canada
| | | | - Catherine KL Too
- Department of Biochemistry & Molecular Biology, Dalhousie University, Faculty of MedicineHalifax, NS B3H 4R2, Canada
| | - Jason N Berman
- IWK Health CentreHalifax, NS B3K 6R8, Canada
- Department of Pediatrics, Dalhousie University, Faculty of MedicineHalifax, NS B3H 4R2, Canada
- Department of Pathology, Dalhousie University, Faculty of MedicineHalifax, NS B3H 4R2, Canada
| | - HP Vasantha Rupasinghe
- Department of Plant, Food, & Environmental Sciences, Faculty of Agriculture, Dalhousie UniversityTruro, NS B2N 5E3, Canada
- Department of Pathology, Dalhousie University, Faculty of MedicineHalifax, NS B3H 4R2, Canada
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Szarzyńska-Zawadzka B, Kosmalska M, Sędek Ł, Sonsala A, Twardoch M, Kowalczyk JR, Szczepański T, Witt M, Dawidowska M. Cost-effective screening of DNMT3A coding sequence identifies somatic mutation in pediatric T-cell acute lymphoblastic leukemia. Eur J Haematol 2017; 99:514-519. [PMID: 28905428 DOI: 10.1111/ejh.12964] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND OBJECTIVES In pediatric T-cell acute lymphoblastic leukemia (T-ALL), risk assignment schemes preclude reliable prediction of outcome, and thus, new prognostic factors are needed. Mutations in DNMT3A are candidate prognostic and classification markers in adults with acute myeloid leukemia (AML) and T-ALL and thus were considered as candidates prognostic markers in pediatric T-ALL. PATIENTS AND METHODS DNMT3A mutational status was investigated in 74 pediatric T-ALL samples collected at diagnosis. We applied high-resolution melt (HRM) analysis and Sanger sequencing to study the hotspot position (R882) within catalytic MTase domain and exons coding for other functional domains of the protein, known to be mutated in the wide spectrum of hematological malignancies. RESULTS We demonstrate a low frequency of mutations in DNMT3A coding sequence in pediatric T-ALL (1.4%, n = 1/74). We identified missense mutation, p.Ala644Thr, which has not been described previously in pediatric T-ALL, but is recurrent in adults with T-ALL and AML. CONCLUSIONS Low frequency of DNMT3A mutations in pediatric T-ALL is in striking contrast to adult T-ALL and renders the necessity for the search of other candidate prognostic markers. Combined Sanger sequencing-HRM approach offers a cost-effective option for genotyping DNMT3A coding sequence, with potential clinical application in other hematological malignancies.
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Affiliation(s)
| | - Maria Kosmalska
- Institute of Human Genetics Polish Academy of Sciences, Poznań, Poland
| | - Łukasz Sędek
- Department of Microbiology and Immunology, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Alicja Sonsala
- Department of Pediatric Hematology and Oncology, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Magdalena Twardoch
- Department of Pediatric Hematology and Oncology, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology and Transplantology, Cytogenetic Laboratory, Children's University Hospital, Medical University of Lublin, Lublin, Poland
| | - Tomasz Szczepański
- Department of Pediatric Hematology and Oncology, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Michał Witt
- Institute of Human Genetics Polish Academy of Sciences, Poznań, Poland
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Bone marrow sites differently imprint dormancy and chemoresistance to T-cell acute lymphoblastic leukemia. Blood Adv 2017; 1:1760-1772. [PMID: 29296822 DOI: 10.1182/bloodadvances.2017004960] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 07/17/2017] [Indexed: 12/21/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) expands in various bone marrow (BM) sites of the body. We investigated whether different BM sites could differently modulate T-ALL propagation using in vivo animal models. We observed that mouse and human T-ALL develop slowly in the BM of tail vertebrae compared with the BM from thorax vertebrae. T-ALL recovered from tail BM displays lower cell-surface marker expression and decreased metabolism and cell-cycle progression, demonstrating a dormancy phenotype. Functionally, tail-derived T-ALL exhibit a deficient short-term ex vivo growth and a delayed in vivo propagation. These features are noncell-autonomous because T-ALL from tail and thorax shares identical genomic abnormalities and functional disparities disappear in vivo and in prolonged in vitro assays. Importantly tail-derived T-ALL displays higher intrinsic resistance to cell-cycle-related drugs (ie, vincristine sulfate and cytarabine). Of note, T-ALL recovered from gonadal adipose tissues or from cocultures with adipocytes shares metabolic, cell-cycle, and phenotypic or chemoresistance features, with tail-derived T-ALL suggesting adipocytes may participate in the tail BM imprints on T-ALL. Altogether these results demonstrate that BM sites differentially orchestrate T-ALL propagation stamping specific features to leukemic cells such as quiescence and decreased response to cell-cycle-dependent chemotherapy.
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Nordlund J, Syvänen AC. Epigenetics in pediatric acute lymphoblastic leukemia. Semin Cancer Biol 2017; 51:129-138. [PMID: 28887175 DOI: 10.1016/j.semcancer.2017.09.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/21/2017] [Accepted: 09/02/2017] [Indexed: 12/11/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common malignancy in children. ALL arises from the malignant transformation of progenitor B- and T-cells in the bone marrow into leukemic cells, but the mechanisms underlying this transformation are not well understood. Recent technical advances and decreasing costs of methods for high-throughput DNA sequencing and SNP genotyping have stimulated systematic studies of the epigenetic changes in leukemic cells from pediatric ALL patients. The results emerging from these studies are increasing our understanding of the epigenetic component of leukemogenesis and have demonstrated the potential of DNA methylation as a biomarker for lineage and subtype classification, prognostication, and disease progression in ALL. In this review, we provide a concise examination of the epigenetic studies in ALL, with a focus on DNA methylation and mutations perturbing genes involved in chromatin modification, and discuss the future role of epigenetic analyses in research and clinical management of ALL.
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Affiliation(s)
- Jessica Nordlund
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Sweden.
| | - Ann-Christine Syvänen
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Sweden
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