1
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Borin C, Pieters T, Serafin V, Ntziachristos P. Emerging Epigenetic and Posttranslational Mechanisms Controlling Resistance to Glucocorticoids in Acute Lymphoblastic Leukemia. Hemasphere 2023; 7:e916. [PMID: 37359189 PMCID: PMC10289758 DOI: 10.1097/hs9.0000000000000916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
Glucocorticoids are extensively used for the treatment of acute lymphoblastic leukemia as they pressure cancer cells to undergo apoptosis. Nevertheless, glucocorticoid partners, modifications, and mechanisms of action are hitherto poorly characterized. This hampers our understanding of therapy resistance, frequently occurring in leukemia despite the current therapeutic combinations using glucocorticoids in acute lymphoblastic leukemia. In this review, we initially cover the traditional view of glucocorticoid resistance and ways of targeting this resistance. We discuss recent progress in our understanding of chromatin and posttranslational properties of the glucocorticoid receptor that might be proven beneficial in our efforts to understand and target therapy resistance. We discuss emerging roles of pathways and proteins such as the lymphocyte-specific kinase that antagonizes glucocorticoid receptor activation and nuclear translocation. In addition, we provide an overview of ongoing therapeutic approaches that sensitize cells to glucocorticoids including small molecule inhibitors and proteolysis-targeting chimeras.
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Affiliation(s)
- Cristina Borin
- Department of Biomolecular Medicine, Ghent University, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Belgium
- Cancer Research Institute Ghent (CRIG), Belgium
| | - Tim Pieters
- Department of Biomolecular Medicine, Ghent University, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Belgium
- Cancer Research Institute Ghent (CRIG), Belgium
| | - Valentina Serafin
- Department of Surgery Oncology and Gastroenterology, Oncology and Immunology Section, University of Padova, Italy
| | - Panagiotis Ntziachristos
- Department of Biomolecular Medicine, Ghent University, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Belgium
- Cancer Research Institute Ghent (CRIG), Belgium
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2
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Hlozkova K, Hermanova I, Safrhansova L, Alquezar-Artieda N, Kuzilkova D, Vavrova A, Sperkova K, Zaliova M, Stary J, Trka J, Starkova J. PTEN/PI3K/Akt pathway alters sensitivity of T-cell acute lymphoblastic leukemia to L-asparaginase. Sci Rep 2022; 12:4043. [PMID: 35260738 PMCID: PMC8904819 DOI: 10.1038/s41598-022-08049-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 02/21/2022] [Indexed: 12/22/2022] Open
Abstract
Childhood T-cell acute lymphoblastic leukemia (T-ALL) still remains a therapeutic challenge due to relapses which are resistant to further treatment. l-asparaginase (ASNase) is a key therapy component in pediatric T-ALL and lower sensitivity of leukemia cells to this drug negatively influences overall treatment efficacy and outcome. PTEN protein deletion and/or activation of the PI3K/Akt signaling pathway leading to altered cell growth and metabolism are emerging as a common feature in T-ALL. We herein investigated the relationship amongst PTEN deletion, ASNase sensitivity and glucose metabolism in T-ALL cells. First, we found significant differences in the sensitivity to ASNase amongst T-ALL cell lines. While cell lines more sensitive to ASNase were PTEN wild type (WT) and had no detectable level of phosphorylated Akt (P-Akt), cell lines less sensitive to ASNase were PTEN-null with high P-Akt levels. Pharmacological inhibition of Akt in the PTEN-null cells rendered them more sensitive to ASNase and lowered their glycolytic function which then resembled PTEN WT cells. In primary T-ALL cells, although P-Akt level was not dependent exclusively on PTEN expression, their sensitivity to ASNase could also be increased by pharmacological inhibition of Akt. In summary, we highlight a promising therapeutic option for T-ALL patients with aberrant PTEN/PI3K/Akt signaling.
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Affiliation(s)
- Katerina Hlozkova
- CLIP (Childhood Leukaemia Investigation Prague), Prague, Czech Republic.,Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ivana Hermanova
- CLIP (Childhood Leukaemia Investigation Prague), Prague, Czech Republic.,Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lucie Safrhansova
- CLIP (Childhood Leukaemia Investigation Prague), Prague, Czech Republic.,Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Natividad Alquezar-Artieda
- CLIP (Childhood Leukaemia Investigation Prague), Prague, Czech Republic.,Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Daniela Kuzilkova
- CLIP (Childhood Leukaemia Investigation Prague), Prague, Czech Republic.,Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Adela Vavrova
- CLIP (Childhood Leukaemia Investigation Prague), Prague, Czech Republic.,Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Kristyna Sperkova
- CLIP (Childhood Leukaemia Investigation Prague), Prague, Czech Republic.,Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marketa Zaliova
- CLIP (Childhood Leukaemia Investigation Prague), Prague, Czech Republic.,Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic.,University Hospital Motol, Prague, Czech Republic
| | - Jan Stary
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic.,University Hospital Motol, Prague, Czech Republic
| | - Jan Trka
- CLIP (Childhood Leukaemia Investigation Prague), Prague, Czech Republic.,Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic.,University Hospital Motol, Prague, Czech Republic
| | - Julia Starkova
- CLIP (Childhood Leukaemia Investigation Prague), Prague, Czech Republic. .,Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic. .,University Hospital Motol, Prague, Czech Republic.
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3
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Skhoun H, Khattab M, Belkhayat A, Takki Chebihi Z, Dakka N, El Baghdadi J. A prognostic approach on a case of pediatric Philadelphia chromosome-positive acute lymphoblastic leukemia with monosomy-7. Clin Case Rep 2021; 9:e05207. [PMID: 34963805 PMCID: PMC8710846 DOI: 10.1002/ccr3.5207] [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: 08/25/2021] [Revised: 11/04/2021] [Accepted: 11/14/2021] [Indexed: 11/21/2022] Open
Abstract
In this work, we present the first case of a Ph-positive ALL Moroccan girl with t(9;22)(q34;q11) and monosomy-7. She was diagnosed with Ph-positive ALL based on bone marrow examination, immunophenotyping, and cytogenetic analysis. She relapsed after treatment with the persistence of the Ph chromosome and the appearance of a monosomy-7.
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Affiliation(s)
- Hanaa Skhoun
- Genetics UnitMilitary Hospital Mohammed VRabatMorocco
- Laboratory of Human Pathologies BiologyGenomic Center of Human PathologiesFaculty of SciencesMohammed V University in RabatRabatMorocco
| | - Mohammed Khattab
- Department of Pediatric Hemato‐OncologyChildren's Hospital of RabatRabatMorocco
| | | | | | - Nadia Dakka
- Laboratory of Human Pathologies BiologyGenomic Center of Human PathologiesFaculty of SciencesMohammed V University in RabatRabatMorocco
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4
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TET2 as a tumor suppressor and therapeutic target in T-cell acute lymphoblastic leukemia. Proc Natl Acad Sci U S A 2021; 118:2110758118. [PMID: 34413196 PMCID: PMC8403940 DOI: 10.1073/pnas.2110758118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy in need of novel targeted therapies to prevent relapse and lessen treatment toxicity. We reveal frequent (∼88%) transcriptional silencing or repression of the tumor suppressor TET2 in T-ALL. We show that loss of TET2 in T-ALL is correlated with hypermethylation of the TET2 promoter and that TET2 expression can be rescued by treatment with the DNA demethylating agent, 5-azacytidine (5-aza). We further reveal that the TET2 cofactor vitamin C exerts a strong synergistic effect on global transcriptional changes when added to 5-aza treatment. Importantly, 5-aza treatment results in increased cell death, specifically in T-ALL cells lacking TET2. Thus, we clearly identify 5-aza as a potentially targeted therapy for TET2-silenced T-ALL. Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy resulting from overproduction of immature T-cells in the thymus and is typified by widespread alterations in DNA methylation. As survival rates for relapsed T-ALL remain dismal (10 to 25%), development of targeted therapies to prevent relapse is key to improving prognosis. Whereas mutations in the DNA demethylating enzyme TET2 are frequent in adult T-cell malignancies, TET2 mutations in T-ALL are rare. Here, we analyzed RNA-sequencing data of 321 primary T-ALLs, 20 T-ALL cell lines, and 25 normal human tissues, revealing that TET2 is transcriptionally repressed or silenced in 71% and 17% of T-ALL, respectively. Furthermore, we show that TET2 silencing is often associated with hypermethylation of the TET2 promoter in primary T-ALL. Importantly, treatment with the DNA demethylating agent, 5-azacytidine (5-aza), was significantly more toxic to TET2-silenced T-ALL cells and resulted in stable re-expression of the TET2 gene. Additionally, 5-aza led to up-regulation of methylated genes and human endogenous retroviruses (HERVs), which was further enhanced by the addition of physiological levels of vitamin C, a potent enhancer of TET activity. Together, our results clearly identify 5-aza as a potential targeted therapy for TET2-silenced T-ALL.
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5
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Single-cell DNA amplicon sequencing reveals clonal heterogeneity and evolution in T-cell acute lymphoblastic leukemia. Blood 2021; 137:801-811. [PMID: 32812017 DOI: 10.1182/blood.2020006996] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/28/2020] [Indexed: 01/27/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive leukemia that is most frequent in children and is characterized by the presence of few chromosomal rearrangements and 10 to 20 somatic mutations in protein-coding regions at diagnosis. The majority of T-ALL cases harbor activating mutations in NOTCH1 together with mutations in genes implicated in kinase signaling, transcriptional regulation, or protein translation. To obtain more insight in the level of clonal heterogeneity at diagnosis and during treatment, we used single-cell targeted DNA sequencing with the Tapestri platform. We designed a custom ALL panel and obtained accurate single-nucleotide variant and small insertion-deletion mutation calling for 305 amplicons covering 110 genes in about 4400 cells per sample and time point. A total of 108 188 cells were analyzed for 25 samples of 8 T-ALL patients. We typically observed a major clone at diagnosis (>35% of the cells) accompanied by several minor clones of which some were less than 1% of the total number of cells. Four patients had >2 NOTCH1 mutations, some of which present in minor clones, indicating a strong pressure to acquire NOTCH1 mutations in developing T-ALL cells. By analyzing longitudinal samples, we detected the presence and clonal nature of residual leukemic cells and clones with a minor presence at diagnosis that evolved to clinically relevant major clones at later disease stages. Therefore, single-cell DNA amplicon sequencing is a sensitive assay to detect clonal architecture and evolution in T-ALL.
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6
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T-cell lymphoblastic lymphoma and leukemia: different diseases from a common premalignant progenitor? Blood Adv 2021; 4:3466-3473. [PMID: 32722786 DOI: 10.1182/bloodadvances.2020001822] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/18/2020] [Indexed: 01/03/2023] Open
Abstract
T-cell lymphoblastic lymphoma (T-LBL) and lymphoblastic leukemia (T-ALL) represent malignancies that arise from the transformation of immature precursor T cells. Similarities in T-LBL and T-ALL have raised the question whether these entities represent 1 disease or reflect 2 different diseases. The genetic profiles of T-ALL have been thoroughly investigated over the last 2 decades, whereas fairly little is known about genetic driver mutations in T-LBL. Nevertheless, the comparison of clinical, immunophenotypic, and molecular observations from independent T-LBL and T-ALL studies lent strength to the theory that T-LBL and T-ALL reflect different presentations of the same disease. Alternatively, T-LBL and T-ALL may simultaneously evolve from a common malignant precursor cell, each having their own specific pathogenic requirements or cellular dependencies that differ among stroma-embedded blasts in lymphoid tissues compared with solitary leukemia cells. This review aims to cluster recent findings with regard to clinical presentation, genetic predisposition, and the acquisition of additional mutations that may give rise to differences in gene expression signatures among T-LBL and T-ALL patients. Improved insight in T-LBL in relation to T-ALL may further help to apply confirmed T-ALL therapies to T-LBL patients.
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7
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Maćkowska N, Drobna-Śledzińska M, Witt M, Dawidowska M. DNA Methylation in T-Cell Acute Lymphoblastic Leukemia: In Search for Clinical and Biological Meaning. Int J Mol Sci 2021; 22:ijms22031388. [PMID: 33573325 PMCID: PMC7866817 DOI: 10.3390/ijms22031388] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 12/21/2022] Open
Abstract
Distinct DNA methylation signatures, related to different prognosis, have been observed across many cancers, including T-cell acute lymphoblastic leukemia (T-ALL), an aggressive hematological neoplasm. By global methylation analysis, two major phenotypes might be observed in T-ALL: hypermethylation related to better outcome and hypomethylation, which is a candidate marker of poor prognosis. Moreover, DNA methylation holds more than a clinical meaning. It reflects the replicative history of leukemic cells and most likely different mechanisms underlying leukemia development in these T-ALL subtypes. The elucidation of the mechanisms and aberrations specific to (epi-)genomic subtypes might pave the way towards predictive diagnostics and precision medicine in T-ALL. We present the current state of knowledge on the role of DNA methylation in T-ALL. We describe the involvement of DNA methylation in normal hematopoiesis and T-cell development, focusing on epigenetic aberrations contributing to this leukemia. We further review the research investigating distinct methylation phenotypes in T-ALL, related to different outcomes, pointing to the most recent research aimed to unravel the biological mechanisms behind differential methylation. We highlight how technological advancements facilitated broadening the perspective of the investigation into DNA methylation and how this has changed our understanding of the roles of this epigenetic modification in T-ALL.
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8
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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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9
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Burns MA, Place AE, Stevenson KE, Gutiérrez A, Forrest S, Pikman Y, Vrooman LM, Harris MH, Weinberg OK, Hunt SK, O’Brien JE, Asselin BL, Athale UH, Clavell LA, Cole PD, Gennarini LM, Kahn JM, Kelly KM, Laverdiere C, Leclerc JM, Michon B, Schorin MA, Sulis ML, Welch JJ, Neuberg DS, Sallan SE, Silverman LB. Identification of prognostic factors in childhood T-cell acute lymphoblastic leukemia: Results from DFCI ALL Consortium Protocols 05-001 and 11-001. Pediatr Blood Cancer 2021; 68:e28719. [PMID: 33026184 PMCID: PMC8369809 DOI: 10.1002/pbc.28719] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/11/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND/OBJECTIVES While outcomes for pediatric T-cell acute lymphoblastic leukemia (T-ALL) are favorable, there are few widely accepted prognostic factors, limiting the ability to risk stratify therapy. DESIGN/METHODS Dana-Farber Cancer Institute (DFCI) Protocols 05-001 and 11-001 enrolled pediatric patients with newly diagnosed B- or T-ALL from 2005 to 2011 and from 2012 to 2015, respectively. Protocol therapy was nearly identical for patients with T-ALL (N = 123), who were all initially assigned to the high-risk arm. End-induction minimal residual disease (MRD) was assessed by reverse transcription polymerase chain reaction (RT-PCR) or next-generation sequencing (NGS), but was not used to modify postinduction therapy. Early T-cell precursor (ETP) status was determined by flow cytometry. Cases with sufficient diagnostic DNA were retrospectively evaluated by targeted NGS of known genetic drivers of T-ALL, including Notch, PI3K, and Ras pathway genes. RESULTS The 5-year event-free survival (EFS) and overall survival (OS) for patients with T-ALL was 81% (95% CI, 73-87%) and 90% (95% CI, 83-94%), respectively. ETP phenotype was associated with failure to achieve complete remission, but not with inferior OS. Low end-induction MRD (<10-4 ) was associated with superior disease-free survival (DFS). Pathogenic mutations of the PI3K pathway were mutually exclusive of ETP phenotype and were associated with inferior 5-year DFS and OS. CONCLUSIONS Together, our findings demonstrate that ETP phenotype, end-induction MRD, and PI3K pathway mutation status are prognostically relevant in pediatric T-ALL and should be considered for risk classification in future trials. DFCI Protocols 05-001 and 11-001 are registered at www.clinicaltrials.gov as NCT00165087 and NCT01574274, respectively.
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Affiliation(s)
- Melissa A. Burns
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| | - Andrew E. Place
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| | - Kristen E. Stevenson
- Department of Biostatistics and Computational Biology,
Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Alejandro Gutiérrez
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| | - Suzanne Forrest
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| | - Lynda M. Vrooman
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| | - Marian H. Harris
- Department of Pathology, Boston Children’s Hospital,
Harvard Medical School, Boston, MA
| | | | - Sarah K. Hunt
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
| | - Jane E. O’Brien
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
| | - Barbara L. Asselin
- Department of Pediatrics, Golisano Children’s
Hospital, University of Rochester Medical Center, Rochester, NY
| | - Uma H. Athale
- Division of Pediatric Hematology/Oncology, McMaster
University, Hamilton, ON, Canada
| | - Luis A. Clavell
- Division of Pediatric Oncology, San Jorge Children’s
Hospital, San Juan, Puerto Rico
| | - Peter D. Cole
- Division of Pediatric Hematology/Oncology, Rutgers Cancer
Institute of New Jersey, Rutgers ;Robert Wood Johnson School of Medicine, New
Brunswick, NJ
| | - Lisa M. Gennarini
- Division of Pediatric Hematology/Oncology,
Children’s Hospital at Montefiore, Bronx, NY
| | - Justine M. Kahn
- Division of Pediatric Hematology, Oncology, and Stem Cell
Transplantation, Columbia University, New York, NY
| | - Kara M. Kelly
- Department of Pediatric Oncology, Roswell Park
Comprehensive Cancer Center, University at Buffalo, Buffalo, NY
| | - Caroline Laverdiere
- Division of Hematology and Oncology, Hospital
Sainte-Justine, University of Montreal, Montreal, Canada
| | - Jean-Marie Leclerc
- Division of Hematology and Oncology, Hospital
Sainte-Justine, University of Montreal, Montreal, Canada
| | - Bruno Michon
- Division of Hematology-Oncology, Centre Hospitalier
Universite de Quebec, Quebec City, Canada
| | | | - Maria Luisa Sulis
- Pediatric Hematologic Malignancies Service, Department of
Pediatric Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jennifer J.G. Welch
- Division of Pediatric Hematology-Oncology, Hasbro
Children’s Hospital, Warren Alpert Medical School of Brown University,
Providence, RI
| | - Donna S. Neuberg
- Department of Biostatistics and Computational Biology,
Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Stephen E. Sallan
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
| | - Lewis B. Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer
Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children’s
Hospital, Harvard Medical School, Boston, MA
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10
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Tottone L, Lancho O, Loh JW, Singh A, Kimura S, Roels J, Kuchmiy A, Strubbe S, Lawlor MA, da Silva-Diz V, Luo S, Gachet S, García-Prieto CA, Hagelaar R, Esteller M, Meijerink JPP, Soulier J, Taghon T, Van Vlierberghe P, Mullighan CG, Khiabanian H, Rocha PP, Herranz D. A Tumor Suppressor Enhancer of PTEN in T-cell development and leukemia. Blood Cancer Discov 2020; 2:92-109. [PMID: 33458694 DOI: 10.1158/2643-3230.bcd-20-0201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Long-range oncogenic enhancers play an important role in cancer. Yet, whether similar regulation of tumor suppressor genes is relevant remains unclear. Loss of expression of PTEN is associated with the pathogenesis of various cancers, including T-cell leukemia (T-ALL). Here, we identify a highly conserved distal enhancer (PE) that interacts with the PTEN promoter in multiple hematopoietic populations, including T-cells, and acts as a hub of relevant transcription factors in T-ALL. Consistently, loss of PE leads to reduced PTEN levels in T-ALL cells. Moreover, PE-null mice show reduced Pten levels in thymocytes and accelerated development of NOTCH1-induced T-ALL. Furthermore, secondary loss of PE in established leukemias leads to accelerated progression and a gene expression signature driven by Pten loss. Finally, we uncovered recurrent deletions encompassing PE in T-ALL, which are associated with decreased PTEN levels. Altogether, our results identify PE as the first long-range tumor suppressor enhancer directly implicated in cancer.
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Affiliation(s)
- Luca Tottone
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Olga Lancho
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Jui-Wan Loh
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Amartya Singh
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Shunsuke Kimura
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Juliette Roels
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Anna Kuchmiy
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Steven Strubbe
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Matthew A Lawlor
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Victoria da Silva-Diz
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Shirley Luo
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Stéphanie Gachet
- INSERM U944 and University de Paris, Hopital Saint-Louis, Paris, France
| | - Carlos A García-Prieto
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Barcelona Supercomputing Center (BSC), Barcelona, Catalonia, Spain
| | - Rico Hagelaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Madrid, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | | | - Jean Soulier
- INSERM U944 and University de Paris, Hopital Saint-Louis, Paris, France
| | - Tom Taghon
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Hossein Khiabanian
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey
| | - Pedro P Rocha
- Unit on Genome Structure and Regulation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Daniel Herranz
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey.
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey
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11
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Bonnet R, Nebout M, Brousse C, Reinier F, Imbert V, Rohrlich PS, Peyron JF. New Drug Repositioning Candidates for T-ALL Identified Via Human/Murine Gene Signature Comparison. Front Oncol 2020; 10:557643. [PMID: 33240808 PMCID: PMC7680901 DOI: 10.3389/fonc.2020.557643] [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: 04/30/2020] [Accepted: 10/07/2020] [Indexed: 12/30/2022] Open
Abstract
T-cell Acute Lymphoblastic Leukemia (T-ALL) is an aggressive subtype of leukemia for which important progress in treatment efficiency have been made in the past decades to reach a cure rate of 75%-80% nowadays. It is nevertheless mandatory to find new targets and active molecules for innovative therapeutic strategies as relapse is associated with a very dismal outcome. We designed an experimental workflow to highlight the conserved core pathways associated with leukemogenesis by confronting the gene expression profiles (GEPs) of human T-ALL cases to the GEP of a murine T-ALL representative model, generated by the conditional deletion of the PTEN tumor suppressor gene in T cell precursors (tPTEN-/-). We identified 844 differentially expressed genes, common GEPs (cGEP) that were conserved between human T-ALL and murine signatures, and also similarly differentially expressed, compared to normal T cells. Using bioinformatic tools we highlighted in cGEPan upregulation of E2F, MYC and mTORC1. Next, using Connectivity Map (CMAP) and CMAPViz a visualization procedure for CMAP data that we developed, we selected in silico three FDA-approved, bioactive molecule candidates: α-estradiol (α-E), nordihydroguaiaretic acid (NDGA) and prochlorperazine dimaleate (PCZ). At a biological level, we showed that the three drugs triggered an apoptotic cell death in a panel of T-ALL cell lines, activated a DNA damage response and interfered with constitutive mTORC1 activation and c-MYC expression. This analysis shows that the investigation of conserved leukemogenesis pathways could be a strategy to reveal new avenues for pharmacological intervention.
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Affiliation(s)
| | | | | | | | | | - Pierre Simon Rohrlich
- Université Côte d’Azur, INSERM, C3M, Nice, France
- Pediatric Hematology-Oncology, CHU de Nice, Nice, France
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12
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Roels J, Thénoz M, Szarzyńska B, Landfors M, De Coninck S, Demoen L, Provez L, Kuchmiy A, Strubbe S, Reunes L, Pieters T, Matthijssens F, Van Loocke W, Erarslan-Uysal B, Richter-Pechańska P, Declerck K, Lammens T, De Moerloose B, Deforce D, Van Nieuwerburgh F, Cheung LC, Kotecha RS, Mansour MR, Ghesquière B, Van Camp G, Berghe WV, Kowalczyk JR, Szczepański T, Davé UP, Kulozik AE, Goossens S, Curtis DJ, Taghon T, Dawidowska M, Degerman S, Van Vlierberghe P. Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia. Blood Cancer Discov 2020; 1:274-289. [PMID: 33179015 PMCID: PMC7116343 DOI: 10.1158/2643-3230.bcd-20-0059] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/06/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
Cancer cells display DNA hypermethylation at specific CpG islands in comparison to their normal healthy counterparts, but the mechanism that drives this so-called CpG island methylator phenotype (CIMP) remains poorly understood. Here, we show that CpG island methylation in human T-cell acute lymphoblastic leukemia (T-ALL) mainly occurs at promoters of Polycomb Repressor Complex 2 (PRC2) target genes that are not expressed in normal or malignant T-cells and which display a reciprocal association with H3K27me3 binding. In addition, we revealed that this aberrant methylation profile reflects the epigenetic history of T-ALL and is established already in pre-leukemic, self-renewing thymocytes that precede T-ALL development. Finally, we unexpectedly uncover that this age-related CpG island hypermethylation signature in T-ALL is completely resistant to the FDA-approved hypomethylating agent Decitabine. Altogether, we here provide conceptual evidence for the involvement of a pre-leukemic phase characterized by self-renewing thymocytes in the pathogenesis of human T-ALL.
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Affiliation(s)
- Juliette Roels
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Morgan Thénoz
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | - Mattias Landfors
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Stien De Coninck
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lisa Demoen
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lien Provez
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Anna Kuchmiy
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Steven Strubbe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Lindy Reunes
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Tim Pieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Filip Matthijssens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - 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
| | - 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
| | - Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES) and Integrated Personalized and Precision Oncology Network (IPPON), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Tim Lammens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Barbara De Moerloose
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | | | - Laurence C Cheung
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Western Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Western Australia
| | - Rishi S Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Western Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Western Australia
| | - Marc R Mansour
- Department of Haematology, University College London Cancer Institute, London, England
| | - Bart Ghesquière
- Metabolomics Expertise Center, VIB Center for Cancer Biology, Leuven, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES) and Integrated Personalized and Precision Oncology Network (IPPON), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Tomasz Szczepański
- Department of Pediatric Hematology and Oncology, Zabrze, Medical University of Silesia, Katowice, Poland
| | - Utpal P Davé
- Roudebush Veterans Affairs Medical Center and Indiana University School of Medicine, Indianapolis, Indiana
| | - 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
| | - Steven Goossens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - David J Curtis
- Australian Centre for Blood Diseases (ACBD), Monash University, Melbourne, Australia
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | | | - Sofie Degerman
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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13
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Lejman M, Włodarczyk M, Styka B, Pastorczak A, Zawitkowska J, Taha J, Sędek Ł, Skonieczka K, Braun M, Haus O, Szczepański T, Młynarski W, Kowalczyk JR. Advantages and Limitations of SNP Array in the Molecular Characterization of Pediatric T-Cell Acute Lymphoblastic Leukemia. Front Oncol 2020; 10:1184. [PMID: 32766158 PMCID: PMC7379740 DOI: 10.3389/fonc.2020.01184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/11/2020] [Indexed: 01/03/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a highly heterogeneous disease, and numerous genetic aberrations in the leukemic genome are responsible for the biological and clinical differences among particular ALL subtypes. However, there is limited knowledge regarding the association of whole-genome copy number abnormalities (CNAs) in childhood T-ALL with the course of leukemia and its outcome. The aim of this study was to identify the pattern of whole-genome CNAs in 86 newly diagnosed childhood T-ALL cases using a high-density single-nucleotide polymorphism array. We analyzed the presence of whole-genome CNAs with respect to immunophenotype, clinical features, and treatment outcomes. A total of 769 CNAs, including trisomies, duplications, deletions, and segmental loss of heterozygosity, were detected in 86 analyzed samples. Gain or loss of chromosomal regions exceeding 10 Mb occurred in 46 cases (53%), including six cases (7%) with complex chromosomal alterations. We observed that microdeletions in selected genes (e.g., FIP1L1 and PDGFRB) were related to the clinical features. Interestingly, 13% of samples have a duplication of the two loci (MYB and AIH1—6q23.3), which never occurred alone. Single-nucleotide polymorphism array significantly improved the molecular characterization of pediatric T-ALL. Further studies with larger cohorts of patients may contribute to the selection of prognostic CNAs in this group of patients.
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Affiliation(s)
- Monika Lejman
- Laboratory of Genetic Diagnostics, Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Monika Włodarczyk
- Laboratory of Genetic Diagnostics, University Children's Hospital, Lublin, Poland
| | - Borys Styka
- Laboratory of Genetic Diagnostics, University Children's Hospital, Lublin, Poland
| | - Agata Pastorczak
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódz, Łódź, Poland
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Joanna Taha
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódz, Łódź, Poland
| | - Łukasz Sędek
- Department of Microbiology and Oncology, Medical University of Silesia in Katowice, Katowice, Poland
| | - Katarzyna Skonieczka
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Marcin Braun
- Department of Pathology, Chair of Oncology, Medical University of Łódz, Łódź, Poland
| | - Olga Haus
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Tomasz Szczepański
- Department of Microbiology and Oncology, Medical University of Silesia in Katowice, Katowice, Poland
| | - Wojciech Młynarski
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódz, Łódź, Poland
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
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14
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Küçükcankurt F, Erbilgin Y, Fırtına S, Hatırnaz Ng Ö, Karakaş Z, Celkan T, Ünüvar A, Özbek U, Sayitoğlu M. PTEN and AKT1 Variations in Childhood T-Cell Acute Lymphoblastic Leukemia. Turk J Haematol 2020; 37:98-103. [PMID: 31744268 PMCID: PMC7236415 DOI: 10.4274/tjh.galenos.2019.2019.0282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Objective: PTEN/AKT pathway deregulations have been reported to be associated with treatment response in acute leukemia. This study examined pediatric T-cell acute lymphoblastic leukemia (T-ALL) samples for PTEN and AKT1 gene variations and evaluated the clinical findings. Materials and Methods: Fifty diagnostic bone marrow samples of childhood T-ALL cases were investigated for the hotspot regions of the PTEN and AKT1 genes by targeted next-generation sequencing. Results: A total of five PTEN variations were found in three of the 50 T-ALL cases (6%). Three of the PTEN variations were first reported in this study. Furthermore, one patient clearly had two different mutant clones for PTEN. Two intronic single-nucleotide variations were found in AKT1 and none of the patients carried pathogenic AKT1 variations. Conclusion: Targeted deep sequencing allowed us to detect both low-level variations and clonal diversity. Low-level PTEN/AKT1 variation frequency makes it harder to investigate the clinical associations of the variants. On the other hand, characterization of the PTEN/AKT signaling members is important for improving case-specific therapeutic strategies.
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Affiliation(s)
- Fulya Küçükcankurt
- İstanbul University, Aziz Sancar Institute of Experimental Medicine, Department of Genetics, İstanbul, Turkey,Altınbaş University Faculty of Medicine, İstanbul, Turkey,F.K. and Y.E. contributed equally to this work
| | - Yücel Erbilgin
- İstanbul University, Aziz Sancar Institute of Experimental Medicine, Department of Genetics, İstanbul, Turkey,F.K. and Y.E. contributed equally to this work
| | - Sinem Fırtına
- İstanbul University, Aziz Sancar Institute of Experimental Medicine, Department of Genetics, İstanbul, Turkey,İstinye University Faculty of Art and Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Özden Hatırnaz Ng
- İstanbul University, Aziz Sancar Institute of Experimental Medicine, Department of Genetics, İstanbul, Turkey,Acıbadem Mehmet Ali Aydınlar University Faculty of Medicine, Department of Medical Biology, İstanbul, Turkey
| | - Zeynep Karakaş
- İstanbul University Faculty of Medicine, Department of Pediatrics Hematology, İstanbul, Turkey
| | - Tiraje Celkan
- İstanbul University-Cerrahpaşa Cerrahpaşa Faculty of Medicine, Department of Pediatric Hematology, İstanbul, Turkey
| | - Ayşegül Ünüvar
- İstanbul University Faculty of Medicine, Department of Pediatrics Hematology, İstanbul, Turkey
| | - Uğur Özbek
- İstanbul University, Aziz Sancar Institute of Experimental Medicine, Department of Genetics, İstanbul, Turkey,Acıbadem Mehmet Ali Aydınlar University Faculty of Medicine, Department of Medical Genetics, İstanbul, Turkey
| | - Müge Sayitoğlu
- İstanbul University, Aziz Sancar Institute of Experimental Medicine, Department of Genetics, İstanbul, Turkey
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15
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hsa-miR-20b-5p and hsa-miR-363-3p Affect Expression of PTEN and BIM Tumor Suppressor Genes and Modulate Survival of T-ALL Cells In Vitro. Cells 2020; 9:cells9051137. [PMID: 32380791 PMCID: PMC7290785 DOI: 10.3390/cells9051137] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 12/17/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy arising from T lymphocyte precursors. We have previously shown by miRNA-seq, that miRNAs from the mir-106a-363 cluster are overexpressed in pediatric T-ALL. In silico analysis indicated their potential involvement in the regulation of apoptosis. Here, we aimed to test the hypothesis on the pro-tumorigenic roles of these miRNAs in T-ALL cells in vitro. We demonstrate, for the first time, that hsa-miR-20b-5p and hsa-miR-363-3p from the mir-106a-363 cluster, when upregulated in T-ALL cells in vitro, protect leukemic cells from apoptosis, enhance proliferation, and contribute to growth advantage. We show, using dual luciferase reporter assays, Ago2-RNA immunoprecipitation, RT-qPCR, and Western blots, that the oncogenic effects of these upregulated miRNAs might, at least in part, be mediated by the downregulation of two important tumor suppressor genes, PTEN and BIM, targeted by both miRNAs. Additionally, we demonstrate the cooperative effects of these two miRNAs by simultaneous inhibition of both miRNAs as compared to the inhibition of single miRNAs. We postulate that hsa-miR-20b-5p and hsa-miR-363-3p from the mir-106a-363 cluster might serve as oncomiRs in T-ALL, by contributing to post-transcriptional repression of key tumor suppressors, PTEN and BIM.
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16
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Comprehensive profiling of disease-relevant copy number aberrations for advanced clinical diagnostics of pediatric acute lymphoblastic leukemia. Mod Pathol 2020; 33:812-824. [PMID: 31857684 DOI: 10.1038/s41379-019-0423-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/30/2022]
Abstract
Acute lymphoblastic leukemia is the most common pediatric cancer characterized by a heterogeneous genomic landscape with copy number aberrations occurring at various stages of pathogenesis, disease progression, and treatment resistance. In this study, disease-relevant copy number aberrations were profiled in bone marrow samples of 91 children with B- or T-cell precursor acute lymphoblastic leukemia using digital multiplex ligation-dependent probe amplification (digitalMLPATM). Whole chromosome gains and losses, subchromosomal copy number aberrations, as well as unbalanced alterations conferring intrachromosomal gene fusions were simultaneously identified with results available within 36 hours. Aberrations were observed in 96% of diagnostic patient samples, and increased numbers of copy number aberrations were detected at the time of relapse as compared with diagnosis. Comparative scrutiny of 24 matching diagnostic and relapse samples from 11 patients revealed three different patterns of clonal relationships with (i) one patient displaying identical copy number aberration profiles at diagnosis and relapse, (ii) six patients showing clonal evolution with all lesions detected at diagnosis being present at relapse, and (iii) four patients displaying conserved as well as lost or gained copy number aberrations at the time of relapse, suggestive of the presence of a common ancestral cell compartment giving rise to clinically manifest leukemia at different time points during the disease course. A newly introduced risk classifier combining cytogenetic data with digitalMLPATM-based copy number aberration profiles allowed for the determination of four genetic subgroups of B-cell precursor acute lymphoblastic leukemia with distinct event-free survival rates. DigitalMLPATM provides fast, robust, and highly optimized copy number aberration profiling for the genomic characterization of acute lymphoblastic leukemia samples, facilitates the decipherment of the clonal origin of relapse and provides highly relevant information for clinical prognosis assessment.
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17
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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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18
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De Smedt R, Morscio J, Goossens S, Van Vlierberghe P. Targeting steroid resistance in T-cell acute lymphoblastic leukemia. Blood Rev 2019; 38:100591. [PMID: 31353059 DOI: 10.1016/j.blre.2019.100591] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 12/16/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is characterized by a variable response to steroids during induction and/or consolidation therapy. Notably, recent work suggested that these differences in glucocorticoid sensitivity might, at least in part, be mediated by hyperactivation of specific oncogenic pathways such as RAS/MEK/ERK, PI3K/AKT and IL7R/JAK/STAT. In this review, we elaborate on putative associations between aberrant signaling, therapy resistance, incidence of relapse and clinical outcome in human T-ALL. Furthermore, we emphasize that this potential association with clinical parameters might also be mediated by the tumor microenvironment as a result of increased sensitivity of leukemic T-cells towards cytokine induced signaling pathway activation. With this in mind, we provide an overview of small molecule inhibitors that might have clinical potential for the treatment of human T-ALL in the near future as a result of their ability to overcome steroid resistance thereby potentially increasing survival rates in this aggressive hematological neoplasm.
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Affiliation(s)
- Renate De Smedt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Julie Morscio
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Steven Goossens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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19
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Martelli AM, Paganelli F, Fazio A, Bazzichetto C, Conciatori F, McCubrey JA. The Key Roles of PTEN in T-Cell Acute Lymphoblastic Leukemia Development, Progression, and Therapeutic Response. Cancers (Basel) 2019; 11:cancers11050629. [PMID: 31064074 PMCID: PMC6562458 DOI: 10.3390/cancers11050629] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/16/2019] [Accepted: 05/04/2019] [Indexed: 02/07/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive blood cancer that comprises 10–15% of pediatric and ~25% of adult ALL cases. Although the curative rates have significantly improved over the past 10 years, especially in pediatric patients, T-ALL remains a challenge from a therapeutic point of view, due to the high number of early relapses that are for the most part resistant to further treatment. Considerable advances in the understanding of the genes, signaling networks, and mechanisms that play crucial roles in the pathobiology of T-ALL have led to the identification of the key drivers of the disease, thereby paving the way for new therapeutic approaches. PTEN is critical to prevent the malignant transformation of T-cells. However, its expression and functions are altered in human T-ALL. PTEN is frequently deleted or mutated, while PTEN protein is often phosphorylated and functionally inactivated by casein kinase 2. Different murine knockout models recapitulating the development of T-ALL have demonstrated that PTEN abnormalities are at the hub of an intricate oncogenic network sustaining and driving leukemia development by activating several signaling cascades associated with drug-resistance and poor outcome. These aspects and their possible therapeutic implications are highlighted in this review.
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Affiliation(s)
- Alberto M Martelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy.
| | - Francesca Paganelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy.
| | - Antonietta Fazio
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy.
| | - Chiara Bazzichetto
- Medical Oncology 1, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy.
| | - Fabiana Conciatori
- Medical Oncology 1, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy.
| | - James A McCubrey
- Department of Microbiology & Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA.
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