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Mandell JD, Diviti S, Xu M, Townsend JP. Rare Drivers at Low Prevalence with High Cancer Effects in T-Cell and B-Cell Pediatric Acute Lymphoblastic Leukemia. Int J Mol Sci 2024; 25:6589. [PMID: 38928295 PMCID: PMC11203805 DOI: 10.3390/ijms25126589] [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: 05/17/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
The genomic analyses of pediatric acute lymphoblastic leukemia (ALL) subtypes, particularly T-cell and B-cell lineages, have been pivotal in identifying potential therapeutic targets. Typical genomic analyses have directed attention toward the most commonly mutated genes. However, assessing the contribution of mutations to cancer phenotypes is crucial. Therefore, we estimated the cancer effects (scaled selection coefficients) for somatic substitutions in T-cell and B-cell cohorts, revealing key insights into mutation contributions. Cancer effects for well-known, frequently mutated genes like NRAS and KRAS in B-ALL were high, which underscores their importance as therapeutic targets. However, less frequently mutated genes IL7R, XBP1, and TOX also demonstrated high cancer effects, suggesting pivotal roles in the development of leukemia when present. In T-ALL, KRAS and NRAS are less frequently mutated than in B-ALL. However, their cancer effects when present are high in both subtypes. Mutations in PIK3R1 and RPL10 were not at high prevalence, yet exhibited some of the highest cancer effects in individual T-cell ALL patients. Even CDKN2A, with a low prevalence and relatively modest cancer effect, is potentially highly relevant for the epistatic effects that its mutated form exerts on other mutations. Prioritizing investigation into these moderately frequent but potentially high-impact targets not only presents novel personalized therapeutic opportunities but also enhances the understanding of disease mechanisms and advances precision therapeutics for pediatric ALL.
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Affiliation(s)
- Jeffrey D. Mandell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA;
| | | | - Mina Xu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA;
- Program in Genetics, Genomics, and Epigenetics, Yale Cancer Center, New Haven, CT 06520, USA
| | - Jeffrey P. Townsend
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA;
- Program in Genetics, Genomics, and Epigenetics, Yale Cancer Center, New Haven, CT 06520, USA
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
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2
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Singh M, Sharma P, Bhatia P, Trehan A, Thakur R, Sreedharanunni S. Integrated analysis of transcriptome and genome variations in pediatric T cell acute lymphoblastic leukemia: data from north Indian tertiary care center. BMC Cancer 2024; 24:325. [PMID: 38459434 PMCID: PMC10924344 DOI: 10.1186/s12885-024-12063-6] [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: 11/23/2023] [Accepted: 02/26/2024] [Indexed: 03/10/2024] Open
Abstract
INTRODUCTION T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease with poor prognosis and inferior outcome. Although multiple studies have been perform on genomics of T-ALL, data from Indian sub-continent is scarce. METHODS In the current study we aimed to identify the genetic variability of T-ALL in an Indian cohort of pediatric (age ≤ 12 years) T-ALL patients (n = 25) by whole transcriptome sequencing along with whole exome sequencing and correlated the findings with clinical characteristics and disease outcome. RESULTS The median age was 7 years (range 3 -12 years). RNA sequencing revealed a definitive fusion event in 14 cases (56%) (including a novel fusions) with STIL::TAL1 in 4 (16%), followed by NUP21::ABL1, TCF7::SPI1, ETV6::HDAC8, LMO1::RIC3, DIAPH1::JAK2, SETD2::CCDC12 and RCBTB2::LPAR6 in 1 (4%) case each. Significant aberrant expression was noted in RAG1 (64%), RAG2 (80%), MYCN (52%), NKX3-1 (52%), NKX3-2 (32%), TLX3 (28%), LMO1 (20%) and MYB (16%) genes. WES data showed frequent mutations in NOTCH1 (35%) followed by WT1 (23%), FBXW7 (12%), KRAS (12%), PHF6 (12%) and JAK3 (12%). Nearly 88.2% of cases showed a deletion of CDKN2A/CDKN2B/MTAP genes. Clinically significant association of a better EFS and OS (p=0.01) was noted with RAG2 over-expression at a median follow up of 22 months, while a poor EFS (p=0.041) and high relapse rate (p=0.045) was observed with MYB over-expression. CONCLUSION Overall, the present study demonstrates the frequencies of transcriptomic and genetic alterations from Indian cohort of pediatric T-ALL and is a salient addition to current genomics data sets available in T-ALL.
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Affiliation(s)
- Minu Singh
- Haematology-Oncology Unit, Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Sector -12, 160012, Chandigarh, India.
| | - Pankaj Sharma
- Haematology-Oncology Unit, Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Sector -12, 160012, Chandigarh, India
| | - Prateek Bhatia
- Haematology-Oncology Unit, Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Sector -12, 160012, Chandigarh, India
| | - Amita Trehan
- Haematology-Oncology Unit, Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Sector -12, 160012, Chandigarh, India
| | - Rozy Thakur
- Haematology-Oncology Unit, Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Sector -12, 160012, Chandigarh, India
| | - Sreejesh Sreedharanunni
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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3
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Pinton A, Courtois L, Doublet C, Cabannes-Hamy A, Andrieu G, Smith C, Balducci E, Cieslak A, Touzart A, Simonin M, Lhéritier V, Huguet F, Balsat M, Dombret H, Rousselot P, Spicuglia S, Macintyre E, Boissel N, Asnafi V. PHF6-altered T-ALL Harbor Epigenetic Repressive Switch at Bivalent Promoters and Respond to 5-Azacitidine and Venetoclax. Clin Cancer Res 2024; 30:94-105. [PMID: 37889114 DOI: 10.1158/1078-0432.ccr-23-2159] [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: 09/27/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023]
Abstract
PURPOSE To assess the impact of PHF6 alterations on clinical outcome and therapeutical actionability in T-cell acute lymphoblastic leukemia (T-ALL). EXPERIMENTAL DESIGN We described PHF6 alterations in an adult cohort of T-ALL from the French trial Group for Research on Adult Acute Lymphoblastic Leukemia (GRAALL)-2003/2005 and retrospectively analyzed clinical outcomes between PHF6-altered (PHF6ALT) and wild-type patients. We also used EPIC and chromatin immunoprecipitation sequencing data of patient samples to analyze the epigenetic landscape of PHF6ALT T-ALLs. We consecutively evaluated 5-azacitidine efficacy, alone or combined with venetoclax, in PHF6ALT T-ALL. RESULTS We show that PHF6 alterations account for 47% of cases in our cohort and demonstrate that PHF6ALT T-ALL presented significantly better clinical outcomes. Integrative analysis of DNA methylation and histone marks shows that PHF6ALT are characterized by DNA hypermethylation and H3K27me3 loss at promoters physiologically bivalent in thymocytes. Using patient-derived xenografts, we show that PHF6ALT T-ALL respond to the 5-azacytidine alone. Finally, synergism with the BCL2-inhibitor venetoclax was demonstrated in refractory/relapsing (R/R) PHF6ALT T-ALL using fresh samples. Importantly, we report three cases of R/R PHF6ALT patients who were successfully treated with this combination. CONCLUSIONS Overall, our study supports the use of PHF6 alterations as a biomarker of sensitivity to 5-azacytidine and venetoclax combination in R/R T-ALL.
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Affiliation(s)
- Antoine Pinton
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Lucien Courtois
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | | | | | - Guillaume Andrieu
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Charlotte Smith
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Estelle Balducci
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Agata Cieslak
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Aurore Touzart
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Mathieu Simonin
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Véronique Lhéritier
- Coordination du Groupe Group for Research in Adult Acute Lymphoblastic Leukemia, Hospices Civils de Lyon, Hôpital Lyon Sud, Lyon, France
| | - Françoise Huguet
- Service d'Hématologie, CHU de Toulouse, IUCT-Oncopole, Toulouse, France
| | - Marie Balsat
- Service d'Hématologie Clinique, Hôpital Lyon Sud, Lyon, France
| | - Hervé Dombret
- Service d'Hématologie Adolescents et Jeunes Adultes, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
- Institut de Recherche Saint-Louis, UPR-3518, Université Paris Cité, Paris, France
| | - Philippe Rousselot
- Centre Hospitalier de Versailles, Versailles, France
- Université Versailles Saint Quentin en Yvelines Paris Saclay, INSERM U1184, Paris, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Elizabeth Macintyre
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Nicolas Boissel
- Service d'Hématologie Adolescents et Jeunes Adultes, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
- Institut de Recherche Saint-Louis, UPR-3518, Université Paris Cité, Paris, France
| | - Vahid Asnafi
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
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4
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Gou Y, Tang Y, Liu S, Cheng S, Deng X, Wen Q, Feng Y, Peng X, Wang P, Zhang X. Myeloid/Lymphoid Neoplasms with ETV6::PDGFRB Fusion Gene: A Rare Case of Poor Response to Imatinib and Possible Transformation Mechanisms from Myeloid Neoplasms of Bone Marrow to T-Cell Lymphoblastic Lymphoma Invasion in Lymph Nodes. J Inflamm Res 2023; 16:5163-5170. [PMID: 38026242 PMCID: PMC10649033 DOI: 10.2147/jir.s427995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/20/2023] [Indexed: 12/01/2023] Open
Abstract
The ETV6::PDGFRB fusion gene is commonly reported in chronic myelomonocytic leukemia with eosinophilia, yet patients with ETV6::PDGFRB presenting myeloid and lymphoid neoplasms successively have not been reported. Here, we report the first case of a 35-year-old man with myeloid and lymphoid neoplasms harboring an ETV6::PDGFRB fusion gene who demonstrated poor response to imatinib. The patient was diagnosed with an ETV6::PDGFRB fusion gene myeloid neoplasm on initial diagnosis at our hospital. After 5 months of treatment with imatinib, he was diagnosed with T-cell lymphoblastic lymphoma. ETV6::PDGFRB turned negative after increasing the dose of imatinib, but enlarged superficial lymph nodes reappeared the following year. Notably, the patient exhibited a worse response to imatinib treatment. This study describes this rare case and speculates on a possible mechanism.
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Affiliation(s)
- Yang Gou
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, People’s Republic of China
| | - Yongjie Tang
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, People’s Republic of China
| | - Shuiqing Liu
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, People’s Republic of China
| | - Siyu Cheng
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, People’s Republic of China
| | - Xiaojuan Deng
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, People’s Republic of China
| | - Qin Wen
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, People’s Republic of China
| | - Yimei Feng
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, People’s Republic of China
| | - Xiangui Peng
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, People’s Republic of China
| | - Ping Wang
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, People’s Republic of China
| | - Xi Zhang
- Medical Center of Hematology, Xinqiao Hospital of Army Medical University, Chongqing, People’s Republic of China
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5
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Fuchs S, Danßmann C, Klironomos F, Winkler A, Fallmann J, Kruetzfeldt LM, Szymansky A, Naderi J, Bernhart SH, Grunewald L, Helmsauer K, Rodriguez-Fos E, Kirchner M, Mertins P, Astrahantseff K, Suenkel C, Toedling J, Meggetto F, Remke M, Stadler PF, Hundsdoerfer P, Deubzer HE, Künkele A, Lang P, Fuchs J, Henssen AG, Eggert A, Rajewsky N, Hertwig F, Schulte JH. Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN. Nat Commun 2023; 14:3936. [PMID: 37402719 DOI: 10.1038/s41467-023-38747-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 05/12/2023] [Indexed: 07/06/2023] Open
Abstract
Circular RNAs (circRNAs) are a regulatory RNA class. While cancer-driving functions have been identified for single circRNAs, how they modulate gene expression in cancer is not well understood. We investigate circRNA expression in the pediatric malignancy, neuroblastoma, through deep whole-transcriptome sequencing in 104 primary neuroblastomas covering all risk groups. We demonstrate that MYCN amplification, which defines a subset of high-risk cases, causes globally suppressed circRNA biogenesis directly dependent on the DHX9 RNA helicase. We detect similar mechanisms in shaping circRNA expression in the pediatric cancer medulloblastoma implying a general MYCN effect. Comparisons to other cancers identify 25 circRNAs that are specifically upregulated in neuroblastoma, including circARID1A. Transcribed from the ARID1A tumor suppressor gene, circARID1A promotes cell growth and survival, mediated by direct interaction with the KHSRP RNA-binding protein. Our study highlights the importance of MYCN regulating circRNAs in cancer and identifies molecular mechanisms, which explain their contribution to neuroblastoma pathogenesis.
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Affiliation(s)
- Steffen Fuchs
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany.
- The German Cancer Consortium (DKTK), Partner Site Berlin, 10117, Berlin, Germany.
- The German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10178, Berlin, Germany.
- CRCT, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, 31037, Toulouse, France.
- Laboratoire d'Excellence Toulouse Cancer-TOUCAN, 31037, Toulouse, France.
| | - Clara Danßmann
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Filippos Klironomos
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Annika Winkler
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany
| | - Louisa-Marie Kruetzfeldt
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Julian Naderi
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Stephan H Bernhart
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany
| | - Laura Grunewald
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, 10117, Berlin, Germany
- The German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Konstantin Helmsauer
- Experimental and Clinical Research Center (ECRC) of the Charité and Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, 13125, Berlin, Germany
| | - Elias Rodriguez-Fos
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the Charité and Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, 13125, Berlin, Germany
| | - Marieluise Kirchner
- Core Unit Proteomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany
| | - Philipp Mertins
- Core Unit Proteomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany
| | - Kathy Astrahantseff
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Christin Suenkel
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Straße 28, 10115, Berlin, Germany
- Lonza Drug Product Services, 4057, Basel, Switzerland
| | - Joern Toedling
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, 10117, Berlin, Germany
- The German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Fabienne Meggetto
- CRCT, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, 31037, Toulouse, France
- Laboratoire d'Excellence Toulouse Cancer-TOUCAN, 31037, Toulouse, France
| | - Marc Remke
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich Heine University Düsseldorf, Medical Faculty, and University Hospital Düsseldorf, 40225, Düsseldorf, Germany
- The German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, 40225, Düsseldorf, Germany
- Institute of Neuropathology, Heinrich Heine University Düsseldorf, Medical Faculty, and University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany
| | - Patrick Hundsdoerfer
- Department of Pediatric Oncology, Helios Klinikum Berlin-Buch, 13125, Berlin, Germany
| | - Hedwig E Deubzer
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, 10117, Berlin, Germany
- The German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10178, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the Charité and Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, 13125, Berlin, Germany
| | - Annette Künkele
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, 10117, Berlin, Germany
- The German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Peter Lang
- Department I - General Pediatrics, Hematology/Oncology, University Children's Hospital, Eberhard Karls University Tuebingen, 72076, Tuebingen, Germany
| | - Jörg Fuchs
- Department of Pediatric Surgery and Pediatric Urology, University Children's Hospital, Eberhard Karls University Tuebingen, 72076, Tuebingen, Germany
| | - Anton G Henssen
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, 10117, Berlin, Germany
- The German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Experimental and Clinical Research Center (ECRC) of the Charité and Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, 13125, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, 10117, Berlin, Germany
- The German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10178, Berlin, Germany
| | - Nikolaus Rajewsky
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Straße 28, 10115, Berlin, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, 10117, Berlin, Germany
- The German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany.
- The German Cancer Consortium (DKTK), Partner Site Berlin, 10117, Berlin, Germany.
- The German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10178, Berlin, Germany.
- Department I - General Pediatrics, Hematology/Oncology, University Children's Hospital, Eberhard Karls University Tuebingen, 72076, Tuebingen, Germany.
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6
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Pottosin I, Olivas-Aguirre M, Dobrovinskaya O. In vitro simulation of the acute lymphoblastic leukemia niche: a critical view on the optimal approximation for drug testing. J Leukoc Biol 2023; 114:21-41. [PMID: 37039524 DOI: 10.1093/jleuko/qiad039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/12/2023] Open
Abstract
Acute lymphoblastic leukemia with the worst prognosis is related to minimal residual disease. Minimal residual disease not only depends on the individual peculiarities of leukemic clones but also reflects the protective role of the acute lymphoblastic leukemia microenvironment. In this review, we discuss in detail cell-to-cell interactions in the 2 leukemic niches, more explored bone marrow and less studied extramedullary adipose tissue. A special emphasis is given to multiple ways of interactions of acute lymphoblastic leukemia cells with the bone marrow or extramedullary adipose tissue microenvironment, indicating observed differences in B- and T-cell-derived acute lymphoblastic leukemia behavior. This analysis argued for the usage of coculture systems for drug testing. Starting with a review of available sources and characteristics of acute lymphoblastic leukemia cells, mesenchymal stromal cells, endothelial cells, and adipocytes, we have then made an update of the available 2-dimensional and 3-dimensional systems, which bring together cellular elements, components of the extracellular matrix, or its imitation. We discussed the most complex available 3-dimensional systems like "leukemia-on-a-chip," which include either a prefabricated microfluidics platform or, alternatively, the microarchitecture, designed by using the 3-dimensional bioprinting technologies. From our analysis, it follows that for preclinical antileukemic drug testing, in most cases, intermediately complex in vitro cell systems are optimal, such as a "2.5-dimensional" coculture of acute lymphoblastic leukemia cells with niche cells (mesenchymal stromal cells, endothelial cells) plus matrix components or scaffold-free mesenchymal stromal cell organoids, populated by acute lymphoblastic leukemia cells. Due to emerging evidence for the correlation of obesity and poor prognosis, a coculture of adipocytes with acute lymphoblastic leukemia cells as a drug testing system is gaining shape.
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Affiliation(s)
- Igor Pottosin
- Laboratory of Immunobiology and Ionic Transport Regulation, University Center for Biomedical Research, University of Colima, Av. Enrique Arreola Silva 883, Guzmán City, Jalisco, 49000, Mexico
| | - Miguel Olivas-Aguirre
- Laboratory of Immunobiology and Ionic Transport Regulation, University Center for Biomedical Research, University of Colima, Av. Enrique Arreola Silva 883, Guzmán City, Jalisco, 49000, Mexico
- Division of Exact, Natural and Technological Sciences, South University Center (CUSUR), University of Guadalajara, Jalisco, Mexico
| | - Oxana Dobrovinskaya
- Laboratory of Immunobiology and Ionic Transport Regulation, University Center for Biomedical Research, University of Colima, Av. Enrique Arreola Silva 883, Guzmán City, Jalisco, 49000, Mexico
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7
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Eisa YA, Guo Y, Yang FC. The Role of PHF6 in Hematopoiesis and Hematologic Malignancies. Stem Cell Rev Rep 2023; 19:67-75. [PMID: 36008597 DOI: 10.1007/s12015-022-10447-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2022] [Indexed: 01/29/2023]
Abstract
Epigenetic regulation of gene expression represents an important mechanism in the maintenance of stem cell function. Alterations in epigenetic regulation contribute to the pathogenesis of hematological malignancies. Plant homeodomain finger protein 6 (PHF6) is a member of the plant homeodomain (PHD)-like zinc finger family of proteins that is involved in transcriptional regulation through the modification of the chromatin state. Germline mutation of PHF6 is the causative genetic alteration of the X-linked mental retardation Borjeson-Forssman-Lehmann syndrome (BFLS). Somatic mutations in PHF6 are identified in human leukemia, such as adult T-cell acute lymphoblastic leukemia (T-ALL, ~ 38%), pediatric T-ALL (~ 16%), acute myeloid leukemia (AML, ~ 3%), chronic myeloid leukemia (CML, ~ 2.5%), mixed phenotype acute leukemia (MPAL, ~ 20%), and high-grade B-cell lymphoma (HGBCL, ~ 3%). More recent studies imply an oncogenic effect of PHF6 in B-cell acute lymphoblastic leukemia (B-ALL) and solid tumors. These data demonstrate that PHF6 could act as a double-edged sword, either a tumor suppressor or an oncogene, in a lineage-dependent manner. However, the underlying mechanisms of PHF6 in normal hematopoiesis and leukemogenesis remain largely unknown. In this review, we summarize current knowledge of PHF6, emphasizing the role of PHF6 in hematological malignancies. Epigenetic regulation of PHF6 in B-ALL. PHF6 maintains a chromatin structure that is permissive to B-cell identity genes, but not T-cell-specific genes (left). Loss of PHF6 leads to aberrant expression of B-cell- and T-cell-specific genes resulting from lineage promiscuity and binding of T-cell transcription factors (right).
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Affiliation(s)
- Yusra A Eisa
- Department of Cell Systems & Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Ying Guo
- Department of Cell Systems & Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Feng-Chun Yang
- Department of Cell Systems & Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA. .,Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, USA.
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8
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Rehn J, Mayoh C, Heatley SL, McClure BJ, Eadie LN, Schutz C, Yeung DT, Cowley MJ, Breen J, White DL. RaScALL: Rapid (Ra) screening (Sc) of RNA-seq data for prognostically significant genomic alterations in acute lymphoblastic leukaemia (ALL). PLoS Genet 2022; 18:e1010300. [PMID: 36251721 PMCID: PMC9612819 DOI: 10.1371/journal.pgen.1010300] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/27/2022] [Accepted: 09/22/2022] [Indexed: 12/05/2022] Open
Abstract
RNA-sequencing (RNA-seq) efforts in acute lymphoblastic leukaemia (ALL) have identified numerous prognostically significant genomic alterations which can guide diagnostic risk stratification and treatment choices when detected early. However, integrating RNA-seq in a clinical setting requires rapid detection and accurate reporting of clinically relevant alterations. Here we present RaScALL, an implementation of the k-mer based variant detection tool km, capable of identifying more than 100 prognostically significant lesions observed in ALL, including gene fusions, single nucleotide variants and focal gene deletions. We compared genomic alterations detected by RaScALL and those reported by alignment-based de novo variant detection tools in a study cohort of 180 Australian patient samples. Results were validated using 100 patient samples from a published North American cohort. RaScALL demonstrated a high degree of accuracy for reporting subtype defining genomic alterations. Gene fusions, including difficult to detect fusions involving EPOR and DUX4, were accurately identified in 98% of reported cases in the study cohort (n = 164) and 95% of samples (n = 63) in the validation cohort. Pathogenic sequence variants were correctly identified in 75% of tested samples, including all cases involving subtype defining variants PAX5 p.P80R (n = 12) and IKZF1 p.N159Y (n = 4). Intragenic IKZF1 deletions resulting in aberrant transcript isoforms were also detectable with 98% accuracy. Importantly, the median analysis time for detection of all targeted alterations averaged 22 minutes per sample, significantly shorter than standard alignment-based approaches. The application of RaScALL enables rapid identification and reporting of previously identified genomic alterations of known clinical relevance.
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Affiliation(s)
- Jacqueline Rehn
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Chelsea Mayoh
- Children’s Cancer Institute, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - Susan L Heatley
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Australian and New Zealand Children’s Oncology Group (ANZCHOG), Clayton, Victoria, Australia
| | - Barbara J McClure
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Laura N Eadie
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Caitlin Schutz
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
| | - David T Yeung
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, South Australia, Australia
| | - Mark J Cowley
- Children’s Cancer Institute, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - James Breen
- Black Ochre Data Labs, Telethon Kids Institute, Adelaide, South Australia, Australia
- Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail:
| | - Deborah L White
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Faculty of Health and Medical Science, University of Adelaide, Adelaide, South Australia, Australia
- Australian and New Zealand Children’s Oncology Group (ANZCHOG), Clayton, Victoria, Australia
- Australian Genomics Health Alliance (AGHA), Parkville, Victoria, Australia
- Faculty of Sciences, University of Adelaide, Adelaide, South Australia, Australia
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Neveu B, Richer C, Cassart P, Caron M, Jimenez-Cortes C, St-Onge P, Fuchs C, Garnier N, Gobeil S, Sinnett D. Identification of new ETV6 modulators through a high-throughput functional screening. iScience 2022; 25:103858. [PMID: 35198911 PMCID: PMC8851229 DOI: 10.1016/j.isci.2022.103858] [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: 08/13/2021] [Revised: 01/01/2022] [Accepted: 01/28/2022] [Indexed: 12/02/2022] Open
Abstract
ETV6 transcriptional activity is critical for proper blood cell development in the bone marrow. Despite the accumulating body of evidence linking ETV6 malfunction to hematological malignancies, its regulatory network remains unclear. To uncover genes that modulate ETV6 repressive transcriptional activity, we performed a specifically designed, unbiased genome-wide shRNA screen in pre-B acute lymphoblastic leukemia cells. Following an extensive validation process, we identified 13 shRNAs inducing overexpression of ETV6 transcriptional target genes. We showed that the silencing of AKIRIN1, COMMD9, DYRK4, JUNB, and SRP72 led to an abrogation of ETV6 repressive activity. We identified critical modulators of the ETV6 function which could participate in cellular transformation through the ETV6 transcriptional network. We develop a genome-wide shRNAs screen for ETV6 modulators The screen uncovered 13 novel putative ETV6 modulator genes The modulators demonstrated a broad impact on the ETV6 transcriptional network T-ALL cells results suggest modulators are conserved in other cellular contexts
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Affiliation(s)
- Benjamin Neveu
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Chantal Richer
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Pauline Cassart
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Maxime Caron
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Camille Jimenez-Cortes
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Molecular Biology Program, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Pascal St-Onge
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Claire Fuchs
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Nicolas Garnier
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Stéphane Gobeil
- CHU de Québec-Université Laval Research Center, Quebec City, QC G1V 4G2, Canada
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Corresponding author
| | - Daniel Sinnett
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
- Corresponding author
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Population-based Targeted RNA Sequencing Reveals Novel Disease-related Gene Fusions in pediatric and adult T-ALL. Leuk Res 2022; 116:106825. [DOI: 10.1016/j.leukres.2022.106825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 11/21/2022]
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11
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Kdm6a deficiency restricted to mouse hematopoietic cells causes an age- and sex-dependent myelodysplastic syndrome-like phenotype. PLoS One 2021; 16:e0255706. [PMID: 34780480 PMCID: PMC8592440 DOI: 10.1371/journal.pone.0255706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/19/2021] [Indexed: 12/18/2022] Open
Abstract
Kdm6a/Utx, a gene on the X chromosome, encodes a histone H3K27me3 demethylase that has an orthologue on the Y chromosome (Uty) (Zheng et al. 2018). We previously identified inactivating mutations of Kdm6a in approximately 50% of mouse acute promyelocytic leukemia samples; however, somatic mutations of KDM6A are more rare in human AML samples, ranging in frequency from 2–15% in different series of patients, where their role in pathogenesis is not yet clear. In this study, we show that female Kdm6aflox/flox mice (with allele inactivation initiated by Vav1-Cre in hematopoietic stem and progenitor cells (HSPCs) have a sex-specific phenotype that emerges with aging, with features resembling a myelodysplastic syndrome (MDS). Female Kdm6a-knockout (KO) mice have an age-dependent expansion of their HSPCs with aberrant self-renewal, but they did not differentiate normally into downstream progeny. These mice became mildly anemic and thrombocytopenic, but did not develop overt leukemia, or die from these cytopenias. ChIP-seq and ATAC-seq studies showed only minor changes in H3K27me3, H3K27ac, H3K4me, H3K4me3 and chromatin accessibility between Kdm6a-WT and Kdm6a-KO mice. Utilizing scRNA-seq, Kdm6a loss was linked to the transcriptional repression of genes that mediate hematopoietic cell fate determination. These data demonstrate that Kdm6a plays an important role in normal hematopoiesis, and that its inactivation may contribute to AML pathogenesis.
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12
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Afkhami M, Ally F, Pullarkat V, Pillai RK. Genetics and Diagnostic Approach to Lymphoblastic Leukemia/Lymphoma. Cancer Treat Res 2021; 181:17-43. [PMID: 34626353 DOI: 10.1007/978-3-030-78311-2_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Our understanding of the genetics and biology of lymphoblastic leukemia/lymphoma (acute lymphoblastic leukemia, ALL) has advanced rapidly in the past decade with advances in sequencing and other molecular techniques. Besides recurrent chromosomal abnormalities detected by karyotyping or fluorescence in situ hybridization, these leukemias/lymphomas are characterized by a variety of mutations, gene rearrangements as well as copy number alterations. This is particularly true in the case of Philadelphia-like (Ph-like) ALL, a major subset which has the same gene expression signature as Philadelphia chromosome-positive ALL but lacks BCR-ABL1 translocation. Ph-like ALL is associated with a worse prognosis and hence its detection is critical. However, techniques to detect this entity are complex and are not widely available. This chapter discusses various subsets of ALL and describes our approach to the accurate classification and prognostication of these cases.
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Affiliation(s)
- Michelle Afkhami
- City of Hope Medical Center, 1500 E Duarte Rd., Duarte, CA, 91010, USA.
| | - Feras Ally
- City of Hope Medical Center, 1500 E Duarte Rd., Duarte, CA, 91010, USA
| | - Vinod Pullarkat
- City of Hope Medical Center, 1500 E Duarte Rd., Duarte, CA, 91010, USA
| | - Raju K Pillai
- City of Hope Medical Center, 1500 E Duarte Rd., Duarte, CA, 91010, USA
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13
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Bilineal evolution of a U2AF1-mutated clone associated with acquisition of distinct secondary mutations. Blood Adv 2021; 5:5612-5616. [PMID: 34581783 PMCID: PMC8714722 DOI: 10.1182/bloodadvances.2021005308] [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: 05/18/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022] Open
Abstract
Rare hematologic malignancies display evidence of both myeloid and lymphoid differentiation. Here, we describe such a novel bilineal event discovered in an adult woman with B-lymphoblastic leukemia (BLL). At the time of BLL diagnosis, the patient had a normal karyotype and a bulk sequencing panel identified pathogenic variants in BCOR, EZH2, RUNX1, and U2AF1, a genotype more typical of myeloid neoplasia. Additionally, the patient was noted to have 3-year history of cytopenias, and morphologic dyspoiesis was noted on post-treatment samples, raising the possibility of an antecedent hematologic disorder. To investigate the clonal architecture of her disease, we performed targeted sequencing on fractionated samples enriched for either B-lymphoblasts or circulating granulocytes. These studies revealed a truncal founder mutation in the spliceosome gene U2AF1 in both fractions, while distinct secondary mutations were present only in B-lymphoblasts (BCOR, NRAS) or myeloid cells (ASXL1, EZH2, RUNX1). These results indicate that both processes evolved from a common U2AF1-mutated precursor, which then acquired additional mutations during a process of divergent evolution and bilineal differentiation. Our findings highlight novel mechanisms in BLL leukemogenesis and expand the spectrum of observed bilineal neoplasms.
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PHF6 and JAK3 mutations cooperate to drive T-cell acute lymphoblastic leukemia progression. Leukemia 2021; 36:370-382. [PMID: 34465864 PMCID: PMC8807395 DOI: 10.1038/s41375-021-01392-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a malignant hematologic disease caused by gene mutations in T-cell progenitors. As an important epigenetic regulator, PHF6 mutations frequently coexist with JAK3 mutations in T-ALL patients. However, the role(s) of PHF6 mutations in JAK3-driven leukemia remain unclear. Here, the cooperation between JAK3 activation and PHF6 inactivation is examined in leukemia patients and in mice models. We found that the average survival time is shorter in patients with JAK/STAT and PHF6 comutation than that in other patients, suggesting a potential role of PHF6 in leukemia progression. We subsequently found that Phf6 deficiency promotes JAK3M511I-induced T-ALL progression in mice by inhibiting the Bai1-Mdm2-P53 signaling pathway, which is independent of the JAK3/STAT5 signaling pathway. Furthermore, combination therapy with a JAK3 inhibitor (tofacitinib) and a MDM2 inhibitor (idasanutlin) reduces the Phf6 KO and JAK3M511I leukemia burden in vivo. Taken together, our study suggests that combined treatment with JAK3 and MDM2 inhibitors may potentially increase the drug benefit for T-ALL patients with PHF6 and JAK3 comutation.
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Kurzer JH, Weinberg OK. PHF6 Mutations in Hematologic Malignancies. Front Oncol 2021; 11:704471. [PMID: 34381727 PMCID: PMC8350393 DOI: 10.3389/fonc.2021.704471] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/28/2021] [Indexed: 11/23/2022] Open
Abstract
Next generation sequencing has uncovered several genes with associated mutations in hematologic malignancies that can serve as potential biomarkers of disease. Keeping abreast of these genes is therefore of paramount importance in the field of hematology. This review focuses on PHF6, a highly conserved epigenetic transcriptional regulator that is important for neurodevelopment and hematopoiesis. PHF6 serves as a tumor suppressor protein, with PHF6 mutations and deletions often implicated in the development of T-lymphoblastic leukemia and less frequently in acute myeloid leukemia and other myeloid neoplasms. PHF6 inactivation appears to be an early event in T-lymphoblastic leukemogenesis, requiring cooperating events, including NOTCH1 mutations or overexpression of TLX1 and TLX3 for full disease development. In contrast, PHF6 mutations tend to occur later in myeloid malignancies, are frequently accompanied by RUNX1 mutations, and are often associated with disease progression. Moreover, PHF6 appears to play a role in lineage plasticity within hematopoietic malignancies, with PHF6 mutations commonly present in mixed phenotype acute leukemias with a predilection for T-lineage marker expression. Due to conflicting data, the prognostic significance of PHF6 mutations remains unclear, with a subset of studies showing no significant difference in outcomes compared to malignancies with wild-type PHF6, and other studies showing inferior outcomes in certain patients with mutated PHF6. Future studies are necessary to elucidate the role PHF6 plays in development of T-lymphoblastic leukemia, progression of myeloid malignancies, and its overall prognostic significance in hematopoietic neoplasms.
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Affiliation(s)
- Jason H. Kurzer
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Olga K. Weinberg
- Department of Pathology, UT Southwestern, Dallas, TX, United States
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Chen W, Song J, Liu S, Tang B, Shen L, Zhu J, Fang S, Wu F, Zheng L, Qiu R, Chen C, Gao Y, Tu J, Zhao Z, Ji J. USP9X promotes apoptosis in cholangiocarcinoma by modulation expression of KIF1Bβ via deubiquitinating EGLN3. J Biomed Sci 2021; 28:44. [PMID: 34112167 PMCID: PMC8191029 DOI: 10.1186/s12929-021-00738-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
Background Cholangiocarcinoma represents the second most common primary liver malignancy. The incidence rate has constantly increased over the last decades. Cholangiocarcinoma silent nature limits early diagnosis and prevents efficient treatment. Methods Immunoblotting and immunohistochemistry were used to assess the expression profiling of USP9X and EGLN3 in cholangiocarcinoma patients. ShRNA was used to silence gene expression. Cell apoptosis, cell cycle, CCK8, clone formation, shRNA interference and xenograft mouse model were used to explore biological function of USP9X and EGLN3. The underlying molecular mechanism of USP9X in cholangiocarcinoma was determined by immunoblotting, co-immunoprecipitation and quantitative real time PCR (qPCR). Results Here we demonstrated that USP9X is downregulated in cholangiocarcinoma which contributes to tumorigenesis. The expression of USP9X in cholangiocarcinoma inhibited cell proliferation and colony formation in vitro as well as xenograft tumorigenicity in vivo. Clinical data demonstrated that expression levels of USP9X were positively correlated with favorable clinical outcomes. Mechanistic investigations further indicated that USP9X was involved in the deubiquitination of EGLN3, a member of 2-oxoglutarate and iron-dependent dioxygenases. USP9X elicited tumor suppressor role by preventing degradation of EGLN3. Importantly, knockdown of EGLN3 impaired USP9X-mediated suppression of proliferation. USP9X positively regulated the expression level of apoptosis pathway genes de through EGLN3 thus involved in apoptosis of cholangiocarcinoma. Conclusion These findings help to understand that USP9X alleviates the malignant potential of cholangiocarcinoma through upregulation of EGLN3. Consequently, we provide novel insight into that USP9X is a potential biomarker or serves as a therapeutic or diagnostic target for cholangiocarcinoma. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-021-00738-2.
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Affiliation(s)
- Weiqian Chen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Jingjing Song
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Siyu Liu
- Clinical Laboratory, Lishui Central Hospital, Lishui, 323000, China
| | - Bufu Tang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Lin Shen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Jinyu Zhu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Shiji Fang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Fazong Wu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Liyun Zheng
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Rongfang Qiu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Chunmiao Chen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Yang Gao
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Jianfei Tu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Zhongwei Zhao
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China.
| | - Jiansong Ji
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China.
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Plasek LM, Valadkhan S. lncRNAs in T lymphocytes: RNA regulation at the heart of the immune response. Am J Physiol Cell Physiol 2021; 320:C415-C427. [PMID: 33296288 PMCID: PMC8294623 DOI: 10.1152/ajpcell.00069.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genome-wide analyses in the last decade have uncovered the presence of a large number of long non-protein-coding transcripts that show highly tissue- and state-specific expression patterns. High-throughput sequencing analyses in diverse subsets of immune cells have revealed a complex and dynamic expression pattern for these long noncoding RNAs (lncRNAs) that correlate with the functional states of immune cells. Although the vast majority of lncRNAs expressed in immune cells remain unstudied, functional studies performed on a small subset have indicated that their state-specific expressions pattern frequently has a regulatory impact on the function of immune cells. In vivo and in vitro studies have pointed to the involvement of lncRNAs in a wide variety of cellular processes, including both the innate and adaptive immune response through mechanisms ranging from epigenetic and transcriptional regulation to sequestration of functional molecules in subcellular compartments. This review will focus mainly on the role of lncRNAs in CD4+ and CD8+ T cells, which play pivotal roles in adaptive immunity. Recent studies have pointed to key physiological functions for lncRNAs during several developmental and functional stages of the life cycle of lymphocytes. Although lncRNAs play important physiological roles in lymphocytic response to antigenic stimulation, differentiation into effector cells, and secretion of cytokines, their dysregulated expression can promote or sustain pathological states such as autoimmunity, chronic inflammation, cancer, and viremia. This, together with their highly cell type-specific expression patterns, makes lncRNAs ideal therapeutic targets and underscores the need for additional studies into the role of these understudied transcripts in adaptive immune response.
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Lin C, Chen D, Xiao T, Lin D, Lin D, Lin L, Zhu H, Xu J, Huang W, Yang T. DNA methylation-mediated silencing of microRNA-204 enhances T cell acute lymphoblastic leukemia by up-regulating MMP-2 and MMP-9 via NF-κB. J Cell Mol Med 2021; 25:2365-2376. [PMID: 33566449 PMCID: PMC7933971 DOI: 10.1111/jcmm.15896] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 01/24/2023] Open
Abstract
T cell acute lymphoblastic leukaemia (T‐ALL) is a highly aggressive haematological cancer of the bone marrow. The abnormal expression of microRNAs (miRNAs) is reportedly involved in T‐ALL development and progression. Thus, we aimed to decipher the involvement of miR‐204 silencing mediated by DNA methylation in the occurrence of T cell acute lymphoblastic leukaemia (T‐ALL). miR‐204 expression was determined in bone marrow and peripheral blood samples from T‐ALL patients by real‐time quantitative PCR (RT‐qPCR) with its effect on cell proliferation evaluated by functional assays. In addition, bisulphite sequencing PCR was employed to detect the DNA methylation level of the miR‐204 promoter region, and the binding site between miR‐204 and IRAK1 was detected by luciferase assay. We found that miR‐204 was down‐regulated in T cells of T‐ALL patients, which was caused by the increased DNA methylation in the promoter region of miR‐204. Moreover, overexpression of miR‐204 inhibited T‐ALL cell proliferation while enhancing their apoptosis through interleukin receptor‐associated kinase 1 (IRAK1), which enhanced the expression of matrix metalloproteinase‐2 (MMP‐2) and MMP‐9 through activation of p‐p65. Thus, miR‐204 modulated MMP‐2 and MMP‐9 through IRAK1/NF‐κB signalling pathway, which was confirmed by in vivo assay. Taken together, DNA methylation‐mediated miR‐204 silencing increased the transcription of IRAK1, thus activating the NF‐κB signalling pathway and up‐regulating the downstream targets MMP‐2/MMP‐9.
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Affiliation(s)
- Congmeng Lin
- Department of Hematology, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, China
| | - Dabing Chen
- Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Tingting Xiao
- Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Dandan Lin
- Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory of Hematology, Fujian Medical University Union Hospital, Fuzhou, China.,Minxi Vocational & Technical College, Longyan, China
| | - Dayi Lin
- Department of Hematology, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, China
| | - Luhui Lin
- Department of Hematology, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, China
| | - Haojie Zhu
- Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Jingjing Xu
- Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Wenwen Huang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Ting Yang
- Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
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19
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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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20
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Zhang P, Zhang Y, Li X, Ying P, Tang Y. U2AF1 expression is a novel and independent prognostic indicator of childhood T-lineage acute lymphoblastic leukemia. Int J Lab Hematol 2020; 43:675-682. [PMID: 33314767 DOI: 10.1111/ijlh.13433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 11/28/2022]
Abstract
INTRODUCTION U2AF1 gene is associated with various types of hematological malignancies in adults. However, the expression level of U2AF1 gene and its prognostic significance are unclear in pediatric ALL patients. The study aimed to study the mRNA level of U2AF1 in pediatric ALL patients and its clinical relevance with long-term survival. METHODS We quantitatively determined U2AF1 gene expression at diagnosis in 132 children with ALL by real-time PCR. According to the patients' median U2AF1 value, the patients' samples were classified into low U2AF1 and high U2AF1 expression groups. Twenty-two bone marrow samples from 22 patients with ITP were recruited as control. The correlation between the expression level of U2AF1 and clinical treatment outcome was analyzed. RESULTS Pediatric patients with ALL showed higher U2AF1 mRNA levels than controls (P = .034). The relapse rates of patients in low U2AF1 levels group were obviously higher than those of U2AF1 high expression group (28.8% vs 12.1%, P = .030). Patients of low U2AF1 expression presented worse 5-year EFS than those of high U2AF1 expression (60% vs 81%, P = .035). For T-ALL, patients with low U2AF1 mRNA level showed lower BM blast percentages (P = .031), worse EFS (37.8% vs 92.3%, P = .003), and CIR (62.2% vs 7.7%, P = .003) than those in high U2AF1 expression group. Multivariate analysis confirmed low U2AF1 mRNA level could be used as an independent risk indicator of poor EFS and CIR of children with T-ALL. CONCLUSION Low U2AF1 mRNA level is related to inferior prognosis and can be served as a prognostic indicator for risk stratification in children with T-ALL.
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Affiliation(s)
- Ping Zhang
- Department of Hematology-Oncology, Pediatric Hematology-Oncology Center, Zhejiang Provincial Pediatric Leukemia Diagnostic and Therapeutic Research Center, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yao Zhang
- Department of Hematology-Oncology, Pediatric Hematology-Oncology Center, Zhejiang Provincial Pediatric Leukemia Diagnostic and Therapeutic Research Center, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China.,Children's Hospital of Shanxi Province, Taiyuan, China
| | - Xiaoxiao Li
- Department of Hematology-Oncology, Pediatric Hematology-Oncology Center, Zhejiang Provincial Pediatric Leukemia Diagnostic and Therapeutic Research Center, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Peiting Ying
- Department of Hematology-Oncology, Pediatric Hematology-Oncology Center, Zhejiang Provincial Pediatric Leukemia Diagnostic and Therapeutic Research Center, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yongmin Tang
- Department of Hematology-Oncology, Pediatric Hematology-Oncology Center, Zhejiang Provincial Pediatric Leukemia Diagnostic and Therapeutic Research Center, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
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21
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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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22
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Zhang J, Shu Y, Zhang H, Jiang T, Gong M, Zhu D, Wang H, Zou L. [β-arrestin1 overexpression suppresses progression of human T-cell acute lymphatic leukemia Molt-4 cell xenograft in mice]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2020; 40:654-660. [PMID: 32897219 DOI: 10.12122/j.issn.1673-4254.2020.05.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the effect of β-arrestin1 overexpression on tumor progression in a NCG mouse model bearing T-cell acute lymphocytic leukemia (T-ALL) Molt-4 cell xenograft. METHODS Molt-4 cells were tagged with firefly-luciferase (F-Luc) by lentiviral infection, and fluorescence intensity of the cells was detected using a luminescence detector. Molt-4 cell lines with β-arrestin1 overexpression or knockdown were constructed by lentivirus infection and injected via the tail vein in sub-lethal irradiated NCG mice. Body weight changes and survival time of the xenografted mice were observed, and the progression of T-ALL in the mice was evaluated using an in vivo fluorescence imaging system. Sixteen days after xenografting, the mice were euthanatized and tumor cell infiltration was observed in the slices of the liver and spleen. RESULTS We successfully tagged Molt-4 cells with F-Luc and overexpressed or knocked down β-arrestin1 in the tagged cells. Bioluminescent imaging showed obvious luminescence catalyzed by F-Luc in Molt-4 cells. After injection of Molt-4-Luc cells into irradiated NCG mice, a gradual enhancement of luminescence in the xenografted mice was observed over time, while the body weight of the mice decreased. Compared with the control mice, the mice xenografted with β-arrestin1-overexpressing Molt-4 cells had significantly prolonged survival time (P < 0.001), while the survival time of the mice xenografted with Molt-4 cells with β- arrestin1 knockdown was significantly shortened (P < 0.001). Histological examination revealed fewer infiltrating tumor cells in the liver and spleen of the mice xenografted with β-arrestin1-overexpressing Molt-4 cells in comparison with the mice bearing parental Molt-4 cell xenografts. CONCLUSIONS β-arrestin1 overexpression suppresses tumor progression in mice bearing Molt-4 cell xenograft.
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Affiliation(s)
- Jia Zhang
- Center for Clinical Molecular Medicine, Children's Hospital, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing Engineering Research Center of Stem Cell Therapy, Chongqing 400014, China
| | - Yi Shu
- Center for Clinical Molecular Medicine, Children's Hospital, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing Engineering Research Center of Stem Cell Therapy, Chongqing 400014, China
| | - Hongyang Zhang
- Center for Clinical Molecular Medicine, Children's Hospital, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing Engineering Research Center of Stem Cell Therapy, Chongqing 400014, China
| | - Tingting Jiang
- Center for Clinical Molecular Medicine, Children's Hospital, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing Engineering Research Center of Stem Cell Therapy, Chongqing 400014, China
| | - Maoyuan Gong
- Center for Clinical Molecular Medicine, Children's Hospital, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing Engineering Research Center of Stem Cell Therapy, Chongqing 400014, China
| | - Dan Zhu
- Center for Clinical Molecular Medicine, Children's Hospital, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing Engineering Research Center of Stem Cell Therapy, Chongqing 400014, China
| | - Haobiao Wang
- Center for Clinical Molecular Medicine, Children's Hospital, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing Engineering Research Center of Stem Cell Therapy, Chongqing 400014, China
| | - Lin Zou
- Center for Clinical Molecular Medicine, Children's Hospital, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing Engineering Research Center of Stem Cell Therapy, Chongqing 400014, China
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23
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Gutierrez-Diaz BT, Gu W, Ntziachristos P. Deubiquitinases: Pro-oncogenic Activity and Therapeutic Targeting in Blood Malignancies. Trends Immunol 2020; 41:327-340. [PMID: 32139316 PMCID: PMC7258259 DOI: 10.1016/j.it.2020.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 12/18/2022]
Abstract
Deubiquitinases are enzymes that remove ubiquitin moieties from the vast majority of cellular proteins, controlling their stability, interactions, and localization. The expression and activity of deubiquitinases are critical for physiology and can go awry in various diseases, including cancer. Based on recent findings in human blood cancers, we discuss the functions of selected deubiquitinases in acute leukemia and efforts to target these enzymes with the aim of blocking leukemia growth and improving disease outcomes. We focus on the emergence of the newest generation of preclinical inhibitors by discussing their modes of inhibition and their effects on leukemia biology.
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Affiliation(s)
- Blanca T Gutierrez-Diaz
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Chicago, IL 60611, USA
| | - Wei Gu
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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24
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Park KJ, Kim IS, Yang EJ, Lim YT, Cho SH. Mutation analysis in Korean patients with T-cell acute lymphoblastic leukemia. Pediatr Hematol Oncol 2020; 37:129-139. [PMID: 31852326 DOI: 10.1080/08880018.2019.1701160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Genomic studies have illuminated the alterations in pathways underlying T-cell acute lymphoblastic leukemia (T-ALL) pathogenesis, but detailed mutation data by next-generation sequencing have not been reported in Korean patients. We aimed to investigate mutation frequency, spectrum, and pattern in the Korean patients with T-ALL. We designed a multigene panel targeting 101 genes and validated it using 10 reference materials. The mutation analysis was done in a total of 10 patients with T-ALL. Clinical data and laboratory tests including immunophenotyping, cytogenetics, and molecular genetic tests were also investigated. All of the 10 patients harbored at least one mutation (range 1-6 per patient). A total of 34 clinically significant mutations including 15 novel mutations were identified in 23 genes. The median of variant allelic frequencies (VAFs) and blasts were counted upto 33% (range 5-91%) and 79% (range 38-90%), respectively. Recurrent mutations were involved in epigenetic regulators (60%), NOTCH1 signaling (40%), PI3K-AKT (40%), JAK-STAT (30%), and transcription factors (30%). We found that both NOTCH signaling and JAK-STAT signaling were positively associated with epigenetic regulators, while showed mutually exclusive patterns with PI3K-AKT pathway. This study showed that the frequency of mutations in epigenetic regulators in Korean patients was significantly higher than expected. Distribution of VAF as well as mutation spectrum is considerably heterogeneous in Korean patients with T-ALL. Although from a limited number of patients, this study provides the first detailed mutational portrait of T-ALL of Korean patients, and gives additional insight into molecular pathogenesis of the disease.
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Affiliation(s)
- Kyoung-Jin Park
- Department of Laboratory Medicine, Myongji Hospital, Goyang, Republic of Korea
| | - In-Suk Kim
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Eu Jeen Yang
- Department of Pediatrics, Pusan National University Children's Hospital, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Young Tak Lim
- Department of Pediatrics, Pusan National University Children's Hospital, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Su-Hee Cho
- Department of Internal Medicine, Pusan National University Yangsan Hospital, Pusan National University School of Medicine, Yangsan, Republic of Korea
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25
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Zhang S, O'Regan R, Xu W. The emerging role of mediator complex subunit 12 in tumorigenesis and response to chemotherapeutics. Cancer 2019; 126:939-948. [PMID: 31869450 DOI: 10.1002/cncr.32672] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/07/2019] [Accepted: 11/22/2019] [Indexed: 12/18/2022]
Abstract
Transcriptional dysregulation induced by disease-defining genetic alterations of proteins in transcriptional machinery is a key feature of cancers. Mediator complex subunit 12 (MED12) is the central architectural subunit in the kinase module of Mediator, a large transcriptional regulatory complex that controls essential steps of transcription. Emerging evidence links deregulated MED12 to human cancers. MED12 is frequently mutated in benign tumors and cancers. Although the missense mutations of MED12 in benign tumors disrupt the kinase activity of Mediator, MED12 mutations in cancers could eliminate the interaction between Mediator complex and RNA polymerase II, leading to severe transcriptional misregulation. Aberrant expression of MED12 is associated with the prognosis of various types of human cancers. Loss of MED12 function has been associated with the development of resistance to chemotherapeutics. Moreover, MED12 is modified by posttranscriptional regulations. Arginine methylation of MED12 has been shown to regulate MED12-mediated transcriptional regulation and response to chemotherapeutics in human cancer cell lines. In this mini-review, the authors provide an overview of the roles of MED12 in the development of benign and malignant tumors as well as its roles in chemoresistance. The studies of MED12 exemplify that aberrant transcriptional programming is a therapeutic vulnerability for certain types of cancer.
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Affiliation(s)
- Shengjie Zhang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin.,Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Ruth O'Regan
- Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
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26
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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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27
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Md Nasir ND, Ng CCY, Rajasegaran V, Wong SF, Liu W, Ng GXP, Lee JY, Guan P, Lim JQ, Thike AA, Koh VCY, Loke BN, Chang KTE, Gudi MA, Lian DWQ, Madhukumar P, Tan BKT, Tan VKM, Wong CY, Yong WS, Ho GH, Ong KW, Tan P, Teh BT, Tan PH, Rahman NA, Nahar Begum SMK, Cheah PL, Chen CJ, Dela Fuente E, Han A, Harada O, Kanomata N, Lee CS, Han Lee JY, Kamal M, Nishimura R, Ohi Y, Sawyer EJ, Teoh KH, Tsang AKH, Tsang JY, Tse GMK, Yamaguchi R. Genomic characterisation of breast fibroepithelial lesions in an international cohort. J Pathol 2019; 249:447-460. [DOI: 10.1002/path.5333] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 07/11/2019] [Accepted: 08/01/2019] [Indexed: 12/31/2022]
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28
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Harris MH, Czuchlewski DR, Arber DA, Czader M. Genetic Testing in the Diagnosis and Biology of Acute Leukemia. Am J Clin Pathol 2019; 152:322-346. [PMID: 31367767 DOI: 10.1093/ajcp/aqz093] [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] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES The 2017 Workshop of the Society for Hematopathology/European Association for Haematopathology examined the role of molecular genetics in the diagnosis and biology of acute leukemia. METHODS Acute leukemias were reviewed in two sessions: "Genetic Testing in Diagnosis of Acute Leukemias" (53 cases) and "Genetics Revealing the Biology of Acute Leukemias" (41 cases). RESULTS Cases included acute lymphoblastic leukemia, acute myeloid leukemia, and acute leukemia of ambiguous lineage. Many cases demonstrated genetic alterations of known diagnostic, prognostic, and/or therapeutic significance, while others exhibited alterations that illuminated disease biology. The workshop highlighted the complexity of acute leukemia diagnosis and follow-up, while illustrating advantages and pitfalls of molecular genetic testing. CONCLUSIONS Our understanding of the molecular genetics of acute leukemias continues to grow rapidly. Awareness of the potential complexity of genetic architecture and environment is critical and emphasizes the importance of integrating clinical information with morphologic, immunophenotypic, and molecular genetic evaluation.
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Affiliation(s)
- Marian H Harris
- Department of Pathology, Boston Children’s Hospital, Boston, MA
| | - David R Czuchlewski
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque
| | - Daniel A Arber
- Department of Pathology, University of Chicago, Chicago, IL
| | - Magdalena Czader
- Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis
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Loss of KDM6A confers drug resistance in acute myeloid leukemia. Leukemia 2019; 34:50-62. [PMID: 31201358 PMCID: PMC7214274 DOI: 10.1038/s41375-019-0497-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 03/25/2019] [Accepted: 04/18/2019] [Indexed: 01/19/2023]
Abstract
Acute myeloid leukemia (AML) is an aggressive hematologic neoplasm resulting from the malignant transformation of myeloid progenitors. Despite intensive chemotherapy leading to initial treatment responses, relapse caused by intrinsic or acquired drug resistance represents a major challenge. Here, we report that histone 3 lysine 27 demethylase KDM6A (UTX) is targeted by inactivating mutations and mutation-independent regulation in relapsed AML. Analyses of matched diagnosis and relapse specimens from individuals with KDM6A mutations showed an outgrowth of the KDM6A mutated tumor population at relapse. KDM6A expression is heterogeneously regulated and relapse-specific loss of KDM6A was observed in 45.7% of CN-AML patients. KDM6A-null myeloid leukemia cells were more resistant to treatment with the chemotherapeutic agents cytarabine (AraC) and daunorubicin. Inducible re-expression of KDM6A in KDM6A-null cell lines suppressed proliferation and sensitized cells again to AraC treatment. RNA expression analysis and functional studies revealed that resistance to AraC was conferred by downregulation of the nucleoside membrane transporter ENT1 (SLC29A1) by reduced H3K27 acetylation at the ENT1 locus. Our results show that loss of KDM6A provides cells with a selective advantage during chemotherapy, which ultimately leads to the observed outgrowth of clones with KDM6A mutations or reduced KDM6A expression at relapse.
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Noronha EP, Marques LVC, Andrade FG, Thuler LCS, Terra-Granado E, Pombo-de-Oliveira MS. The Profile of Immunophenotype and Genotype Aberrations in Subsets of Pediatric T-Cell Acute Lymphoblastic Leukemia. Front Oncol 2019; 9:316. [PMID: 31338319 PMCID: PMC6503680 DOI: 10.3389/fonc.2019.00316] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/08/2019] [Indexed: 12/20/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a biologically heterogeneous malignancy, which reflects distinctive stages of T-cell differentiation arrest. We have revisited a cohort of pediatric T-ALL, in order to test if immunophenotypes associated with molecular alterations would predict the patient's outcome. Genetic mutations, translocations and copy number alterations were identified through Sanger sequencing, RT-PCR, FISH and multiplex ligation-dependent probe amplification (MLPA). We defined 8 immunophenotypic T-ALL subtypes through multiparametric flow cytometry: early T-cell precursor (ETP, n = 27), immature (n = 38), early cortical (n = 15), cortical (n = 50), late cortical (n = 53), CD4/CD8 double negative mature (n = 31), double positive mature (n = 35) and simple positive mature (n = 31) T-ALL. Deletions (del) or amplifications (amp) in at least one gene were observed in 87% of cases. The most frequent gene alterations were CDKN2A/Bdel (71.4%), NOTCH1mut (47.6%) and FBXW7mut (17%). ETP-ALL had frequent FLT3mut (22.2%) and SUZ12del (16.7%) (p < 0.001), while CDKN2A/Bdel were rarely found in this subtype (p < 0.001). The early cortical T-ALL subtype had high frequencies of NOTCH1mut and IL7Rmut (71%, 28.6%, respectively), whereas, mature T-ALL with double positive CD4/CD8 had the highest frequencies of STIL-TAL1 (36.7%), LEF1del (27.3%) and CASP8AP2del (22.7%). The co-existence of two groups of T-ALL with NOTCH1mut/IL7Rmut, and with TLX3/SUZ12del/NF1del/IL7Rmut, were characterized with statistical significance (p < 0.05) but only STIL-TAL1 (pOS 47.5%) and NOTCH1WT/FBXW7WT (pOS 55.3%) are predictors of poor T-ALL outcomes. In conclusion, we have observed that 8 T-ALL subgroups are characterized by distinct molecular profiles. The mutations in NOTCH1/FBXW7 and STIL-TAL1 rearrangement had a prognostic impact, independent of immunophenotype.
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Affiliation(s)
- Elda Pereira Noronha
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Luísa Vieira Codeço Marques
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Francianne Gomes Andrade
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | | - Eugênia Terra-Granado
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Maria S Pombo-de-Oliveira
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
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Khater F, Vairy S, Langlois S, Dumoucel S, Sontag T, St-Onge P, Bittencourt H, Dal Soglio D, Champagne J, Duval M, Leclerc JM, Laverdiere C, Tran TH, Patey N, Ellezam B, Perreault S, Piché N, Samson Y, Teira P, Jabado N, Michon B, Brossard J, Marzouki M, Cellot S, Sinnett D. Molecular Profiling of Hard-to-Treat Childhood and Adolescent Cancers. JAMA Netw Open 2019; 2:e192906. [PMID: 31026031 PMCID: PMC6487576 DOI: 10.1001/jamanetworkopen.2019.2906] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
IMPORTANCE Little progress in pediatric cancer treatment has been noted in the past decade, urging the development of novel therapeutic strategies for adolescents and children with hard-to-treat cancers. Use of comprehensive molecular profiling in the clinical management of children and adolescents with cancer appears a suitable approach to improve patient care and outcomes, particularly for hard-to-treat cases. OBJECTIVE To assess the feasibility of identifying potentially actionable mutations using next-generation sequencing-based assays in a clinically relevant time frame. DESIGN, SETTING, AND PARTICIPANTS This diagnostic study reports the results of the TRICEPS study, a prospective genome sequencing study conducted in Québec, Canada. Participants, aged 18 years or younger at diagnosis, with refractory or relapsed childhood and adolescent cancers were enrolled from April 2014 through January 2018. Whole-exome sequencing (WES) of matched tumor normal samples and RNA sequencing of tumor were performed to identify single-nucleotide variants, fusion transcripts, differential gene expression, and copy number alterations. Results reviewed by a team of experts were further annotated, synthesized into a report, and subsequently discussed in a multidisciplinary molecular tumor board. MAIN OUTCOMES AND MEASURES Molecular profiling of pediatric patients with hard-to-treat cancer, identification of actionable and targetable alteration needed for the management of these patients, and proposition of targeted and personalized novel therapeutic strategies. RESULTS A total of 84 patients with hard-to-treat cancers were included in the analysis. These patients had a mean (range) age of 10.1 (1-21) years and a similar proportion of male (45 [54%]) and female (39 [46%]). Sixty-two patients (74%) had suitable tissues for multimodal molecular profiling (WES and RNA sequencing). The process from DNA or RNA isolation to genomic sequencing and data analysis steps took a median (range) of 24 (4-41) days. Potentially actionable alterations were identified in 54 of 62 patients (87%). Actions were taken in 22 of 54 patients (41%), and 18 (33%) either were on a second or third line of treatment, were in remission, or had stable disease and thus no actions were taken. CONCLUSIONS AND RELEVANCE Incorporating genomic sequencing into the management of hard-to-treat childhood and adolescent cancers appeared feasible; molecular profiling may enable the identification of potentially actionable alterations with clinical implications for most patients, including targeted therapy and clinically relevant information of diagnostic, prognostic, and monitoring significance.
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Affiliation(s)
- Fida Khater
- Research Centre, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Stephanie Vairy
- Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Sylvie Langlois
- Research Centre, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Sophie Dumoucel
- Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Thomas Sontag
- Research Centre, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Pascal St-Onge
- Research Centre, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Henrique Bittencourt
- Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Dorothée Dal Soglio
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Josette Champagne
- Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Michel Duval
- Research Centre, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
- Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Jean-Marie Leclerc
- Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Caroline Laverdiere
- Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Thai Hoa Tran
- Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Natalie Patey
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Benjamin Ellezam
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Sébastien Perreault
- Division of Neurology, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Nelson Piché
- Department of Surgery, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Yvan Samson
- Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Pierre Teira
- Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Nada Jabado
- Department of Pediatrics, McGill University, Montreal, Québec, Canada
| | - Bruno Michon
- Division of Hematology-Oncology, Centre Hospitalier Universitaire de Québec, Québec City, Québec, Canada
| | - Josée Brossard
- Division of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada
| | - Monia Marzouki
- Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Sonia Cellot
- Research Centre, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
- Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
| | - Daniel Sinnett
- Research Centre, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
- Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Québec, Canada
- Department of Pediatrics, Montreal University, Montreal, Québec, Canada
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Luo H, Jing B, Xia Y, Zhang Y, Hu M, Cai H, Tong Y, Zhou L, Yang L, Yang J, Lei H, Xu H, Liu C, Wu Y. WP1130 reveals USP24 as a novel target in T-cell acute lymphoblastic leukemia. Cancer Cell Int 2019; 19:56. [PMID: 30911287 PMCID: PMC6415346 DOI: 10.1186/s12935-019-0773-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/06/2019] [Indexed: 12/20/2022] Open
Abstract
Background T-cell acute lymphoblastic leukemia (T-ALL) is a lymphoid malignancy caused by the oncogenic transformation of immature T-cell progenitors with poor outcomes. WP1130 has shown potent activity against a variety of cancer but whether WP1130 has anti-T-ALL activity is not clear. USP24, one target of WP1130, is one of the largest deubiquitinases and its detailed mechanism is poorly understood. The aim of this study was to explore whether WP1130 could suppress T-ALL and the role of USP24 in T-ALL. Methods Molecular docking and cellular thermal shift assay were performed to determine whether and how WP1130 directly interact with USP24. Mitochondrial transmembrane potential assay was measured via Rhodamine 123 staining. USP24 was reactivated using the deactivated CRISPR-associated protein 9 (dCas9)-synergistic activation mediator (SAM) system. The in vivo results were examined by tumor xenografts in NOD-SCID mice. All statistical analyses were performed with the SPSS software package. Results WP1130 treatment decreased the viability and induces apoptosis of T-ALL cells both in vitro and in vivo. Furthermore, we demonstrated that knockdown of USP24 but not USP9X could significantly induce growth inhibition and apoptosis of T-ALL cells. Oncomine database showed that USP24 expression was upregulated in T-ALL samples and Kaplan–Meier results indicated that the USP24 was negatively but USP9X was positively associated with survival in T-ALL patients. Additionally, we proposed that WP1130 directly interacts with the activity site pocket of USP24 in T-ALL cells, which leads to the decrease of its substrates Mcl-1. Mechanistically, WP1130 induces apoptosis by accelerating the collapse of mitochondrial transmembrane potential via USP24-Mcl-1 axis. Conclusions Altogether, using WP1130 as a chemical probe, we demonstrate that USP24 but not USP9X is a novel target in T-ALL cells. Moreover, we uncovered that WP1130 induces apoptosis by accelerating the collapse of mitochondrial transmembrane potential via USP24-Mcl-1 axis. These results provide that USP24-Mcl-1 axis may represent a novel strategy in the treatment of T-ALL and WP1130 is a promising lead compound for developing anti-T-ALL drugs. Electronic supplementary material The online version of this article (10.1186/s12935-019-0773-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Luo
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Bo Jing
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Yu Xia
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Yugen Zhang
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Meng Hu
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Haiyan Cai
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Yin Tong
- 2Department of Hematology, Shanghai First People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Li Zhou
- 3State Key Laboratory of Medical Genomics, Department of Hematology, Faculty of Medical Laboratory Science, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025 China
| | - Li Yang
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Junmei Yang
- 4Department of Clinical Laboratory, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018 China
| | - Hu Lei
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Hanzhang Xu
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Chuanxu Liu
- 5Department of Hematology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Yingli Wu
- 1Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
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Mutational dynamics of early and late relapsed childhood ALL: rapid clonal expansion and long-term dormancy. Blood Adv 2019; 2:177-188. [PMID: 29365312 DOI: 10.1182/bloodadvances.2017011510] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/29/2017] [Indexed: 12/18/2022] Open
Abstract
Childhood acute lymphoblastic leukemia (cALL) is the most frequent pediatric cancer. Refractory/relapsed cALL presents a survival rate of ∼45% and is still one of the leading causes of death by disease among children. Mechanisms, such as clonal competition and evolutionary adaptation, govern treatment resistance. However, the underlying clonal dynamics leading to multiple relapses and differentiating early (<36 months postdiagnosis) from late relapse events remain elusive. Here, we use an integrative genome-based analysis combined with serial sampling of relapsed tumors (from primary tumor to ≤4 relapse events) from 19 pre-B-cell cALL patients (8 early and 11 late relapses) to assess the fitness of somatic mutations and infer their ancestral relationships. By quantifying both general clonal dynamics and newly acquired subclonal diversity, we show that 2 distinct evolutionary patterns govern early and late relapse: on one hand, a highly dynamic pattern, sustained by a putative defect of DNA repair processes, illustrating the quick emergence of fitter clones, and on the other hand, a quasi-inert evolution pattern, suggesting the escape from dormancy of leukemia stem cells likely spared from initial cytoreductive therapy. These results offer new insights into cALL relapse mechanisms and highlight the pressing need for adapted treatment strategies to circumvent resistance mechanisms.
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34
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Ohki K, Kiyokawa N, Saito Y, Hirabayashi S, Nakabayashi K, Ichikawa H, Momozawa Y, Okamura K, Yoshimi A, Ogata-Kawata H, Sakamoto H, Kato M, Fukushima K, Hasegawa D, Fukushima H, Imai M, Kajiwara R, Koike T, Komori I, Matsui A, Mori M, Moriwaki K, Noguchi Y, Park MJ, Ueda T, Yamamoto S, Matsuda K, Yoshida T, Matsumoto K, Hata K, Kubo M, Matsubara Y, Takahashi H, Fukushima T, Hayashi Y, Koh K, Manabe A, Ohara A. Clinical and molecular characteristics of MEF2D fusion-positive B-cell precursor acute lymphoblastic leukemia in childhood, including a novel translocation resulting in MEF2D-HNRNPH1 gene fusion. Haematologica 2019; 104:128-137. [PMID: 30171027 PMCID: PMC6312004 DOI: 10.3324/haematol.2017.186320] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 08/29/2018] [Indexed: 11/10/2022] Open
Abstract
Fusion genes involving MEF2D have recently been identified in precursor B-cell acute lymphoblastic leukemia, mutually exclusive of the common risk stratifying genetic abnormalities, although their true incidence and associated clinical characteristics remain unknown. We identified 16 cases of acute lymphoblastic leukemia and 1 of lymphoma harboring MEF2D fusions, including MEF2D-BCL9 (n=10), MEF2D-HNRNPUL1 (n=6), and one novel MEF2D-HNRNPH1 fusion. The incidence of MEF2D fusions overall was 2.4% among consecutive precursor B-cell acute lymphoblastic leukemia patients enrolled onto a single clinical trial. They frequently showed a cytoplasmic μ chain-positive pre-B immunophenotype, and often expressed an aberrant CD5 antigen. Besides up- and down-regulation of HDAC9 and MEF2C, elevated GATA3 expression was also a characteristic feature of MEF2D fusion-positive patients. Mutations of PHF6, recurrent in T-cell acute lymphoblastic leukemia, also showed an unexpectedly high frequency (50%) in these patients. MEF2D fusion-positive patients were older (median age 9 years) with elevated WBC counts (median: 27,300/ml) at presentation and, as a result, were mostly classified as NCI high risk. Although they responded well to steroid treatment, MEF2D fusion-positive patients showed a significantly worse outcome, with 53.3% relapse and subsequent death. Stem cell transplantation was ineffective as salvage therapy. Interestingly, relapse was frequently associated with the presence of CDKN2A/CDKN2B gene deletions. Our observations indicate that MEF2D fusions comprise a distinct subgroup of precursor B-cell acute lymphoblastic leukemia with a characteristic immunophenotype and gene expression signature, associated with distinct clinical features.
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Affiliation(s)
- Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Yuya Saito
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
- Department of Hematology/Oncology, Tokyo Metropolitan Children's Medical Center, Fuchu-shi
| | - Shinsuke Hirabayashi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
- Department of Pediatrics, St. Luke's International Hospital, Chuo-ku, Tokyo
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Hitoshi Ichikawa
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Chuo-ku, Tokyo
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama-shi, Kanagawa
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Ai Yoshimi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
- Division of Pediatric Hematology and Oncology, Ibaraki Children's Hospital, Mito-shi
| | - Hiroko Ogata-Kawata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Hiromi Sakamoto
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Chuo-ku, Tokyo
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | | | - Daisuke Hasegawa
- Department of Pediatrics, St. Luke's International Hospital, Chuo-ku, Tokyo
| | - Hiroko Fukushima
- Department of Pediatrics, University of Tsukuba Hospital, Ibaraki
| | - Masako Imai
- Department of Pediatrics, Japanese Red Cross Musashino Hospital, Tokyo
| | - Ryosuke Kajiwara
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa
| | - Takashi Koike
- Department of Pediatrics, Tokai University School of Medicine, Kanagawa
| | - Isao Komori
- Department of Pediatrics, Matsudo City Hospital, Chiba
| | - Atsushi Matsui
- Department of Pediatrics, Japanese Red Cross Maebashi Hospital, Gunma
| | - Makiko Mori
- Department of Hematology/Oncology, Saitama Children's Medical Center
| | - Koichi Moriwaki
- Department of Pediatrics, Saitama Medical Center, Saitama Medical University
| | - Yasushi Noguchi
- Department of Pediatrics, Japanese Red Cross Narita Hospital, Chiba
| | - Myoung-Ja Park
- Department of Hematology/Oncology, Gunma Children's Medical Center, Shibukawa-shi
| | - Takahiro Ueda
- Department of Pediatrics, Nippon Medical School, Bunkyo-ku, Tokyo
| | - Shohei Yamamoto
- Department of Pediatrics, Showa University Fujigaoka Hospital, Yokohama-shi, Kanagawa
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences, The University of Tokyo, Minato-ku
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Chuo-ku, Tokyo
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama-shi, Kanagawa
| | - Yoichi Matsubara
- Director, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo
| | | | - Takashi Fukushima
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Ibaraki
| | - Yasuhide Hayashi
- Institute of Physiology and Medicine, Jobu University, Takasaki-shi, Gunma, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center
| | - Atsushi Manabe
- Department of Pediatrics, St. Luke's International Hospital, Chuo-ku, Tokyo
| | - Akira Ohara
- Department of Pediatrics, Toho University Omori Medical Center, Tokyo
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35
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Recurrent somatic BRAF insertion (p.V504_R506dup): a tumor marker and a potential therapeutic target in pilocytic astrocytoma. Oncogene 2018; 38:2994-3002. [PMID: 30575814 PMCID: PMC6484687 DOI: 10.1038/s41388-018-0623-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 09/10/2018] [Accepted: 11/23/2018] [Indexed: 12/19/2022]
Abstract
Pilocytic astrocytoma (PA) is emerging as a tumor entity with dysregulated RAS/RAF/MEK/ERK signaling. In this study, we report the identification of a novel recurrent BRAF insertion (p.V504_R506dup) in five PA cases harboring exclusively this somatic tandem duplication. This recurrent alteration leads to an addition of three amino acids in the kinase domain of BRAF and has functional impact on activating MAPK phosphorylation. Importantly, we show that this mutation confers resistance to RAF inhibitors without changing effectiveness while downstream MEK inhibitors remain effective. Our results further emphasize the importance of BRAF alterations in PA and the need to characterize them in a given tumor as this can affect therapeutic strategies and their potential use as tumor marker in molecular diagnostics.
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Verboom K, Van Loocke W, Volders PJ, Decaesteker B, Cobos FA, Bornschein S, de Bock CE, Atak ZK, Clappier E, Aerts S, Cools J, Soulier J, Taghon T, Van Vlierberghe P, Vandesompele J, Speleman F, Durinck K. A comprehensive inventory of TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia through polyA+ and total RNA sequencing. Haematologica 2018; 103:e585-e589. [PMID: 29954933 DOI: 10.3324/haematol.2018.190587] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Karen Verboom
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium
| | - Wouter Van Loocke
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium
| | - Pieter-Jan Volders
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium.,Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.,Bioinformatics Institute Ghent from Nucleotides to Networks, BIG N2N, Belgium
| | - Bieke Decaesteker
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium
| | - Francisco Avila Cobos
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium.,Bioinformatics Institute Ghent from Nucleotides to Networks, BIG N2N, Belgium
| | - Simon Bornschein
- KU Leuven Center for Human Genetics, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - Charles E de Bock
- KU Leuven Center for Human Genetics, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - Zeynep Kalender Atak
- KU Leuven Center for Human Genetics, Belgium.,VIB Center for Brain & Disease Research, Laboratory of Computational Biology, Leuven, Belgium
| | | | - Stein Aerts
- KU Leuven Center for Human Genetics, Belgium.,VIB Center for Brain & Disease Research, Laboratory of Computational Biology, Leuven, Belgium
| | - Jan Cools
- KU Leuven Center for Human Genetics, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - Jean Soulier
- Hôpital Saint Louis, Institut Universitaire d'Hématologie, Paris, France
| | - Tom Taghon
- Cancer Research Institute Ghent, Belgium.,Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Belgium
| | - Pieter Van Vlierberghe
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium.,Bioinformatics Institute Ghent from Nucleotides to Networks, BIG N2N, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium
| | - Kaat Durinck
- Center for Medical Genetics, Ghent University, Belgium .,Cancer Research Institute Ghent, Belgium
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Genetic alterations crossing the borders of distinct hematopoetic lineages and solid tumors: Diagnostic challenges in the era of high-throughput sequencing in hemato-oncology. Crit Rev Oncol Hematol 2018; 126:64-79. [DOI: 10.1016/j.critrevonc.2018.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/03/2018] [Accepted: 03/25/2018] [Indexed: 02/07/2023] Open
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38
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Wang S, Ma J, Yu MK, Zheng F, Huang EW, Han J, Peng J, Ideker T. Annotating gene sets by mining large literature collections with protein networks. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018; 23:602-613. [PMID: 29218918 PMCID: PMC5806628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Analysis of patient genomes and transcriptomes routinely recognizes new gene sets associated with human disease. Here we present an integrative natural language processing system which infers common functions for a gene set through automatic mining of the scientific literature with biological networks. This system links genes with associated literature phrases and combines these links with protein interactions in a single heterogeneous network. Multiscale functional annotations are inferred based on network distances between phrases and genes and then visualized as an ontology of biological concepts. To evaluate this system, we predict functions for gene sets representing known pathways and find that our approach achieves substantial improvement over the conventional text-mining baseline method. Moreover, our system discovers novel annotations for gene sets or pathways without previously known functions. Two case studies demonstrate how the system is used in discovery of new cancer-related pathways with ontological annotations.
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Affiliation(s)
- Sheng Wang
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jianzhu Ma
- School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Michael Ku Yu
- School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Fan Zheng
- School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Edward W Huang
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jiawei Han
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Trey Ideker
- School of Medicine, University of California San Diego, San Diego, CA, USA
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39
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Pan MR, Hsu MC, Chen LT, Hung WC. Orchestration of H3K27 methylation: mechanisms and therapeutic implication. Cell Mol Life Sci 2018; 75:209-223. [PMID: 28717873 PMCID: PMC5756243 DOI: 10.1007/s00018-017-2596-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/06/2017] [Accepted: 07/13/2017] [Indexed: 01/08/2023]
Abstract
Histone proteins constitute the core component of the nucleosome, the basic unit of chromatin. Chemical modifications of histone proteins affect their interaction with genomic DNA, the accessibility of recognized proteins, and the recruitment of enzymatic complexes to activate or diminish specific transcriptional programs to modulate cellular response to extracellular stimuli or insults. Methylation of histone proteins was demonstrated 50 years ago; however, the biological significance of each methylated residue and the integration between these histone markers are still under intensive investigation. Methylation of histone H3 on lysine 27 (H3K27) is frequently found in the heterochromatin and conceives a repressive marker that is linked with gene silencing. The identification of enzymes that add or erase the methyl group of H3K27 provides novel insights as to how this histone marker is dynamically controlled under different circumstances. Here we summarize the methyltransferases and demethylases involved in the methylation of H3K27 and show the new evidence by which the H3K27 methylation can be established via an alternative mechanism. Finally, the progress of drug development targeting H3K27 methylation-modifying enzymes and their potential application in cancer therapy are discussed.
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Affiliation(s)
- Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Ming-Chuan Hsu
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan
- Division of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, 704, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 804, Taiwan
| | - Wen-Chun Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan.
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 804, Taiwan.
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40
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Virasami A, Farndon SJ, McDermott U, Sebire N, Behjati S. Molecular diagnoses of century-old childhood tumours. Lancet Oncol 2017; 18:e237. [DOI: 10.1016/s1470-2045(17)30226-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 12/23/2022]
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41
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Keightley MC, Nilsson SK, Lieschke GJ. MED12 in hematopoietic stem cells-cell specific function despite ubiquitous expression. Stem Cell Investig 2017; 4:3. [PMID: 28217705 DOI: 10.21037/sci.2016.12.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 12/08/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Maria-Cristina Keightley
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Susan K Nilsson
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia;; CSIRO Manufacturing, Clayton, Victoria 3800, Australia
| | - Graham J Lieschke
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
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42
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Spinella JF, Mehanna P, Vidal R, Saillour V, Cassart P, Richer C, Ouimet M, Healy J, Sinnett D. SNooPer: a machine learning-based method for somatic variant identification from low-pass next-generation sequencing. BMC Genomics 2016; 17:912. [PMID: 27842494 PMCID: PMC5109690 DOI: 10.1186/s12864-016-3281-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 11/09/2016] [Indexed: 12/31/2022] Open
Abstract
Background Next-generation sequencing (NGS) allows unbiased, in-depth interrogation of cancer genomes. Many somatic variant callers have been developed yet accurate ascertainment of somatic variants remains a considerable challenge as evidenced by the varying mutation call rates and low concordance among callers. Statistical model-based algorithms that are currently available perform well under ideal scenarios, such as high sequencing depth, homogeneous tumor samples, high somatic variant allele frequency (VAF), but show limited performance with sub-optimal data such as low-pass whole-exome/genome sequencing data. While the goal of any cancer sequencing project is to identify a relevant, and limited, set of somatic variants for further sequence/functional validation, the inherently complex nature of cancer genomes combined with technical issues directly related to sequencing and alignment can affect either the specificity and/or sensitivity of most callers. Results For these reasons, we developed SNooPer, a versatile machine learning approach that uses Random Forest classification models to accurately call somatic variants in low-depth sequencing data. SNooPer uses a subset of variant positions from the sequencing output for which the class, true variation or sequencing error, is known to train the data-specific model. Here, using a real dataset of 40 childhood acute lymphoblastic leukemia patients, we show how the SNooPer algorithm is not affected by low coverage or low VAFs, and can be used to reduce overall sequencing costs while maintaining high specificity and sensitivity to somatic variant calling. When compared to three benchmarked somatic callers, SNooPer demonstrated the best overall performance. Conclusions While the goal of any cancer sequencing project is to identify a relevant, and limited, set of somatic variants for further sequence/functional validation, the inherently complex nature of cancer genomes combined with technical issues directly related to sequencing and alignment can affect either the specificity and/or sensitivity of most callers. The flexibility of SNooPer’s random forest protects against technical bias and systematic errors, and is appealing in that it does not rely on user-defined parameters. The code and user guide can be downloaded at https://sourceforge.net/projects/snooper/. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3281-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Pamela Mehanna
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Ramon Vidal
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Virginie Saillour
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Pauline Cassart
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Chantal Richer
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Manon Ouimet
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Jasmine Healy
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Daniel Sinnett
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada. .,Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada. .,Division of Hematology-Oncology, CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, Montreal, QC, H3T 1C5, Canada.
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