1
|
Pagliaro L, Chen SJ, Herranz D, Mecucci C, Harrison CJ, Mullighan CG, Zhang M, Chen Z, Boissel N, Winter SS, Roti G. Acute lymphoblastic leukaemia. Nat Rev Dis Primers 2024; 10:41. [PMID: 38871740 DOI: 10.1038/s41572-024-00525-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 06/15/2024]
Abstract
Acute lymphoblastic leukaemia (ALL) is a haematological malignancy characterized by the uncontrolled proliferation of immature lymphoid cells. Over past decades, significant progress has been made in understanding the biology of ALL, resulting in remarkable improvements in its diagnosis, treatment and monitoring. Since the advent of chemotherapy, ALL has been the platform to test for innovative approaches applicable to cancer in general. For example, the advent of omics medicine has led to a deeper understanding of the molecular and genetic features that underpin ALL. Innovations in genomic profiling techniques have identified specific genetic alterations and mutations that drive ALL, inspiring new therapies. Targeted agents, such as tyrosine kinase inhibitors and immunotherapies, have shown promising results in subgroups of patients while minimizing adverse effects. Furthermore, the development of chimeric antigen receptor T cell therapy represents a breakthrough in ALL treatment, resulting in remarkable responses and potential long-term remissions. Advances are not limited to treatment modalities alone. Measurable residual disease monitoring and ex vivo drug response profiling screening have provided earlier detection of disease relapse and identification of exceptional responders, enabling clinicians to adjust treatment strategies for individual patients. Decades of supportive and prophylactic care have improved the management of treatment-related complications, enhancing the quality of life for patients with ALL.
Collapse
Affiliation(s)
- Luca Pagliaro
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics (THEC), University of Parma, Parma, Italy
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Daniel Herranz
- Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Cristina Mecucci
- Department of Medicine, Hematology and Clinical Immunology, University of Perugia, Perugia, Italy
| | - Christine J Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ming Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Nicolas Boissel
- Hôpital Saint-Louis, APHP, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Stuart S Winter
- Children's Minnesota Cancer and Blood Disorders Program, Minneapolis, MN, USA
| | - Giovanni Roti
- Department of Medicine and Surgery, University of Parma, Parma, Italy.
- Translational Hematology and Chemogenomics (THEC), University of Parma, Parma, Italy.
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy.
| |
Collapse
|
2
|
García-Aznar JM, Alonso Alvarez S, Bernal Del Castillo T. Pivotal role of BCL11B in the immune, hematopoietic and nervous systems: a review of the BCL11B-associated phenotypes from the genetic perspective. Genes Immun 2024; 25:232-241. [PMID: 38472338 PMCID: PMC11178493 DOI: 10.1038/s41435-024-00263-w] [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: 08/22/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
The transcription factor BCL11B plays an essential role in the development of central nervous system and T cell differentiation by regulating the expression of numerous genes involved in several pathways. Monoallelic defects in the BCL11B gene leading to loss-of-function are associated with a wide spectrum of phenotypes, including neurological disorders with or without immunological features and susceptibility to hematological malignancies. From the genetic point of view, the landscape of BCL11B mutations reported so far does not fully explain the genotype-phenotype correlation. In this review, we sought to compile the phenotypic and genotypic variables associated with previously reported mutations in this gene in order to provide a better understanding of the consequences of deleterious variants. We also highlight the importance of a careful evaluation of the mutation type, its location and the pattern of inheritance of the variants in order to assign the most accurate pathogenicity and actionability of the genetic findings.
Collapse
Affiliation(s)
- José María García-Aznar
- Healthincode, A Coruña, Spain.
- Universitary Institute of Oncology of Principado de Asturias (IUOPA), Oviedo, Spain.
- Health Research Institute of Principado de Asturias, Oviedo, Spain.
| | - Sara Alonso Alvarez
- Universitary Institute of Oncology of Principado de Asturias (IUOPA), Oviedo, Spain
- Health Research Institute of Principado de Asturias, Oviedo, Spain
- Hematology Department, Hospital Universitario Clínico de Asturias, Oviedo, Spain
| | - Teresa Bernal Del Castillo
- Universitary Institute of Oncology of Principado de Asturias (IUOPA), Oviedo, Spain
- Health Research Institute of Principado de Asturias, Oviedo, Spain
- Hematology Department, Hospital Universitario Clínico de Asturias, Oviedo, Spain
| |
Collapse
|
3
|
Steinemann D, Dawidowska M, Russell LJ, Harrison CJ, Göhring G. Genetic alterations in lymphoblastic leukaemia / lymphoma - a practical guide to WHO HAEM5. MED GENET-BERLIN 2024; 36:39-45. [PMID: 38835965 PMCID: PMC11006319 DOI: 10.1515/medgen-2024-2007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
We present a practical guide for analyzing the genetic aspects of lymphoblastic leukaemia/lymphoma according to the 5th edition of the World Health Organization (WHO) classification of haematolymphoid neoplasms (WHO-HAEM5) issued in 2024. The WHO-HAEM5 acknowledges the increasing importance of genetics in the diagnosis of lymphoid neoplasia. Classification is based on the established genetic subtypes according to cell lineage, with precursor cell neoplasms followed by mature malignancies. This guide describes those genetic abnormalities in acute precursor B- and T-cell neoplasms required for risk stratification, and for treatment, providing diagnostic algorithms under the headings of 'essential' and 'desirable' diagnostic criteria.
Collapse
Affiliation(s)
- Doris Steinemann
- Hannover Medical School Department of Human Genetics Hannover Germany
| | - Małgorzata Dawidowska
- Institute of Human Genetics Department of Molecular and Clinical Genetics Poznan Poland
| | - Lisa J Russell
- Newcastle University Centre for Cancer Biosciences Institute Newcastle upon Tyne UK
| | - Christine J Harrison
- Newcastle University Centre for Cancer Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle upon Tyne UK
| | - Gudrun Göhring
- Amedes genetics MVZ wagnerstibbe für Laboratoriumsmedizin, Hämostaseologie, Humangenetik und Mikrobiologie Hannover Germany
| |
Collapse
|
4
|
Testa U, Chiusolo P, Pelosi E, Castelli G, Leone G. CAR-T Cell Therapy for T-Cell Malignancies. Mediterr J Hematol Infect Dis 2024; 16:e2024031. [PMID: 38468828 PMCID: PMC10927222 DOI: 10.4084/mjhid.2024.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Chimeric antigen receptor T-cell (CAR-T) therapy has revolutionized the treatment of B-cell lymphoid neoplasia and, in some instances, improved disease outcomes. Thus, six FDA-approved commercial CAR-T cell products that target antigens preferentially expressed on malignant B-cells or plasma cells have been introduced in the therapy of B-cell lymphomas, B-ALLs, and multiple myeloma. These therapeutic successes have triggered the application of CAR-T cell therapy to other hematologic tumors, including T-cell malignancies. However, the success of CAR-T cell therapies in T-cell neoplasms was considerably more limited due to the existence of some limiting factors, such as: 1) the sharing of mutual antigens between normal T-cells and CAR-T cells and malignant cells, determining fratricide events and severe T-cell aplasia; 2) the contamination of CAR-T cells used for CAR transduction with malignant T-cells. Allogeneic CAR-T products can avoid tumor contamination but raise other problems related to immunological incompatibility. In spite of these limitations, there has been significant progress in CD7- and CD5-targeted CAR-T cell therapy of T-cell malignancies in the last few years.
Collapse
Affiliation(s)
- Ugo Testa
- Istituto Superiore di Sanità, Roma, Italy
| | - Patrizia Chiusolo
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy. Sezione Di Ematologia. Roma, Italy
- Dipartimento Di Scienze Radiologiche Ed Ematologiche, Università Cattolica Del Sacro Cuore, Roma, Italy
| | | | | | - Giuseppe Leone
- Dipartimento Di Scienze Radiologiche Ed Ematologiche, Università Cattolica Del Sacro Cuore, Roma, Italy
| |
Collapse
|
5
|
Kubota Y, Gu X, Terkawi L, Bodo J, Przychodzen BP, Awada H, Williams N, Gurnari C, Kawashima N, Aly M, Durmaz A, Mori M, Ponvilawan B, Kewan T, Bahaj W, Meggendorfer M, Jha BK, Visconte V, Rogers HJ, Haferlach T, Maciejewski JP. Molecular and clinical analyses of PHF6 mutant myeloid neoplasia provide their pathogenesis and therapeutic targeting. Nat Commun 2024; 15:1832. [PMID: 38418452 PMCID: PMC10901781 DOI: 10.1038/s41467-024-46134-w] [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: 03/27/2023] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
PHF6 mutations (PHF6MT) are identified in various myeloid neoplasms (MN). However, little is known about the precise function and consequences of PHF6 in MN. Here we show three main findings in our comprehensive genomic and proteomic study. Firstly, we show a different pattern of genes correlating with PHF6MT in male and female cases. When analyzing male and female cases separately, in only male cases, RUNX1 and U2AF1 are co-mutated with PHF6. In contrast, female cases reveal co-occurrence of ASXL1 mutations and X-chromosome deletions with PHF6MT. Next, proteomics analysis reveals a direct interaction between PHF6 and RUNX1. Both proteins co-localize in active enhancer regions that define the context of lineage differentiation. Finally, we demonstrate a negative prognostic role of PHF6MT, especially in association with RUNX1. The negative effects on survival are additive as PHF6MT cases with RUNX1 mutations have worse outcomes when compared to cases carrying single mutation or wild-type.
Collapse
Affiliation(s)
- Yasuo Kubota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xiaorong Gu
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Laila Terkawi
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Juraj Bodo
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Bartlomiej P Przychodzen
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hussein Awada
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Nakisha Williams
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Naomi Kawashima
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mai Aly
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Minako Mori
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ben Ponvilawan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Tariq Kewan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Waled Bahaj
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Babal K Jha
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Center for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute (LRI) Cleveland Clinic, Cleveland, OH, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Heesun J Rogers
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | | | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
| |
Collapse
|
6
|
Aoki K, Hyuga M, Tarumoto Y, Nishibuchi G, Ueda A, Ochi Y, Sugino S, Mikami T, Kobushi H, Kato I, Akahane K, Inukai T, Takaori-Kondo A, Takita J, Ogawa S, Yusa K. Canonical BAF complex regulates the oncogenic program in human T-cell acute lymphoblastic leukemia. Blood 2024; 143:604-618. [PMID: 37922452 DOI: 10.1182/blood.2023020857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/05/2023] Open
Abstract
ABSTRACT Acute leukemia cells require bone marrow microenvironments, known as niches, which provide leukemic cells with niche factors that are essential for leukemic cell survival and/or proliferation. However, it remains unclear how the dynamics of the leukemic cell-niche interaction are regulated. Using a genome-wide CRISPR screen, we discovered that canonical BRG1/BRM-associated factor (cBAF), a variant of the switch/sucrose nonfermenting chromatin remodeling complex, regulates the migratory response of human T-cell acute lymphoblastic leukemia (T-ALL) cells to a niche factor CXCL12. Mechanistically, cBAF maintains chromatin accessibility and allows RUNX1 to bind to CXCR4 enhancer regions. cBAF inhibition evicts RUNX1 from the genome, resulting in CXCR4 downregulation and impaired migration activity. In addition, cBAF maintains chromatin accessibility preferentially at RUNX1 binding sites, ensuring RUNX1 binding at these sites, and is required for expression of RUNX1-regulated genes, such as CDK6; therefore, cBAF inhibition negatively impacts cell proliferation and profoundly induces apoptosis. This anticancer effect was also confirmed using T-ALL xenograft models, suggesting cBAF as a promising therapeutic target. Thus, we provide novel evidence that cBAF regulates the RUNX1-driven leukemic program and governs migration activity toward CXCL12 and cell-autonomous growth in human T-ALL.
Collapse
Affiliation(s)
- Kazunari Aoki
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Mizuki Hyuga
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Tarumoto
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Gohei Nishibuchi
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Atsushi Ueda
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yotaro Ochi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Seiichi Sugino
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takashi Mikami
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hirokazu Kobushi
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koshi Akahane
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Takeshi Inukai
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Kosuke Yusa
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| |
Collapse
|
7
|
Kimura S, Polonen P, Montefiori L, Park CS, Iacobucci I, Yeoh AE, Attarbaschi A, Moore AS, Brown A, Manabe A, Buldini B, Freeman BB, Chen C, Cheng C, Kean Hui C, Li CK, Pui CH, Qu C, Tomizawa D, Teachey DT, Varotto E, Paietta EM, Arnold ED, Locatelli F, Escherich G, Elisa Muhle H, Marquart HV, de Groot-Kruseman HA, Rowe JM, Stary J, Trka J, Choi JK, Meijerink JPP, Yang JJ, Takita J, Pawinska-Wasikowska K, Roberts KG, Han K, Caldwell KJ, Schmiegelow K, Crews KR, Eguchi M, Schrappe M, Zimmerman M, Takagi M, Maybury M, Svaton M, Reiterova M, Kicinski M, Prater MS, Kato M, Reyes N, Spinelli O, Thomas P, Mazilier P, Gao Q, Masetti R, Kotecha RS, Pieters R, Elitzur S, Luger SM, Mitchell S, Pruett-Miller SM, Shen S, Jeha S, Köhrer S, Kornblau SM, Skoczeń S, Miyamura T, Vincent TL, Imamura T, Conter V, Tang Y, Liu YC, Chang Y, Gu Z, Cheng Z, Yinmei Z, Inaba H, Mullighan CG. Biologic and clinical features of childhood gamma delta T-ALL: identification of STAG2/LMO2 γδ T-ALL as an extremely high risk leukemia in the very young. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.06.23298028. [PMID: 37986997 PMCID: PMC10659466 DOI: 10.1101/2023.11.06.23298028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
PURPOSE Gamma delta T-cell receptor-positive acute lymphoblastic leukemia (γδ T-ALL) is a high-risk but poorly characterized disease. METHODS We studied clinical features of 200 pediatric γδ T-ALL, and compared the prognosis of 93 cases to 1,067 protocol-matched non-γδ T-ALL. Genomic features were defined by transcriptome and genome sequencing. Experimental modeling was used to examine the mechanistic impacts of genomic alterations. Therapeutic vulnerabilities were identified by high throughput drug screening of cell lines and xenografts. RESULTS γδ T-ALL in children under three was extremely high-risk with 5-year event-free survival (33% v. 70% [age 3-<10] and 73% [age ≥10], P =9.5 x 10 -5 ) and 5-year overall survival (49% v. 78% [age 3-<10] and 81% [age ≥10], P =0.002), differences not observed in non-γδ T-ALL. γδ T-ALL in this age group was enriched for genomic alterations activating LMO2 activation and inactivating STAG2 inactivation ( STAG2/LMO2 ). Mechanistically, we show that inactivation of STAG2 profoundly perturbs chromatin organization by altering enhancer-promoter looping resulting in deregulation of gene expression associated with T-cell differentiation. Drug screening showed resistance to prednisolone, consistent with clinical slow treatment response, but identified a vulnerability in DNA repair pathways arising from STAG2 inactivation, which was efficaciously targeted by Poly(ADP-ribose) polymerase (PARP) inhibition, with synergism with HDAC inhibitors. Ex-vivo drug screening on PDX cells validated the efficacy of PARP inhibitors as well as other potential targets including nelarabine. CONCLUSION γδ T-ALL in children under the age of three is extremely high-risk and enriched for STAG2/LMO2 ALL. STAG2 loss perturbs chromatin conformation and differentiation, and STAG2/LMO2 ALL is sensitive to PARP inhibition. These data provide a diagnostic and therapeutic framework for pediatric γδ T-ALL. SUPPORT The authors are supported by the American and Lebanese Syrian Associated Charities of St Jude Children's Research Hospital, NCI grants R35 CA197695, P50 CA021765 (C.G.M.), the Henry Schueler 41&9 Foundation (C.G.M.), and a St. Baldrick's Foundation Robert J. Arceci Innovation Award (C.G.M.), Gabriella Miller Kids First X01HD100702 (D.T.T and C.G.M.) and R03CA256550 (D.T.T. and C.G.M.), F32 5F32CA254140 (L.M.), and a Garwood Postdoctoral Fellowship of the Hematological Malignancies Program of the St Jude Children's Research Hospital Comprehensive Cancer Center (S.K.). This project was supported by the National Cancer Institute of the National Institutes of Health under the following award numbers: U10CA180820, UG1CA189859, U24CA114766, U10CA180899, U10CA180866 and U24CA196173. DISCLAIMER The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The funding agencies were not directly involved in the design of the study, gathering, analysis and interpretation of the data, writing of the manuscript, or decision to submit the manuscript for publication.
Collapse
|
8
|
De Bie J, Quessada J, Tueur G, Lefebvre C, Luquet I, Toujani S, Cuccuini W, Lafage-Pochitaloff M, Michaux L. Cytogenetics in the management of T-cell acute lymphoblastic leukemia (T-ALL): Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103431. [PMID: 38016418 DOI: 10.1016/j.retram.2023.103431] [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: 07/03/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Molecular analysis is the hallmark of T-cell acute lymphoblastic leukemia (T-ALL) categorization. Several T-ALL sub-groups are well recognized based on the aberrant expression of specific transcription factors. This recently resulted in the implementation of eight provisional T-ALL entities into the novel 2022 International Consensus Classification, albeit not into the updated World Health Organization classification system. Despite this extensive molecular characterization, cytogenetic analysis remains the backbone of T-ALL diagnosis in many countries as chromosome banding analysis and fluorescence in situ hybridization are relatively inexpensive techniques to obtain results of diagnostic, prognostic and therapeutic interest. Here, we provide an overview of recurrent chromosomal abnormalities detectable in T-ALL patients and propose guidelines regarding their detection. By referring in parallel to the more general molecular classification approach, we hope to offer a diagnostic framework useful in a broad clinical genetic setting.
Collapse
Affiliation(s)
- Jolien De Bie
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Julie Quessada
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France; CRCM, Inserm UMR1068, CNRS UMR7258, Aix Marseille Université U105, Institut Paoli Calmettes, Marseille 13009, France
| | - Giulia Tueur
- Laboratoire d'hématologie, Hôpital Avicenne, AP-HP, Bobigny 93000, France
| | - Christine Lefebvre
- Unité de Génétique des Hémopathies, Service d'Hématologie Biologique, CHU Grenoble Alpes, Grenoble 38000, France
| | - Isabelle Luquet
- Laboratoire d'Hématologie, CHU Toulouse (IUCT-O), Toulouse 31000, France
| | - Saloua Toujani
- Service de Cytogénétique et Biologie Cellulaire, CHU de Rennes, Rennes 35033, France
| | - Wendy Cuccuini
- Laboratoire d'Hématologie, Unité de Cytogénétique, Hôpital Saint-Louis, AP-HP, Paris 75010, France
| | - Marina Lafage-Pochitaloff
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France
| | - Lucienne Michaux
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium; Katholieke Universiteit Leuven, Leuven 3000, Belgium.
| |
Collapse
|
9
|
Zhang X, Cui B, Li Y, Li Z, Zheng J, Chu X, Xiao P, Lu J, Wang Z, Cen J, Liu Y, Hu S. Transcriptome sequencing identifies novel EVX fusions involved in transcriptional activation of HOX family genes in pediatric immature T-cell acute lymphoblastic leukemia: two cases reports and a literature review. Int J Hematol 2023; 118:508-513. [PMID: 37243888 DOI: 10.1007/s12185-023-03619-6] [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: 01/17/2023] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 05/29/2023]
Abstract
Driver genomic alterations in pediatric immature T-cell acute lymphoblastic leukemia are not fully known. We report two cases of novel EVX fusions involved in the transcriptional activation of HOX family genes, ETV6::EVX2 and MSI2::EVX1/HOXA13, which activate HOXD and HOXA cluster genes transcription through enhancer hijacking. HOXA and HOXD were the only key transcription factors activated in these cases, which indicates their important roles in leukemogenesis. Our findings elucidate potential drivers for development of T-cell lymphoblastic leukemia, and are valuable for diagnosis and risk stratification of pediatric T-ALL in the era of precision medicine.
Collapse
Affiliation(s)
- Xiao Zhang
- Department of Hematology, Jiangsu Children's Hematology and Oncology Center, and the Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Bowen Cui
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yizhen Li
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place MS313, Memphis, TN, 38105, USA
| | - Zhiheng Li
- Department of Hematology, Jiangsu Children's Hematology and Oncology Center, and the Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Jiajia Zheng
- Department of Hematology, Jiangsu Children's Hematology and Oncology Center, and the Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Xinran Chu
- Department of Hematology, Jiangsu Children's Hematology and Oncology Center, and the Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Peifang Xiao
- Department of Hematology, Jiangsu Children's Hematology and Oncology Center, and the Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Jun Lu
- Department of Hematology, Jiangsu Children's Hematology and Oncology Center, and the Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Zheng Wang
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Jiannong Cen
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Yu Liu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Shaoyan Hu
- Department of Hematology, Jiangsu Children's Hematology and Oncology Center, and the Children's Hospital of Soochow University, Suzhou, 215025, China.
| |
Collapse
|
10
|
Pawlikowska P, Delestré L, Gregoricchio S, Oppezzo A, Esposito M, Diop MB, Rosselli F, Guillouf C. FANCA deficiency promotes leukaemic progression by allowing the emergence of cells carrying oncogenic driver mutations. Oncogene 2023; 42:2764-2775. [PMID: 37573408 PMCID: PMC10491493 DOI: 10.1038/s41388-023-02800-9] [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: 09/12/2022] [Revised: 07/21/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023]
Abstract
Leukaemia is caused by the clonal evolution of a cell that accumulates mutations/genomic rearrangements, allowing unrestrained cell growth. However, recent identification of leukaemic mutations in the blood cells of healthy individuals revealed that additional events are required to expand the mutated clones for overt leukaemia. Here, we assessed the functional consequences of deleting the Fanconi anaemia A (Fanca) gene, which encodes a DNA damage response protein, in Spi1 transgenic mice that develop preleukaemic syndrome. FANCA loss increases SPI1-associated disease penetrance and leukaemic progression without increasing the global mutation load of leukaemic clones. However, a high frequency of leukaemic FANCA-depleted cells display heterozygous activating mutations in known oncogenes, such as Kit or Nras, also identified but at low frequency in FANCA-WT mice with preleukaemic syndrome, indicating that FANCA counteracts the emergence of oncogene mutated leukaemic cells. A unique transcriptional signature is associated with the leukaemic status of FANCA-depleted cells, leading to activation of MDM4, NOTCH and Wnt/β-catenin pathways. We show that NOTCH signalling improves the proliferation capacity of FANCA-deficient leukaemic cells. Collectively, our observations indicate that loss of the FANC pathway, known to control genetic instability, fosters the expansion of leukaemic cells carrying oncogenic mutations rather than mutation formation. FANCA loss may contribute to this leukaemogenic progression by reprogramming transcriptomic landscape of the cells.
Collapse
Affiliation(s)
- Patrycja Pawlikowska
- CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France
- Inserm U981, Gustave Roussy Cancer Campus, CNRS UMS3655, Inserm US23AMMICA, Villejuif, France
| | - Laure Delestré
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France
- Inserm UMR1170, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
| | - Sebastian Gregoricchio
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France
- Inserm UMR1170, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alessia Oppezzo
- CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France
| | - Michela Esposito
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France
- Inserm UMR1170, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
| | - M' Boyba Diop
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France
- Inserm UMR1170, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
| | - Filippo Rosselli
- CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France.
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France.
| | - Christel Guillouf
- Equipe Labellisée Ligue Nationale Contre le Cancer, Villejuif, France.
- Inserm UMR1170, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France.
| |
Collapse
|
11
|
Davis K, Sheikh T, Aggarwal N. Emerging molecular subtypes and therapies in acute lymphoblastic leukemia. Semin Diagn Pathol 2023; 40:202-215. [PMID: 37120350 DOI: 10.1053/j.semdp.2023.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 05/01/2023]
Abstract
Tremendous strides have been made in the molecular and cytogenetic classification of acute lymphoblastic leukemia based on gene expression profiling data, leading to an expansion of entities in the recent International Consensus Classification (ICC) of myeloid neoplasms and acute leukemias and 2022 WHO Classification of Tumours: Haematolymphoid Tumors, 5th edition. This increased diagnostic and therapeutic complexity can be overwhelming, and this review compares nomenclature differences between the ICC and WHO 5th edition publications, compiles key features of each entity, and provides a diagnostic algorithmic approach. In covering B-lymphoblastic leukemia (B-ALL), we divided the entities into established (those present in the revised 4th edition WHO) and novel (those added to either the ICC or WHO 5th edition) groups. The established B-ALL entities include B-ALL with BCR::ABL1 fusion, BCR::ABL1-like features, KMT2A rearrangement, ETV6::RUNX1 rearrangement, high hyperdiploidy, hypodiploidy (focusing on near haploid and low hypodiploid), IGH::IL3 rearrangement, TCF3::PBX1 rearrangement, and iAMP21. The novel B-ALL entities include B-ALL with MYC rearrangement; DUX4 rearrangement; MEF2D rearrangement; ZNF384 or ZNF362 rearrangement, NUTM1 rearrangement; HLF rearrangement; UBTF::ATXN7L3/PAN3,CDX2; mutated IKZF1 N159Y; mutated PAX5 P80R; ETV6::RUNX1-like features; PAX5 alteration; mutated ZEB2 (p.H1038R)/IGH::CEBPE; ZNF384 rearranged-like; KMT2A-rearranged-like; and CRLF2 rearrangement (non-Ph-like). Classification of T-ALL is complex with some variability in how the subtypes are defined in recent literature. It was classified as early T-precursor lymphoblastic leukemia/lymphoma and T-ALL, NOS in the WHO revised 4th edition and WHO 5th edition. The ICC added an entity into early T-cell precursor ALL, BCL11B-activated, and also added provisional entities subclassified based on transcription factor families that are aberrantly activated.
Collapse
Affiliation(s)
- Katelynn Davis
- Department of Hematopathology, School of Medicine and UPMC, University of Pittsburgh, USA
| | | | - Nidhi Aggarwal
- Department of Hematopathology, School of Medicine and UPMC, University of Pittsburgh, USA.
| |
Collapse
|
12
|
Yarani R, Palasca O, Doncheva NT, Anthon C, Pilecki B, Svane CAS, Mirza AH, Litman T, Holmskov U, Bang-Berthelsen CH, Vilien M, Jensen LJ, Gorodkin J, Pociot F. Cross-species high-resolution transcriptome profiling suggests biomarkers and therapeutic targets for ulcerative colitis. Front Mol Biosci 2023; 9:1081176. [PMID: 36685283 PMCID: PMC9850088 DOI: 10.3389/fmolb.2022.1081176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023] Open
Abstract
Background: Ulcerative colitis (UC) is a disorder with unknown etiology, and animal models play an essential role in studying its molecular pathophysiology. Here, we aim to identify common conserved pathological UC-related gene expression signatures between humans and mice that can be used as treatment targets and/or biomarker candidates. Methods: To identify differentially regulated protein-coding genes and non-coding RNAs, we sequenced total RNA from the colon and blood of the most widely used dextran sodium sulfate Ulcerative colitis mouse. By combining this with public human Ulcerative colitis data, we investigated conserved gene expression signatures and pathways/biological processes through which these genes may contribute to disease development/progression. Results: Cross-species integration of human and mouse Ulcerative colitis data resulted in the identification of 1442 genes that were significantly differentially regulated in the same direction in the colon and 157 in blood. Of these, 51 genes showed consistent differential regulation in the colon and blood. Less known genes with importance in disease pathogenesis, including SPI1, FPR2, TYROBP, CKAP4, MCEMP1, ADGRG3, SLC11A1, and SELPLG, were identified through network centrality ranking and validated in independent human and mouse cohorts. Conclusion: The identified Ulcerative colitis conserved transcriptional signatures aid in the disease phenotyping and future treatment decisions, drug discovery, and clinical trial design.
Collapse
Affiliation(s)
- Reza Yarani
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark,*Correspondence: Reza Yarani, ; Flemming Pociot,
| | - Oana Palasca
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nadezhda T. Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bartosz Pilecki
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Cecilie A. S. Svane
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Aashiq H. Mirza
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Thomas Litman
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Uffe Holmskov
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Claus H. Bang-Berthelsen
- Research Group for Microbial Biotechnology and Biorefining, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark,Department of Gastroenterology, North Zealand Hillerød Hospital, Hillerød, Denmark
| | - Mogens Vilien
- Department of Surgery, North Zealand Hospital, Hillerød, Denmark
| | - Lars J. Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Pociot
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Copenhagen Diabetes Research Center, Department of Pediatrics, Herlev University Hospital, Herlev, Denmark,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark,*Correspondence: Reza Yarani, ; Flemming Pociot,
| |
Collapse
|
13
|
Akter H, Rahman MM, Sarker S, Basiruzzaman M, Islam MM, Rahaman MA, Rahaman MA, Eshaque TB, Dity NJ, Sarker S, Amin MR, Hossain MM, Lopa M, Jahan N, Hossain S, Islam A, Mondol A, Faruk MO, Saha N, Kundu GK, Kanta SI, Kazal RK, Fatema K, Rahman MA, Hasan M, Hossain Mollah MA, Hosen MI, Karuvantevida N, Begum G, Zehra B, Nassir N, Nabi AHMN, Uddin KMF, Uddin M. Construction of copy number variation landscape and characterization of associated genes in a Bangladeshi cohort of neurodevelopmental disorders. Front Genet 2023; 14:955631. [PMID: 36959829 PMCID: PMC10028086 DOI: 10.3389/fgene.2023.955631] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023] Open
Abstract
Introduction: Copy number variations (CNVs) play a critical role in the pathogenesis of neurodevelopmental disorders (NDD) among children. In this study, we aim to identify clinically relevant CNVs, genes and their phenotypic characteristics in an ethnically underrepresented homogenous population of Bangladesh. Methods: We have conducted chromosomal microarray analysis (CMA) for 212 NDD patients with male to female ratio of 2.2:1.0 to identify rare CNVs. To identify candidate genes within the rare CNVs, gene constraint metrics [i.e., "Critical-Exon Genes (CEGs)"] were applied to the population data. Autism Diagnostic Observation Schedule-Second Edition (ADOS-2) was followed in a subset of 95 NDD patients to assess the severity of autism and all statistical tests were performed using the R package. Results: Of all the samples assayed, 12.26% (26/212) and 57.08% (121/212) patients carried pathogenic and variant of uncertain significance (VOUS) CNVs, respectively. While 2.83% (6/212) patients' pathogenic CNVs were found to be located in the subtelomeric regions. Further burden test identified females are significant carriers of pathogenic CNVs compared to males (OR = 4.2; p = 0.0007). We have observed an increased number of Loss of heterozygosity (LOH) within cases with 23.85% (26/109) consanguineous parents. Our analyses on imprinting genes show, 36 LOH variants disrupting 69 unique imprinted genes and classified these variants as VOUS. ADOS-2 subset shows severe social communication deficit (p = 0.014) and overall ASD symptoms severity (p = 0.026) among the patients carrying duplication CNV compared to the CNV negative group. Candidate gene analysis identified 153 unique CEGs in pathogenic CNVs and 31 in VOUS. Of the unique genes, 18 genes were found to be in smaller (<1 MB) focal CNVs in our NDD cohort and we identified PSMC3 gene as a strong candidate gene for Autism Spectrum Disorder (ASD). Moreover, we hypothesized that KMT2B gene duplication might be associated with intellectual disability. Conclusion: Our results show the utility of CMA for precise genetic diagnosis and its integration into the diagnosis, therapy and management of NDD patients.
Collapse
Affiliation(s)
- Hosneara Akter
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Muhammad Mizanur Rahman
- Department of Paediatric Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shaoli Sarker
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Paediatric Neuroscience, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Mohammed Basiruzzaman
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Neurology, National Institute of Neurosciences and Hospital, Dhaka, Bangladesh
| | - Md. Mazharul Islam
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Neurology, National Institute of Neurosciences and Hospital, Dhaka, Bangladesh
| | - Md. Atikur Rahaman
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
| | | | | | - Nushrat Jahan Dity
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Shouvik Sarker
- Institute of Plant Genetics, Department of Plant Biotechnology, Leibniz University Hannover, Hanover, Germany
| | - Md. Robed Amin
- Department of Medicine, Dhaka Medical College, Dhaka, Bangladesh
| | - Mohammad Monir Hossain
- Department of Paediatric Neurology, National Institute of Neuroscience and Hospital, Dhaka, Bangladesh
| | - Maksuda Lopa
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Nargis Jahan
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Shafaat Hossain
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Amirul Islam
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Cellular Intelligence Lab, GenomeArc Inc, Toronto, ON, Canada
| | | | - Md Omar Faruk
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Narayan Saha
- Department of Paediatric Neurology, National Institute of Neuroscience and Hospital, Dhaka, Bangladesh
| | - Gopen kumar Kundu
- Department of Child Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shayla Imam Kanta
- Department of Paediatric Neuroscience, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Rezaul Karim Kazal
- Department of Obstetrics and Gynaecology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Kanij Fatema
- Department of Paediatric Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Md. Ashrafur Rahman
- Department of Pharmaceutical Sciences, Wilkes University, Pennsylvania, PA, United States
| | - Maruf Hasan
- Department of Biomedical Engineering, Military Institute of Science and Technology, Dhaka, Bangladesh
| | | | - Md. Ismail Hosen
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Ghausia Begum
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Binte Zehra
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Nasna Nassir
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - A. H. M. Nurun Nabi
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - K. M. Furkan Uddin
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Biochemistry, Holy Family Red Crescent Medical College, Dhaka, Bangladesh
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Cellular Intelligence (Ci) Lab, GenomeArc Inc, Toronto, ON, Canada
- *Correspondence: Mohammed Uddin,
| |
Collapse
|
14
|
García-Aznar JM, Alonso S, Iglesias DDU, de Ugarriza PL, López CÁ, Balbín M, del Castillo TB. Mapping the genetic features of T-ALL cases through simplified NGS approach. Clin Immunol 2022; 245:109151. [DOI: 10.1016/j.clim.2022.109151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/25/2022] [Accepted: 10/03/2022] [Indexed: 11/03/2022]
|
15
|
He Y, Zhang J, Zhang Y, Hu Z, Wang P, Gan W, Xie S, Qian M, Pui CH, Jiang H, Zhu X, Zhang H, Zhang W. Dasatinib-therapy induced sustained remission in a child with refractory TCF7-SPI1 T-cell acute lymphoblastic leukemia. Pediatr Blood Cancer 2022; 69:e29724. [PMID: 35441457 DOI: 10.1002/pbc.29724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/06/2022] [Accepted: 03/28/2022] [Indexed: 12/25/2022]
Abstract
The prognosis of patients with T-cell acute lymphoblastic leukemia (T-ALL) has been largely lacked behind than that of patients with B-cell ALL, especially in refractory or relapsed cases. Here, we describe a 4.7-year-old male child with TCF-SPI1-postitve T-ALL who developed refractoriness disease after a seven drugs-conventional therapy. Several studies have suggested the therapeutic potential of dasatinib in refractory T-ALL. Actually, dasatinib-included therapy dramatically reduces the leukemic burden and re-induces this patient into complete remission without systemic adverse events. Although this is a single exceptional case, the translational potential evidence of dasatinib in specific T-ALL subtype should not be under-estimated.
Collapse
Affiliation(s)
- Yingyi He
- Department of Pediatric Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Jingliao Zhang
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yingchi Zhang
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Zhengbin Hu
- Department of Pediatric Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Pengfei Wang
- Department of Pediatric Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Wenting Gan
- Department of Pediatric Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Shao Xie
- Institute of Pediatrics and Department of Hematology and Oncology, Children's Hospital of Fudan University, National Children's Medical Center, the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Maoxiang Qian
- Institute of Pediatrics and Department of Hematology and Oncology, Children's Hospital of Fudan University, National Children's Medical Center, the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Hua Jiang
- Department of Pediatric Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xiaofan Zhu
- Division of Pediatric Blood Diseases Center, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Hui Zhang
- Department of Pediatric Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Department of Hematology & Oncology, Fujian Branch of Shanghai Children's Medical Center, Fujian Children's Hospital, Fuzhou, China (current address).,Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weina Zhang
- Department of Pediatric Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| |
Collapse
|
16
|
Gregoricchio S, Polit L, Esposito M, Berthelet J, Delestré L, Evanno E, Diop M, Gallais I, Aleth H, Poplineau M, Zwart W, Rosenbauer F, Rodrigues-Lima F, Duprez E, Boeva V, Guillouf C. HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia. Nucleic Acids Res 2022; 50:7938-7958. [PMID: 35871293 PMCID: PMC9371914 DOI: 10.1093/nar/gkac613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/18/2022] [Accepted: 06/30/2022] [Indexed: 11/23/2022] Open
Abstract
Although originally described as transcriptional activator, SPI1/PU.1, a major player in haematopoiesis whose alterations are associated with haematological malignancies, has the ability to repress transcription. Here, we investigated the mechanisms underlying gene repression in the erythroid lineage, in which SPI1 exerts an oncogenic function by blocking differentiation. We show that SPI1 represses genes by binding active enhancers that are located in intergenic or gene body regions. HDAC1 acts as a cooperative mediator of SPI1-induced transcriptional repression by deacetylating SPI1-bound enhancers in a subset of genes, including those involved in erythroid differentiation. Enhancer deacetylation impacts on promoter acetylation, chromatin accessibility and RNA pol II occupancy. In addition to the activities of HDAC1, polycomb repressive complex 2 (PRC2) reinforces gene repression by depositing H3K27me3 at promoter sequences when SPI1 is located at enhancer sequences. Moreover, our study identified a synergistic relationship between PRC2 and HDAC1 complexes in mediating the transcriptional repression activity of SPI1, ultimately inducing synergistic adverse effects on leukaemic cell survival. Our results highlight the importance of the mechanism underlying transcriptional repression in leukemic cells, involving complex functional connections between SPI1 and the epigenetic regulators PRC2 and HDAC1.
Collapse
Affiliation(s)
- Sebastian Gregoricchio
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute , Amsterdam , The Netherlands
| | - Lélia Polit
- CNRS UMR8104, Inserm U1016, Université Paris Cité, Cochin Institute , F-75014 Paris , France
| | - Michela Esposito
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | | | - Laure Delestré
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | - Emilie Evanno
- Curie Institute , Inserm U830, F- 75005 Paris, France
| | - M’Boyba Diop
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | | | - Hanna Aleth
- Institute of Molecular Tumor Biology, University of Münster , Münster, Germany
| | - Mathilde Poplineau
- CNRS UMR7258, Inserm U1068, Université Aix Marseille, Paoli-Calmettes Institute , CRCM, F-13009 Marseille , France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute , Amsterdam , The Netherlands
| | - Frank Rosenbauer
- Institute of Molecular Tumor Biology, University of Münster , Münster, Germany
| | | | - Estelle Duprez
- CNRS UMR7258, Inserm U1068, Université Aix Marseille, Paoli-Calmettes Institute , CRCM, F-13009 Marseille , France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | - Valentina Boeva
- CNRS UMR8104, Inserm U1016, Université Paris Cité, Cochin Institute , F-75014 Paris , France
- Department of Computer Science and Department of Biology , ETH Zurich, 8092 Zurich , Switzerland
| | - Christel Guillouf
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| |
Collapse
|
17
|
Childhood acute myeloid leukemia with 5q deletion and HNRNPH1-MLLT10 fusion: the first case report. Blood Adv 2022; 6:3162-3166. [PMID: 35139176 PMCID: PMC9131903 DOI: 10.1182/bloodadvances.2021006383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/31/2022] [Indexed: 12/30/2022] Open
|
18
|
Fukuhara S, Oshikawa-Kumade Y, Kogure Y, Shingaki S, Kariyazono H, Kikukawa Y, Koya J, Saito Y, Tabata M, Yoshifuji K, Mizuno K, Maeshima AM, Matsushita H, Sugiyama M, Ogawa C, Inamoto Y, Fukuda T, Sugano M, Yamauchi N, Minami Y, Hirata M, Yoshida T, Kohno T, Kohsaka S, Mano H, Shiraishi Y, Ogawa S, Izutsu K, Kataoka K. Feasibility and clinical utility of comprehensive genomic profiling of hematological malignancies. Cancer Sci 2022; 113:2763-2777. [PMID: 35579198 PMCID: PMC9357666 DOI: 10.1111/cas.15427] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/26/2022] [Accepted: 05/12/2022] [Indexed: 12/01/2022] Open
Abstract
Identification of genetic alterations through next‐generation sequencing (NGS) can guide treatment decision‐making by providing information on diagnosis, therapy selection, and prognostic stratification in patients with hematological malignancies. Although the utility of NGS‐based genomic profiling assays was investigated in hematological malignancies, no assays sufficiently cover driver mutations, including recently discovered ones, as well as fusions and/or pathogenic germline variants. To address these issues, here we have devised an integrated DNA/RNA profiling assay to detect various types of somatic alterations and germline variants at once. Particularly, our assay can successfully identify copy number alterations and structural variations, including immunoglobulin heavy chain translocations, IKZF1 intragenic deletions, and rare fusions. Using this assay, we conducted a prospective study to investigate the feasibility and clinical usefulness of comprehensive genomic profiling for 452 recurrently altered genes in hematological malignancies. In total, 176 patients (with 188 specimens) were analyzed, in which at least one alteration was detected in 171 (97%) patients, with a median number of total alterations of 7 (0–55). Among them, 145 (82%), 86 (49%), and 102 (58%) patients harbored at least one clinically relevant alteration for diagnosis, treatment, and prognosis, respectively. The proportion of patients with clinically relevant alterations was the highest in acute myeloid leukemia, whereas this assay was less informative in T/natural killer‐cell lymphoma. These results suggest the clinical utility of NGS‐based genomic profiling, particularly for their diagnosis and prognostic prediction, thereby highlighting the promise of precision medicine in hematological malignancies.
Collapse
Affiliation(s)
- Suguru Fukuhara
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuji Oshikawa-Kumade
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Diagnostic Division, Otsuka Pharmaceutical Co., Ltd. Tokushima, Japan
| | - Yasunori Kogure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Sumito Shingaki
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hirokazu Kariyazono
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Diagnostic Division, Otsuka Pharmaceutical Co., Ltd. Tokushima, Japan
| | - Yoshiya Kikukawa
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Diagnostic Division, Otsuka Pharmaceutical Co., Ltd. Tokushima, Japan
| | - Junji Koya
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Mariko Tabata
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kota Yoshifuji
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Hematology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kota Mizuno
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | | | - Hiromichi Matsushita
- Department of Laboratory Medicine, National Cancer Center Hospital, Tokyo, Japan
| | - Masanaka Sugiyama
- Department of Pediatric Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Chitose Ogawa
- Department of Pediatric Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshihiro Inamoto
- Department of Hematopoietic Stem Cell Transplantation, National Cancer Center Hospital, Tokyo, Japan
| | - Takahiro Fukuda
- Department of Hematopoietic Stem Cell Transplantation, National Cancer Center Hospital, Tokyo, Japan
| | - Masato Sugano
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa, Japan
| | - Nobuhiko Yamauchi
- Department of Hematology and Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yosuke Minami
- Department of Hematology and Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Makoto Hirata
- Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Teruhiko Yoshida
- Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koji Izutsu
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| |
Collapse
|
19
|
Canté-Barrett K, Meijer MT, Cordo' V, Hagelaar R, Yang W, Yu J, Smits WK, Nulle ME, Jansen JP, Pieters R, Yang JJ, Haigh JJ, Goossens S, Meijerink JP. MEF2C opposes Notch in lymphoid lineage decision and drives leukemia in the thymus. JCI Insight 2022; 7:150363. [PMID: 35536646 PMCID: PMC9310523 DOI: 10.1172/jci.insight.150363] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 05/04/2022] [Indexed: 11/25/2022] Open
Abstract
Rearrangements that drive ectopic MEF2C expression have recurrently been found in patients with human early thymocyte progenitor acute lymphoblastic leukemia (ETP-ALL). Here, we show high levels of MEF2C expression in patients with ETP-ALL. Using both in vivo and in vitro models of ETP-ALL, we demonstrate that elevated MEF2C expression blocks NOTCH-induced T cell differentiation while promoting a B-lineage program. MEF2C activates a B cell transcriptional program in addition to RUNX1, GATA3, and LMO2; upregulates the IL-7R; and boosts cell survival by upregulation of BCL2. MEF2C and the Notch pathway, therefore, demarcate opposite regulators of B- or T-lineage choices, respectively. Enforced MEF2C expression in mouse or human progenitor cells effectively blocks early T cell differentiation and promotes the development of biphenotypic lymphoid tumors that coexpress CD3 and CD19, resembling human mixed phenotype acute leukemia. Salt-inducible kinase (SIK) inhibitors impair MEF2C activity and alleviate the T cell developmental block. Importantly, this sensitizes cells to prednisolone treatment. Therefore, SIK-inhibiting compounds such as dasatinib are potentially valuable additions to standard chemotherapy for human ETP-ALL.
Collapse
Affiliation(s)
| | - Mariska T Meijer
- Princess Máxima Center for pediatric oncology, Utrecht, Netherlands
| | - Valentina Cordo'
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Rico Hagelaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Wentao Yang
- Department of Pharmaceutical Sciences, St. Jude Childen's Research Hospital, Memphis, United States of America
| | - Jiyang Yu
- Computational Biology Department, St. Jude Childen's Research Hospital, Memphis, United States of America
| | - Willem K Smits
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Marloes E Nulle
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Joris P Jansen
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Rob Pieters
- Pieters Group, Princess Máxima Center for pediatric oncology, Utrecht, Netherlands
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, United States of America
| | - Jody J Haigh
- Research Institute of Oncology and Hematology, University of Manitoba, Manitoba, Canada
| | - Steven Goossens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jules Pp Meijerink
- Meijerink Group, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| |
Collapse
|
20
|
Oksa L, Mäkinen A, Nikkilä A, Hyvärinen N, Laukkanen S, Rokka A, Haapaniemi P, Seki M, Takita J, Kauko O, Heinäniemi M, Lohi O. Arginine Methyltransferase PRMT7 Deregulates Expression of RUNX1 Target Genes in T-Cell Acute Lymphoblastic Leukemia. Cancers (Basel) 2022; 14:2169. [PMID: 35565298 PMCID: PMC9101393 DOI: 10.3390/cancers14092169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 02/05/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy with no well-established prognostic biomarkers. We examined the expression of protein arginine methyltransferases across hematological malignancies and discovered high levels of PRMT7 mRNA in T-ALL, particularly in the mature subtypes of T-ALL. The genetic deletion of PRMT7 by CRISPR-Cas9 reduced the colony formation of T-ALL cells and changed arginine monomethylation patterns in protein complexes associated with the RNA and DNA processing and the T-ALL pathogenesis. Among them was RUNX1, whose target gene expression was consequently deregulated. These results suggest that PRMT7 plays an active role in the pathogenesis of T-ALL.
Collapse
Affiliation(s)
- Laura Oksa
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (A.M.); (A.N.); (N.H.); (S.L.); (O.L.)
| | - Artturi Mäkinen
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (A.M.); (A.N.); (N.H.); (S.L.); (O.L.)
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, FI-33520 Tampere, Finland
| | - Atte Nikkilä
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (A.M.); (A.N.); (N.H.); (S.L.); (O.L.)
| | - Noora Hyvärinen
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (A.M.); (A.N.); (N.H.); (S.L.); (O.L.)
| | - Saara Laukkanen
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (A.M.); (A.N.); (N.H.); (S.L.); (O.L.)
| | - Anne Rokka
- Turku Bioscience Center, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland; (A.R.); (P.H.); (O.K.)
| | - Pekka Haapaniemi
- Turku Bioscience Center, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland; (A.R.); (P.H.); (O.K.)
| | - Masafumi Seki
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-17165 Solna, Sweden;
| | - Junko Takita
- Graduate School of Medicine, Kyoto University, Kyoto JP-606-8501, Japan;
| | - Otto Kauko
- Turku Bioscience Center, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland; (A.R.); (P.H.); (O.K.)
| | - Merja Heinäniemi
- The Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland;
| | - Olli Lohi
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (A.M.); (A.N.); (N.H.); (S.L.); (O.L.)
- Tays Cancer Center, Tampere University Hospital, FI-33520 Tampere, Finland
| |
Collapse
|
21
|
Transcriptome-wide subtyping of pediatric and adult T cell acute lymphoblastic leukemia in an international study of 707 cases. Proc Natl Acad Sci U S A 2022; 119:e2120787119. [PMID: 35385357 PMCID: PMC9169777 DOI: 10.1073/pnas.2120787119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We provide transcriptomic insights into differences between pediatric and adult T cell acute lymphoblastic leukemia (T-ALL) patients through an international collaborative effort integrating RNA-sequencing data of 707 patients. Ten subtypes were identified, each characterized by distinct gene mutation profiles and dysregulated expression signatures of leukemogenic factors, and associated with T cell development stages. Adult T-ALL tends to have characteristics of early T cell precursor ALL, mostly corresponding to the mixed phenotype acute leukemia, whereas pediatric T-ALL shows a wide spectrum of aberrant molecular features, from early T cell precursor to mature T cell compartments. Our findings have important implications for disease mechanism of T-ALL that differs between pediatric and adult patients, facilitating further refined targeted therapy. T cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy of T cell progenitors, known to be a heterogeneous disease in pediatric and adult patients. Here we attempted to better understand the disease at the molecular level based on the transcriptomic landscape of 707 T-ALL patients (510 pediatric, 190 adult patients, and 7 with unknown age; 599 from published cohorts and 108 newly investigated). Leveraging the information of gene expression enabled us to identify 10 subtypes (G1–G10), including the previously undescribed one characterized by GATA3 mutations, with GATA3R276Q capable of affecting lymphocyte development in zebrafish. Through associating with T cell differentiation stages, we found that high expression of LYL1/LMO2/SPI1/HOXA (G1–G6) might represent the early T cell progenitor, pro/precortical/cortical stage with a relatively high age of disease onset, and lymphoblasts with TLX3/TLX1 high expression (G7–G8) could be blocked at the cortical/postcortical stage, while those with high expression of NKX2-1/TAL1/LMO1 (G9–G10) might correspond to cortical/postcortical/mature stages of T cell development. Notably, adult patients harbored more cooperative mutations among epigenetic regulators, and genes involved in JAK-STAT and RAS signaling pathways, with 44% of patients aged 40 y or above in G1 bearing DNMT3A/IDH2 mutations usually seen in acute myeloid leukemia, suggesting the nature of mixed phenotype acute leukemia.
Collapse
|
22
|
Novel TENM3–ALK fusion is an alternate mechanism for ALK activation in neuroblastoma. Oncogene 2022; 41:2789-2797. [DOI: 10.1038/s41388-022-02301-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 03/16/2022] [Accepted: 03/25/2022] [Indexed: 11/09/2022]
|
23
|
Sato-Otsubo A, Osumi T, Yoshida M, Iguchi A, Fukushima T, Nakabayashi K, Ogawa S, Hata K, Kato M. Genomic analysis of two rare cases of pediatric Ph-positive T-ALL. Pediatr Blood Cancer 2022; 69:e29427. [PMID: 34719840 DOI: 10.1002/pbc.29427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/07/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Aiko Sato-Otsubo
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, The University of Tokyo, Tokyo, Japan
| | - Tomoo Osumi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Masanori Yoshida
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akihiro Iguchi
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Hokkaido University, Sapporo, Japan
| | - Takashi Fukushima
- Department of Pediatric Hematology and Oncology, Saitama Medical University International Medical Center, Saitama, Japan.,Department of Pediatrics, University of Tsukuba Hospital, Tsukuba, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Molecular Hematology, Karolinska Institute, Stockholm, Sweden
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, The University of Tokyo, Tokyo, Japan.,Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| |
Collapse
|
24
|
Ben-David Y, Gajendran B, Sample KM, Zacksenhaus E. Current insights into the role of Fli-1 in hematopoiesis and malignant transformation. Cell Mol Life Sci 2022; 79:163. [PMID: 35412146 PMCID: PMC11072361 DOI: 10.1007/s00018-022-04160-1] [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: 11/01/2021] [Revised: 01/05/2022] [Accepted: 01/19/2022] [Indexed: 11/27/2022]
Abstract
Fli-1, a member of the ETS family of transcription factors, was discovered in 1991 through retroviral insertional mutagenesis as a driver of mouse erythroleukemias. In the past 30 years, nearly 2000 papers have defined its biology and impact on normal development and cancer. In the hematopoietic system, Fli-1 controls self-renewal of stem cells and their differentiation into diverse mature blood cells. Fli-1 also controls endothelial survival and vasculogenesis, and high and low levels of Fli-1 are implicated in the auto-immune diseases systemic lupus erythematosus and systemic sclerosis, respectively. In addition, aberrant Fli-1 expression is observed in, and is essential for, the growth of multiple hematological malignancies and solid cancers. Here, we review the historical context and latest research on Fli-1, focusing on its role in hematopoiesis, immune response, and malignant transformation. The importance of identifying Fli-1 modulators (both agonists and antagonists) and their potential clinical applications is discussed.
Collapse
Affiliation(s)
- Yaacov Ben-David
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Province Science City, High Tech Zone, Baiyun District, Guiyang, 550014, Guizhou Province, People's Republic of China.
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Babu Gajendran
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Province Science City, High Tech Zone, Baiyun District, Guiyang, 550014, Guizhou Province, People's Republic of China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Klarke M Sample
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Province Science City, High Tech Zone, Baiyun District, Guiyang, 550014, Guizhou Province, People's Republic of China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Eldad Zacksenhaus
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Research Institute, Max Bell Research Centre, University Health Network, 101 College Street, Toronto, ON, Canada
| |
Collapse
|
25
|
Huang J, Chen W, Jie Z, Jiang M. Comprehensive Analysis of Immune Implications and Prognostic Value of SPI1 in Gastric Cancer. Front Oncol 2022; 12:820568. [PMID: 35237521 PMCID: PMC8882873 DOI: 10.3389/fonc.2022.820568] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/19/2022] [Indexed: 01/13/2023] Open
Abstract
Background The transcription factor Spi-1 proto-oncogene (SPI1, also known as PU.1) is a key regulator of signal communication in the immune system and is essential for the development of myeloid cells and lymphocytes. However, the potential role of SPI1 in gastric cancer (GC) and the correlations between SPI1 and immune infiltration remain unclear. Methods In the present study, multiple databases including ONCOMINE, TIMER, Kaplan–Meier Plotter, and The Cancer Genome Atlas were used to explore the expression levels and prognostic value of SPI1 in GC. cBioPortal was used to explore the possible reasons for the increased expression of SPI1 in GC. The correlations between SPI1 expression and tumor-infiltrating immune cells (TICs) were analyzed using CIBERSORT and TIMER. Gene set enrichment analysis was used to determine the biological function of SPI1 in the development of GC. In addition, a risk signature based on SPI1-related immunomodulators was constructed to accurately evaluate the prognosis of patients with GC. The upregulation of SPI1 expression in GC was further confirmed through immunohistochemistry, western blotting, and real-time quantitative PCR (RT-qPCR) assay. Results The expression of SPI1 was increased significantly in GC according to multiple databases, and high expression of SPI1 was related to poor prognosis and progression of GC. The main factor influencing the high expression of SPI1 mRNA in GC may be diploidy, not DNA methylation. Moreover, immunohistochemistry, western blotting, and RT-qPCR assays also confirmed the upregulated expression of SPI1 in GC. CIBERSORT analysis revealed that SPI1 expression was correlated with seven types of TICs (naive B cells, resting memory CD4 T cells, activated memory CD4 T cells, activated natural killer cells, resting natural killer cells, M2 macrophages, and resting dendritic cells). Gene set enrichment analysis indicated that SPI1 might be related to immune activation in GC and participate in cell cycle regulation. In addition, based on SPI1-related immunomodulators, we developed multiple-gene risk prediction signatures and constructed a nomogram that can independently predict the clinical outcome of GC. Conclusion The results of the present study suggest that SPI1 has a critical role in determining the prognosis of GC patients and may be a potential immunotherapeutic target.
Collapse
Affiliation(s)
- Jianfeng Huang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wenzheng Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhigang Jie
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Mengmeng Jiang, ; Zhigang Jie,
| | - Mengmeng Jiang
- Department of Emergency Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Mengmeng Jiang, ; Zhigang Jie,
| |
Collapse
|
26
|
Integrated genomic analyses identify high-risk factors and actionable targets in T-cell acute lymphoblastic leukemia. BLOOD SCIENCE 2022; 4:16-28. [PMID: 35399540 PMCID: PMC8974951 DOI: 10.1097/bs9.0000000000000102] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/12/2022] [Indexed: 11/26/2022] Open
Abstract
T cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy often associated with poor outcomes. To identify high-risk factors and potential actionable targets for T-ALL, we perform integrated genomic and transcriptomic analyses on samples from 165 Chinese pediatric and adult T-ALL patients, of whom 85% have outcome information. The genomic mutation landscape of this Chinese cohort is very similar to the Western cohort published previously, except that the rate of NOTCH1 mutations is significant lower in the Chinese T-ALL patients. Among 47 recurrently mutated genes in 7 functional categories, we identify RAS pathway and PTEN mutations as poor survival factors for non-TAL and TAL subtypes, respectively. Mutations in the PI3K pathway are mutually exclusive with mutations in the RAS and NOTCH1 pathways as well as transcription factors. Further analysis demonstrates that approximately 43% of the high-risk patients harbor at least one potential actionable alteration identified in this study, and T-ALLs with RAS pathway mutations are hypersensitive to MEKi in vitro and in vivo. Thus, our integrated genomic analyses not only systematically identify high-risk factors but suggest that these high-risk factors are promising targets for T-ALL therapies.
Collapse
|
27
|
Steimlé T, Dourthe ME, Alcantara M, Touzart A, Simonin M, Mondesir J, Lhermitte L, Bond J, Graux C, Grardel N, Cayuela JM, Arnoux I, Gandemer V, Balsat M, Vey N, Macintyre E, Ifrah N, Dombret H, Petit A, Baruchel A, Ruminy P, Boissel N, Asnafi V. Clinico-biological features of T-cell acute lymphoblastic leukemia with fusion proteins. Blood Cancer J 2022; 12:14. [PMID: 35082269 PMCID: PMC8791998 DOI: 10.1038/s41408-022-00613-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/01/2022] [Accepted: 01/06/2022] [Indexed: 12/23/2022] Open
Abstract
T-cell acute lymphoblastic leukemias (T-ALL) represent 15% of pediatric and 25% of adult ALL. Since they have a particularly poor outcome in relapsed/refractory cases, identifying prognosis factors at diagnosis is crucial to adapting treatment for high-risk patients. Unlike acute myeloid leukemia and BCP ALL, chromosomal rearrangements leading to chimeric fusion-proteins with strong prognosis impact are sparsely reported in T-ALL. To address this issue an RT-MPLA assay was applied to a consecutive series of 522 adult and pediatric T-ALLs and identified a fusion transcript in 20% of cases. PICALM-MLLT10 (4%, n = 23), NUP214-ABL1 (3%, n = 19) and SET-NUP214 (3%, n = 18) were the most frequent. The clinico-biological characteristics linked to fusion transcripts in a subset of 235 patients (138 adults in the GRAALL2003/05 trials and 97 children from the FRALLE2000 trial) were analyzed to identify their prognosis impact. Patients with HOXA trans-deregulated T-ALLs with MLLT10, KMT2A and SET fusion transcripts (17%, 39/235) had a worse prognosis with a 5-year EFS of 35.7% vs 63.7% (HR = 1.63; p = 0.04) and a trend for a higher cumulative incidence of relapse (5-year CIR = 45.7% vs 25.2%, HR = 1.6; p = 0.11). Fusion transcripts status in T-ALL can be robustly identified by RT-MLPA, facilitating risk adapted treatment strategies for high-risk patients.
Collapse
Affiliation(s)
- Thomas Steimlé
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Marie-Emilie Dourthe
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
- Department of Pediatric Hematology and Immunology, Robert Debré University Hospital (AP-HP), Université de Paris, Paris, France
| | - Marion Alcantara
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
- Department of Pediatric Hematology and Immunology, Robert Debré University Hospital (AP-HP), Université de Paris, Paris, France
- Center for Cancer Immunotherapy, INSERM U932, Institut Curie, PSL Research University, Paris, France
| | - Aurore Touzart
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Mathieu Simonin
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
- Department of Pediatric Hematology and Immunology, Robert Debré University Hospital (AP-HP), Université de Paris, Paris, France
- Center for Cancer Immunotherapy, INSERM U932, Institut Curie, PSL Research University, Paris, France
- Department of Pediatric Hematology and Oncology, Assistance Publique-Hôpitaux de Paris (AP-HP), GH HUEP, Armand Trousseau Hospital, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 938, CDR Saint-Antoine, GRC n°07, GRC MyPAC, Paris, France
| | - Johanna Mondesir
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Ludovic Lhermitte
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Jonathan Bond
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Carlos Graux
- Department of Hematology, Université catholique de Louvain, CHU UCL Namur - site Godinne, Yvoir, Belgium
| | - Nathalie Grardel
- Laboratory of Hematology, CHRU Lille, Lille, France and U1172, INSERM, Lille, France
| | - Jean-Michel Cayuela
- Laboratory of Hematology and EA 3518 University Hospital Saint-Louis, AP-HP and Université de Paris, Paris, France
| | - Isabelle Arnoux
- Hematology Laboratory, Marseille University Hospital Timone, Marseille, France
| | - Virginie Gandemer
- Department of Pediatric Hematology and Oncology, University Hospital of Rennes, Rennes, France
| | - Marie Balsat
- Service d'hématologie clinique, Hôpital Lyon Sud, Marseille, France
| | - Norbert Vey
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Elizabeth Macintyre
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Norbert Ifrah
- PRES LUNAM, CHU Angers service des Maladies du Sang et CRCINA INSERM, Angers, France
| | - Hervé Dombret
- Institut de Recherche Saint-Louis, Université de Paris, EA-3518, Paris, France
| | - Arnaud Petit
- Department of Pediatric Hematology and Oncology, Assistance Publique-Hôpitaux de Paris (AP-HP), GH HUEP, Armand Trousseau Hospital, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 938, CDR Saint-Antoine, GRC n°07, GRC MyPAC, Paris, France
| | - André Baruchel
- Department of Pediatric Hematology and Immunology, Robert Debré University Hospital (AP-HP), Université de Paris, Paris, France
- Institut de Recherche Saint-Louis, Université de Paris, EA-3518, Paris, France
| | - Philippe Ruminy
- Inserm U1245, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Nicolas Boissel
- Institut de Recherche Saint-Louis, Université de Paris, EA-3518, Paris, France
- Inserm U1245, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
- AP-HP, Hôpital Saint Louis, Unité d'Hématologie Adolescents et Jeunes Adultes, Paris, France
| | - Vahid Asnafi
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France.
| |
Collapse
|
28
|
Fishman H, Madiwale S, Geron I, Bari V, Van Loocke W, Kirschenbaum Y, Ganmore I, Kugler E, Rein-Gil A, Friedlander G, Schiby G, Birger Y, Strehl S, Soulier J, Knoechel B, Ferrando A, Noy-Lotan S, Nagler A, Mulloy JC, Van Vlierberghe P, Izraeli S. ETV6-NCOA2 fusion induces T/myeloid mixed-phenotype leukemia through transformation of nonthymic hematopoietic progenitor cells. Blood 2022; 139:399-412. [PMID: 34624096 PMCID: PMC9906988 DOI: 10.1182/blood.2020010405] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 09/26/2021] [Indexed: 01/05/2023] Open
Abstract
Mixed-phenotype acute leukemia is a rare subtype of leukemia in which both myeloid and lymphoid markers are co-expressed on the same malignant cells. The pathogenesis is largely unknown, and the treatment is challenging. We previously reported the specific association of the recurrent t(8;12)(q13;p13) chromosomal translocation that creates the ETV6-NCOA2 fusion with T/myeloid leukemias. Here we report that ETV6-NCOA2 initiates T/myeloid leukemia in preclinical models; ectopic expression of ETV6-NCOA2 in mouse bone marrow hematopoietic progenitors induced T/myeloid lymphoma accompanied by spontaneous Notch1-activating mutations. Similarly, cotransduction of human cord blood CD34+ progenitors with ETV6-NCOA2 and a nontransforming NOTCH1 mutant induced T/myeloid leukemia in immunodeficient mice; the immunophenotype and gene expression pattern were similar to those of patient-derived ETV6-NCOA2 leukemias. Mechanistically, we show that ETV6-NCOA2 forms a transcriptional complex with ETV6 and the histone acetyltransferase p300, leading to derepression of ETV6 target genes. The expression of ETV6-NCOA2 in human and mouse nonthymic hematopoietic progenitor cells induces transcriptional dysregulation, which activates a lymphoid program while failing to repress the expression of myeloid genes such as CSF1 and MEF2C. The ETV6-NCOA2 induced arrest at an early immature T-cell developmental stage. The additional acquisition of activating NOTCH1 mutations transforms the early immature ETV6-NCOA2 cells into T/myeloid leukemias. Here, we describe the first preclinical model to depict the initiation of T/myeloid leukemia by a specific somatic genetic aberration.
Collapse
Affiliation(s)
- Hila Fishman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Shreyas Madiwale
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Ifat Geron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Vase Bari
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital, Cincinnati, OH
| | - Wouter Van Loocke
- Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - Yael Kirschenbaum
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Cancer Research Center, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Itamar Ganmore
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Cancer Research Center, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Eitan Kugler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Avigail Rein-Gil
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Gilgi Friedlander
- The Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Ginette Schiby
- Institute for Pathology Laboratory, Hematology Institute, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Yehudit Birger
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Sabine Strehl
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Jean Soulier
- Genomes and Cell Biology of Disease, Hôpital Saint-Louis, Paris, France
| | - Birgit Knoechel
- Dana-Farber Cancer Institute, Boston Children's Hospital, Boston, MA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Sharon Noy-Lotan
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Arnon Nagler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Hematology Division Bone Marrow Transplants and Cord-Blood Bank, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - James C. Mulloy
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital, Cincinnati, OH
| | | | - Shai Izraeli
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
- Department of System Biology, City of Hope, Duarte, CA
| |
Collapse
|
29
|
Montefiori LE, Bendig S, Gu Z, Chen X, Pölönen P, Ma X, Murison A, Zeng A, Garcia-Prat L, Dickerson K, Iacobucci I, Abdelhamed S, Hiltenbrand R, Mead PE, Mehr CM, Xu B, Cheng Z, Chang TC, Westover T, Ma J, Stengel A, Kimura S, Qu C, Valentine MB, Rashkovan M, Luger S, Litzow MR, Rowe JM, den Boer ML, Wang V, Yin J, Kornblau SM, Hunger SP, Loh ML, Pui CH, Yang W, Crews KR, Roberts KG, Yang JJ, Relling MV, Evans WE, Stock W, Paietta EM, Ferrando AA, Zhang J, Kern W, Haferlach T, Wu G, Dick JE, Klco JM, Haferlach C, Mullighan CG. Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia. Cancer Discov 2021; 11:2846-2867. [PMID: 34103329 PMCID: PMC8563395 DOI: 10.1158/2159-8290.cd-21-0145] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/27/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022]
Abstract
Lineage-ambiguous leukemias are high-risk malignancies of poorly understood genetic basis. Here, we describe a distinct subgroup of acute leukemia with expression of myeloid, T lymphoid, and stem cell markers driven by aberrant allele-specific deregulation of BCL11B, a master transcription factor responsible for thymic T-lineage commitment and specification. Mechanistically, this deregulation was driven by chromosomal rearrangements that juxtapose BCL11B to superenhancers active in hematopoietic progenitors, or focal amplifications that generate a superenhancer from a noncoding element distal to BCL11B. Chromatin conformation analyses demonstrated long-range interactions of rearranged enhancers with the expressed BCL11B allele and association of BCL11B with activated hematopoietic progenitor cell cis-regulatory elements, suggesting BCL11B is aberrantly co-opted into a gene regulatory network that drives transformation by maintaining a progenitor state. These data support a role for ectopic BCL11B expression in primitive hematopoietic cells mediated by enhancer hijacking as an oncogenic driver of human lineage-ambiguous leukemia. SIGNIFICANCE: Lineage-ambiguous leukemias pose significant diagnostic and therapeutic challenges due to a poorly understood molecular and cellular basis. We identify oncogenic deregulation of BCL11B driven by diverse structural alterations, including de novo superenhancer generation, as the driving feature of a subset of lineage-ambiguous leukemias that transcend current diagnostic boundaries.This article is highlighted in the In This Issue feature, p. 2659.
Collapse
Affiliation(s)
- Lindsey E Montefiori
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Zhaohui Gu
- Department of Computational and Quantitative Medicine, City of Hope Comprehensive Cancer Center, Duarte, California
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Petri Pölönen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Alex Murison
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Andy Zeng
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Laura Garcia-Prat
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Kirsten Dickerson
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Paul E Mead
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Cyrus M Mehr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zhongshan Cheng
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Shunsuke Kimura
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Marcus B Valentine
- Cytogenetics Core Facility, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Marissa Rashkovan
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Selina Luger
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mark R Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jacob M Rowe
- Department of Hematology, Shaare Zedek Medical Center, Jerusalem, Israel
| | | | - Victoria Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jun Yin
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, Minnesota
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen P Hunger
- Department of Pediatrics, Children's Hospital of Philadelphia, and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kristine R Crews
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Wendy Stock
- University of Chicago Comprehensive Cancer Center, Chicago, Illinois
| | | | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, New York
- Department of Pediatrics, Columbia University, New York, New York
- Department of Pathology and Cell Biology, Columbia University, New York, New York
- Department of Systems Biology, Columbia University, New York, New York
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | - Gang Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John E Dick
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | | | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| |
Collapse
|
30
|
van der Kouwe E, Heller G, Czibere A, Pulikkan JA, Agreiter C, Castilla LH, Delwel R, Di Ruscio A, Ebralidze AK, Forte M, Grebien F, Heyes E, Kazianka L, Klinger J, Kornauth C, Le T, Lind K, Barbosa IAM, Pemovska T, Pichler A, Schmolke AS, Schweicker CM, Sill H, Sperr WR, Spittler A, Surapally S, Trinh BQ, Valent P, Vanura K, Welner RS, Zuber J, Tenen DG, Staber PB. Core-binding factor leukemia hijacks the T-cell-prone PU.1 antisense promoter. Blood 2021; 138:1345-1358. [PMID: 34010414 PMCID: PMC8525333 DOI: 10.1182/blood.2020008971] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/09/2021] [Indexed: 11/20/2022] Open
Abstract
The blood system serves as a key model for cell differentiation and cancer. It is orchestrated by precise spatiotemporal expression of crucial transcription factors. One of the key master regulators in the hematopoietic systems is PU.1. Reduced levels of PU.1 are characteristic for human acute myeloid leukemia (AML) and are known to induce AML in mouse models. Here, we show that transcriptional downregulation of PU.1 is an active process involving an alternative promoter in intron 3 that is induced by RUNX transcription factors driving noncoding antisense transcription. Core-binding factor (CBF) fusions RUNX1-ETO and CBFβ-MYH11 in t(8;21) and inv(16) AML, respectively, activate the PU.1 antisense promoter that results in a shift from sense toward antisense transcription and myeloid differentiation blockade. In patients with CBF-AML, we found that an elevated antisense/sense transcript and promoter accessibility ratio represents a hallmark compared with normal karyotype AML or healthy CD34+ cells. Competitive interaction of an enhancer with the proximal or the antisense promoter forms a binary on/off switch for either myeloid or T-cell development. Leukemic CBF fusions thus use a physiological mechanism used by T cells to decrease sense transcription. Our study is the first example of a sense/antisense promoter competition as a crucial functional switch for gene expression perturbation by oncogenes. Hence, this disease mechanism reveals a previously unknown Achilles heel for future precise therapeutic targeting of oncogene-induced chromatin remodeling.
Collapse
Affiliation(s)
- E van der Kouwe
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - G Heller
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | | | | | - C Agreiter
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - L H Castilla
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - R Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - A Di Ruscio
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - A K Ebralidze
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA
| | - M Forte
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - F Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - E Heyes
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - L Kazianka
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - J Klinger
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - C Kornauth
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - T Le
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - K Lind
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - I A M Barbosa
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - T Pemovska
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - A Pichler
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - A-S Schmolke
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - C M Schweicker
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - H Sill
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - W R Sperr
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - A Spittler
- Core Facility Flow Cytometry and Surgical Research Laboratories, and
| | - S Surapally
- Versiti Blood Research Institute, Milwaukee, WI
| | - B Q Trinh
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA
| | - P Valent
- Department of Medicine I, Division of Hematology and Hemostaseology, and
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - K Vanura
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - R S Welner
- Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL; and
| | - J Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - D G Tenen
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA
- Cancer Science Institute, National University of Singapore, Singapore
| | - P B Staber
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| |
Collapse
|
31
|
Lilljebjörn H, Orsmark-Pietras C, Mitelman F, Hagström-Andersson A, Fioretos T. Transcriptomics paving the way for improved diagnostics and precision medicine of acute leukemia. Semin Cancer Biol 2021; 84:40-49. [PMID: 34606984 DOI: 10.1016/j.semcancer.2021.09.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 11/26/2022]
Abstract
Transcriptional profiling of acute leukemia, specifically by RNA-sequencing or whole transcriptome sequencing (WTS), has provided fundamental insights into its underlying disease biology and allows unbiased detection of oncogenic gene fusions, as well as of gene expression signatures that can be used for improved disease classification. While used as a research tool for many years, RNA-sequencing is becoming increasingly used in clinical diagnostics. Here, we highlight key transcriptomic studies of acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) that have improved our biological understanding of these heterogeneous malignant disorders and have paved the way for translation into clinical diagnostics. Recent single-cell transcriptomic studies of ALL and AML, which provide new insights into the cellular ecosystem of acute leukemia and point to future clinical utility, are also reviewed. Finally, we discuss current challenges that need to be overcome for a more wide-spread adoption of RNA-sequencing in clinical diagnostics and how this technology significantly can aid the identification of genetic alterations in current guidelines and of newly emerging disease entities, some of which are critical to identify because of the availability of targeted therapies, thereby paving the way for improved precision medicine of acute leukemia.
Collapse
Affiliation(s)
- Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
| | - Christina Orsmark-Pietras
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anna Hagström-Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Center for Translational Genomics, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Center for Translational Genomics, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden.
| |
Collapse
|
32
|
Association of allele-specific methylation of the ASNS gene with asparaginase sensitivity and prognosis in T-ALL. Blood Adv 2021; 6:212-224. [PMID: 34535013 PMCID: PMC8753197 DOI: 10.1182/bloodadvances.2021004271] [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: 01/14/2021] [Accepted: 07/05/2021] [Indexed: 12/02/2022] Open
Abstract
Allele-specific methylation of the ASNS gene is associated with asparaginase sensitivity and therapeutic outcome in T-ALL. Pediatric T-ALL patients with poor prognostic SPI1 fusion exclusively exhibited ASNS hypomethylation status.
Asparaginase therapy is a key component of chemotherapy for patients with T-cell acute lymphoblastic leukemia (T-ALL). Asparaginase depletes serum asparagine by deamination into aspartic acid. Normal hematopoietic cells can survive due to asparagine synthetase (ASNS) activity, whereas leukemia cells are supposed to undergo apoptosis due to silencing of the ASNS gene. Because the ASNS gene has a typical CpG island in its promoter, its methylation status in T-ALL cells may be associated with asparaginase sensitivity. Thus, we investigated the significance of ASNS methylation status in asparaginase sensitivity of T-ALL cell lines and prognosis of childhood T-ALL. Sequencing of bisulfite polymerase chain reaction products using next-generation sequencing technology in 22 T-ALL cell lines revealed a stepwise allele-specific methylation of the ASNS gene, in association with an aberrant methylation of a 7q21 imprinted gene cluster. T-ALL cell lines with ASNS hypermethylation status showed significantly higher in vitro l-asparaginase sensitivity in association with insufficient asparaginase-induced upregulation of ASNS gene expression and lower basal ASNS protein expression. A comprehensive analysis of diagnostic samples from pediatric patients with T-ALL in Japanese cohorts (N = 77) revealed that methylation of the ASNS gene was associated with an aberrant methylation of the 7q21 imprinted gene cluster. In pediatric T-ALL patients in Japanese cohorts (n = 75), ASNS hypomethylation status was significantly associated with poor therapeutic outcome, and all cases with poor prognostic SPI1 fusion exclusively exhibited ASNS hypomethylation status. These observations show that ASNS hypomethylation status is associated with asparaginase resistance and is a poor prognostic biomarker in childhood T-ALL.
Collapse
|
33
|
Iacobucci I, Kimura S, Mullighan CG. Biologic and Therapeutic Implications of Genomic Alterations in Acute Lymphoblastic Leukemia. J Clin Med 2021; 10:3792. [PMID: 34501239 PMCID: PMC8432032 DOI: 10.3390/jcm10173792] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most successful paradigm of how risk-adapted therapy and detailed understanding of the genetic alterations driving leukemogenesis and therapeutic response may dramatically improve treatment outcomes, with cure rates now exceeding 90% in children. However, ALL still represents a leading cause of cancer-related death in the young, and the outcome for older adolescents and young adults with ALL remains poor. In the past decade, next generation sequencing has enabled critical advances in our understanding of leukemogenesis. These include the identification of risk-associated ALL subtypes (e.g., those with rearrangements of MEF2D, DUX4, NUTM1, ZNF384 and BCL11B; the PAX5 P80R and IKZF1 N159Y mutations; and genomic phenocopies such as Ph-like ALL) and the genomic basis of disease evolution. These advances have been complemented by the development of novel therapeutic approaches, including those that are of mutation-specific, such as tyrosine kinase inhibitors, and those that are mutation-agnostic, including antibody and cellular immunotherapies, and protein degradation strategies such as proteolysis-targeting chimeras. Herein, we review the genetic taxonomy of ALL with a focus on clinical implications and the implementation of genomic diagnostic approaches.
Collapse
Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
| | - Shunsuke Kimura
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
- Comprehensive Cancer Center, Hematological Malignancies Program, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| |
Collapse
|
34
|
Hosokawa H, Koizumi M, Masuhara K, Romero-Wolf M, Tanaka T, Nakayama T, Rothenberg EV. Stage-specific action of Runx1 and GATA3 controls silencing of PU.1 expression in mouse pro-T cells. J Exp Med 2021; 218:e20202648. [PMID: 34180951 PMCID: PMC8241539 DOI: 10.1084/jem.20202648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/01/2021] [Accepted: 06/10/2021] [Indexed: 12/16/2022] Open
Abstract
PU.1 (encoded by Spi1), an ETS-family transcription factor with many hematopoietic roles, is highly expressed in the earliest intrathymic T cell progenitors but must be down-regulated during T lineage commitment. The transcription factors Runx1 and GATA3 have been implicated in this Spi1 repression, but the basis of the timing was unknown. We show that increasing Runx1 and/or GATA3 down-regulates Spi1 expression in pro-T cells, while deletion of these factors after Spi1 down-regulation reactivates its expression. Leveraging the stage specificities of repression and transcription factor binding revealed an unconventional but functional site in Spi1 intron 2. Acute Cas9-mediated deletion or disruption of the Runx and GATA motifs in this element reactivates silenced Spi1 expression in a pro-T cell line, substantially more than disruption of other candidate elements, and counteracts the repression of Spi1 in primary pro-T cells during commitment. Thus, Runx1 and GATA3 work stage specifically through an intronic silencing element in mouse Spi1 to control strength and maintenance of Spi1 repression during T lineage commitment.
Collapse
Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Maria Koizumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Kaori Masuhara
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Maile Romero-Wolf
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan
| | - Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Van Thillo Q, De Bie J, Seneviratne JA, Demeyer S, Omari S, Balachandran A, Zhai V, Tam WL, Sweron B, Geerdens E, Gielen O, Provost S, Segers H, Boeckx N, Marshall GM, Cheung BB, Isobe K, Kato I, Takita J, Amos TG, Deveson IW, McCalmont H, Lock RB, Oxley EP, Garwood MM, Dickins RA, Uyttebroeck A, Carter DR, Cools J, de Bock CE. Oncogenic cooperation between TCF7-SPI1 and NRAS(G12D) requires β-catenin activity to drive T-cell acute lymphoblastic leukemia. Nat Commun 2021; 12:4164. [PMID: 34230493 PMCID: PMC8260768 DOI: 10.1038/s41467-021-24442-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
Spi-1 Proto-Oncogene (SPI1) fusion genes are recurrently found in T-cell acute lymphoblastic leukemia (T-ALL) cases but are insufficient to drive leukemogenesis. Here we show that SPI1 fusions in combination with activating NRAS mutations drive an immature T-ALL in vivo using a conditional bone marrow transplant mouse model. Addition of the oncogenic fusion to the NRAS mutation also results in a higher leukemic stem cell frequency. Mechanistically, genetic deletion of the β-catenin binding domain within Transcription factor 7 (TCF7)-SPI1 or use of a TCF/β-catenin interaction antagonist abolishes the oncogenic activity of the fusion. Targeting the TCF7-SPI1 fusion in vivo with a doxycycline-inducible knockdown results in increased differentiation. Moreover, both pharmacological and genetic inhibition lead to down-regulation of SPI1 targets. Together, our results reveal an example where TCF7-SPI1 leukemia is vulnerable to pharmacological targeting of the TCF/β-catenin interaction.
Collapse
Affiliation(s)
- Quentin Van Thillo
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Jolien De Bie
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, UZ Leuven, Leuven, Belgium
| | - Janith A Seneviratne
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Sofie Demeyer
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Sofia Omari
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Anushree Balachandran
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Vicki Zhai
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Wai L Tam
- Technology Innovation Lab, VIB, Gent, Belgium
| | - Bram Sweron
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Ellen Geerdens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Olga Gielen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Sarah Provost
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Heidi Segers
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pediatric Hemato-Oncology, UZ Leuven, Leuven, Belgium
| | - Nancy Boeckx
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Laboratory Medicine, UZ Leuven, Leuven, Belgium
| | - Glenn M Marshall
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Belamy B Cheung
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Kiyotaka Isobe
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Timothy G Amos
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Hannah McCalmont
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Richard B Lock
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Ethan P Oxley
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Maximilian M Garwood
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Ross A Dickins
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Anne Uyttebroeck
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pediatric Hemato-Oncology, UZ Leuven, Leuven, Belgium
| | - Daniel R Carter
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
- School of Biomedical Engineering, University of Technology, Sydney, NSW, Australia
| | - Jan Cools
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Center for Cancer Biology, VIB, Leuven, Belgium.
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium.
| | - Charles E de Bock
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia.
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia.
| |
Collapse
|
37
|
Wang J, Wu Y, Uddin MN, Chen R, Hao JP. Identification of Potential Key Genes and Regulatory Markers in Essential Thrombocythemia Through Integrated Bioinformatics Analysis and Clinical Validation. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:767-784. [PMID: 34267539 PMCID: PMC8275175 DOI: 10.2147/pgpm.s309166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/16/2021] [Indexed: 12/11/2022]
Abstract
Introduction Essential thrombocytosis (ET) is a group of myeloproliferative neoplasms characterized by abnormal proliferation of platelet and megakaryocytes. Research on potential key genes and novel regulatory markers in essential thrombocythemia (ET) is still limited. Methods Downloading array profiles from the Gene Expression Omnibus database, we identified the differentially expressed genes (DEGs) through comprehensive bioinformatic analysis. GO, and REACTOME pathway enrichment analysis was used to predict the potential functions of DEGs. Besides, constructing a protein–protein interaction (PPI) network through the STRING database, we validated the expression level of hub genes in an independent cohort of ET, and the transcription factors (TFs) were detected in the regulatory networks of TFs and DEGs. And the candidate drugs that are targeting hub genes were identified using the DGIdb database. Results We identified 63 overlap DEGs that included 21 common up-regulated and 42 common down-regulated genes from two datasets. Functional enrichment analysis shows that the DEGs are mainly enriched in the immune system and inflammatory processes. Through PPI network analysis, ACTB, PTPRC, ACTR2, FYB, STAT1, ETS1, IL7R, IKZF1, FGL2, and CTSS were selected as hub genes. Interestingly, we found that the dysregulated hub genes are also aberrantly expressed in a bone marrow cohort of ET. Moreover, we found that the expression of CTSS, FGL2, IKZF1, STAT1, FYB, ACTR2, PTPRC, and ACTB genes were significantly under-expressed in ET (P<0.05), which is consistent with our bioinformatics analysis. The ROC curve analysis also shows that these hub genes have good diagnostic value. Besides, we identified 4 TFs (SPI1, IRF4, SRF, and AR) as master transcriptional regulators that were associated with regulating the DEGs in ET. Cyclophosphamide, prednisone, fluorouracil, ruxolitinib, and lenalidomide were predicted as potential candidate drugs for the treatment of ET. Discussion These dysregulated genes and predicted key regulators had a significant relationship with the occurrence of ET with affecting the immune system and inflammation of the processes. Some of the immunomodulatory drugs have potential value by targeting ACTB, PTPRC, IL7R, and IKZF1 genes in the treatment of ET.
Collapse
Affiliation(s)
- Jie Wang
- Department of Pharmacy, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, People's Republic of China.,School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Yun Wu
- Department of General Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, People's Republic of China
| | - Md Nazim Uddin
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China.,Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Rong Chen
- Department of Hematology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, People's Republic of China
| | - Jian-Ping Hao
- Department of Hematology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, People's Republic of China
| |
Collapse
|
38
|
3D genome alterations associated with dysregulated HOXA13 expression in high-risk T-lineage acute lymphoblastic leukemia. Nat Commun 2021; 12:3708. [PMID: 34140506 PMCID: PMC8211852 DOI: 10.1038/s41467-021-24044-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/01/2021] [Indexed: 02/06/2023] Open
Abstract
3D genome alternations can dysregulate gene expression by rewiring enhancer-promoter interactions and lead to diseases. We report integrated analyses of 3D genome alterations and differential gene expressions in 18 newly diagnosed T-lineage acute lymphoblastic leukemia (T-ALL) patients and 4 healthy controls. 3D genome organizations at the levels of compartment, topologically associated domains and loop could hierarchically classify different subtypes of T-ALL according to T cell differentiation trajectory, similar to gene expressions-based classification. Thirty-four previously unrecognized translocations and 44 translocation-mediated neo-loops are mapped by Hi-C analysis. We find that neo-loops formed in the non-coding region of the genome could potentially regulate ectopic expressions of TLX3, TAL2 and HOXA transcription factors via enhancer hijacking. Importantly, both translocation-mediated neo-loops and NUP98-related fusions are associated with HOXA13 ectopic expressions. Patients with HOXA11-A13 expressions, but not other genes in the HOXA cluster, have immature immunophenotype and poor outcomes. Here, we highlight the potentially important roles of 3D genome alterations in the etiology and prognosis of T-ALL. The non-coding genome of T-ALL has not been extensively studied. Here, the authors conduct RNA-seq, ATAC-seq and Hi-C seq analyses and find that T-ALL associated neo-loops may regulate key transcription factors including HOXA13; the aberrant expression of which is associated with poor prognosis.
Collapse
|
39
|
Zhang C, Amanda S, Wang C, King Tan T, Zulfaqar Ali M, Zhong Leong W, Moy Ng L, Kitajima S, Li Z, Eng Juh Yeoh A, Hao Tan S, Sanda T. Oncorequisite role of an aldehyde dehydrogenase in the pathogenesis of T-cell acute lymphoblastic leukemia. Haematologica 2021; 106:1545-1558. [PMID: 32414855 PMCID: PMC8168519 DOI: 10.3324/haematol.2019.245639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 12/11/2022] Open
Abstract
Aldehyde dehydrogenases (ALDH) are overexpressed in various types of cancers. One of the ALDH family genes, ALDH1A2, is aberrantly expressed in more than 50% of cases of T-cell acute lymphoblastic leukemia (T-ALL). However, its molecular function and role in the pathogenesis of T-ALL are largely unknown. Chromatin immunoprecipitation-sequencing and RNA-sequencing analyses showed that the oncogenic transcription factor TAL1 and its regulatory partners bind to the intronic regulatory element of the ALDH1A2 gene, directly inducing a T-ALL-specific isoform with enzymatic activity. ALDH1A2 was preferentially expressed in the TAL1-positive T-ALL subgroup. In TALL cell lines, depletion of ALDH1A2 inhibited cell viability and induced apoptosis. Interestingly, gene expression and metabolomic profiling revealed that ALDH1A2 supported glycolysis and the tricarboxylic acid cycle, accompanied by NADH production, by affecting multiple metabolic enzymes to promote ATP production. Depletion of ALDH1A2 increased the levels of reactive oxygen species, while the levels were reduced by ALDH1A2 overexpression both in vitro and in vivo. Overexpression of ALDH1A2 accelerated tumor onset and increased tumor penetrance in a zebrafish model of T-ALL. Taken together, our results indicate that ALDH1A2 protects against intracellular stress and promotes T-ALL cell metabolism and survival. ALDH1A2 overexpression enables leukemic clones to sustain a hyper-proliferative state driven by oncogenes.
Collapse
Affiliation(s)
- Chujing Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Stella Amanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Cheng Wang
- Department of Anatomy, National University of Singapore, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Wei Zhong Leong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ley Moy Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Shojiro Kitajima
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Zhenhua Li
- Department of Paediatrics, National University of Singapore, Singapore
| | - Allen Eng Juh Yeoh
- Dept of Paediatrics, National University of Singapore and Cancer Science Institute of Singapore
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| |
Collapse
|
40
|
BCOR gene alterations in hematological diseases. Blood 2021; 138:2455-2468. [PMID: 33945606 DOI: 10.1182/blood.2021010958] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/14/2021] [Indexed: 11/20/2022] Open
Abstract
The BCL6 co-repressor (BCOR) is a transcription factor involved in the control of embryogenesis, mesenchymal stem cells function, hematopoiesis and lymphoid development. Recurrent somatic clonal mutations of the BCOR gene and its homologue BCORL1 have been detected in several hematological malignancies and aplastic anemia. They are scattered across the whole gene length and mostly represent frameshifts (deletions, insertions), nonsense and missence mutations. These disruptive events lead to the loss of full-length BCOR protein and to the lack or low expression of a truncated form of the protein, both consistent with the tumor suppressor role of BCOR. BCOR and BCORL1 mutations are similar to those causing two rare X-linked diseases: the oculo-facio-cardio-dental (OFCD) and the Shukla-Vernon syndromes, respectively. Here, we focus on the structure and function of normal BCOR and BCORL1 in normal hematopoietic and lymphoid tissues and review the frequency and clinical significance of the mutations of these genes in malignant and non-malignant hematological diseases. Moreover, we discuss the importance of mouse models to better understand the role of Bcor loss, alone and combined with alterations of other genes (e.g. Dnmt3a and Tet2), in promoting hematological malignancies and in providing a useful platform for the development of new targeted therapies.
Collapse
|
41
|
Giaimo BD, Robert-Finestra T, Oswald F, Gribnau J, Borggrefe T. Chromatin Regulator SPEN/SHARP in X Inactivation and Disease. Cancers (Basel) 2021; 13:cancers13071665. [PMID: 33916248 PMCID: PMC8036811 DOI: 10.3390/cancers13071665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Carcinogenesis is a multistep process involving not only the activation of oncogenes and disabling tumor suppressor genes, but also epigenetic modulation of gene expression. X chromosome inactivation (XCI) is a paradigm to study heterochromatin formation and maintenance. The double dosage of X chromosomal genes in female mammals is incompatible with early development. XCI is an excellent model system for understanding the establishment of facultative heterochromatin initiated by the expression of a 17,000 nt long non-coding RNA, known as Xinactivespecifictranscript (Xist), on the X chromosome. This review focuses on the molecular mechanisms of how epigenetic modulators act in a step-wise manner to establish facultative heterochromatin, and we put these in the context of cancer biology and disease. An in depth understanding of XCI will allow a better characterization of particular types of cancer and hopefully facilitate the development of novel epigenetic therapies. Abstract Enzymes, such as histone methyltransferases and demethylases, histone acetyltransferases and deacetylases, and DNA methyltransferases are known as epigenetic modifiers that are often implicated in tumorigenesis and disease. One of the best-studied chromatin-based mechanism is X chromosome inactivation (XCI), a process that establishes facultative heterochromatin on only one X chromosome in females and establishes the right dosage of gene expression. The specificity factor for this process is the long non-coding RNA Xinactivespecifictranscript (Xist), which is upregulated from one X chromosome in female cells. Subsequently, Xist is bound by the corepressor SHARP/SPEN, recruiting and/or activating histone deacetylases (HDACs), leading to the loss of active chromatin marks such as H3K27ac. In addition, polycomb complexes PRC1 and PRC2 establish wide-spread accumulation of H3K27me3 and H2AK119ub1 chromatin marks. The lack of active marks and establishment of repressive marks set the stage for DNA methyltransferases (DNMTs) to stably silence the X chromosome. Here, we will review the recent advances in understanding the molecular mechanisms of how heterochromatin formation is established and put this into the context of carcinogenesis and disease.
Collapse
Affiliation(s)
- Benedetto Daniele Giaimo
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
- Correspondence: (B.D.G.); (T.B.); Tel.: +49-641-9947-400 (T.B.)
| | - Teresa Robert-Finestra
- Department of Developmental Biology, Erasmus MC, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (T.R.-F.); (J.G.)
| | - Franz Oswald
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany;
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (T.R.-F.); (J.G.)
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
- Correspondence: (B.D.G.); (T.B.); Tel.: +49-641-9947-400 (T.B.)
| |
Collapse
|
42
|
Zimmer TS, Korotkov A, Zwakenberg S, Jansen FE, Zwartkruis FJT, Rensing NR, Wong M, Mühlebner A, van Vliet EA, Aronica E, Mills JD. Upregulation of the pathogenic transcription factor SPI1/PU.1 in tuberous sclerosis complex and focal cortical dysplasia by oxidative stress. Brain Pathol 2021; 31:e12949. [PMID: 33786950 PMCID: PMC8412124 DOI: 10.1111/bpa.12949] [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: 12/15/2020] [Revised: 02/23/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is a congenital disorder characterized by cortical malformations and concomitant epilepsy caused by loss‐of‐function mutations in the mTOR suppressors TSC1 or TSC2. While the underlying molecular changes caused by mTOR activation in TSC have previously been investigated, the drivers of these transcriptional change have not been fully elucidated. A better understanding of the perturbed transcriptional regulation could lead to the identification of novel pathways for therapeutic intervention not only in TSC, but other genetic epilepsies in which mTOR activation plays a key role, such as focal cortical dysplasia 2b (FCD). Here, we analyzed RNA sequencing data from cortical tubers and a tsc2−/− zebrafish. We identified differential expression of the transcription factors (TFs) SPI1/PU.1, IRF8, GBX2, and IKZF1 of which SPI1/PU.1 and IRF8 targets were enriched among the differentially expressed genes. Furthermore, for SPI1/PU.1 these findings were conserved in TSC zebrafish model. Next, we confirmed overexpression of SPI1/PU.1 on the RNA and protein level in a separate cohort of surgically resected TSC tubers and FCD tissue, in fetal TSC tissue, and a Tsc1GFAP−/− mouse model of TSC. Subsequently, we validated the expression of SPI1/PU.1 in dysmorphic cells with mTOR activation in TSC tubers. In fetal TSC, we detected SPI1/PU.1 expression prenatally and elevated RNA Spi1 expression in Tsc1GFAP−/− mice before the development of seizures. Finally, in vitro, we identified that in astrocytes and neurons SPI1 transcription was driven by H2O2‐induced oxidative stress, independent of mTOR. We identified SPI1/PU.1 as a novel TF involved in the pro‐inflammatory gene expression of malformed cells in TSC and FCD 2b. This transcriptional program is activated in response to oxidative stress and already present prenatally. Importantly, SPI1/PU.1 protein appears to be strictly limited to malformed cells, as we did not find SPI1/PU.1 protein expression in mice nor in our in vitro models.
Collapse
Affiliation(s)
- Till S Zimmer
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Anatoly Korotkov
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Susan Zwakenberg
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Floor E Jansen
- Department of Pediatric Neurology, Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Fried J T Zwartkruis
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Michael Wong
- Department of Neurology, Washington University, Saint Louis, MO, USA
| | - Angelika Mühlebner
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Erwin A van Vliet
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, the Netherlands
| | - James D Mills
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Department of Clinical and Experimental Epilepsy, UCL, London, UK.,Chalfont Centre for Epilepsy, Chalfont St Peter, UK
| |
Collapse
|
43
|
Gocho Y, Liu J, Hu J, Yang W, Dharia NV, Zhang J, Shi H, Du G, John A, Lin TN, Hunt J, Huang X, Ju B, Rowland L, Shi L, Maxwell D, Smart B, Crews KR, Yang W, Hagiwara K, Zhang Y, Roberts K, Wang H, Jabbour E, Stock W, Eisfelder B, Paietta E, Newman S, Roti G, Litzow M, Easton J, Zhang J, Peng J, Chi H, Pounds S, Relling MV, Inaba H, Zhu X, Kornblau S, Pui CH, Konopleva M, Teachey D, Mullighan CG, Stegmaier K, Evans WE, Yu J, Yang JJ. Network-based systems pharmacology reveals heterogeneity in LCK and BCL2 signaling and therapeutic sensitivity of T-cell acute lymphoblastic leukemia. NATURE CANCER 2021; 2:284-299. [PMID: 34151288 PMCID: PMC8208590 DOI: 10.1038/s43018-020-00167-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy, and novel therapeutics are much needed. Profiling patient leukemia' drug sensitivities ex vivo, we discovered that 44.4% of childhood and 16.7% of adult T-ALL cases exquisitely respond to dasatinib. Applying network-based systems pharmacology analyses to examine signal circuitry, we identified preTCR-LCK activation as the driver of dasatinib sensitivity, and T-ALL-specific LCK dependency was confirmed in genome-wide CRISPR-Cas9 screens. Dasatinib-sensitive T-ALLs exhibited high BCL-XL and low BCL2 activity and venetoclax resistance. Discordant sensitivity of T-ALL to dasatinib and venetoclax is strongly correlated with T-cell differentiation, particularly with the dynamic shift in LCK vs. BCL2 activation. Finally, single-cell analysis identified leukemia heterogeneity in LCK and BCL2 signaling and T-cell maturation stage, consistent with dasatinib response. In conclusion, our results indicate that developmental arrest in T-ALL drives differential activation of preTCR-LCK and BCL2 signaling in this leukemia, providing unique opportunities for targeted therapy.
Collapse
Affiliation(s)
- Yoshihiro Gocho
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jingjing Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jianzhong Hu
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wentao Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jingliao Zhang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hao Shi
- Department of Immunology,, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guoqing Du
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - August John
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ting-Nien Lin
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeremy Hunt
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Huang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bensheng Ju
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lauren Rowland
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Dylan Maxwell
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brandon Smart
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kristine R Crews
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yingchi Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Kathryn Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hong Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wendy Stock
- University of Chicago Medical Center, Chicago, IL, USA
| | | | | | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Giovanni Roti
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Mark Litzow
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongbo Chi
- Department of Immunology,, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Steven Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Marina Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Teachey
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| |
Collapse
|
44
|
Hosokawa H, Rothenberg EV. How transcription factors drive choice of the T cell fate. Nat Rev Immunol 2021; 21:162-176. [PMID: 32918063 PMCID: PMC7933071 DOI: 10.1038/s41577-020-00426-6] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2020] [Indexed: 12/21/2022]
Abstract
Recent evidence has elucidated how multipotent blood progenitors transform their identities in the thymus and undergo commitment to become T cells. Together with environmental signals, a core group of transcription factors have essential roles in this process by directly activating and repressing specific genes. Many of these transcription factors also function in later T cell development, but control different genes. Here, we review how these transcription factors work to change the activities of specific genomic loci during early intrathymic development to establish T cell lineage identity. We introduce the key regulators and highlight newly emergent insights into the rules that govern their actions. Whole-genome deep sequencing-based analysis has revealed unexpectedly rich relationships between inherited epigenetic states, transcription factor-DNA binding affinity thresholds and influences of given transcription factors on the activities of other factors in the same cells. Together, these mechanisms determine T cell identity and make the lineage choice irreversible.
Collapse
Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| |
Collapse
|
45
|
Hosokawa H, Masuhara K, Koizumi M. Transcription factors regulate early T cell development via redeployment of other factors: Functional dynamics of constitutively required factors in cell fate decisions. Bioessays 2021; 43:e2000345. [PMID: 33624856 DOI: 10.1002/bies.202000345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/30/2021] [Accepted: 02/08/2021] [Indexed: 01/02/2023]
Abstract
Establishment of cell lineage identity from multipotent progenitors is controlled by cooperative actions of lineage-specific and stably expressed transcription factors, combined with input from environmental signals. Lineage-specific master transcription factors activate and repress gene expression by recruiting consistently expressed transcription factors and chromatin modifiers to their target loci. Recent technical advances in genome-wide and multi-omics analysis have shed light on unexpected mechanisms that underlie more complicated actions of transcription factors in cell fate decisions. In this review, we discuss functional dynamics of stably expressed and continuously required factors, Notch and Runx family members, throughout developmental stages of early T cell development in the thymus. Pre- and post-commitment stage-specific transcription factors induce dynamic redeployment of Notch and Runx binding genomic regions. Thus, together with stage-specific transcription factors, shared transcription factors across distinct developmental stages regulate acquisition of T lineage identity.
Collapse
Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan.,Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
| | - Kaori Masuhara
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Maria Koizumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| |
Collapse
|
46
|
Maćkowska N, Drobna-Śledzińska M, Witt M, Dawidowska M. DNA Methylation in T-Cell Acute Lymphoblastic Leukemia: In Search for Clinical and Biological Meaning. Int J Mol Sci 2021; 22:ijms22031388. [PMID: 33573325 PMCID: PMC7866817 DOI: 10.3390/ijms22031388] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 12/21/2022] Open
Abstract
Distinct DNA methylation signatures, related to different prognosis, have been observed across many cancers, including T-cell acute lymphoblastic leukemia (T-ALL), an aggressive hematological neoplasm. By global methylation analysis, two major phenotypes might be observed in T-ALL: hypermethylation related to better outcome and hypomethylation, which is a candidate marker of poor prognosis. Moreover, DNA methylation holds more than a clinical meaning. It reflects the replicative history of leukemic cells and most likely different mechanisms underlying leukemia development in these T-ALL subtypes. The elucidation of the mechanisms and aberrations specific to (epi-)genomic subtypes might pave the way towards predictive diagnostics and precision medicine in T-ALL. We present the current state of knowledge on the role of DNA methylation in T-ALL. We describe the involvement of DNA methylation in normal hematopoiesis and T-cell development, focusing on epigenetic aberrations contributing to this leukemia. We further review the research investigating distinct methylation phenotypes in T-ALL, related to different outcomes, pointing to the most recent research aimed to unravel the biological mechanisms behind differential methylation. We highlight how technological advancements facilitated broadening the perspective of the investigation into DNA methylation and how this has changed our understanding of the roles of this epigenetic modification in T-ALL.
Collapse
|
47
|
Kimura S, Sekiguchi M, Watanabe K, Hiwatarai M, Seki M, Yoshida K, Isobe T, Shiozawa Y, Suzuki H, Hoshino N, Hayashi Y, Oka A, Miyano S, Ogawa S, Takita J. Association of high-risk neuroblastoma classification based on expression profiles with differentiation and metabolism. PLoS One 2021; 16:e0245526. [PMID: 33465163 PMCID: PMC7815088 DOI: 10.1371/journal.pone.0245526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 01/02/2021] [Indexed: 11/19/2022] Open
Abstract
Neuroblastoma, the most common extracranial solid malignancy among children, originates from undifferentiated neural crest cells (NCC). Despite recent intensified treatment, high-risk patients still have a high mortality rate. To explore a new therapeutic strategy, we performed an integrated genomic and transcriptomic analysis of 30 high-risk neuroblastoma cases. Based on the expression profiling of RNA sequencing, neuroblastoma was classified into Mesenchymal (MES; n = 5) and Noradrenergic (ADRN; n = 25) clusters, as previously reported in the super-enhancer landscape. The expression patterns in MES-cluster cases were similar to normal adrenal glands, with enrichment in secretion-related pathways, suggesting chromaffin cell-like features built from NCC-derived Schwann cell precursors (SCPs). In contrast, neuron-related pathways were enriched in the ADRN-cluster, indicating sympathoblast features reported to originate from NCC but not via SCPs. Thus, MES- and ADRN-clusters were assumed to be corresponding to differentiation pathways through SCP and sympathoblast, respectively. ADRN-cluster cases were further classified into MYCN- and ATRX-clusters, characterized by genetic alterations, MYCN amplifications and ATRX alterations, respectively. MYCN-cluster cases showed high expression of ALDH18A1, encoding P5CS related to proline production. As reported in other cancers, this might cause reprogramming of proline metabolism leading to tumor specific proline vulnerability candidate for a target therapy of metabolic pathway. In ATRX-cluster, SLC18A2 (VMAT2), an enzyme known to prevent cell toxicity due to the oxidation of dopamine, was highly expressed and VMAT2 inhibitor (GZ-793A) represented significant attenuation of cell growth in NB-69 cell line (high SLC18A2 expression, no MYCN amplification) but not in IMR-32 cell line (MYCN amplification). In addition, the correlation of VMAT2 expression with metaiodobenzylguanidine (MIBG) avidity suggested a combination of VMAT2 inhibitor and MIBG radiation for a novel potential therapeutic strategy in ATRX-cluster cases. Thus, targeting the characteristics of unique neuroblastomas may prospectively improve prognosis.
Collapse
Affiliation(s)
- Shunsuke Kimura
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Pediatrics, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Masahiro Sekiguchi
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kentaro Watanabe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mitsuteru Hiwatarai
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masafumi Seki
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoya Isobe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yusuke Shiozawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Noriko Hoshino
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuhide Hayashi
- Institute of Physiology and Medicine, Jobu University, Gunma, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Human Genome Center Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Pediatrics, Kyoto University, Kyoto, Japan
| |
Collapse
|
48
|
Targeted sequencing to identify genetic alterations and prognostic markers in pediatric T-cell acute lymphoblastic leukemia. Sci Rep 2021; 11:769. [PMID: 33436855 PMCID: PMC7804301 DOI: 10.1038/s41598-020-80613-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/22/2020] [Indexed: 01/06/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is caused by the accumulation of multiple genetic alterations. To determine the frequency of common genetic mutations and possible prognostic markers in childhood T-ALL, we performed targeted sequencing of 67 genes across 64 cases treated according to Taiwan Pediatric Oncology Group protocols between January 2002 and December 2015. Together, 302 variants were identified in 60 genes including 233 single nucleotide variants and 69 indels. Sixty-four samples had a median number of six genetic lesions each (range 1–17). Thirteen genes had mutation frequencies > 10%, and 5 were > 20%, with the highest being NOTCH1 (70.31%). Protocadherins FAT1 (32.81%) and FAT3 (17.19%), and the ubiquitin ligase component FBXW7 (28.13%) had higher mutation frequencies than previously reported. Other mutation frequencies (PHF6, DNM2, DNMT3A, CNOT3, and WT1) were within previously reported ranges. Three epigenetic-related genes (KMT2D, DNMT3A, and EZH2) were mutated in our cohort. JAK-STAT signaling pathway genes had mutation frequencies of 3–13% and were observed in 23 cases (35.94%). Changes to genes in the ErbB signaling pathway were detected in 20 cases (31.25%). Patients with NOTCH1/FBXW7 mutations and RAS/PTEN germline exhibited better 5-year overall survival rates.
Collapse
|
49
|
Emerging molecular subtypes and therapeutic targets in B-cell precursor acute lymphoblastic leukemia. Front Med 2021; 15:347-371. [PMID: 33400146 DOI: 10.1007/s11684-020-0821-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/04/2020] [Indexed: 12/13/2022]
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is characterized by genetic alterations with high heterogeneity. Precise subtypes with distinct genomic and/or gene expression patterns have been recently revealed using high-throughput sequencing technology. Most of these profiles are associated with recurrent non-overlapping rearrangements or hotspot point mutations that are analogous to the established subtypes, such as DUX4 rearrangements, MEF2D rearrangements, ZNF384/ZNF362 rearrangements, NUTM1 rearrangements, BCL2/MYC and/or BCL6 rearrangements, ETV6-RUNX1-like gene expression, PAX5alt (diverse PAX5 alterations, including rearrangements, intragenic amplifications, or mutations), and hotspot mutations PAX5 (p.Pro80Arg) with biallelic PAX5 alterations, IKZF1 (p.Asn159Tyr), and ZEB2 (p.His1038Arg). These molecular subtypes could be classified by gene expression patterns with RNA-seq technology. Refined molecular classification greatly improved the treatment strategy. Multiagent therapy regimens, including target inhibitors (e.g., imatinib), immunomodulators, monoclonal antibodies, and chimeric antigen receptor T-cell (CAR-T) therapy, are transforming the clinical practice from chemotherapy drugs to personalized medicine in the field of risk-directed disease management. We provide an update on our knowledge of emerging molecular subtypes and therapeutic targets in BCP-ALL.
Collapse
|
50
|
Porcine model elucidates function of p53 isoform in carcinogenesis and reveals novel circTP53 RNA. Oncogene 2021; 40:1896-1908. [PMID: 33603167 PMCID: PMC7946636 DOI: 10.1038/s41388-021-01686-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/19/2021] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Recent years have seen an increasing number of genetically engineered pig models of human diseases including cancer. We previously generated pigs with a modified TP53 allele that carries a Cre-removable transcriptional stop signal in intron 1, and an oncogenic mutation TP53R167H (orthologous to human TP53R175H) in exon 5. Pigs with the unrecombined mutant allele (flTP53R167H) develop mainly osteosarcoma but also nephroblastomas and lymphomas. This observation suggested that TP53 gene dysfunction is itself the key initiator of bone tumorigenesis, but raises the question which aspects of the TP53 regulation lead to the development of such a narrow tumour spectrum. Molecular analysis of p53 revealed the presence of two internal TP53 promoters (Pint and P2) equivalent to those found in human. Consequently, both pig and human express TP53 isoforms. Data presented here strongly suggest that P2-driven expression of the mutant R167H-Δ152p53 isoform (equivalent to the human R175H-Δ160p53 isoform) and its circular counterpart circTP53 determine the tumour spectrum and play a critical role in the malignant transformation in flTP53R167H pigs. The detection of Δ152p53 isoform mRNA in serum is indicative of tumorigenesis. Furthermore, we showed a tissue-specific p53-dependent deregulation of the p63 and p73 isoforms in these tumours. This study highlights important species-specific differences in the transcriptional regulation of TP53. Considering the similarities of TP53 regulation between pig and human, these observations provide useful pointers for further investigation into isoform function including the novel circTP53 in both the pig model and human patients.
Collapse
|